SARS-CoV-2 Update

11/22/2022 davidcwrightmd

It’s time for our next 14-day moving average determinations for SARS-CoV-2 for the United States and my thoughts on vaccines, SARS-CoV-2 therapeutic agents and mutant viruses. We use the WORLDOMETERS aggregators data set to make any projections since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

SARS-CoV-2 infections per day in the United States have increased for the second time in 16 weeks. There is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have decreased by 54 deaths per day. Many states are not reporting deaths or infections in a timely manner. The number of infections per day has increased by 494. On 11/19/22 the CDC estimates that BA.5 accounted for 24% of infections (a 28.4% drop from 10/21/22), BQ.1 accounted for 25.5% (a 16.1% increase since 10/21/22), BQ.1.1 accounted for 24.2% (a 17.0% increase since 10/21/22), BA.4.6 accounted for 4.4% (a 5.1% decrease from 10/21/22), BF.7 accounted for 7.8% (a 1.2% decrease from 10/21/22), and BA.2.75.2 accounted for 0.8%. A new variant BN.1 accounted for 5.1% of isolates on 11/19/22. In the week ending November 19, 2022 BQ isolates accounted for 49.7% of infections (a 14.4% increase in infections caused by these BQ variants since 10/21/22). BQ.1.1 has five spike mutations that are different from BA.5. Four of these mutations allow escape from immunity from monoclonal antibodies, any prior infection (including Omicron BA.5), or any vaccine to include the bivalent Omicron BA.5 vaccine.

The total percentage of BQ variant infections in the region that includes New York and New Jersey was 52.3% two weeks ago and is now 64.8%. BA.5 accounts for 14% of infections, BN.7 accounts for 5.6%, and a new isolate, BN.1, accounts for 2.2% of isolates. BA.5.2.6 isolates now account for 1.9% of infections. The BA.2.75 lineages account for 3.2% of infections.

The total percentage of BQ variant infections in the region that includes California, Nevada, Arizona, and Hawaii was 13.6% two weeks ago and is now 36.9%. BA.5.2.6 isolates now account for 2.4% of cases. The BA.2.75 lineages account for 4.2%.

Data on the rapid spread of a dangerous variant category, the BQ variants, was withheld by the CDC in their weekly reports until three weeks ago. The data on BQ.1 and BQ.1.1, the last being a variant with five significant spike protein mutations leading to escape from immunity from prior infections or vaccination. In addition, our monoclonal antibody therapies do not work for these isolates. Infections and hospitalizations in New York are rapidly increasing, secondary to BQ variants. BQ variants have been found in all 10 regions in the United States. Since New York has been a harbinger of things to come throughout the pandemic, we expect the pattern of increased infections, hospitalizations and deaths to continue in many states. These emerging BQ variants are descendants of BA.5. It’s troubling that, despite the availability of a BA.5 bivalent SARS-CoV-2 vaccine, few people are getting vaccinated. As of November 17, 2022, the CDC reports that the Pfizer Omicron BA.5 mRNA booster was administered to 22,681,194 people and the Moderna Omicron BA.5 mRNA booster was administered to 12,715,605 people. In total, 35,396,799 people in the United States (5 years and up) have received the bivalent vaccine. That’s only 15.5% of people who received the primary series and 10.6% of the overall population.

Children under the age of 5 have not been approved to receive either Omicron BA.5 mRNA boosters. Sadly, in children between 0 and 5 years of age only 1.5 million have received at least one dose of any SARS-CoV-2 mRNA vaccine based on the original Wuhan isolate. In the United States, at least 1,360 children have died of COVID-19, and another 74 have died of multisystem inflammatory syndrome (MIS-C). Worldwide, according to UNICEF, over 16,100 children and young adults aged 0-20 have died of COVID-19.

The October 28 UK Health Security Agency Technical Briefing identifies lineages BQ.1, BQ.1.1, XBB, and BF.7 as isolates of concern. Although BA.5 remains the dominant lineage in the UK, the authors explain, “In the most recent week, logistic growth of variants with 1, 2 or 3 convergent and antigenically significant RBD mutations was respectively 23%, 47%, and 66% per week. The category with 3 RBD mutations consisted largely of BQ.1.1 (59%) with the remainder consisting primarily of a mixture of BA.2.75 sub-lineages (29%).”

Variant	Sublineage of	Spike Mutations	Global Sequences	UK Sequences
BF.7	BA.5.2.1	R346T	11,922	2,644
BQ.1	BA.5	L452RN460KK444T	2,490	3,207
BQ.1.1	BA.5	N460KK444TR346T	2,304(35 countries)	1,272
BS.1	BA.2.3.2	R346TL452RN460KG476S	79	2

In Monterey County during the pandemic we have had 96,339 reported SARS-CoV-2 infections, 2,983 hospitalizations and 795 reported deaths as of 11/18/22. The Monterey County Health Department reports that, as of 11/21/22, 3.1% of 0-4 year-olds and 40.1% of 5-11 year-olds have received the first two doses of vaccine, while 73.3% of 12-17 year-olds have received two doses. Only 55% of Monterey County residents have received a third dose of the vaccine. The Monterey County Health Department does not publish data on how many residents have received the new BA.5 bivalent booster vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. All Monterey County residents should get up to date on COVID-19 vaccinations, including the bivalent BA.5 booster, as soon as possible.

On 11/18/22, the United States had 22,851 documented new infections. There were also 160 deaths. Thirty-four states did not report their infections, and 36 states didn’t report their deaths. In the United States on 11/18/22 the number of hospitalized patients (27,868) has increased slightly (+2% compared to the previous 14 days) in many areas and was 27,395 on November 5. On 11/18/22 there were 3,362 patients who were seriously or critically ill; that number was 3,146 two weeks ago. The number of critically ill patients has increased by 216 in the last 14 days, while at least 4,401 new deaths occurred. The number of critically ill patients has increased for the seventh time in thirty-one 14-day periods. Patients are still dying each day (average 314/day). Two new Omicron variants BQ.1 and BQ.1.1 are causing increased numbers of infections and hospitalizations in New York and the rest of the country. BA.2.75, BA.4.6, BA.5, BF.7 and BN.1 and other variants are still causing infections. In Singapore a different Omicron BA.2 variant, XBB, has caused rapidly increasing infections and now has been named a designated variant along with BQ.1 in the October 28 UK Health Security Agency Technical Briefing. Past infections with a BA.1, BA.2 or BA.5 variants will not prevent infections with any of the newer variants. Monoclonal antibodies are not effective against newer BQ variants and other spike protein mutated variants. Paxlovid was only 89% effective in the original clinical trials against SARS-CoV-2. If resistance develops this winter to oral Paxlovid, we will have more Paxlovid failures and increased hospitalizations and deaths.

As of 11/18/22, we have had 1,102,439 deaths and 100,156,325 SARS-CoV-2 infections in the United States. We have had 553,847 new infections in the last 14 days. We are adding an average of 276,934 new infections every seven days. For the pandemic in the United States we are averaging one death for every 90.84 infections or over 11,007 deaths for each one million infections. As of 11/18/22, thirty-nine states have had greater than 500,000 total infections, and 38 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 33 states have greater than 3,000 deaths per million population. Seven states have over 4,000 deaths per million population: Mississippi (4,374), Arizona (4,348), Alabama (4,205), West Virginia (4,230), New Mexico (4,147), Tennessee (4,134), and Arkansas (4,153). . Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Eight states have had greater than 40,000 deaths: Florida (82,875 deaths), Texas (91,854 deaths), New York (73,831 deaths), Pennsylvania (48,126 deaths), Georgia (40,915 deaths), Ohio (40,391 deaths) , Illinois (40,198 deaths), and California (97,239 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (23 months), there were 835,338 new deaths from SARS-CoV-2. For twenty of those months, vaccines have been available to all adults. During these twenty months, 530,340 people have died of SARS-CoV-2 infections. Clearly, a vaccine-only approach is not working anywhere, especially not in the United States. In addition to getting more people vaccinated, most of the hospitalizations and deaths could have been prevented by proper masking (N95 or better), social distancing, and treatment with oral antiviral agents like Paxlovid. We recommend all of these precautions and treatments to every patient in our clinic, and we have only lost one patient to COVID in 2.5 years.

As of 11/18/22, California was ranked 33rd in the USA in infection percentage at 28.86%. In California, 24.89% of the people were infected in the last 20 months. As of 11/18/22, 28 states have had greater than 30% of their population infected. Fifty states, the District of Columbia and Puerto Rico have greater than 20% of their population infected.

Worldwide, average deaths per day are 1,459 for the last 14 days, which is a 178 deaths-per-day decrease over the previous 14 days. The United States accounts for 21.52% (314 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 376,514 the last two weeks. The United States accounts for 10.51% of those infections (or 39,561 infections per day).

FDA-Approved Oral Drug Treatments for SARS-CoV-2

Pfizer has developed PAXLOVID™, an oral reversible inhibitor of C3-like protease of SARS-CoV-2. The drug inhibits this key enzyme that is crucial for virus production. The compound, also called Compound 6 (PF-07321332), is part of the drug combination PAXLOVID™ (PF-07321332; ritonavir), which just successfully completed a Phase 2-3 trial in humans in multiple countries. The preliminary results were announced on 11/5/21 by Pfizer. The results show that 89% of the hospitalizations and deaths were prevented in the drug treatment arm. The drug was administered twice a day for five days. No deaths occurred in the treatment group, and ten deaths occurred in the placebo group. The study was stopped by an independent data safety monitoring board, and the FDA concurred with this decision. Pfizer applied for an Emergency Use Authorization for this drug on 11/15/21. This drug was approved on 12/23/21. We have only been able to obtain PAXLOVID™ for two patients who we successfully treated with this drug obtained from CVS in Salinas (East Alisal Street; phone number 831-424-0026). They were expecting another shipment on 1/28/22. In my opinion, this agent, if more widely available, could markedly alter the course of every coronavirus infection throughout the world.

Merck has developed the oral drug Molnupiravir, which induces RNA mutagenesis by viral RNA-dependent RNA polymerase of SARS-CoV-2 and other viruses. According to Kabinger et al, “Viral RNA-dependent RNA polymerase uses the active form of Molnupiravir, β-D-N4-hydroxycytidine triphosphate, as a substrate instead of cytidine triphosphate or uridine triphosphate. When the RNA-dependent RNA polymerase uses the resulting RNA as a template, β-D-N4-hydroxycytidine triphosphate directs incorporation of either guanine or adenine, leading to mutated (viral) RNA products. Analysis of RNA-dependent RNA polymerase–RNA complexes that contain mutagenesis products has demonstrated that β-D-N4-hydroxycytidine (the active form of Molnupiravir) can form stable base pairs with either guanine or adenine in RNA-dependent RNA polymerase explaining how the polymerase escapes proofreading and synthesizes mutated RNA” (quotation modified for clarity). The results of the phase 3 trial of Molnupiravir were published in the NEJM article “Molnupiravir for Oral Treatment of Covid-19 in Nonhospitalized Patients” by Angélica Jayk Bernal, M.D. et al. (December 16, 2021 DOI: 10.1056/NEJMoa2116044). In this phase 3 study in the Molnupiravir group, 28 patients were hospitalized and one death occurred. In the placebo group, 53 patients were hospitalized and 9 died. Overall, 47% of hospitalizations and deaths were prevented by Molnupiravir. If you do a post hoc analysis and just look at deaths, Molnupiravir would prevent 89% of deaths. An Emergency Use Authorization by the FDA for Molnupiravir was approved on 12/24/21.The dose of Molnupiravir approved is four 200 mg capsules orally twice a day for five days. Diarrhea is reportedly a side effect in two percent of patients. I treated my first patient with Molnupiravir on 1/28/22. Currently more Molnupiravir is available weekly in the United States than PAXLOVID™ (see chart below; data from PHE.gov). Locally Molnupiravir is still available at CVS in Monterey (Fremont Blvd.; phone number: 831-375-5135) and CVS in Salinas (East Alisal Street; phone number 831-424-0026).

FDA-Approved Intravenous Monoclonal Antibody Treatment for Non-Hospitalized SARS-CoV-2 Patients

Bebtelovimab is a monoclonal antibody treatment for mild-to-moderate COVID-19 in adults and pediatric patients (12 years of age and older weighing at least 40 kg) with positive results of direct SARS-CoV-2 viral testing, and who are at high risk for progression to severe COVID-19, including hospitalization or death, and for whom alternative COVID-19 treatment options approved or authorized by FDA are not accessible or clinically appropriate. The authorized dose of bebtelovimab is 175 mg, given as an intravenous injection over at least 30 seconds. The U.S. Food and Drug Administration (FDA) has issued an Emergency Use Authorization (EUA) for this drug on 2/11/22. Bebtelovimab is a human antibody that demonstrates neutralization against the Omicron variants and is available in every state and many hospitals and some clinics. If you are planning on using a monoclonal antibody to treat a SARS-CoV-2 infection, currently only bebtelovimab has activity against all Omicron variants, including BA.4.6. Researchers at Columbia University recently reported that “The loss of activity of tixagevimab and cilgavimab [components of Evusheld] against BA.4.6 leaves us with bebtelovimab as the only therapeutic mAb that has retained potent activity against all circulating forms of SARS-CoV-2.” For this reason, we no longer recommend Evusheld for immunocompromised patients with Omicron infections.

An examination of the three variants that Wang et al identified as capable of immune escape in patients who receive the two monoclonal antibodies that are contained in Evusheld reveals that all three variants have a mutation in the spike protein at position 346. The changes substitute an uncharged amino acid— threonine (T), serine (S), or isoleucine (I)—for a positively-charged amino acid, arginine. This just goes to show that a single point mutation in the spike protein can render a monoclonal antibody treatment ineffective. Policy makers should keep in mind that the only way to prevent new drug-resistant variants like BA.4.6 from emerging is to prevent transmission of SARS-CoV-2 in the first place, using non-pharmaceutical interventions. The lack of use of N95 masks, with impending winter and influenza outbreaks, on top of COVID-19, is not wise public health and infectious disease policy. If we don’t make effective use of the non-pharmaceutical interventions available to us (masks, ventilation, social distancing), then the pharmaceutical interventions we have will all eventually be useless.

Two virologists collaborated on Twitter to create the figure below, which Professor Johnson titled “Convergent Evolution on Steroids.” It shows the key mutations present in many of the currently-circulating Omicron subvariants and demonstrates that mutation at site 346 is becoming more and more common. This means that even if prevalence of BA.4.6 wanes, we are still likely to have drug resistance issues with other newer variants.

From Daniele Focosi, M.D., Ph.D. @dfocosi on Twitter

Watching World Data

Over the next few months, we’ll be paying close attention to correlations between the SARS-CoV-2 data, the number of isolates identified in various countries and states, and the non-pharmaceutical interventions (like mask mandates and lockdowns) put in place by state and national governments. Data on infections, deaths, and percent of population infected was compiled from Worldometers. Data for this table for SARS-CoV-2 Isolates Currently Known in Location was compiled from GISAID and the CDC. It’s worth noting that GISAID provided more data than the CDC.

Location	Total Infections as of 11/18/22	New Infections on 11/18/22	Total Deaths	New Deaths on 11/18/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	642,552,835(5,271,193 new infections in 14 days).	344,837	6,624,873(20,425 new deaths in last 14 days)	1,083	8.24%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)BF.7BJ.1XBBBQ.1BQ.1.1BS.1BN.1*	No	No
USA	100,156,325(ranked #1) 553,847 new infections in the last 14 days or 39,561/day.	22,851(ranked #6) 34 states and D,C. failed to report infections on 11/18/22.	1,102,439(ranked #1) 4,401 new deaths reported in the last 14 days or 388/day.	160 36 states and D.C. failed to report deaths on 11/18/22.	29.91%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)BQ.1BQ.1.1BN.1*	No	No
Brazil	35,039,614(ranked #5) 149,371 new infections in the last 14 days.	30,438 (ranked#4)	688,958(ranked #2; 574 new deaths in 14 days)	72	16.27%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,669,527(ranked #2); 10,080 new infections in 2 weeks.	576	530,533(ranked #3) 47 new deaths in 2 weeks.	–	3.17%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,977,637(ranked #6) 49,596 new infections in 2 weeks.	–	196,241 (ranked #7) 1,537 new deaths in 2 weeks	–	35.00%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,405,188(ranked #14 in the world; 51,292 new infections in the last 14 days).	2,217	97,239 (ranked #20 in world) 255 new deaths in the last 14 days	7	28.86%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BQ.1BQ.1.1BN.1*	No	No
Mexico	7,118,933(ranked #19) 5,801 new infections in 14 days).	–	330,444(ranked #5)29 new deaths in 14 days)	–	5.41%		No	No
South Africa	4,037,221(ranked #37; 7,484 new infections in 14 days).	598	102,371 (ranked #18) 8 new deaths in 14 days)	–	6.64%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,377,070(ranked #33) 40,210 new infections in 14 days).	–	47,118(ranked #25 ) 749 new deaths in the last 14 days	–	11.40%		No	No
Poland	6,348,380(ranked #21; 14,789 new infections in 14 days).	359	118,267 (ranked #15)110 new deaths in the last 14 days	15	16.82%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	21,525,567 (ranked #10), 71,900 new infections in 14 days).	5,546 (ranked #12)	391,333(ranked #4)874 new deaths in 14 days	60	14.76%		No	No
Peru	4,159,132(ranked #35, 25,059 new infections in 14 days).	3,357	217,229(ranked #6) 257 new deaths in the last 14 days	11	12.42%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,559,211(ranked #18; 1,189 new infections in last 14 days)	47	144,620(ranked #12) 33 new deaths in the last 14 days	3	8.78%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,573,721(ranked #12; 44,078 new infections in 14 days).	3,168	115,641 (ranked #16)402 new deaths in 14 days	38	29.0%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	37,287,547(ranked #3; 367,483 new infections in the last 14 days).	37,177 (ranked #3)	158,163 (ranked #10)886 new deaths in 14 days.	74	56.29% a 0.56% increase in 14 days.	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinantBQ.1.1	No	No
Germany	36,205,405(ranked #4; 381,634 new infections in 14 days.)	25,238 (ranked #5)	156,613 (ranked #11)2,078 new deaths in 14 days	203	43.16% 0.46% increase in 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinantBQ.1.1	No	No
South Korea	26,462,319 (ranked #6 701,618 new infections in 14 days).	49,418(ranked #2)	29,925 (ranked #35) 609 new deaths in 14 days	63	51.55%2.37% increase in 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,510,919 (ranked #13; 5,670 new infections in 14 days).	435	43,168(ranked #26)	1	11.63%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,534,144 (ranked #16; 11,415 new infections in 14 days).	853	22,892 (ranked #41)	2	49.58%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,143,261 (ranked #40) 6,511 new infections in 14 days.	290	7,470 (ranked #78 83 new deaths in the last 14 days)	–	53.86%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	8,130,219(ranked #17)292,561 new infections in 14 days	17,991 (ranked #7)	13,848 (ranked #58 764 new deaths in the last 14 days)	58	34.03% 1.22% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	23,604,176(ranked #9)1,069,799 new infections in the last 14 days	84,375(ranked #1)	48,058(ranked #24) 1,160 new deaths in the last 14 days	99	18.79% 0.85% of the population infected in the last 14 days.	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No
Argentina	9,721,718 (ranked #15)	–	130,011(ranked #14)	–	21.12%		No	No
Italy	24,031,538 (ranked #7) 389,527 new infections in the last 14 days.	–	180,581(ranked #8) 1,145 new deaths in the last 14 days	–	39.87% 0.64% of population infected in last 14 days.		No	No
Chile	4,865,658(ranked #28) 88,450 new infections in14 days..	6,457 (ranked#11)	62,130(ranked #22) 398 new deaths in the last 14 days.	28	25.27% 0.46% of population infected in the last 14 days.		No	No
Colombia	6,312,657(ranked #22)	–	141,881(ranked #13)	–	12.25%		No	No
Australia	10,552,678(ranked #14) 833,801 new infections in 14 days.	10,925 (ranked #8)	15,967(ranked #55) 191 new deaths in 14 days.	14	40.48% 0.53% of population infected in last 14 days.		No	No
Turkey	16,976,729(ranked #11)57,091 new infections in 14 days.	–	101,327(ranked #19) 124 new deaths in 14 days..	–	19.84%		No	No
Indonesia	6,596,,812 (ranked #20) 83,899 new infections in last 14 days.	6,699 (ranked #10)	159,323 (ranked #9) 555 new deaths in the last 14 days.	32	23.63%		No	No
Malaysia	4,963,216 (ranked #27) 44,299 new infections in the last 14 days.	3,037 (ranked #17)	36,588 (ranked #29) 124 new deaths in the last 14 days.	5	14.95%		No	No
Hong Kong	2,020,885(ranked#47)	8,008 (ranked#9)	10,577 (ranked#65)	8	26.57%		No	No
China	279,431	2,388	5,226	–	–	–	–	–

What Our Team Is Reading This Week

Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States (Preprint) https://doi.org/10.1101/2022.05.23.22275458
Post-COVID-19-associated morbidity in children, adolescents, and adults: A matched cohort study including more than 157,000 individuals with COVID-19 in Germany (PLOS Medicine) https://journals.plos.org/plosmedicine/article?id=10.1371%2Fjournal.pmed.1004122
Endothelial dysfunction in COVID-19: an overview of evidence, biomarkers, mechanisms and potential therapies (Acta Pharmacologica Sinica) https://doi.org/10.1038/s41401-022-00998-0
Cognitive Deficits in Long Covid-19 (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMcibr2210069
Brain 18F-FDG PET imaging in outpatients with post-COVID-19 conditions: findings and associations with clinical characteristics (European Journal of Nuclear Medicine and Molecular Imaging) https://doi.org/10.1007/s00259-022-06013-2
Acute and postacute sequelae associated with SARS-CoV-2 reinfection (Nature) https://doi.org/10.1038/s41591-022-02051-3
Associations between indoor relative humidity and global COVID-19 outcomes (Journal of the Royal Society) https://doi.org/10.1098/rsif.2021.0865
Successful treatment of prolonged, severe COVID-19 lower respiratory tract disease in a B-cell ALL patient with an extended course of remdesivir and nirmatrelvir/ritonavir (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac868
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis (Preprint) https://doi.org/10.1101/2022.10.18.512708
Anti-PF4 antibodies associated with disease severity in COVID-19 (PNAS) https://www.pnas.org/doi/10.1073/pnas.2213361119
A multinational Delphi consensus to end the COVID-19 public health threat (Nature) https://doi.org/10.1038/s41586-022-05398-2
Pfizer and BioNTech Announce Updated Clinical Data for Omicron BA.4/BA.5-Adapted Bivalent Booster Demonstrating Substantially Higher Immune Response in Adults Compared to the Original COVID-19 Vaccine https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-announce-updated-clinical-data-omicron
Paxlovid and Long Covid (Ground Truths, Eric Topol) https://erictopol.substack.com/p/paxlovid-and-long-covid?utm_source=substack&utm_medium=email
Risk of Infection and Hospitalization Among Children and Adolescents in New York After Emergence of the SARS-CoV-2 Omicron Variant – Comment and Response (JAMA) https://jamanetwork.com/journals/jama/article-abstract/2797231
Myocarditis (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMra2114478
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 47 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1115077/Technical-Briefing-47.pdf
Effectiveness of Monovalent mRNA Vaccines Against COVID-19–Associated Hospitalization Among Immunocompetent Adults During BA.1/BA.2 and BA.4/BA.5 Predominant Periods of SARS-CoV-2 Omicron Variant in the United States — IVY Network, 18 States, December 26, 2021–August 31, 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7142a3.htm
- “Three-dose monovalent mRNA VE estimates against COVID-19–associated hospitalization decreased with time since vaccination. Three-dose VE during the BA.1/BA.2 and BA.4/BA.5 periods was 79% and 60%, respectively, during the initial 120 days after the third dose and decreased to 41% and 29%, respectively, after 120 days from vaccination.”
Saliva antibody-fingerprint of reactivated latent viruses after mild/asymptomatic COVID-19 is unique in patients with myalgic-encephalomyelitis/chronic fatigue syndrome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.949787
SARS-CoV-2 Nsp6 causes cardiac defects through MGA/MAX complex-mediated increased glycolysis (Preprint) https://doi.org/10.21203/rs.3.rs-1677754/v1
WHO’s Therapeutics and COVID-19 Living Guideline on mAbs needs to be reassessed (The Lancet) https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)01938-9/fulltext
SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry (Nature) https://doi.org/10.1038/s41586-022-05282-z
Real-world effectiveness of molnupiravir and nirmatrelvir plus ritonavir against mortality, hospitalisation, and in-hospital outcomes among community-dwelling, ambulatory patients with confirmed SARS-CoV-2 infection during the omicron wave in Hong Kong: an observational study (The Lancet) https://doi.org/10.1016/S0140-6736(22)01586-0
An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines (PLOS Pathogens) https://doi.org/10.1371/journal.ppat.1010828
Plasma cytokine levels reveal deficiencies in IL-8 and gamma interferon in Long-COVID (Preprint) https://doi.org/10.1101/2022.10.03.22280661
Lingering cardiac involvement in previously well people after mild COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02002-y
SARS-CoV-2 variants of concern and variants under investigation in England: technical briefing 46 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1109820/Technical-Briefing-46.pdf
Rapid initiation of nasal saline irrigation to reduce severity in high-risk COVID+ outpatients (Ear, Nose, and Throat Journal) https://doi.org/10.1177/01455613221123737
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://doi.org/10.1101/2022.09.22.509040
Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.15.507787v2
- Note: This is a frightening paper and if the conclusions are accurate humans in general are in trouble. From other papers the facts that HERV-M and EBV are activated by SARS-CoV-2 infection does not bode well for humans moving forward.
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.22.509040v1
Evolution of antibody immunity following Omicron BA.1 breakthrough infection (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.21.508922v1
SARS-CoV-2 Spike protein promotes vWF secretion and thrombosis via endothelial cytoskeleton-associated protein 4 (CKAP4) (Signal Transduction and Targeted Therapy) https://www.nature.com/articles/s41392-022-01183-9
Long-term neurologic outcomes of COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02001-z
Pulmonary Dysfunction after Pediatric COVID-19 (Radiology) https://pubs.rsna.org/doi/10.1148/radiol.221250
Severe Respiratory Illnesses Associated with Rhinoviruses and/or Enteroviruses Including EV-D68 – Multistate, 2022 (CDC) https://emergency.cdc.gov/han/2022/han00474.asp
VACCINE INFORMATION FACT SHEET FOR RECIPIENTS AND CAREGIVERS ABOUT COMIRNATY (COVID-19 VACCINE, mRNA), THE PFIZER-BIONTECH COVID-19 VACCINE, AND THE PFIZER-BIONTECH COVID-19 VACCINE BIVALENT (ORIGINAL AND OMICRON BA.4/BA.5) TO PREVENT CORONAVIRUS DISEASE 2019 (COVID-19) FOR USE IN INDIVIDUALS 12 YEARS OF AGE AND OLDER https://labeling.pfizer.com/ShowLabeling.aspx?id=14472
Pfizer/BioNTech COVID-19 Omicron-Modified Bivalent Vaccine https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2022-09-01/07-covid-swanson-508.pdf
Coronavirus (COVID-19) Update: FDA Authorizes Moderna, Pfizer-BioNTech Bivalent COVID-19 Vaccines for Use as a Booster Dose (FDA) https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-moderna-pfizer-biontech-bivalent-covid-19-vaccines-use
Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.05.506628v1.full
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 45, 9 September 2022 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1103869/Technical-Briefing-45-9September2022.pdf
SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors (Biophysics and Computational Biology) https://doi.org/10.1073/pnas.2119761119

COVID-19

SARS-CoV-2 Update

11/06/202211/06/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have increased for the first time in 14 weeks. There is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have increased by 34 deaths per day. Many states are not reporting deaths or infections in a timely manner. The number of infections per day has increased by 1,683. The CDC estimates that BA.5 accounted for 39.2% (a 23% drop from 10/21/22), BQ.1 accounted for 16.5% (a 7.1% increase since 10/21/22), BQ.1.1 accounted for 18.8% (a 11.6% increase since 10/21/22), BA.4.6 accounted for 9.5%, BF.7 accounted for 9%, BA.2.75.2 accounted for 1.3%, and BA.4 accounted for 0.2%. In the week ending November 5, 2022 BQ isolates accounted for 35.3% of infections. BQ.1.1 has five spike mutations that are different from BA.5. Four of these mutations allow escape from immunity from monoclonal antibodies, any prior infection (including BA.5), or any vaccine to include a BA.5 vaccine.

The total percentage of BQ variant infections in the region that includes New York and New Jersey was 28.4% two weeks ago and is now 52.3%. BA.5.2.6 isolates now account for 3.1% of cases. The BA.2.75 lineages account for 4.2%.

The total percentage of BQ variant infections in the region that includes Pennsylvania, Delaware, Maryland, West Virginia, and Virginia was 17.8% two weeks ago and is now 36.6%. BA.5.2.6 isolates now account for 3.4% of cases. The BA.2.75 lineages account for 3% of cases.

Data on the rapid spread of a dangerous variant category, the BQ variants, was withheld by the CDC in their weekly reports until three weeks ago. The data on BQ.1 and BQ.1.1, the last being a variant with five significant spike protein mutations leading to escape from immunity from prior infections or vaccination. In addition, our monoclonal antibody therapies do not work for these isolates. Infections and hospitalizations in New York are rapidly increasing, secondary to BQ variants. BQ variants have been found in all 10 regions in the United States. Since New York has been a harbinger of things to come throughout the pandemic, we expect the pattern of increased infections, hospitalizations and deaths to continue in many states. These emerging BQ variants are descendants of BA.5. It’s troubling that, despite the availability of a BA.5 bivalent SARS-CoV-2 vaccine, few people are getting vaccinated. As of November 2, 2022, the CDC reports that only 26,378,963 people have received the bivalent vaccine. The Pfizer Omicron BA.5 mRNA booster was administered to 16,748,737 people and the Moderna Omicron BA.5 mRNA booster was administered to 9,630,226 people. In total, 26.3 million people (5 years and up) have received the bivalent vaccine. That’s only 11.6% of people who received the primary series and 7.9% of the overall population.

Children under the age of 5 have not been approved to receive either Omicron BA.5 mRNA boosters. Sadly, in children between 0 and 5 years of age only 1.47 million have received at least one dose of any SARS-CoV-2 mRNA vaccine. In the United States, at least 1,332 children have died of COVID-19, and another 74 have died of multisystem inflammatory syndrome (MIS-C). Worldwide, according to UNICEF, over 16,100 children and young adults aged 0-20 have died of COVID-19.

Variant	Sublineage of	Spike Mutations	Global Sequences	UK Sequences
BF.7	BA.5.2.1	R346T	11,922	2,644
BQ.1	BA.5	L452RN460KK444T	2,490	3,207
BQ.1.1	BA.5	N460KK444TR346T	2,304(35 countries)	1,272
BS.1	BA.2.3.2	R346TL452RN460KG476S	79	2

Data from UK Health Security Agency

In Monterey County, as of 11/5/22, 2.6% of 0-4 year-olds and 40.1% of 5-11 year-olds have received the first two doses of vaccine, while 73.4% of 12-17 year-olds have received two doses. Only 54.5% of Monterey County residents have received a third dose of the vaccine. The Monterey County Health Department does not publish data on how many residents have received the new BA.5 bivalent booster vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. All Monterey County residents should get up to date on COVID-19 vaccinations, including the bivalent BA.5 booster, as soon as possible.

On 11/04/22, the United States had 21,312 documented new infections. There were also 148 deaths. Thirty-five states did not report their infections, and 37 states didn’t report their deaths. In the United States the number of hospitalized patients has increased slightly (+2% compared to the previous 14 days) in many areas and was 27,395 on November 5. On 11/05/22 there were 3,146 patients who were seriously or critically ill; that number was 2,707 two weeks ago. The number of critically ill patients has increased by 439 in the last 14 days, while at least 5,432 new deaths occurred. The number of critically ill patients has decreased for the sixth time in thirty 14-day periods. Patients are still dying each day (average 388/day). Two new Omicron variants BQ.1 and BQ.1.1 are causing increased numbers of infections and hospitalizations in New York. BA.4, BA.4.6, BA.5, and BF.7 variants are still causing infections. In Singapore a different Omicron BA.2 variant, XBB, has caused rapidly increasing infections and now has been named a designated variant along with BQ.1 in the October 28 UK Health Security Agency Technical Briefing. Past infections with a BA.1, BA.2 or BA.5 variants will not prevent infections with any of the newer variants.

As of 11/04/22, we have had 1,098,038 deaths and 99,602,478 SARS-CoV-2 infections in the United States. We have had 546,941 new infections in the last 14 days. We are adding an average of 273,348 new infections every seven days. For the pandemic in the United States we are averaging one death for every 90.71 infections or over 11,024 deaths for each one million infections. As of 11/04/22, thirty-eight states have had greater than 500,000 total infections, and 38 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 43 states have greater than 2,000 deaths per million population. Seven states have over 4,000 deaths per million population: Mississippi (4,365), Arizona (4,338), Alabama (4,193), West Virginia (4,202), New Mexico (4,132), Tennessee (4,118), and Arkansas (4,148). . Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Eight states have had greater than 40,000 deaths: Florida (82,357 deaths), Texas (91,737 deaths), New York (73,549 deaths), Pennsylvania (47,840 deaths), Georgia (40,696 deaths), Ohio (40,249 deaths) , Illinois (40,058 deaths), and California (96,984 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (23 months), there were 830,937 new deaths from SARS-CoV-2. For nineteen of those months, vaccines have been available to all adults. During these nineteen months, 525,939 people have died of SARS-CoV-2 infections. Clearly, a vaccine-only approach is not working anywhere, especially not in the United States. In addition to getting more people vaccinated, most of the hospitalizations and deaths could have been prevented by proper masking (N95 or better), social distancing, and treatment with oral antiviral agents like Paxlovid. We recommend all of these precautions and treatments to every patient in our clinic, and we have only lost one patient to COVID in 2.5 years.

As of 11/04/22, California was ranked 33rd in the USA in infection percentage at 28.73%. In California, 24.76% of the people were infected in the last 20 months. As of 11/06/22, 24 states have had greater than 30% of their population infected. Fifty states have greater than 20% of their population infected.

Worldwide, average deaths per day are 1,637 for the last 14 days, which is a 68 deaths-per-day increase over the previous 14 days. The United States accounts for 23.70% (388 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 346,369. The United States accounts for 11.28% of those infections (or 39,067 infections per day).

FDA-Approved Oral Drug Treatments for SARS-CoV-2

28, p740–746 (2021)with four 200 mg capsules orally twice a day for five dayfour 200 mg capsules orally twice a day for five daysIntravenous Drug Treatment for non-hospitalized SARS-CoV-2 Infected Patient

FDA-Approved Intravenous Monoclonal Antibody Treatment for Non-Hospitalized SARS-CoV-2 Patients

From Daniele Focosi, M.D., Ph.D. @dfocosi on Twitter

Watching World Data

Location	Total Infections as of 11/04/22	New Infections on 11/04/22	Total Deaths	New Deaths on 11/04/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	637,281,842(4,849,164 new infections in 14 days).	273,333	6,604,448(22,918 new deaths in last 14 days)	1,091	8.17%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)BF.7BJ.1XBBBQ.1BQ.1.1BS.1*	No	No
USA	99,602,478(ranked #1) 546,941 new infections in the last 14 days or 39,067/day.	19,652(ranked #6) 35 states and D,C. failed to report infections on 11/04/22.	1,098,038(ranked #1) 5,432 new deaths reported in the last 14 days or 388/day.	148 37 states and D.C. failed to report deaths on 11/04/22.	29.74%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,890,243(ranked #5) 62,069 new infections in the last 14 days.	2,738	688,384(ranked #2; 803 new deaths in 14 days)	68	16.20%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,659,447(ranked #2); 18,699 new infections in 2 weeks.	1,082	530,486(ranked #3) 1,529 new deaths in 2 weeks.	7	3.17%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,930,041(ranked #7) 74,519 new infections in 2 weeks.	–	194,704 (ranked #7) 2,022 new deaths in 2 weeks	–	34.93%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,353,896(ranked #13 in the world; 21,351 new infections in the last 14 days).	1,434	96,984 (ranked #20 in world) 303 new deaths in the last 14 days	7	28.73%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	7,113,132(ranked #19) 7,114 new infections in 14 days).	628	330,415(ranked #5)94 new deaths in 14 days)	5	5.40%		No	No
South Africa	4,029,737(ranked #37; 4,362 new infections in 14 days).	241	102,363 (ranked #18) 106 new deaths in 14 days)	52	6.63%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,336,860(ranked #33) 22,142 new infections in 14 days).	–	46,389(ranked #25 ) 364 new deaths in the last 14 days	–	11.29%		No	No
Poland	6,333,591 (ranked #21; 9,506 new infections in 14 days).	693	118,157 (ranked #15)142 new deaths in the last 14 days	14	16.80%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	21,453667(ranked #10), 98,753 new infections in 14 days).	6,149 (ranked #9)	390,459(ranked #4)1,100 new deaths in 14 days	71	14.71%		No	No
Peru	4,159,132(ranked #36, 7,113new infections in 14 days).	598	216,972(ranked #6) 95 new deaths in the last 14 days	5	12.34%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,558,002(ranked #17; 2,308 new infections in last 14 days)	40	144,587(ranked #12) 47 new deaths in the last 14 days	4	8.78%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,529,643(ranked #12; 41,628 new infections in 14 days).	2,551	115,239 (ranked #16)381 new deaths in 14 days	23	28.95%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	36,920,064 (ranked #3; 395,459 new infections in the last 14 days).	29,438 (ranked #4)	157,277 (ranked #10)940 new deaths in 14 days.	78	56.29% a 0.60% increase in 14 days.	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	35,823,771(ranked #4; 651,078 new infections in 14 days.)	38,859 (ranked #2)	154,535 (ranked #11)2,053 new deaths in 14 days	207	42.70% 0.77% increase in 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	25,760,701 (ranked #6 516,446 new infections in 14 days).	43,424(ranked #1)	29,315 (ranked #36) 363 new deaths in 14 days	35	49.18%1.00% increase in 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,505,249 (ranked #13; 8,895 new infections in 14 days).	339	43,165(ranked #26)	–	11.62%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,521,729 (ranked #16; 27,024 new infections in 14 days).	1,225	22,845 (ranked #41)	3	49.51%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,138,750 (ranked #40) 7,601 new infections in 14 days.	355	7,387 (ranked #78 139 new deaths in the last 14 days)	12	53.79%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	7,837,658(ranked #17)458,453 new infections in 14 days	27,594 (ranked #5)	13,084 (ranked #59 878 new deaths in the last 14 days)	74	32.80% 1.91% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	22,534,377(ranked #9)608,146 new infections in the last 14 days	34,064(ranked #5)	46,898(ranked #24) 757 new deaths in the last 14 days	59	17.94%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No
Argentina	9,718,875 (ranked #15)	–	129,991(ranked #14)	–	21.12%		No	No
Italy	23,642,011 (ranked #8)	–	179,436(ranked #8)		39,23%		No	No
Chile	4,777,208(ranked #28)	7,570	61,737(ranked #22)	12	24.81%		No	No
Colombia	6,310,332(ranked #14)	–	141,850(ranked #13)	–	12.25%		No	No
Australia	9,718,875(ranked #14)	15,618 (ranked #7)	15,776(ranked #55)	59	39.95%		No	No
Turkey	16,919,638(ranked #11)	–	101,203(ranked #19)	–	19.77%		No	No
Indonesia	6,512,913 (ranked #20)	5,303 (ranked #11)	158,768 (ranked #9)	31	23,23%		No	No
Malaysia	4,918,917 (ranked #29)	4,360 (ranked #13)	36,481 (ranked #29)	1	14.75%		No	No

What Our Team Is Reading This Week

Successful treatment of prolonged, severe COVID-19 lower respiratory tract disease in a B-cell ALL patient with an extended course of remdesivir and nirmatrelvir/ritonavir (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac868
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis (Preprint) https://doi.org/10.1101/2022.10.18.512708
Anti-PF4 antibodies associated with disease severity in COVID-19 (PNAS) https://www.pnas.org/doi/10.1073/pnas.2213361119
A multinational Delphi consensus to end the COVID-19 public health threat (Nature) https://doi.org/10.1038/s41586-022-05398-2
Pfizer and BioNTech Announce Updated Clinical Data for Omicron BA.4/BA.5-Adapted Bivalent Booster Demonstrating Substantially Higher Immune Response in Adults Compared to the Original COVID-19 Vaccine https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-announce-updated-clinical-data-omicron
Paxlovid and Long Covid (Ground Truths, Eric Topol) https://erictopol.substack.com/p/paxlovid-and-long-covid?utm_source=substack&utm_medium=email
Risk of Infection and Hospitalization Among Children and Adolescents in New York After Emergence of the SARS-CoV-2 Omicron Variant – Comment and Response (JAMA) https://jamanetwork.com/journals/jama/article-abstract/2797231
Myocarditis (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMra2114478
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 47 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1115077/Technical-Briefing-47.pdf
Effectiveness of Monovalent mRNA Vaccines Against COVID-19–Associated Hospitalization Among Immunocompetent Adults During BA.1/BA.2 and BA.4/BA.5 Predominant Periods of SARS-CoV-2 Omicron Variant in the United States — IVY Network, 18 States, December 26, 2021–August 31, 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7142a3.htm
- “Three-dose monovalent mRNA VE estimates against COVID-19–associated hospitalization decreased with time since vaccination. Three-dose VE during the BA.1/BA.2 and BA.4/BA.5 periods was 79% and 60%, respectively, during the initial 120 days after the third dose and decreased to 41% and 29%, respectively, after 120 days from vaccination.”
Saliva antibody-fingerprint of reactivated latent viruses after mild/asymptomatic COVID-19 is unique in patients with myalgic-encephalomyelitis/chronic fatigue syndrome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.949787
SARS-CoV-2 Nsp6 causes cardiac defects through MGA/MAX complex-mediated increased glycolysis (Preprint) https://doi.org/10.21203/rs.3.rs-1677754/v1
WHO’s Therapeutics and COVID-19 Living Guideline on mAbs needs to be reassessed (The Lancet) https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)01938-9/fulltext
SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry (Nature) https://doi.org/10.1038/s41586-022-05282-z
Real-world effectiveness of molnupiravir and nirmatrelvir plus ritonavir against mortality, hospitalisation, and in-hospital outcomes among community-dwelling, ambulatory patients with confirmed SARS-CoV-2 infection during the omicron wave in Hong Kong: an observational study (The Lancet) https://doi.org/10.1016/S0140-6736(22)01586-0
An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines (PLOS Pathogens) https://doi.org/10.1371/journal.ppat.1010828
Plasma cytokine levels reveal deficiencies in IL-8 and gamma interferon in Long-COVID (Preprint) https://doi.org/10.1101/2022.10.03.22280661
Lingering cardiac involvement in previously well people after mild COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02002-y
SARS-CoV-2 variants of concern and variants under investigation in England: technical briefing 46 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1109820/Technical-Briefing-46.pdf
Rapid initiation of nasal saline irrigation to reduce severity in high-risk COVID+ outpatients (Ear, Nose, and Throat Journal) https://doi.org/10.1177/01455613221123737
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://doi.org/10.1101/2022.09.22.509040
Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.15.507787v2
- Note: This is a frightening paper and if the conclusions are accurate humans in general are in trouble. From other papers the facts that HERV-M and EBV are activated by SARS-CoV-2 infection does not bode well for humans moving forward.
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.22.509040v1
Evolution of antibody immunity following Omicron BA.1 breakthrough infection (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.21.508922v1
SARS-CoV-2 Spike protein promotes vWF secretion and thrombosis via endothelial cytoskeleton-associated protein 4 (CKAP4) (Signal Transduction and Targeted Therapy) https://www.nature.com/articles/s41392-022-01183-9
Long-term neurologic outcomes of COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02001-z
Pulmonary Dysfunction after Pediatric COVID-19 (Radiology) https://pubs.rsna.org/doi/10.1148/radiol.221250
Severe Respiratory Illnesses Associated with Rhinoviruses and/or Enteroviruses Including EV-D68 – Multistate, 2022 (CDC) https://emergency.cdc.gov/han/2022/han00474.asp
VACCINE INFORMATION FACT SHEET FOR RECIPIENTS AND CAREGIVERS ABOUT COMIRNATY (COVID-19 VACCINE, mRNA), THE PFIZER-BIONTECH COVID-19 VACCINE, AND THE PFIZER-BIONTECH COVID-19 VACCINE BIVALENT (ORIGINAL AND OMICRON BA.4/BA.5) TO PREVENT CORONAVIRUS DISEASE 2019 (COVID-19) FOR USE IN INDIVIDUALS 12 YEARS OF AGE AND OLDER https://labeling.pfizer.com/ShowLabeling.aspx?id=14472
Pfizer/BioNTech COVID-19 Omicron-Modified Bivalent Vaccine https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2022-09-01/07-covid-swanson-508.pdf
Coronavirus (COVID-19) Update: FDA Authorizes Moderna, Pfizer-BioNTech Bivalent COVID-19 Vaccines for Use as a Booster Dose (FDA) https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-moderna-pfizer-biontech-bivalent-covid-19-vaccines-use
Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.05.506628v1.full
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 45, 9 September 2022 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1103869/Technical-Briefing-45-9September2022.pdf
SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261

COVID-19

SARS-CoV-2 Update

10/25/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have decreased for the fourth time in 12 weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have decreased by 81 deaths per day; however, many states are not reporting deaths in a timely manner. The number of infections per day has decreased by 8,524. The CDC estimates that BA.5 accounted for 62.2% (a 17% drop from 10/7/22), BQ.1 accounted for 9.4%, BQ.1.1 accounted for 7.2%, BA.4.6 accounted for 11.3%, BF.7 accounted for 6.7%, BA.2.75 accounted for 1.6%, BA.2.27.2 accounted for 1.3%, and BA.4 accounted for 0.4%, in the week ending October 22.

The total percentage of BQ variant infections in the region that includes New York and New Jersey is 28.4%.

The total percentage of BQ variant infections in the region that includes Pennsylvania, Delaware, Maryland, West Virginia, and Virginia is 17.8%.

The total percentage of BQ variant infections in the region that includes California, Nevada, Arizona, and Hawaii is 13.6%.

Data on the rapid spread of a dangerous variant category, the BQ variants, was withheld by the CDC in their weekly reports until last week. The data on BQ.1 and BQ.1.1, the last being a variant with five significant spike protein mutations leading to escape from immunity from prior infections or vaccination. In addition, our monoclonal antibody therapies do not work for these isolates. Infections and hospitalizations in New York are rapidly increasing, secondary to BQ variants. We can expect this pattern to continue in many states, since New York has been a harbinger of things to come throughout the pandemic.

These emerging BQ variants are descendants of BA.5. It’s troubling that, despite the availability of a BA.5 bivalent SARS-CoV-2 vaccine, few people are getting vaccinated. As of October 19, the CDC reports that 19.4 million people have received the bivalent vaccine. That’s only 8.5% of people who received the primary series and 5% of the overall population.

There has been no new UK Health Security Agency Technical Briefing since October 7. The October 7 Technical Briefing says, “From UK data, BQ.X, BA.2.75.2 and BF.7 are the most concerning variants in terms of both growth and neutralisation data at present; there is also supportive animal model data for BA.2.75.”

Variant	Sublineage of	Spike Mutations	Global Sequences	UK Sequences
BF.7	BA.5.2.1	R346T	9,809 (1,752 from Belgium)	663
BQ.1.1	BA.5	N460KK444TR346T	326(20 countries)	60
BJ.1	BA.5	13 non- synonymous spike mutations, 7 in RBD and including4 predicted immune escape locations	123 (10 countries, most cases in India)	1
BS.1	BA.2.3.2	R346TL452RN460KG476S	25 (15 from Japan)	0

Data from UK Health Security Agency

In Monterey County, as of 10/22/22, 2.1% of 0-4 year-olds and 40.1% of 5-11 year-olds have received the first two doses of vaccine, while 73.3% of 12-17 year-olds have received two doses. Only 54.1% of Monterey County residents have received a third dose of the vaccine. The Monterey County Health Department does not publish data on how many residents have received the new BA.5 bivalent booster vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. All Monterey County residents should get up to date on COVID-19 vaccinations, including the bivalent BA.5 booster, as soon as possible.

On 10/21/22, the United States had 19,652 documented new infections. There were also 190 deaths. Thirty-four states did not report their infections, and 36 states didn’t report their deaths. In the United States the number of hospitalized patients has decreased slightly (-1% compared to the previous 14 days) in many areas and was 26,810 on October 22. On 10/21/22 there were 2,707 patients who are seriously or critically ill; that number was 2,753 two weeks ago. The number of critically ill patients has decreased only by 47 in the last 14 days, while at least 4,951 new deaths occurred. The number of critically ill patients has decreased for the fifth time in twenty-nine 14-day periods. Patients are still dying each day (average 354/day). Omicron BA.4, BA.4.6, BA.5, and BF.7 variants are still causing infections. A new variant BQ.1.1, descended from Omicron BA.5, is causing increasing numbers of infections and hospitalizations in New York. In Singapore a different Omicron BA.2 variant, XBB, is causing rapidly increasing infections. Past infections with a BA.1, BA.2 or BA.5 variants will not prevent infections with any of the newer variants.

As of 10/21/22, we have had 1,092,606 deaths and 99,055,537 SARS-CoV-2 infections in the United States. We have had 532,369 new infections in the last 14 days. We are adding an average of 266,185 new infections every seven days. For the pandemic in the United States we are averaging one death for every 90.65 infections or over 11,030 deaths for each one million infections. As of 10/21/22, thirty-eight states have had greater than 500,000 total infections, and 38 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 43 states have greater than 2,000 deaths per million population. Seven states have over 4,000 deaths per million population: Mississippi (4,350), Arizona (4,330), Alabama (4,186), West Virginia (4,178), New Mexico (4,111), Tennessee (4,103) and Arkansas (4,114). . Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Seven states have had greater than 40,000 deaths: Florida (82,065 deaths), Texas (91,584 deaths), New York (72,694 deaths), Pennsylvania (47,582 deaths), Georgia (40,552 deaths), Ohio (40,111 deaths) and California (96,721 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (23 months), there were 825,605 new deaths from SARS-CoV-2. For nineteen of those months, vaccines have been available to all adults. During these eighteen months, 520,509 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 10/21/22, California was ranked 33rd in the USA in infection percentage at 28.65%. In California, 24.68% of people were infected in the last 19 months. As of 10/21/22, 24 states have had greater than 30% of their population infected. Fifty states have greater than 20% of their population infected.

Worldwide, average deaths per day are 1,569 for the last 14 days, which is a 97 deaths-per-day increase over the previous 14 days. The United States accounts for 22.56% (354 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 310,532. The United States accounts for 12.04% of those infections (or 37,384 infections per day).

FDA-Approved Oral Drug Treatments for SARS-CoV-2

FDA-Approved Intravenous Monoclonal Antibody Treatment for Non-Hospitalized SARS-CoV-2 Patients

From Professor Marc Johnson, molecular virologist @SolidEvidence on Twitter and Daniele Focosi, M.D., Ph.D. @dfocosi on Twitter

Watching World Data

Location	Total Infections as of 10/21/22	New Infections on 10/21/22	Total Deaths	New Deaths on 10/21/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	632,432,678(4,347,443 new infections in 14 days).	349,351	6,581,530(21,965 new deaths in last 14 days)	1,189	8.11%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)BF.7BJ.1XBBBQ.1BQ.1.1BS.1*	No	No
USA	99,055,537(ranked #1) 532,369 new infections in the last 14 days.	19,652(ranked #7) 34 states failed to report infections on 10/21/22.	1,092,606(ranked #1) 4,951 new deaths reported in the last 14 days.	190 36 states failed to report deaths on 10/21/22.	29.58%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,822,174(ranked #4) 64,917 new infections in the last 14 days.	3,400	687,581(ranked #2; 732 new deaths in 14 days)	37	16.16%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,640,748(ranked #2); 31,991 new infections in 2 weeks.	2,112	528,957(ranked #3) 199 new deaths in 2 weeks.	4	3.17%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,855,522(ranked #7) 120,249 new infections in 2 weeks.	–	192,682 (ranked #7) 1,794 new deaths in 2 weeks	–	34.82%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,332,345(ranked #14 in the world; 39,798 new infections in the last 14 days).	998	96,721 (ranked #20 in world) 303 new deaths in the last 14 days	14	28.65%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	7,106018(ranked #19) 4,587 new infections in 14 days).	453	330,321(ranked #5)181 new deaths in 14 days)	15	5.40%		No	No
South Africa	4,025,375(ranked #37; 4,587 new infections in 14 days).	416	102,257 (ranked #18) 63 new deaths in 14 days)	11	6.62%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,314,718(ranked #33) 43,827 new infections in 14 days).	3,067	46,025(ranked #25)631 new deaths in the last 14 days	49	11.23%		No	No
Poland	6,333,591 (ranked #21; 22,629 new infections in 14 days).	1,170	118,015 (ranked #15)272 new deaths in the last 14 days	24	16.78%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	21,354,915(ranked #10), 190,973 new infections in 14 days).	9,761 (ranked #8)	389,359(ranked #4)1,368 new deaths in 14 days	93	14.64%		No	No
Peru	4,152,019(ranked #32, 3,858 new infections in 14 days).	314	216,877(ranked #6) 177 new deaths in the last 14 days	–	12.32%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,555,694(ranked #17; 4,672 new infections in last 14 days)	139	144,540(ranked #12) 69 new deaths in the last 14 days	4	8.78%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,488,015(ranked #12; 46,047 new infections in 14 days).	3,630	114,858 (ranked #16)390 new deaths in 14 days	31	28.87%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	36,524,605 (ranked #3; 758,248 new infections in the last 14 days).	49,087 (ranked #2)	156,337 (ranked #10)803 new deaths in 14 days.	81	55.69% a 2.17% increase in 14 days.	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	35,172,693(ranked #4; 1,224,661 new infections in 14 days.)	49,087 (ranked #2)	152,482 (ranked #11)1,947 new deaths in 14 days	204	41.93% 1.71% increase in 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	25,244,255 (ranked #6 310,499 new infections in 14 days).	24,709(ranked #8)	28,952 (ranked #37) 338 new deaths in 14 days	30	49.18%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,496,354 (ranked #13; 10,933 new infections in 14 days).	582	43,159 (ranked #26)	–	11.61%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,494,705 (ranked #16; 33,354 new infections in 14 days).	952	22,683 (ranked #41)	5	49.35%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,131,149(ranked #40) 12,835 new infections in 14 days.	652	7,248 (ranked #79 126 new deaths in the last 14 days)	13	53.66%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	7,379,205(ranked #18)569,950 new infections in 14 days	37,265 (ranked #3)	12,206 (ranked #59 937 new deaths in the last 14 days)	78	30.89% 2.53% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	21,926,231(ranked #9)463,493 new infections in the last 14 days	31,593(ranked #5)	46,152(ranked #25) 831 new deaths in the last 14 days	67	17.45%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No

What Our Team Is Reading This Week

Effectiveness of Monovalent mRNA Vaccines Against COVID-19–Associated Hospitalization Among Immunocompetent Adults During BA.1/BA.2 and BA.4/BA.5 Predominant Periods of SARS-CoV-2 Omicron Variant in the United States — IVY Network, 18 States, December 26, 2021–August 31, 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7142a3.htm
- “Three-dose monovalent mRNA VE estimates against COVID-19–associated hospitalization decreased with time since vaccination. Three-dose VE during the BA.1/BA.2 and BA.4/BA.5 periods was 79% and 60%, respectively, during the initial 120 days after the third dose and decreased to 41% and 29%, respectively, after 120 days from vaccination.”
Saliva antibody-fingerprint of reactivated latent viruses after mild/asymptomatic COVID-19 is unique in patients with myalgic-encephalomyelitis/chronic fatigue syndrome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.949787
SARS-CoV-2 Nsp6 causes cardiac defects through MGA/MAX complex-mediated increased glycolysis (Preprint) https://doi.org/10.21203/rs.3.rs-1677754/v1
WHO’s Therapeutics and COVID-19 Living Guideline on mAbs needs to be reassessed (The Lancet) https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)01938-9/fulltext
SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry (Nature) https://doi.org/10.1038/s41586-022-05282-z
Real-world effectiveness of molnupiravir and nirmatrelvir plus ritonavir against mortality, hospitalisation, and in-hospital outcomes among community-dwelling, ambulatory patients with confirmed SARS-CoV-2 infection during the omicron wave in Hong Kong: an observational study (The Lancet) https://doi.org/10.1016/S0140-6736(22)01586-0
An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines (PLOS Pathogens) https://doi.org/10.1371/journal.ppat.1010828
Plasma cytokine levels reveal deficiencies in IL-8 and gamma interferon in Long-COVID (Preprint) https://doi.org/10.1101/2022.10.03.22280661
Lingering cardiac involvement in previously well people after mild COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02002-y
SARS-CoV-2 variants of concern and variants under investigation in England: technical briefing 46 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1109820/Technical-Briefing-46.pdf
Rapid initiation of nasal saline irrigation to reduce severity in high-risk COVID+ outpatients (Ear, Nose, and Throat Journal) https://doi.org/10.1177/01455613221123737
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://doi.org/10.1101/2022.09.22.509040
Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.15.507787v2
- Note: This is a frightening paper and if the conclusions are accurate humans in general are in trouble. From other papers the facts that HERV-M and EBV are activated by SARS-CoV-2 infection does not bode well for humans moving forward.
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.22.509040v1
Evolution of antibody immunity following Omicron BA.1 breakthrough infection (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.21.508922v1
SARS-CoV-2 Spike protein promotes vWF secretion and thrombosis via endothelial cytoskeleton-associated protein 4 (CKAP4) (Signal Transduction and Targeted Therapy) https://www.nature.com/articles/s41392-022-01183-9
Long-term neurologic outcomes of COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02001-z
Pulmonary Dysfunction after Pediatric COVID-19 (Radiology) https://pubs.rsna.org/doi/10.1148/radiol.221250
Severe Respiratory Illnesses Associated with Rhinoviruses and/or Enteroviruses Including EV-D68 – Multistate, 2022 (CDC) https://emergency.cdc.gov/han/2022/han00474.asp
VACCINE INFORMATION FACT SHEET FOR RECIPIENTS AND CAREGIVERS ABOUT COMIRNATY (COVID-19 VACCINE, mRNA), THE PFIZER-BIONTECH COVID-19 VACCINE, AND THE PFIZER-BIONTECH COVID-19 VACCINE BIVALENT (ORIGINAL AND OMICRON BA.4/BA.5) TO PREVENT CORONAVIRUS DISEASE 2019 (COVID-19) FOR USE IN INDIVIDUALS 12 YEARS OF AGE AND OLDER https://labeling.pfizer.com/ShowLabeling.aspx?id=14472
Pfizer/BioNTech COVID-19 Omicron-Modified Bivalent Vaccine https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2022-09-01/07-covid-swanson-508.pdf
Coronavirus (COVID-19) Update: FDA Authorizes Moderna, Pfizer-BioNTech Bivalent COVID-19 Vaccines for Use as a Booster Dose (FDA) https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-moderna-pfizer-biontech-bivalent-covid-19-vaccines-use
Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.05.506628v1.full
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 45, 9 September 2022 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1103869/Technical-Briefing-45-9September2022.pdf
SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4

COVID-19

SARS-CoV-2 Update

10/13/202210/13/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have decreased for the third time in 10 weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have increased by 60 deaths per day. The number of infections per day has decreased by 15,124. The CDC estimates that BA.5 accounted for 79.2%, BA.4.6 accounted for 13.6%, BF.7 accounted for 4.6%, BA.2.75 accounted for 1.8% and BA.4 accounted for 0.8%, in the week ending October 8. The rise in BA.4.6 cases is especially concerning because the September 9 UK Health Security Agency Technical Briefing says that, “Pseudoviral neutralisation assays performed on BA.4.6 show that titres are reduced 2-fold, compared to neutralisation of BA.4 or BA.5 using sera from triple dosed recipients of the Pfizer BNT162b2 vaccine.” The same briefing also states that BA.4.6 has a growth advantage relative to BA.5. The October 7 UK Health Security Agency Technical Briefing says, “From UK data, BQ.X, BA.2.75.2 and BF.7 are the most concerning variants in terms of both growth and neutralisation data at present; there is also supportive animal model data for BA.2.75.”

Variant	Sublineage of	Spike Mutations	Global Sequences	UK Sequences
BF.7	BA.5.2.1	R346T	9,809 (1,752 from Belgium)	663
BQ.1.1	BA.5	N460K K444T R346T	326(20 countries)	60
BJ.1	BA.5	13 non- synonymous spike mutations, 7 in RBD and including4 predicted immune escape locations	123 (10 countries, most cases in India)	1
BS.1	BA.2.3.2	R346T L452R N460K G476S	25 (15 from Japan)	0

Data from 7 October 2022 UK Health Security Agency Technical Briefing

We frequently hear messaging from health officials and politicians that Omicron is “mild,” especially compared to the Delta variant, and as a result, many of our patients believe that they no longer need to wear their masks. This is a dangerous misconception. SARS-CoV-2 still remains a highly transmissible, airborne virus. The following graph, based on CDC data from April 2, 2022, shows that Omicron deaths in people over 65 are much higher than Delta deaths in the same age group. In fact, the peak of Omicron deaths in people over 65 years of age is 163% higher than the Delta peak. The death rate from Omicron is only lower than Delta in the populations between 12 and 64 years of age. Until we have more data on these newer mutants of SARS-CoV-2, we will not know the lethality of each variant. It may take months to measure objective differences in the death rates of new circulating variants. We recommend that all of our patients and family members continue to wear N95 masks in all enclosed spaces.
In patients treated with Paxlovid for five days who have persistent symptoms and continued positivity, we feel that clinicians should consider giving a second course of Paxlovid for five days. Boucau et al have demonstrated that in a study of seven patients with recurrent symptoms, “High viral loads (median 6.1 log10 copies/mL) were detected after rebound for a median of 17 days after initial diagnosis. Three had culturable virus for up to 16 days after initial diagnosis.” This was not due to resistance-associated mutations of the virus, suggesting that the course of therapy may be inadequate in this group of persistently infected patients.

The Omicron variant has continued to mutate just like Delta. The list of variants was not updated in the last four weeks, but as of six weeks ago, there are now 276 Omicron sub-variants that have been assigned Pango lineages, including 123 sub-lineages of BA.2, one sub-lineage of BA.3, 15 sub-lineages of BA.4, and 45 sub-lineages of BA.5. The BF lineage (new sixteen weeks ago) now has 21 sublineages. The BE lineage (also new sixteen weeks ago), with BE.1 first detected in South Africa, Austria and England, now has 7 sublineages. There are also new lineages from sixteen weeks ago: BC.1 (Japan), BC.2 (Peru), BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel). In the last eight weeks, the BG lineage has expanded to include BG.5 (USA) and BG.6 (Peru). Lastly, two new sublineages were added in the past eight weeks: BH.1 (India) and BK.1 (USA and Canada).

In Monterey County, as of 10/7/22, 1.7% of 0-4 year-olds and 40.0% of 5-11 year-olds have received the first two doses of vaccine, while 73.2% of 12-17 year-olds have received two doses. Only 53.9% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

On 10/07/22, the United States had 23,524 documented new infections. There were also 229 deaths. Thirty states did not report their infections, and 33 states didn’t report their deaths. In the United States the number of hospitalized patients has decreased slightly in many areas and was 30,273 on September 24, a decrease of 6,417 hospitalizations compared to the previous 14 days. On 10/07/22 there are 2,753 patients who are seriously or critically ill; that number was 3,176 two weeks ago. The number of critically ill patients has decreased by 423 in the last 14 days, while at least 6,089 new deaths occurred. The number of critically ill patients has decreased for the fourth time in twenty-eight 14-day periods. Patients are still dying each day (average 435/day). Omicron BA.4, BA.4.6, BA.5, and BF.7 variants are still causing infections. Past infections with a BA.1 or BA.2 variant will not prevent infections with any of the newer variants.

As of 10/07/22, we have had 1,087,655 deaths and 98,523,168 SARS-CoV-2 infections in the United States. We have had 642,717 new infections in the last 14 days. We are adding an average of 321,358 new infections every seven days. For the pandemic in the United States we are averaging one death for every 90.58 infections or over 11,040 deaths for each one million infections. As of 10/07/22, thirty-eight states have had greater than 500,000 total infections, and 38 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 43 states have greater than 2,000 deaths per million population. Vermont, at 1,167 deaths per million, and Hawaii, 1,196 deaths per million, are the states with the lowest death rates. Seven states have over 4,000 deaths per million population: Mississippi (4,344), Arizona (4,315), Alabama (4,175), West Virginia (4,157), New Mexico (4,099), Tennessee (4,087) and Arkansas (4,068). . Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Six states have had greater than 40,000 deaths: Florida (81,566 deaths), Texas (91,394 deaths), New York (72,346 deaths), Pennsylvania (47,323 deaths), Georgia (40,374 deaths) and California (96,418 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (23 months), there were 820,654 new deaths from SARS-CoV-2. For nineteen of those months, vaccines have been available to all adults. During these eighteen months, 515,558 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 10/07/22, California was ranked 32nd in the USA in infection percentage at 28.57%. In California, 24.60% of people were infected in the last 19 months. As of 9/23/22, 23 states have had greater than 30% of their population infected. No state has less than 20% of their population infected.

Below are the variant proportions for Region 9, which includes California, Nevada, and Arizona.

Worldwide, average deaths per day are 1,480 for the last 14 days, which is a 257 deaths-per-day decrease over the previous 14 days. The United States accounts for 29.39% (435 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 464,233. The United States accounts for 9.89% of those infections (or 45,908 infections per day).

FDA-Approved Oral Drug Treatments for SARS-CoV-2

FDA-Approved Intravenous Monoclonal Antibody Treatment for Non-Hospitalized SARS-CoV-2 Patients

Watching World Data

Location	Total Infections as of 10/07/22	New Infections on 10/07/22	Total Deaths	New Deaths on 10/07/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	626,085,235(6,488,266 new infections in 14 days).	458,597	6,559,565(20,715 new deaths in last 14 days)	1,255	8.03%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
USA	98,523,168(ranked #1) 642,717 new infections in the last 14 days.	23,524(ranked #6) 30 states failed to report infections on 10/08/22.	1,087,655(ranked #1) 6,089 new deaths reported in the last 14 days.	229 33 states failed to report deaths on 10/07/22.	29.40%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,757,257(ranked #4) 90,870 new infections in the last 14 days.	7,149	686,849(ranked #2; 1,033 new deaths in 14 days)	90	16.09%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,609,257(ranked #2); 45,920 new infections in 2 weeks.	2,797	528,778(ranked #3) 291 new deaths in 2 weeks.	24	3.16%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,735,273(ranked #7) 13,321 new infections in 2 weeks.	–	190,888 (ranked #7) 969 new deaths in 2 weeks	–	34.55%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,292,547(ranked #14 in the world; 63,757 new infections in the last 14 days).	1,321	96,418 (ranked #20 in world) 616 new deaths in the last 14 days	10	28.57%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	7,090,965(ranked #18) 27,224 new infections in 14 days).	–	330,139(ranked #5)122 new deaths in 14 days)	–	5.37%		No	No
South Africa	4,020,788(ranked #37; 3,113 new infections in 14 days).	359	102,194 (ranked #18) 25 new deaths in 14 days)	–	6.59%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,270,891(ranked #33) 37,423 new infections in 14 days).	2,756	45,394(ranked #24)392 new deaths in the last 14 days	26	11.09%		No	No
Poland	6,310,962 (ranked #21; 42,913 new infections in 14 days).	2,618	117,743 (ranked #15)312 new deaths in the last 14 days	41	16.71%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	21,163,942(ranked #10), 469,048 new infections in 14 days).	22,268 (ranked #7)	387,991(ranked #4)1,386 new deaths in 14 days	104	14.48%		No	No
Peru	4,148,161(ranked #34, 8,032 new infections in 14 days).	339	216,700(ranked #6) 254 new deaths in the last 14 days	55	12.19%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,551,022(ranked #17; 4,746 new infections in last 14 days)	166	144,471(ranked #12) 104 new deaths in the last 14 days	2	8.73%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,441,941(ranked #12; 48,745 new infections in 14 days).	3,615	114,468 (ranked #16)623 new deaths in 14 days	68	28.72%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	35,766,357 (ranked #3; 716,224 new infections in the last 14 days).Double the new infections of the previous 14 days	61,121 (ranked #2)	155,534 (ranked #10)676 new deaths in 14 days.	53	53.52%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	33,948,632(ranked #5; 1,043,546 new infections in 14 days.).More than double the new infections of the previous 14 days.	122,265 (ranked #1)	150,535 (ranked #11)1,167 new deaths in 14 days	129	40.22% 1% increase in 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	24,933,756 (ranked #6 397,816 new infections in 14 days).	22,529(ranked #8)	28,614 (ranked #37) 505 new deaths in 14 days	41	48.53%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,485,361 (ranked #13; 17,742 new infections in 14 days).	702	43,152 (ranked #26)	1	11.56%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,441,351 (ranked #16; 22,819 new infections in 14 days).	–	22,663 (ranked #41)	1	49.01%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,118,314 (ranked #40) 21,226 new infections in 14 days. Has more than doubled new infections last 14 days.	872	7,121 (ranked #79 100 new deaths in the last 14 days)	9	53.41%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	6,782,455(ranked #19)649,711 new infections in 14 days	50,570 (ranked #3)	11,369 (ranked #62 667 new deaths in the last 14 days)	52	28.36% 2.69% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	21,489,738(ranked #9)648,953 new infections in the last 14 days	29,443(ranked #5)	45,321(ranked #25) 1,970 new deaths in the last 14 days	73	17.10% 0.51% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No

What Our Team Is Reading This Week

SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry (Nature) https://doi.org/10.1038/s41586-022-05282-z
Real-world effectiveness of molnupiravir and nirmatrelvir plus ritonavir against mortality, hospitalisation, and in-hospital outcomes among community-dwelling, ambulatory patients with confirmed SARS-CoV-2 infection during the omicron wave in Hong Kong: an observational study (The Lancet) https://doi.org/10.1016/S0140-6736(22)01586-0
An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines (PLOS Pathogens) https://doi.org/10.1371/journal.ppat.1010828
Plasma cytokine levels reveal deficiencies in IL-8 and gamma interferon in Long-COVID (Preprint) https://doi.org/10.1101/2022.10.03.22280661
Lingering cardiac involvement in previously well people after mild COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02002-y
SARS-CoV-2 variants of concern and variants under investigation in England: technical briefing 46 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1109820/Technical-Briefing-46.pdf
Rapid initiation of nasal saline irrigation to reduce severity in high-risk COVID+ outpatients (Ear, Nose, and Throat Journal) https://doi.org/10.1177/01455613221123737
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://doi.org/10.1101/2022.09.22.509040
Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.15.507787v2
- Note: This is a frightening paper and if the conclusions are accurate humans in general are in trouble. From other papers the facts that HERV-M and EBV are activated by SARS-CoV-2 infection does not bode well for humans moving forward.
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.22.509040v1
Evolution of antibody immunity following Omicron BA.1 breakthrough infection (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.21.508922v1
SARS-CoV-2 Spike protein promotes vWF secretion and thrombosis via endothelial cytoskeleton-associated protein 4 (CKAP4) (Signal Transduction and Targeted Therapy) https://www.nature.com/articles/s41392-022-01183-9
Long-term neurologic outcomes of COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02001-z
Pulmonary Dysfunction after Pediatric COVID-19 (Radiology) https://pubs.rsna.org/doi/10.1148/radiol.221250
Severe Respiratory Illnesses Associated with Rhinoviruses and/or Enteroviruses Including EV-D68 – Multistate, 2022 (CDC) https://emergency.cdc.gov/han/2022/han00474.asp
VACCINE INFORMATION FACT SHEET FOR RECIPIENTS AND CAREGIVERS ABOUT COMIRNATY (COVID-19 VACCINE, mRNA), THE PFIZER-BIONTECH COVID-19 VACCINE, AND THE PFIZER-BIONTECH COVID-19 VACCINE BIVALENT (ORIGINAL AND OMICRON BA.4/BA.5) TO PREVENT CORONAVIRUS DISEASE 2019 (COVID-19) FOR USE IN INDIVIDUALS 12 YEARS OF AGE AND OLDER https://labeling.pfizer.com/ShowLabeling.aspx?id=14472
Pfizer/BioNTech COVID-19 Omicron-Modified Bivalent Vaccine https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2022-09-01/07-covid-swanson-508.pdf
Coronavirus (COVID-19) Update: FDA Authorizes Moderna, Pfizer-BioNTech Bivalent COVID-19 Vaccines for Use as a Booster Dose (FDA) https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-moderna-pfizer-biontech-bivalent-covid-19-vaccines-use
Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.05.506628v1.full
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 45, 9 September 2022 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1103869/Technical-Briefing-45-9September2022.pdf
SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7

COVID-19

SARS-CoV-2 Update

09/25/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have decreased for the second time in four weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have decreased by 14 deaths per day. The number of infections per day has decreased by 19,313. The CDC estimates that BA.5 accounted for 83.1%, BA.4.6 accounted for 11.9%, BF.7 accounted for 2.3%, BA.4 accounted for 1.4%, BA.2.12.1 accounted for 0.0% of isolates, BA.2 accounted for 0.0%, BA.1.1 accounted for 0.0%, and B.1.1.529 accounted for 0% in the week ending September 10. The rise in BA.4.6 cases is especially concerning because the September 9 UK Security Agency Technical Briefing says that, “Pseudoviral neutralisation assays performed on BA.4.6 show that titres are reduced 2-fold, compared to neutralisation of BA.4 or BA.5 using sera from triple dosed recipients of the Pfizer BNT162b2 vaccine.” The same briefing also states that BA.4.6 has a growth advantage relative to BA.5.

In patients treated with Paxlovid for five days who have persistent symptoms and continued positivity, we feel that clinicians should consider giving a second course of Paxlovid for five days. Boucau et al have demonstrated that in a study of seven patients with recurrent symptoms, “High viral loads (median 6.1 log10 copies/mL) were detected after rebound for a median of 17 days after initial diagnosis. Three had culturable virus for up to 16 days after initial diagnosis.” This was not due to resistance-associated mutations of the virus, suggesting that the course of therapy may be inadequate in this group of persistently infected patients.

The Omicron variant has continued to mutate just like Delta. The list of variants was not updated in the last four weeks, but as of six weeks ago, there are now 276 Omicron sub-variants that have been assigned Pango lineages, including 123 sub-lineages of BA.2, one sub-lineage of BA.3, 15 sub-lineages of BA.4, and 45 sub-lineages of BA.5. The BF lineage (new fourteen weeks ago) now has 21 sublineages.. The BE lineage (also new fourteen weeks ago), with BE.1 first detected in South Africa, Austria and England, now has 7 sublineages. There are also new lineages from fourteen weeks ago: BC.1 (Japan), BC.2 (Peru), BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel). In the last six weeks, the BG lineage has expanded to include BG.5 (USA) and BG.6 (Peru). Lastly, two new sublineages were added in the past six weeks: BH.1 (India) and BK.1 (USA and Canada).

In Monterey County, as of 9/24/22, 1.1% of 0-4 year-olds and 39.9% of 5-11 year-olds have received the first two doses of vaccine, while 73.1% of 12-17 year-olds have received two doses. Only 53.6% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

On 9/23/22, the United States had 33,238 documented new infections. There were also 259 deaths. Twenty-six states did not report their infections, and 30 states didn’t report their deaths. In the United States the number of hospitalized patients has decreased slightly in many areas and was 30,273 on September 24, a decrease of 6,417 hospitalizations compared to the previous 14 days. On 9/14/22 there are 3,176 patients who are seriously or critically ill; that number was 3,829 two weeks ago. The number of critically ill patients has decreased by 653 in the last 14 days, while at least 5,228 new deaths occurred. The number of critically ill patients has decreased for the fourth time in twenty-eight 14-day periods. Patients are still dying each day (average 375/day). Omicron BA.4, BA.4.6 and BA.5 variants are still causing infections. Past infections with a BA.1 or BA.2 variant will not prevent infections with BA.4, BA.4.6 or BA.5. Evusheld may not prevent BA.4.6 infections.

As of 9/23/22, we have had 1,081,566 deaths and 97,880,451 SARS-CoV-2 infections in the United States. We have had 854,450 new infections in the last 14 days. We are adding an average of 427,225 new infections every seven days. For the pandemic in the United States we are averaging one death for every 90.48 infections or over 11,050 deaths for each one million infections. As of 9/23/22, thirty-eight states have had greater than 500,000 total infections, and 38 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 43 states have greater than 2,000 deaths per million population. Vermont, at 1,152 deaths per million, and Hawaii, 1,186 deaths per million, are the states with the lowest death rates. Six states have over 4,000 deaths per million population: Mississippi (4,327), Arizona (4,304), Alabama (4,160), West Virginia (4,119), New Mexico (4,079) and Tennessee (4,057). Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states have had greater than 70,000 deaths: Florida (81,139 deaths), Texas (91,159 deaths), New York (72,058 deaths), and California (95,970 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (22 months), there were 820,435 new deaths from SARS-CoV-2. For eighteen of those months, vaccines have been available to all adults. During these eighteen months, 509,469 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 9/23/22, California was ranked 32nd in the USA in infection percentage at 28.40%. In California, 24.43% of people were infected in the last 19 months. As of 9/23/22, 43 states have had greater than 25% of their population infected. No state has less than 20% of their population infected. Below are the variant proportions for Region 9, which includes California, Nevada, and Arizona.

Worldwide, average deaths per day are 1,737 for the last 14 days, which is a 340 deaths-per-day decrease over the previous 14 days. The United States accounts for 21.58% (375 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 474,827. The United States accounts for 12.854% of those infections (or 61,032 infections per day).

FDA-Approved Oral Drug Treatments for SARS-CoV-2

FDA-Approved Intravenous Monoclonal Antibody Treatment for Non-Hospitalized SARS-CoV-2 Patients

Watching World Data

Location	Total Infections as of 9/23/22	New Infections on 9/23/22	Total Deaths	New Deaths on 9/23/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	619,585,969(6,647,575 new infections in 14 days).	410,558	6,538,850(24,324 new deaths in last 14 days)	1,312	7.94%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
USA	97,880,451(ranked #1) 854,450 new infections in the last 14 days.	33,238(ranked #5) 26 states failed to report infections on 9/23/22.	1,081,566(ranked #1) 5,228 new deaths reported in the last 14 days.	259 30 states failed to report deaths on 9/23/22.	29.57%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,666,387(ranked #4) 129,467 new infections in the last 14 days.	6,861	685,816(ranked #2; 950 new deaths in 14 days)	91	16.05%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,563,337(ranked #2); 73,054 new infections in 2 weeks.	4,912	528,487(ranked #3) 348 new deaths in 2 weeks.	38	3.16%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,621,952(ranked #7) 67,433 new infections in 2 weeks.	–	189,919 (ranked #7) 893 new deaths in 2 weeks	–	34.39%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,228,790(ranked #14 in the world; 100,708 new infections in the last 14 days).	1,619	95,970 (ranked #20 in world) 616 new deaths in the last 14 days	13	28.40%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	7,080,152(ranked #18) 27,224 new infections in 14 days).	4,147	330,017(ranked #5)312 new deaths in 14 days)	68	5.36%		No	No
South Africa	4,017,163(ranked #37; 3,113 new infections in 14 days).	152	102,169 (ranked #18) 40 new deaths in 14 days)	–	6.58%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,233,468(ranked #33) 35,767 new infections in 14 days).	2,477	44,992(ranked #24) 618new deaths in the last 14 days	36	11.60%		No	No
Poland	6,268,049 (ranked #21; 61,157 new infections in 14 days).	4,438	117,431 (ranked #15)	19	16.60%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	20,694,894(ranked #10), 734,599 new infections in 14 days).	53,335 (ranked #2)	386,551(ranked #4)1,386 new deaths in 14 days	104	14,16%		No	No
Peru	4,140,129(ranked #34, 16,694 new infections in 14 days).	1,150	216,446(ranked #6)	17	12.17%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,546,276(ranked #17; 8,495 new infections in last 14 days)	421	144,367(ranked #12)	–	8.73%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,393,196(ranked #12; 34,671 new infections in 14 days).	-(ranked #18)	113,845(ranked #16)676 new deaths in 14 days	–	28.61%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	35,050,133 (ranked #3; 367,940 new infections in the last 14 days).	38,464 (ranked #6)	154,854 (ranked #10) 386 new deaths in 14 days	30	53.44%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	32,905,086(ranked #5; 452,824 new infections in 14 days.).	50,800 (ranked #3)	149,368 (ranked #11) 1,139 new deaths in 14 days	93	39.22%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	24,535,940 (ranked #6 601,906 new infections in 14 days).	39,972(ranked #8)	28,009 (ranked #37) 628 new deaths in 14 days	59	47.80%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,467,619 (ranked #13; 32,147 new infections in 14 days).	1,928	43,146 (ranked #26)	–	11.58%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,413,532 (ranked #16; 16,553 new infections in 14 days).	1,756	22,633 (ranked #41)	1	48.98%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,097,088 (ranked #40) 7,517 new infections in 14 days	640	7,021 (ranked #79)	53.22%	53.07%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	6,132,744(ranked #22) 518,546 new infections in 14 days	42,420 (ranked #4)	10,702 (ranked #63)	59	25.67% 2.17% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	20,840,785(ranked #9) 958,392 new infections in the last 14 days	61,478(ranked #1)	44,071(ranked #25) 1,970 new deaths in the last 14 days	120	16.59% 0.76% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No

What Our Team Is Reading This Week

Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.15.507787v2
- Note: This is a frightening paper, and if the conclusions are accurate, humans in general are in trouble. From other papers, the fact that HERV-M and EBV are activated by SARS-CoV-2 infection does not bode well for humans moving forward.
SARS-CoV-2 Omicron boosting induces de novo B cell response in humans (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.22.509040v1
Evolution of antibody immunity following Omicron BA.1 breakthrough infection (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.21.508922v1
SARS-CoV-2 Spike protein promotes vWF secretion and thrombosis via endothelial cytoskeleton-associated protein 4 (CKAP4) (Signal Transduction and Targeted Therapy) https://www.nature.com/articles/s41392-022-01183-9
Long-term neurologic outcomes of COVID-19 (Nature Medicine) https://www.nature.com/articles/s41591-022-02001-z
Pulmonary Dysfunction after Pediatric COVID-19 (Radiology) https://pubs.rsna.org/doi/10.1148/radiol.221250
Severe Respiratory Illnesses Associated with Rhinoviruses and/or Enteroviruses Including EV-D68 – Multistate, 2022 (CDC) https://emergency.cdc.gov/han/2022/han00474.asp
VACCINE INFORMATION FACT SHEET FOR RECIPIENTS AND CAREGIVERS ABOUT COMIRNATY (COVID-19 VACCINE, mRNA), THE PFIZER-BIONTECH COVID-19 VACCINE, AND THE PFIZER-BIONTECH COVID-19 VACCINE BIVALENT (ORIGINAL AND OMICRON BA.4/BA.5) TO PREVENT CORONAVIRUS DISEASE 2019 (COVID-19) FOR USE IN INDIVIDUALS 12 YEARS OF AGE AND OLDER https://labeling.pfizer.com/ShowLabeling.aspx?id=14472
Pfizer/BioNTech COVID-19 Omicron-Modified Bivalent Vaccine https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2022-09-01/07-covid-swanson-508.pdf
Coronavirus (COVID-19) Update: FDA Authorizes Moderna, Pfizer-BioNTech Bivalent COVID-19 Vaccines for Use as a Booster Dose (FDA) https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-moderna-pfizer-biontech-bivalent-covid-19-vaccines-use
Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.05.506628v1.full
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 45, 9 September 2022 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1103869/Technical-Briefing-45-9September2022.pdf
SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors (Biophysics and Computational Biology) https://doi.org/10.1073/pnas.2119761119
Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2 (The Lancet) https://doi.org/10.1016/S0140-6736(22)00941-2
Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum (Cell) https://doi.org/10.1016/j.cell.2022.06.005
Immunomodulatory treatment in postural tachycardia syndrome: A case series (European Journal of Neurology) https://doi.org/10.1111/ene.14711
Long COVID-19 Liver Manifestation in Children (JPGN) https://journals.lww.com/jpgn/abstract/9900/long_covid_19_liver_manifestation_in_children.84.aspx
Cross-reactive immunity against the SARS-CoV-2 Omicron variant is low in pediatric patients with prior COVID-19 or MIS-C (Nature Communications) https://doi.org/10.1038/s41467-022-30649-1
C.D.C. Dismisses Airborne Transmission of Monkeypox. Some Experts Disagree. (NY Times) https://www.nytimes.com/2022/06/10/health/monkeypox-airborne.html
Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes (Science Immunology) https://doi.org/10.1126/sciimmunol.abq2427
SARS-CoV-2 Infection and Persistence Throughout the Human Body and Brain (National Institutes of Health) https://videocast.nih.gov/watch=45296?jwsource=twi
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Herpesvirus infections and post-COVID-19 manifestations: a pilot observational study (Observational Research) https://doi.org/10.1007/s00296-022-05146-9

COVID-19

SARS-CoV-2 Update

09/11/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have decreased for the second time in four weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have decreased by 14 deaths per day. The number of infections per day has decreased by 19,313. The CDC estimates that BA.2.12.1 accounted for 0.1% of isolates, BA.2 accounted for 1.0%, BA.5 accounted for 87.5%, BA.4 accounted for 2.2%, BA.4.6 accounted for 9.2%, and B.1.1.529 accounted for 0% in the week ending September 10. The rise in BA.4.6 cases is especially concerning because the September 9 UK Security Agency Technical Briefing says that, “Pseudoviral neutralisation assays performed on BA.4.6 show that titres are reduced 2-fold, compared to neutralisation of BA.4 or BA.5 using sera from triple dosed recipients of the Pfizer BNT162b2 vaccine.” The same briefing also states that BA.4.6 has a growth advantage relative to BA.5.

The Omicron variant has continued to mutate just like Delta. The list of variants was not updated in the last two weeks, but as of four weeks ago, there are now 276 Omicron sub-variants that have been assigned Pango lineages, including 123 sub-lineages of BA.2, one sub-lineage of BA.3, 15 sub-lineages of BA.4, and 45 sub-lineages of BA.5. The BF lineage (new twelve weeks ago) now has 21 sublineages.. The BE lineage (also new twelve weeks ago), with BE.1 first detected in South Africa, Austria and England, now has 7 sublineages.. There are also new lineages from twelve weeks ago: BC.1 (Japan), BC.2 (Peru), BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel). In the last four weeks, the BG lineage has expanded to include BG.5 (USA) and BG.6 (Peru). Lastly, two new sublineages were added in the past four weeks: BH.1 (India) and BK.1 (USA and Canada).

In Monterey County, as of 9/11/22, 0.6% of 0-4 year-olds and 39.7% of 5-11 year-olds have received the first two doses of vaccine, while 73.0% of 12-17 year-olds have received two doses. Only 53.4% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

On 9/09/22, the United States had 50,822 documented new infections. There were also 317 deaths. Twenty-six states did not report their infections, and 29 states didn’t report their deaths. In the United States the number of hospitalized patients has decreased slightly in many areas and was 36,690 on September 6, a decrease of 1,949 hospitalizations compared to the previous 14 days. On 9/09/22 there are 3,829 patients who are seriously or critically ill; that number was 3,992 two weeks ago. The number of critically ill patients has decreased by 153 in the last 14 days, while at least 6,495 new deaths occurred. The number of critically ill patients has decreased for the third time in twenty-seven 14-day periods. Patients are still dying each day (average 464/day). Omicron BA.4, BA.4.6 (a new USA variant) and BA.5 variants causing infections should continue to increase and critically ill patients may increase. Deaths usually lag two to four weeks behind exponential increase in infections. Past infections with a BA.1 or BA.2 variant will not prevent infections with BA.4, BA.4.6 or BA.5. Evusheld may not prevent BA.4.6 infections.

As of 9/09/22, we have had 1,075,338 deaths and 97,026,001 SARS-CoV-2 infections in the United States. We have had 1,055,994 new infections in the last 14 days. We are adding an average of 527,997 new infections every seven days. For the pandemic in the United States we are averaging one death for every 90.23 infections or over 11,083 deaths for each one million infections. As of 9/09/22, thirty-eight states have had greater than 500,000 total infections, and 37 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 46 states have greater than 2,000 deaths per million population. Vermont, at 1,146 deaths per million, and Hawaii, 1,169 deaths per million, are the states with the lowest death rates. Five states have over 4,000 deaths per million population: Mississippi (4,308), Arizona (4,281), Alabama (4,134), West Virginia (4,088), New Mexico (4,046( and Tennessee (4,032). Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states have had greater than 70,000 deaths: Florida (80,384 deaths), Texas (90,860 deaths), New York (71,730 deaths), and California (95,354 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (22 months), there were 815,207 new deaths from SARS-CoV-2. For eighteen of those months, vaccines have been available to all adults. During these eighteen months, 504,241 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 9/09/22, California was ranked 32nd in the USA in infection percentage at 28.16%. In California, 24.19% of people were infected in the last 19 months. As of 9/09/22, 42 states have had greater than 25% of their population infected. No state has less than 20% of their population infected.

Worldwide, average deaths per day are 2,077 for the last 14 days, which is a 322 deaths-per-day decrease over the previous 14 days. The United States accounts for 15.95% (464 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 584,902. The United States accounts for 12.899% of those infections (or 75,428 infections per day).

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Watching World Data

Location	Total Infections as of 9/09/22	New Infections on 9/09/22	Total Deaths	New Deaths on 9/09/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	612,988,394(8,188,628 new infections in 14 days).	492,284	6,514,526(29,079 new deaths in last 14 days)	1,716	7.86%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
USA	97,026,001(ranked #1) 1,055,994 new infections in the last 14 days.	50,822(ranked #4) 26 states failed to report infections on 9096/22.	1,076,338(ranked #1) 6,495 new deaths reported in the last 14 days.	317 29 states failed to report deaths on 9/09/22.	26.72%* *Not updated for 10 weeks by Worldometer.	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,536.920(ranked #4) 195,011 new infections in the last 14 days.	14,005 (ranked #9)	684,866(ranked #2; 1,402 new deaths in 14 days)	82	16.01%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,490,283(ranked #2); 101,587 new infections in 2 weeks.	9,938 (ranked #11)	528,139(ranked #3) 631 new deaths in 2 weeks.	36	3.16%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,554,519(ranked #7) 61,644 new infections in 2 weeks.	–	189,026 (ranked #7) 1,265 new deaths in 2 weeks	–	34.30%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,128,082(ranked #14 in the world; 75,216 new infections in the last 14 days).	2,191	95,354 (ranked #20 in world) 395 new deaths in the last 14 days	14	28.16%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	7,052,928(ranked #18) 51,338 new infections in 14 days).	2,973	329,705(ranked #5)426 new deaths in 14 days)	30	5.34%		No	No
South Africa	4,014,050(ranked #36; 3,418 new infections in 14 days).	329	102,129 (ranked #18) 45 new deaths in 14 days)	–	6.58%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,197,701(ranked #33) 39,219 new infections in 14 days).	2,626	44,374(ranked #24) 550 new deaths in the last 14 days	34	10.93%		No	No
Poland	6,206,982 (ranked #21; 44,320 new infections in 14 days).	4,553	117,233 (ranked #15)	14	16.44%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	19,960,295(ranked #9), 648,322 new infections in 14 days).	52,106 (ranked #4)	385,165(ranked #4)1,255 new deaths in 14 days	96	13.68%		No	No
Peru	4,123,435(ranked #34, 28,783 new infections in 14 days).	2,399	216,045(ranked #6)	42	12.24%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,537,781(ranked #17; 16,788 new infections in last 14 days)	700	144,135(ranked #12)	27	8.76%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,367,647(ranked #12; 34,671 new infections in 14 days).	2,975(ranked #18)	113,130 (ranked #16)676 new deaths in 14 days	69	28.61%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	34,682,193 (ranked #3; 235,339 new infections in the last 14 days).	19,087 (ranked #7)	154,468 (ranked #10) 621 new deaths in 14 days	31	52.88%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	32,452,250(ranked #5; 410,902 new infections in 14 days.).	30,166 (ranked #6)	148,229 (ranked #11) 1,125 new deaths in 14 days	82	38.68%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	23,933,949 (ranked #6 1,130,964 new infections in 14 days).	69,389(ranked #2)	27,381 (ranked #37) 968 new deaths in 14 days	68	46.62%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,435,472 (ranked #13; 36,072 new infections in 14 days).	1,219	43,126 (ranked #25)	–	11.55%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,396,979 (ranked #15; 15,970 new infections in 14 days).	1,219	22,613 (ranked #41)	1	48.78%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,097,088 (ranked #40) 7,970 new infections in 14 days	614	6,968 (ranked #79)	3	53.07%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	5,614,198(ranked #22) 445,249 new infections in 14 days	34,231 (ranked #5)	10,225 (ranked #64)	55	23.50% 1.89% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	19,882,393(ranked #10) 1,918,596 new infections in the last 14 days	112,404(ranked #1)	42,101(ranked #26) 3,904 new deaths in the last 14 days	261	15.83% 1.52% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No

What Our Team Is Reading This Week

Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization (Preprint) https://www.biorxiv.org/content/10.1101/2022.09.05.506628v1.full
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 45, 9 September 2022 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1103869/Technical-Briefing-45-9September2022.pdf
SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html

COVID-19

SARS-CoV-2 Update

08/28/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have decreased for the first time in two weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have decreased by 31 deaths per day. The number of infections have decreased by 19,061 infections per day. The CDC estimates that BA.2.12.1 accounted for 0.2% of isolates, BA.2 accounted for 0%, BA.5 accounted for 88.7%, BA.4 accounted for 3.6%, BA.4.6 accounted for 7.5%, and B.1.1.529 accounted for 0% in the week ending August 27.

The Omicron variant has continued to mutate just like Delta. There are now 276 Omicron sub-variants (an increase of 46 in the last two weeks) that have been assigned Pango lineages, including 123 sub-lineages of BA.2 (an increase of 7 in two weeks), one sub-lineage of BA.3, 15 sub-lineages of BA.4 (an increase of one in two weeks), and 45 sub-lineages of BA.5 (an increase of 21 in two weeks). The BF lineage (new ten weeks ago) now has 21 sublineages, an increase of 10 in two weeks. The BE lineage (also new ten weeks ago), with BE.1 first detected in South Africa, Austria and England, now has 7 sublineages, an increase of 3 in two weeks. There are also new lineages from ten weeks ago: BC.1 (Japan), BC.2 (Peru),BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel). In the last two weeks, the BG lineage has expanded to include BG.5 (USA) and BG.6 (Peru). Lastly, two new sublineages were added in the past two weeks: BH.1 (India) and BK.1 (USA and Canada).

In Monterey County, as of 8/28/22, 0.5% of 0-4 year-olds and 39.4% of 5-11 year-olds have received the first two doses of vaccine, while 72.9% of 12-17 year-olds have received two doses. Only 53.4% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. We would anticipate, with the start of school on August 5 and the low vaccination rates in our county, that we’ll have a marked increase in the number of infected patients. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

On 8/26/22, the United States had 63,798 documented new infections. There were also 312 deaths. Twenty-four states did not report their infections, and 28 states didn’t report their deaths. In the United States the number of hospitalized patients has decreased slightly in many areas and was 38,630 on August 27, a decrease of 9% compared to the previous 14 days. Now there are 3,992 patients who are seriously or critically ill; that number was 4,490 two weeks ago. The number of critically ill patients has decreased by 498 in the last 14 days, while at least 6,692 new deaths occurred. The number of critically ill patients has decreased for the second time in twenty-six 14-day periods. Patients are still dying each day (average 478/day). Omicron BA.4, BA.4.6 (a new USA variant) and BA.5 variants causing infections should continue to increase and critically ill patients may increase. Deaths usually lag two to four weeks behind exponential increase in infections. Past infections with a BA.1 or BA.2 variant will not prevent infections with BA.4, BA.4.6 or BA.5.

As of 8/26/22, we have had 1,068,843 deaths and 95,970,007 SARS-CoV-2 infections in the United States. We have had 1,326,375 new infections in the last 14 days. We are adding an average of 663,188 infections every seven days. For the pandemic in the United States we are averaging one death for every 89.78 infections or over 11,137 deaths for each one million infections. As of 8/26/22, thirty-eight states have had greater than 500,000 total infections, and 37 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 42 states have greater than 2,000 deaths per million population. Vermont, at 1,153 deaths per million, and Hawaii, 1,133 deaths per million, are the states with the lowest death rates. Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states have had greater than 70,000 deaths: Florida (79,568 deaths), Texas (90,539 deaths), New York (71,422 deaths), and California (94,959 deaths, 20th most deaths in the world).

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (21 months), there were 808,712 new deaths from SARS-CoV-2. For seventeen of those months, vaccines have been available to all adults. During these seventeen months, 497,746 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 8/26/22, California was ranked 32nd in the USA in infection percentage at 27.97%. In California, 24.0% of people were infected in the last 19 months. As of 8/26/22, 41 states have had greater than 25% of their population infected. No state has less than 20% of their population infected.

Worldwide, average deaths per day are 2,399 for the last 14 days, which is a 55 deaths-per-day decrease over the previous 14 days. The United States accounts for 19.92% (478 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 774,366. The United States accounts for 12.23% of those infections (or 94,741 infections per day).

Watching World Data

Location	Total Infections as of 8/26/22	New Infections on 8/26/22	Total Deaths	New Deaths on 8/26/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	604,789,766(10,841,118 new infections in 14 days).	689,194	6,485,447(33,589 new deaths in last 14 days)	1,927	7.75%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
USA	95,970,007(ranked #1) 1,326,375 new infections in the last 14 days.	63,798(ranked #3) 24 states failed to report infections on 8/26/22.	1,068,843(ranked #1) 6,692 new deaths reported in the last 14 days.	312 30 states failed to report deaths on 8/26/22.	26.72%* *Not updated for 8 weeks by Worldometer.	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,368,909(ranked #4) 220,778 new infections in the last 14 days.	18,270 (ranked #8)	683,464(ranked #2; 2,147 new deaths in 14 days)	136	15.92%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,398,696(ranked #2); 159,324 new infections in 2 weeks.	9,520 (ranked #12)	527,597(ranked #3) 631 new deaths in 2 weeks.	41	3.15%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom	23,492,875(ranked #6) 72,049 new infections in 2 weeks.	–	187,761 (ranked #7) 1,674 new deaths in 2 weeks	–	34.22%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	11,052,866(ranked #14 in the world; 156,070 new infections in the last 14 days).	11,374	94,959 (ranked #20 in world) 640 new deaths in the last 14 days	55	27.97%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	7,001,590(ranked #18) 7,728 new infections in 14 days).	7,281(ranked #16)	329,289(ranked #5)693 new deaths in 214 days)	64	5.31%	B2 lineageAlpha/B.1.1.7 (UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)*	No	No
South Africa	4,010,632(ranked #36; 2,607 new infections in 14 days).	247	102,084 (ranked #18)	–	6.58%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,158,491(ranked #33) 48,560 new infections in 14 days).	3,270	43,797(ranked #24)	39	10.81%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)*	No	No
Poland	6,162,662 (ranked #21; 48,822 new infections in 14 days).	3,847	117,007 (ranked #15)	40	16.32%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	19,311,973(ranked #9), 487,691 new infections in 14 days).	46,452 (ranked #4)	383,910(ranked #4)899 new deaths in 14 days	81	13.22%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)R1 (Japan) B.1.640.1 (Congo/France)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Peru	4,094,652(ranked #34, 80,821 new infections in 14 days).	3,286	215,566(ranked #6)	42	12.05%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,520,993(ranked #17; 55,414 new infections in last 14 days)	2,019	143,647(ranked #12)	35	8.71%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,332,976(ranked #12; 38,737 new infections in 14 days).	3,064(ranked #26)	112,454 (ranked #16)787 new deaths in 14 days	70	28.49%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	34,446,854 (ranked #3; 254,935 new infections in the last 14 days).	18,116	153,857 (ranked #10) 793 new deaths in 14 days	51	52.52%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	32,041,348(ranked #5; 506,005 new infections in 14 days.).	33,226 (ranked #5)	147,104 (ranked #11) 1,406 new deaths in 14 days	101	37.98%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	22,802,985 (ranked #7 1,691,145 new infections in 14 days).	101,064(ranked #2)	26,413 (ranked #37)	81	44.39%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,399,400 (ranked #13; 36,860 new infections in 14 days).	3,195	43,110 (ranked #25)	–	11.48%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,381,009 (ranked #16; 18.445 new infections in 14 days).	1,156	22,594 (ranked #41)	2	48.68%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,089,118 (ranked #40) 12,476 new infections in 14 days	680	6,893 (ranked #79)	5	52.93%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	5,168,949(ranked #23) 322,462 new infections in 14 days	26,713 (ranked #6)	9,773 (ranked #65)	45	21.61%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	17,983,797(ranked #10) 2,897,493 new infections in the last 14 days	227,139(ranked #1)	38,197(ranked #27) 3,660 new deaths in the last 14 days	310	14.31% 2.31% of population has been infected in the last 14 days	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No

What Our Team Is Reading This Week

SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy (Pediatric Research) https://doi.org/10.1038/s41390-022-02266-7
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization (Nature Communications) https://doi.org/10.1038/s41467-022-32262-8
Is SARS-CoV-2 an oncogenic virus? (Journal of Infection) https://doi.org/10.1016/j.jinf.2022.08.005
Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope (Cell) https://doi.org/10.1016/j.cell.2022.07.002
Neurological and psychiatric risk trajectories after SARS-CoV-2 infection: an analysis of 2-year retrospective cohort studies including 1 284 437 patients (The Lancet Psychiatry) https://doi.org/10.1016/S2215-0366(22)00260-7
An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion (Science Immunology) https://doi.org/10.1126/sciimmunol.add5446
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic (Preprint) https://doi.org/10.1101/2022.08.03.22278363
Evaluation of publication bias for 12 clinical trials of molnupiravir to treat SARS-CoV-2 infection in 13,694 patients (Preprint) https://www.researchsquare.com/article/rs-1913200/v1
Anti-neuronal antibodies against brainstem antigens are associated with COVID-19 (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104211
Risk of SARS-CoV-2 Acquisition in Health Care Workers According to Cumulative Patient Exposure and Preferred Mask Type (JAMA Infectious Diseases) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.26816
Coronavirus spike protein activated natural immune response, damaged heart muscle cells (AHA Basic Cardiovascular Sciences Meeting) https://newsroom.heart.org/news/coronavirus-spike-protein-activated-natural-immune-response-damaged-heart-muscle-cells
Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors (Biophysics and Computational Biology) https://doi.org/10.1073/pnas.2119761119
Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2 (The Lancet) https://doi.org/10.1016/S0140-6736(22)00941-2
Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum (Cell) https://doi.org/10.1016/j.cell.2022.06.005
Immunomodulatory treatment in postural tachycardia syndrome: A case series (European Journal of Neurology) https://doi.org/10.1111/ene.14711
Long COVID-19 Liver Manifestation in Children (JPGN) https://journals.lww.com/jpgn/abstract/9900/long_covid_19_liver_manifestation_in_children.84.aspx
Cross-reactive immunity against the SARS-CoV-2 Omicron variant is low in pediatric patients with prior COVID-19 or MIS-C (Nature Communications) https://doi.org/10.1038/s41467-022-30649-1
C.D.C. Dismisses Airborne Transmission of Monkeypox. Some Experts Disagree. (NY Times) https://www.nytimes.com/2022/06/10/health/monkeypox-airborne.html

COVID-19

SARS-CoV-2 Update

08/14/2022 davidcwrightmd

SARS-CoV-2 infections per day in the United States have decreased for the first time in two weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day had been decelerating at a rapid rate in the United States but are now increased by 57 more deaths per day. The number of infections have increased as the Omicron BA.2.12.1, BA.2, BA.4, and BA.5 variants of SARS CoV-2 have spread across the nation. The CDC estimates that BA.2.12.1 accounted for 0.8% of isolates, BA.2 accounted for 0%, BA.5 accounted for 88.8%, BA.4 accounted for 5.3%, BA.4.6 accounted for 5.1%, and B.1.1.529 accounted for 0% in the week ending August 13.

The Omicron variant has continued to mutate just like Delta. There are now 230 Omicron sub-variants (an unexplained decrease of 9 in the last two weeks) that have been assigned Pango lineages, including 116 sub-lineages of BA.2 (no increase in two weeks), one sub-lineage of BA.3, 14 sub-lineages of BA.4 (no increase in two weeks), and 24 sub-lineages of BA.5 (no increase in two weeks). The BF lineage (new eight weeks ago) now has 11 sublineages, no increase in two weeks. The BE lineage (also new eight weeks ago), with BE.1 first detected in South Africa, Austria and England, still has 4 sublineages. There are also new lineages from eight weeks ago: BC.1 (Japan), BC.2 (Peru),BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel).

Omicron variants have mutations which decrease the effectiveness of current vaccines and monoclonal antibodies. The effectiveness of the new Pfizer drug, PAXLOVID^TM, should not be compromised by any of the current mutations in Omicron or Delta variants. Pfizer completed their filing with the FDA on 11/15/21. The FDA approved PAXLOVID^TM on December 22 , 2021.The FDA approved Merck’s drug Molnupiravir on December 23, 2021. On 12/23/21 CVS announced by fax it was selected by the Government to distribute oral PAXLOVID^TM and Molnupiravir. On 12/27/21, another fax from CVS listed which CVS pharmacies in California would have these drugs. Monterey County covers 3,771 square miles with a population of 434,061. Three CVS pharmacies in Monterey, Salinas, and Soledad are the only listed pharmacies in our county. I have now been able to obtain PAXLOVID^TM for infected patients from the CVS in Salinas (phone 831-424-0026), the CVS on Fremont Street in Monterey (phone 831-375-5135) and the CVS in Soledad in south Monterey County (phone 831-678-5110). All require electronic prescriptions written as Paxlovid three tablets twice daily orally for five days (thirty total tablets). Physicians or their staff probably should call to check on drug availability that day.

In the absence of obtaining intravenous Sotrovimab or Bebtelovimab, only oral PAXLOVID^TM and Molnupiravir are available to treat SARS-CoV-2 as an outpatient. Our first Paxlovid failure in an immunocompromised patient was treated the week of 4/5/22 at the Community Hospital of the Monterey Peninsula (Montage) ER as an outpatient with a single one-minute intravenous injection of Bebtelovimab.

In Monterey County, as of 8/14/22, 0.3% of 0-4 year-olds and 38.9% of 5-11 year-olds have received the first two doses of vaccine, while 72.8% of 12-17 year-olds have received two doses. Only 53.3% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. We would anticipate, with the start of school on August 5 and the low vaccination rates in our county, that we’ll have a marked increase in the number of infected patients. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

FDA Approved Intramuscular Prophylaxis of SARS-CoV-2 Immunocompromised Patients

Evusheld (from AstraZeneca) contains two human monoclonal antibodies, Tixagevimab (150 mg in 1.5 mL) and Cilgavimab (150 mg in 1.5 mL), in separate vials. According to the manufacturer, “Tixagevimab and Cilgavimab are two recombinant human IgG1κ monoclonal antibodies with amino acid substitutions to extend antibody half-life (YTE), reduce antibody effector function, and minimize the potential risk of antibody-dependent enhancement of disease (TM). Tixagevimab and Cilgavimab can simultaneously bind to non-overlapping regions of the receptor binding domain (RBD) of SARS-CoV-2 spike protein. Tixagevimab, Cilgavimab, and their combination bind to spike protein with equilibrium dissociation constants of KD = 2.76 pM, 13.0 pM and 13.7 pM, respectively, blocking its interaction with human ACE2, the SARS-CoV-2 receptor, which is required for virus attachment. Tixagevimab, Cilgavimab, and their combination blocked RBD binding to human ACE2 with IC50 values of 0.32 nM (48 ng/mL), 0.53 nM (80 ng/mL), and 0.43 nM (65 ng/mL), respectively.” Each monoclonal antibody is administered intramuscularly to immunocompromised patients in two separate injections every six months. Evusheld availability in California is limited and has been rationed/distributed by our local Public Health Department only to hospitals. Physicians in Monterey County who want to receive a distribution (or redistribution) of Evusheld need to be added to the list of eligible facilities by the State Therapeutics group. The first step is for the Monterey County EMS Agency (phone: 831-755-5713) to make a request to the State Therapeutics group to have the facility added to the system for further verification. Due to extremely limited availability, evidently the State Therapeutics group is currently only considering additions on a case by case basis. Physicians who wish to submit their facility for consideration will need to provide the following information to the Monterey County EMS Agency:

Facility/Provider Name for Registration
Provider Type (Hospital, Pharmacy, Etc)
Shipping Address
Contact Name(s)
Contact Email(s)
Contact Phone Number(s)

As for my immunocompromised patients: We provided this information by email to the Monterey County EMS Agency on 1/26/22 and will update you when or if we become an eligible provider and receive our first doses of Evusheld.

Watching World Data

Location	Total Infections as of 8/12/22	New Infections on 8/12/22	Total Deaths	New Deaths on 8/12/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	593,948,648(13,178,472 new infections in 14 days).	792,572	6,451,858(34,360 new deaths in last 14 days)	2,241	7.61%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
USA	94,643,632(ranked #1) 1,589,448 new infections in the last 14 days.	85,116(ranked #3) 22 states failed to report infections on 8/12/22.	1,062,151(ranked #1) 7,131 new deaths reported in the last 14 days.	335 28 states failed to report deaths on 8/12/22..	26.72%* *Not updated for 6 weeks by Worldometer.	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)*	No	No
Brazil	34,148,131(ranked #3) 352,939 new infections in the last 14 days.	23,552 (ranked #7)	681,317(ranked #2; 2,942 new deaths in 14 days)	292	15.82%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
India	44,239.372(ranked #2); 239,234 new infections in 2 weeks.	15,815 (ranked#11)	526,966(ranked #3) 654 new deaths in 2 weeks.	68	3.14%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)*	No	No
United Kingdom* *No reported data for 8/12/22	23,420,826(ranked #6) 116,347 new infections in 2 weeks.	–	186,087 (ranked #7) 2,134 new deaths in 2 weeks	–	34.12%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
California, USA	10,896,796(ranked #14 in the world; 198618 new infections in the last 14 days).	13,306	94,319 (ranked #20 in world) 615 new deaths in the last 14 days	50	27.57%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)*	No	No
Mexico	6,903,862(ranked #18) 192,015 new infections in 14 days).	13,313(ranked #12)	328,596(ranked #5)1,071 new deaths in 214 days)	71	5.23%	B2 lineageAlpha/B.1.1.7 (UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)*	No	No
South Africa	4,007,925(ranked #33; 3,370 new infections in 14 days).	313	101,982 (ranked #18) Not updated in last 2 weeks.	–	6.58%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)	No	No
Canada	4,109,931(ranked #33) 87,572 new infections in 14 days).	3,603	43,583(ranked #24)	37	10.69%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)*	No	No
Poland	6,113,840 (ranked #21; 48,508 new infections in 14 days).	4,223	116,751 (ranked #15)	14	16.19%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	18,824,282(ranked #9), 247,309 new infections in 14 days).	27,810	383,011(ranked #4 in world)	57	12.88%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)R1 (Japan) B.1.640.1 (Congo/France)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Peru	4,013,831(ranked #34, 118,345 new infections in 14 days).	10,882	214,890(ranked #6)	72	11.82%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,465,579(ranked #17; 88,785 new infections in last 14 days)	6,404	142,806(ranked #12)	54	8.65%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,294,139(ranked #12; 67,560 new infections in 14 days).	4,528(ranked #22)	111,667 (ranked #16)	110	28.41%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	34,191,919 (ranked #3; 405,153 new infections in the last 14 days).	22,638 (ranked #9)	153,064 (ranked #10) 1,101 new deaths in 14 days	74	52.13%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	31,535,343(ranked #5; 682,031 new infections in 14 days.).	45,859 (ranked #4)	145,698 (ranked #11) 1,726 new deaths in 14 days	137	37.38%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	21,111,840 (ranked #8 1,491,323 new infections in 14 days).	128,671(ranked #2)	25,499 (ranked #37)	58	41.10%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	11,362,540 (ranked #13; 586,056 new infections in 14 days).	2,192	43,096 (ranked #25)	1	11.45%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,362,564 (ranked #16; 31,241 new infections in 14 days).	1,882	22,542 (ranked #41)	4	48.57%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,076,642 (ranked #40) 16,658 new infections in 14 days	1,323	6,792 (ranked #80)	12	52.72%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	4,846,477(ranked #24) 300,841 new infections in 14 days	21,965 (ranked #10)	9,373 (ranked #67)	31	20.27%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	15,086,304(ranked #11) 2,908,192 new infections in the last 14 days	224,929(ranked #1)	34,537(ranked #30) 2,251 new deaths in the last 14 days	214	12.00%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2BA.5	No	No

What Our Team Is Reading This Week

Distinguishing features of Long COVID identified through immune profiling (Preprint) https://doi.org/10.1101/2022.08.09.22278592
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 (Preprint) https://doi.org/10.1101/2022.08.07.503115
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir (Preprint) https://doi.org/10.1101/2022.08.07.499047
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors (Preprint) https://doi.org/10.1101/2022.08.07.503099
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 (Preprint) https://doi.org/10.1101/2022.08.05.502758
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates (Nature Communications) https://doi.org/10.1038/s41467-022-29440-z
SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19 (Journal of Neuropathology and Experimental Neurology) https://doi.org/10.1093/jnen/nlac056
Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology (JAMA) http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.25430
Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection (Nature) https://doi.org/10.1038/nature04295
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID (Preprint) https://doi.org/10.1101/2022.06.21.22276660
Notes from the Field: Increase in Pediatric Intracranial Infections During the COVID-19 Pandemic — Eight Pediatric Hospitals, United States, March 2020–March 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7131a4
Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors (Biophysics and Computational Biology) https://doi.org/10.1073/pnas.2119761119
Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2 (The Lancet) https://doi.org/10.1016/S0140-6736(22)00941-2
Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum (Cell) https://doi.org/10.1016/j.cell.2022.06.005
Immunomodulatory treatment in postural tachycardia syndrome: A case series (European Journal of Neurology) https://doi.org/10.1111/ene.14711

COVID-19

SARS-CoV-2 Update

07/31/2022 davidcwrightmd

SARS-CoV-2 infections per day have been increasing in the United States for 16 consecutive weeks despite underreporting by states and the failure to capture positive home tests and a decreased screening program in most states. Deaths per day had been decelerating at a rapid rate in the United States but are now increased by 65 more deaths per day. The number of infections have increased as the Omicron BA.2.12.1, BA.2, BA.4, and BA.5 variants of SARS CoV-2 have spread across the nation. The CDC estimates that BA.2.12.1 accounted for 5.0% of isolates, BA.2 accounted for 0.3%, BA.5 accounted for 89.1%, BA.4 accounted for 12.9%, and B.1.1.529 accounted for 0% in the week ending July 23.

The Omicron variant has continued to mutate just like Delta. There are now 239 Omicron sub-variants (an increase of 28 in the last two weeks) that have been assigned Pango lineages, including 116 sub-lineages of BA.2 (an increase of 4 in two weeks), one sub-lineage of BA.3, 14 sub-lineages of BA.4 (an increase of 3 in two weeks), and 24 sub-lineages of BA.5 (an increase of 7 in two weeks). The BF lineage (new six weeks ago) now has 11 sublineages, an increase of 5 in two weeks. The BE lineage (also new six weeks ago), with BE.1 first detected in South Africa, Austria and England, still has 4 sublineages. There are also new lineages from six weeks ago: BC.1 (Japan), BC.2 (Peru), BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel).

Unless people continue to wear masks and get vaccinated, including their third dose of the vaccine, we will see further spread of the Omicron variants and increase in deaths in people who are not vaccinated, those who have waning immunity, the immunocompromised population, and others with risk factors, particularly those older over the age of 64. SARS-CoV-2 is now in the top ten most common causes of death for children. Anyone over the age of 5 years can now get vaccinated in the United States at no cost. This should get done immediately.

In Monterey County, as of 7/31/22, 0.1% of 0-4 year-olds and 38.6% of 5-11 year-olds have received the first two doses of vaccine, while 72.6% of 12-17 year-olds have received two doses. Only 53.2% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. We would anticipate, with the start of school on August 5 and the low vaccination rates in our county, that we’ll have a marked increase in the number of infected patients. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

On 7/29/22, the United States had 99,061 documented new infections. There were also 286 deaths. Twenty-two states did not report their infections, and 28 states didn’t report their deaths. In the United States the number of hospitalized patients has been increasing in many areas and was 44,207 on July 29, an increase of 9% compared to the previous 14 days. Now there are 4,723 patients who are seriously or critically ill; that number was 4,180 two weeks ago. The number of critically ill patients has increased by 543 in the last 14 days, while at least 6,327 new deaths occurred (an increase of 65 deaths per day from the previous 14 days). The number of critically ill patients has increased for the seventh time in twenty-four 14-day periods. Patients are still dying each day (average 387/day). Omicron BA.2, BA.2.12.1, BA.4, and BA.5 variants causing infections should continue to increase and critically ill patients may continue to increase. Deaths, which usually lag two to four weeks behind exponential increase in infections, are increasing now. Past infections with a BA.1 or BA.2 variant will not prevent infections with BA.2.12.1, BA.4, or BA.5.

As of 7/29/22, we have had 1,055,020 deaths and 93,054,184 SARS-CoV-2 infections in the United States. We have had 1,883,613 new infections in the last 14 days. We are adding an average of 941,807 infections every seven days. For the pandemic in the United States we are averaging one death for every 88.20 infections or over 11,338 deaths for each one million infections. As of 7/29/22, thirty-eight states have had greater than 500,000 total infections, and 37 states have had greater than 5,000 total deaths. Seventeen states (Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York, and California) have had greater than 70,000 deaths. California and Texas have each had greater than 89,000 deaths with California having 93,704 deaths (20th most deaths in the world).

As of 7/1/22, in the United States, 26.72% of the population has had a documented SARS-CoV-2 infection. In the 18 months preceding 7/1/22, 23.97% of our country became infected with SARS-CoV-2. On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2.

In the last 18 months, there were 794,889 new deaths from SARS-CoV-2. For fifteen of those months, vaccines have been available to all adults. During these fifteen months, 483,923 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 7/29/22, California was ranked 32th in the USA in infection percentage at 27.07%. In California, 23.1% of people were infected in the last 18 months. As of 7/29/22, 38 states have had greater than 25% of their population infected.

Worldwide, average deaths per day are 2,263 for the last 14 days, which is a 417 deaths-per-day increase over the previous 14 days. The United States accounts for 19.97% (452 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 1,030,492. The United States accounts for 13.06% of those infections (or 134,544 infections per day).

FDA-Approved Oral Drug Treatments for SARS-CoV-2

FDA Approved Intramuscular Prophylaxis of SARS-CoV-2 Immunocompromised Patients

Facility/Provider Name for Registration
Provider Type (Hospital, Pharmacy, Etc)
Shipping Address
Contact Name(s)
Contact Email(s)
Contact Phone Number(s)

On 2/24/22, the FDA revised its dosing guidance for Evusheld, doubling the dosage of its two components, Tixagevimab and Cilgavimab, from 150 mg each to 300 mg each. They explain, “Based on the most recent information and data available, Evusheld may be less active against certain Omicron subvariants. The dosing regimen was revised because available data indicate that a higher dose of Evusheld may be more likely to prevent infection by the COVID-19 Omicron subvariants BA.1 and BA.1.1 than the originally authorized Evusheld dose.” Patients who have already received their first administration of Evusheld intramuscularly will need to contact their healthcare provider to get a second 150 mg injection of Tixagevimab and Cilgavimab. If you have not received Evusheld yet, the correct dose is 3 mL/300 mg of each monoclonal antibody injected intramuscularly. This large volume necessitates administration of the antibodies in the gluteus, with two separate injections.

Watching World Data

Location	Total Infections as of 7/29/22	New Infections on 7/29/22	Total Deaths	New Deaths on 7/29/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	580,770,176(14,426,888 new infections in 14 days).	905,405	6,417,498(31,678 new deaths in last 14 days)	2,808	7.45%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1BA.4 (South Africa)BA.5 (South Africa)*	No	No
USA	93,054,184(ranked #1) 1,883,613 new infections in the last 14 days.	99,081(ranked #4) 22 states failed to report infections.	1,055,020(ranked #1) 6,327 new deaths in the last 14 days.	28628 states failed to report deaths.	26.72%* *Not updated for four weeks by Worldometers	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India)*	No	No
Brazil	33,795,192(ranked #3) 545,075 new infections in the last 14 days.	42,816 (ranked #8)	678,375(ranked #2; 3,230 new deaths in 14 days)	228	15.66%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
India	44,000,138(ranked #2); 270,067 new infections in 2 weeks.	20,408	526,312(ranked #3)	54	3.12%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2.75 (India)*	No	No
United Kingdom* *No reported data for 7/29/22	23,304,479(ranked #6) 229,119 new infections in 2 weeks.	–	183,953 (ranked #7) 2,373 new deaths in 2 weeks	–	33.95%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India)*	No	No
California, USA	10,698,178(ranked #14 in the world; 317,309 new infections in the last 14 days).	18,715	93,704 (ranked #20 in world) 687 new deaths in the last 14 days	51	27.07%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa)BA.5 (South Africa)*	No	No
Mexico	6,711,847(ranked #18) 337,971 new infections in 14 days).	24,893(ranked #9)	327,525(ranked #5)	113	5.09%	B2 lineageAlpha/B.1.1.7 (UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)*	No	No
South Africa	4,004,555(ranked #33; 4,704 new infections in 14 days).	354	101,982 (ranked #18)	5	6.58%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.2.12.1BA.4 (South Africa)BA.5 (South Africa)	No	No
Canada	4,012,359(ranked #32) 4,896 new infections in 14 days).	–	43,583(ranked #24)	–	10.44% .	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)*	No	No
Poland	6,065,332 (ranked #21; 35,385 new infections in 14 days).	3,391	116,556 (ranked #15)	9	16.06%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	18,576,973(ranked #9), 96,039 new infections in 14 days).	11,422	382,352(ranked #4 in world)	39	12.71%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)R1 (Japan) B.1.640.1 (Congo/France)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Peru	3,895,486(ranked #37, 181,125 new infections in 14 days).	6,467	214,195(ranked #6)	41	11.48%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,376,794(ranked 17th; 106,771 new infections in last 14 days)	7,849	141,891(ranked #12)	54	8.55%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,226,579(ranked 11th; 136,103 new infections in 14 days).	7,783(ranked #18)	110,719 (ranked #16)	109	28.26%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	33,786,766 (ranked #4; 967,865 new infections in the last 14 days).	45,515 (ranked #6)	151,983 (ranked #10) 1,407 new deaths in 14 days	89	51.52%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	30,853,312(ranked #5; 1,170,323 new infections in 14 days.).	66,003 (ranked #4)	143,972 (ranked #11) 1,437 new deaths in 14 days	117	36.58%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	19,620,517 (ranked #9 940,375 new infections in 14 days).	85,275(ranked #3)	24,999 (ranked #38)	35	38.20%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	10,776,484 (ranked #13; 17,339 new infections in 14 days).	1,803	43,093 (ranked #25)	1	10.86%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,331,315 (ranked #18; 57,081 new infections in 14 days).	3,238	22,492 (ranked #41)	4	48.40%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,059,984 (ranked #39) 20,125 new infections in 14 days	1,037	6,639 (ranked #81)	11	52.44%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Taiwan	4,545,636(ranked #29) 330,436 new infections in 14 days	23,289 (ranked #10)	8,833 (ranked #69) 916 new deaths in 14 days	57	19.01%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	12,118,112(ranked #12) 2,117,392 new infections in the last 14 days	230,055(ranked #1)	32,286(ranked #30)	116	9.64%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No

What Our Team Is Reading This Week

Broadly neutralizing antibodies target the coronavirus fusion peptide (Science) https://doi.org/10.1126/science.abq3773
Efficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2201300
Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2202261
Risk of Reinfection, Vaccine Protection, and Severity of Infection with the BA.5 Omicron Subvariant: A Danish Nation-Wide Population-Based Study (Preprint) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4165630
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors (Biophysics and Computational Biology) https://doi.org/10.1073/pnas.2119761119
Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2 (The Lancet) https://doi.org/10.1016/S0140-6736(22)00941-2
Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum (Cell) https://doi.org/10.1016/j.cell.2022.06.005
Immunomodulatory treatment in postural tachycardia syndrome: A case series (European Journal of Neurology) https://doi.org/10.1111/ene.14711
Long COVID-19 Liver Manifestation in Children (JPGN) https://journals.lww.com/jpgn/abstract/9900/long_covid_19_liver_manifestation_in_children.84.aspx
Cross-reactive immunity against the SARS-CoV-2 Omicron variant is low in pediatric patients with prior COVID-19 or MIS-C (Nature Communications) https://doi.org/10.1038/s41467-022-30649-1
C.D.C. Dismisses Airborne Transmission of Monkeypox. Some Experts Disagree. (NY Times) https://www.nytimes.com/2022/06/10/health/monkeypox-airborne.html
Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes (Science Immunology) https://doi.org/10.1126/sciimmunol.abq2427
SARS-CoV-2 Infection and Persistence Throughout the Human Body and Brain (National Institutes of Health) https://videocast.nih.gov/watch=45296?jwsource=twi
Long COVID is associated with extensive in-vivo neuroinflammation on [18F]DPA-714 PET (Preprint) https://doi.org/10.1101/2022.06.02.22275916
Unexpected worsening of progressive multifocal leucoencephalopathy following COVID-19 pneumonia (Journal of Neurovirology) https://doi.org/10.1007%2Fs13365-021-00980-2
Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5 (Preprint) https://doi.org/10.1101/2022.05.26.493539
During the Omicron Wave, Death Rates Soared for Older People (NY Times with CDC data) https://www.nytimes.com/2022/05/31/health/omicron-deaths-age-65-elderly.html
PD-1 blockade counteracts post–COVID-19 immune abnormalities and stimulates the anti–SARS-CoV-2 immune response (JCI Insight) https://insight.jci.org/articles/view/146701
Adverse effects of immune-checkpoint inhibitors: epidemiology, management and surveillance (Nature Reviews Clinical Oncology) https://doi.org/10.1038/s41571-019-0218-0
Herpesvirus infections and post-COVID-19 manifestations: a pilot observational study (Observational Research) https://doi.org/10.1007/s00296-022-05146-9
An early warning system for emerging SARS-CoV-2 variants (Nature Medicine) https://doi.org/10.1038/s41591-022-01836-w
SARS-CoV-2 Omicron Variant is as Deadly as Previous Waves After Adjusting for Vaccinations, Demographics, and Comorbidities (Preprint) https://doi.org/10.21203/rs.3.rs-1601788/v1
Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1 (Preprint) https://www.medrxiv.org/content/10.1101/2022.04.25.22274187v1
COVID-19 Associated Hepatitis in Children (CAH-C) during the second wave of SARS-CoV-2 infections in Central India: Is it a complication or transient phenomenon. (Preprint) https://doi.org/10.1101/2021.07.23.21260716
Liver and Gastrointestinal Involvement in Patients With COVID-19: A Retrospective Study https://www.cureus.com/articles/90062-liver-and-gastrointestinal-involvement-in-patients-with-covid-19-a-retrospective-study
Cortical Grey Matter Volume Loss links to Neurological Sequelae in post COVID-19 “Long Haulers” (Preprint) https://doi.org/10.21203/rs.3.rs-1582065/v1
Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike (Cell) https://doi.org/10.1016/j.cell.2022.04.035
Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages https://www.krisp.org.za/manuscripts/MEDRXIV-2022-274406v1-deOliveira.pdf
Molecular consequences of SARS-CoV-2 liver tropism (Nature Metabolism) https://doi.org/10.1038/s42255-022-00552-6
China CDC shares latest COVID-19 data (GISAID) https://www.gisaid.org/resources/gisaid-in-the-news/china-shares-latest-11-apr-2022/#c920
Persistent COVID-19 symptoms in a community study of 606,434 people in England (Nature) https://www.nature.com/articles/s41467-022-29521-z
Brain Inflammation and Intracellular α-Synuclein Aggregates in Macaques after SARS-CoV-2 Infection (Viruses) https://www.mdpi.com/1999-4915/14/4/776
Antibody Resistance of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages (Preprint) https://www.biorxiv.org/content/10.1101/2022.04.07.487489v1
Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2 (Nature Medicine) https://www.nature.com/articles/s41591-022-01816-0
Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain (Preprint) https://www.biorxiv.org/content/10.1101/2022.01.07.475453v1
Risks of deep vein thrombosis, pulmonary embolism, and bleeding after covid-19: nationwide self-controlled cases series and matched cohort study (BMJ) https://www.bmj.com/content/377/bmj-2021-069590
SARS-CoV-2 Infection Induces Ferroptosis of Sinoatrial Node Pacemaker Cells (Circulation Research) https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.121.320518
SARS-CoV-2 variants of concern and variants under investigation in England (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1063424/Tech-Briefing-39-25March2022_FINAL.pdf
Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine (Preprint) https://doi.org/10.1101/2022.03.24.485633
COVID-19-Associated Encephalitis: Two Case Reports https://www.cureus.com/articles/86903-covid-19-associated-encephalitis-two-case-reports
First evidence that an emerging mammalian alphacoronavirus is able to infect an avian species (Transboundary and Emerging Diseases) https://doi.org/10.1111/tbed.14535
SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses (The Lancet) https://doi.org/10.1016/S0140-6736(22)00383-X
Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination (Preprint) https://www.medrxiv.org/content/10.1101/2022.03.09.22272113v1
Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France (Preprint) https://www.medrxiv.org/content/10.1101/2022.03.03.22271812v1.full
Mandatory masking in schools reduced COVID-19 cases during Delta surge (NIH press release) https://www.nih.gov/news-events/news-releases/mandatory-masking-schools-reduced-covid-19-cases-during-delta-surge
School Masking Policies and Secondary SARS-CoV-2 Transmission (Pediatrics) https://publications.aap.org/pediatrics/article/doi/10.1542/peds.2022-056687/185379/School-Masking-Policies-and-Secondary-SARS-CoV-2
Transmission of SARS-CoV-2 delta variant (AY.127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study (The Lancet) https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00326-9/fulltext
COVID-19 Variant Dashboard – USA by Raj Rajnarayanan https://public.tableau.com/app/profile/raj.rajnarayanan/viz/USAVariantDB/VariantDashboard
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 38 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1060337/Technical-Briefing-38-11March2022.pdf
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 37 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1057359/Technical-Briefing-37-25February2022.pdf
Engineered extracellular vesicles antagonize SARS-CoV-2 infection by inhibiting mTOR signaling (Biomaterials and Biosystems) https://www.sciencedirect.com/science/article/pii/S2666534422000046?via%3Dihub
Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study (Preprint) https://doi.org/10.21203/rs.3.rs-1385593/v1
Dynamics of the Delta and Omicron variants of SARS-CoV-2 in the United States: the battle of supremacy in the presence of vaccination, mask usage and antiviral treatment (Preprint) https://doi.org/10.21203/rs.3.rs-1420446/v1
Virological characteristics of SARS-CoV-2 BA.2 variant (Preprint) https://www.biorxiv.org/content/10.1101/2022.02.14.480335v1
Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households (Preprint) https://www.medrxiv.org/content/10.1101/2022.01.28.22270044v1
Waning 2-Dose and 3-Dose Effectiveness of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7107e2.htm?s_cid=mm7107e2_e&ACSTrackingID=USCDC_921-DM75599&ACSTrackingLabel=MMWR%20Early%20Release%20-%20Vol.%2071%2C%20February%2011%2C%202022&deliveryName=USCDC_921-DM75599
SARS-CoV-2 B.1.1.529 (Omicron) Variant Transmission Within Households — Four U.S. Jurisdictions, November 2021–February 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7109e1.htm?s_cid=mm7109e1_w
Pediatric Emergency Department Visits Before and During the COVID-19 Pandemic — United States, January 2019–January 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7108e1.htm?s_cid=mm7108e1_w#F2_down
Birth Of The Omicron Family: BA.1, BA.2, BA.3. Each As Different As Alpha Is From Delta. (Forbes) https://www.forbes.com/sites/williamhaseltine/2022/01/26/birth-of-the-omicron-family-ba1-ba2-ba3-each-as-different-as-alpha-is-from-delta/?sh=403de4ee3da9
Take a look at SARS-CoV-2’s family tree. It’s full of surprises (NPR) https://www.npr.org/sections/goatsandsoda/2022/02/09/1047616658/take-a-look-at-sars-cov-2s-family-tree-its-full-of-surprises
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 35 https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1050999/Technical-Briefing-35-28January2022.pdf
Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants (Nature) https://www.nature.com/articles/s41586-022-04466-x_reference.pdf
Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time (Preprint) https://www.medrxiv.org/content/10.1101/2022.01.14.22269235v1
Syncytin, envelope protein of human endogenous retrovirus (HERV): no longer ‘fossil’ in human genome (Animal Cells and Systems) https://doi.org/10.1080/19768354.2021.2019109
Host Chitinase 3-like-1 is a Universal Therapeutic Target for the Delta, Omicron and Other SARS-CoV-2 Viral Variants in COVID 19 (Preprint) https://www.biorxiv.org/content/10.1101/2022.01.21.477274v1
COVID-19 reinfections among naturally infected and vaccinated individuals (Nature) https://www.nature.com/articles/s41598-022-05325-5
Duration of Protection against Mild and Severe Disease by Covid-19 Vaccines (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2115481
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants (Preprint) https://www.medrxiv.org/content/10.1101/2022.01.25.22269794v1
COVID-19 and the Common Cold—Preexisting Coronavirus Antibodies May Hinder SARS-CoV-2 Immunity (JAMA) https://jamanetwork.com/journals/jama/fullarticle/2788621?guestAccessKey=0bbad800-e651-496b-8046-d124bbc63a5a&term=01262022&utm_source=silverchair&utm_medium=email&utm_campaign=article_alert-jama&utm_content=olf&utm_term=012622
Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant https://dash.harvard.edu/handle/1/37370587
Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein (Preprint) https://doi.org/10.1101/2021.12.24.21268174
A living WHO guideline on drugs for covid-19 (BMJ) https://doi.org/10.1136/bmj.m3379
Longitudinal analysis reveals high prevalence of Epstein-Barr virus associated with multiple sclerosis (Science) https://doi.org/10.1126/science.abj8222
Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection (Nature) https://www.nature.com/articles/s41590-021-01113-x
An upper bound on one-to-one exposure to infectious human respiratory particles (PNAS) https://www.pnas.org/content/118/49/e2110117118
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies (Nature) https://doi.org/10.1038/d41586-021-03796-6
Frequent Occurrence of SARS-CoV-2 Transmission among Non-close Contacts Exposed to COVID-19 Patients (Journal of Korean Medical Science) https://doi.org/10.3346/jkms.2021.36.e233
Serial Screening for SARS-CoV-2 in Rectal Swabs of Symptomatic COVID-19 Patients (Journal of Korean Medical Science) https://doi.org/10.3346/jkms.2021.36.e301
Saliva swabs are the preferred sample for Omicron detection (Preprint) https://doi.org/10.1101/2021.12.22.21268246

COVID-19

SARS-CoV-2 Update

07/19/2022 davidcwrightmd

SARS-CoV-2 infections per day have been increasing in the United States for 14 consecutive weeks despite underreporting by states and the failure to capture positive home tests and a decreased screening program in most states. Deaths per day had been decelerating at a rapid rate in the United States but are now increased by 29 more deaths per day. The number of infections have increased as the Omicron BA.2.12.1, BA.2, BA.4, and BA.5 variants of SARS CoV-2 have spread across the nation. The CDC estimates that BA.2.12.1 accounted for 17.3% of isolates, BA.2 accounted for 1.4%, BA.5 accounted for 65.0%, BA.4 accounted for 16.3%, and B.1.1.529 accounted for 0% in the week ending June 25.

The Omicron variant has continued to mutate just like Delta. There are now 211 Omicron sub-variants (an increase of 12 in the last two weeks) that have been assigned Pango lineages, including 112 sub-lineages of BA.2 (an increase of 8 in two weeks), one sub-lineage of BA.3, 11 sub-lineages of BA.4 (an increase of 2 in two weeks), and 17 sub-lineages of BA.5 (an increase of 2 in two weeks). The BF lineage (new four weeks ago), with BF.1 first detected in England, Denmark, Spain and Scotland still has 6 sublineages. The BE lineage (also new four weeks ago), with BE.1 first detected in South Africa, Austria and England, now has 4 sublineages (one new in the past two weeks). There are also new lineages from four weeks ago: BC.1 (Japan), BC.2 (Peru),BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel).

In Monterey County, as of 7/17/22, 0.0% of 0-4 year-olds and 38.3% of 5-11 year-olds have received the first two doses of vaccine, while 72.4% of 12-17 year-olds have received two doses. Only 53% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. We would anticipate, with the start of school on August 5 and the low vaccination rates in our county, that we’ll have a marked increase in the number of infected patients. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible.

On 7/15/22, the United States had 94,037 documented new infections. There were also 207 deaths. Twenty-one states did not report their infections, and 28 states didn’t report their deaths. In the United States the number of hospitalized patients has been increasing in many areas and was 40,650 on July 15, an increase of 20% compared to the previous 14 days. Now there are 4,180 patients who are seriously or critically ill; that number was 3,400 two weeks ago. The number of critically ill patients has increased by 780 in the last 14 days, while at least 5,412 new deaths occurred (an increase of 29 deaths per day from the previous 14 days). The number of critically ill patients has increased for the sixth time in twenty-three 14-day periods. Patients are still dying each day (average 387/day). Omicron BA.2, BA.2.12.1, BA.4, and BA.5 variants causing infections should continue to increase and critically ill patients may continue to increase. Deaths, which usually lag two to four weeks behind exponential increase in infections, are increasing now. Past infections with a BA.1 or BA.2 variant will not prevent infections with BA.2.12.1, BA.4, or BA.5.

As of 7/15/22, we have had 1,048,693 deaths and 91,170,571 SARS-CoV-2 infections in the United States. We have had 1,663,488 new infections in the last 14 days. We are adding an average of 831,744 infections every seven days. For the pandemic in the United States we are averaging one death for every 86.94 infections or over 11,503 deaths for each one million infections. As of 7/15/22, thirty-eight states have had greater than 500,000 total infections, and 37 states have had greater than 5,000 total deaths. Seventeen states (Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York, and California) have had greater than 70,000 deaths. California and Texas have each had greater than 89,000 deaths with California having 93,017 deaths (20th most deaths in the world).

As of 7/1/22, in the United States, 26.72% of the population has had a documented SARS-CoV-2 infection. In the last 18 months, 23.97% of our country became infected with SARS-CoV-2. On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. In the last 18 months, there were 788,562 new deaths from SARS-CoV-2. For fifteen of those months, vaccines have been available to all adults. During these fifteen months, 477,596 people have died of SARS-CoV-2 infections. Most of the hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.

As of 7/15/22, California was ranked 32th in the USA in infection percentage at 26.27%. In California, 22.3% of people were infected in the last 18 months. As of 7/15/22, 38 states have had greater than 25% of their population infected.

Worldwide, average deaths per day are 1,846 for the last 14 days. The United States has 20.96% (387 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 910,374. The United States accounts for 13.05% of those infections (or 118,821 infections per day).

Watching World Data

Location	Total Infections as of 7/15/22	New Infections on 7/15/22	Total Deaths	New Deaths on 7/15/22	% of Pop.Infected	SARS-CoV-2 Isolates Currently Known in Location	National/ State Mask Mandate	Currently in Lockdown
World	566,343,288(12,745,232 new infections in 14 days).	903,272	6,385,820(25,848 new deaths in last 14 days)	1,737	7.26%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1BA.4 (South Africa)BA.5 (South Africa)*	No	No
USA	91,170,571(ranked #1) 1,663,488 new infections in the last 14 days.	94,037(ranked #4) 21 states failed to report infections.	1,048,693(ranked #1) 5,412 new deaths in the last 14 days.	207 27 states failed to report deaths.	26.72%* *Not updated	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan) Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India)*	No	No
Brazil	33,250,117(ranked #3) 816,054 new infections in the last 14 days.	107,959 (ranked #4)	675,145(ranked #2; 3,145 new deaths in 14 days)	299	15.42%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
India	43,730,071(ranked #2); 241,552 new infections in 2 weeks.	20,044	525,660(ranked #3)	56	3.10%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2.75 (India)*	No	No
United Kingdom* *No reported data for 7/14/22- 7/16/22	23,075,360(ranked #6) 334,295 new infections in 2 weeks.	–	181,580 (ranked #7)	–	33.63%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India)*	No	No
California, USA	10,380,889(ranked #12 in the world; 226,544 new infections in the last 14 days).	8,694	93,017 (ranked #20 in world) 397 new deaths in the last 14 days	16	26.27%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa)BA.5 (South Africa)*	No	No
Mexico	6,373,876(ranked #18) 339,174 new infections in 14 days).	34,885(ranked #9)	326,335(ranked #5)	74	4.84%	B2 lineageAlpha/B.1.1.7 (UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)*	No	No
South Africa	3,999,751(ranked #33; 5,528 new infections in 14 days).	406	101,918 (ranked #18)	3	6.57%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India) C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.2.12.1BA.4 (South Africa)BA.5 (South Africa)	No	No
Canada	4,007,463(ranked #32) 61,376 new infections in 14 days).	1,881	43,555(ranked #24)	51	10.43% .	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)*	No	No
Poland	6,029,947 (ranked #21; 14,313 new infections in 14 days).	1,974	116,470 (ranked #15)	2	15.96%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3	No	No
Russia	18,480,934(ranked #9), 47,540 new infections in 14 days).	4,457	381,794(ranked #4 in world)	40	12.65%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)R1 (Japan) B.1.640.1 (Congo/France)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Argentina	9,426,171(ranked #14; 58,999 new infections in 14 days).	———–	140,365 (ranked #14)	——–	20.47%	B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)Gama/P.1 (Brazil)Delta/B.1.617.2 (India)Lambda/C.37 (Peru)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)*	No	No
Colombia	6,223,497(ranked #19, 48,316 new infections in 14 days).	3,523	140,365 (ranked #13)	26	11.97%	B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Epsilon/B.1.427 + B.1.429 (USA)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)*	No	No
Peru	3,714,361(ranked #38, 84,565 new infections in 14 days).	10,610	235,526(ranked #6)	15	10.95%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Iran	7,270,023(ranked 17th; 31,434 new infections in last 14 days)	4,772	141,477(ranked #11)	13	8.43%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)	No	No
Spain	13,090,476(ranked 11th; 272,292 new infections in 14 days).	19,211(ranked #12)	109,348 (ranked #17)	134	27.97%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)	No	No
France	32,818,901 (ranked #4; 1,609,976 new infections in the last 14 days).	119,684 (ranked #1)	150,576 (ranked #10)	108	50.05%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinant	No	No
Germany	29,692,989(ranked #5; 1,300,360 new infections in 14 days.).	123,046 (ranked #2)	142,535 (ranked #11)	134	35.21%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
South Korea	18,680,142 (ranked #9 310,285 new infections in 14 days).	38,864(ranked #8)	24,712 (ranked #38)	16	36.37%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Vietnam	10,759,145 (ranked #12; 11,748 new infections in 14 days).	956	43,090 (ranked #26)	–	10.85%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Netherlands	8,274,234 (ranked #16; 83,979 new infections in 14 days).	6,527	22,422 (ranked #41)	5	48.07%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
Denmark	3,039,859 (ranked #39) 23,810 new infections in 14 days	1,567	6,551 (ranked #81)	8	52.10%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinant	No	No
North Korea (DPRK)	4,770,400 (ranked #24; 25,670 new infections in 14 days)	500	74	–	18.34%	Omicron/B.1.1.529 South Africa November 2021)	No	No
Taiwan	4,215,200(ranked #30) 412,171 new infections in 14 days	25,310 (ranked #10)	7,917 (ranked #73)	114	17.63%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No
Japan	10,000,720(ranked #13) 671,200 new infections in the last 14 days	97,339(ranked #5)	31,528(ranked #34)	34	7.95%	B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)	No	No

What Our Team Is Reading This Week

SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. (Preprint) https://doi.org/10.1101/2022.07.07.22277128
Brain imaging and neuropsychological assessment of individuals recovered from mild to moderate SARS-CoV-2 infection (Preprint) https://doi.org/10.1101/2022.07.08.22277420
Increased Risk of Herpes Zoster in Adults ≥50 Years Old Diagnosed With COVID-19 in the United States (Open Forum Infectious Diseases) https://doi.org/10.1093/ofid/ofac118
Neutralization sensitivity of Omicron BA.2.75 to therapeutic monoclonal antibodies (Preprint) https://doi.org/10.1101/2022.07.14.500041
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2 (Nature Microbiology) https://doi.org/10.1038/s41564-022-01163-3
How COVID-19 affects microvessels in the brain (Brain) https://doi.org/10.1093/brain/awac211
Fine Analysis of Lymphocyte Subpopulations in SARS-CoV-2 Infected Patients: Differential Profiling of Patients With Severe Outcome (Frontiers in Immunology) https://doi.org/10.3389/fimmu.2022.889813
SARS-CoV-2 accelerated clearance using a novel nitric oxide nasal spray (NONS) treatment: A randomized trial (The Lancet Regional Health – Southeast Asia) https://doi.org/10.1016/j.lansea.2022.100036
Effectiveness of 2, 3, and 4 COVID-19 mRNA Vaccine Doses Among Immunocompetent Adults During Periods when SARS-CoV-2 Omicron BA.1 and BA.2/BA.2.12.1 Sublineages Predominated — VISION Network, 10 States, December 2021–June 2022 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7129e1
Characterization of virologic rebound following nirmatrelvir-ritonavir treatment for COVID-19 (Clinical Infectious Diseases) https://doi.org/10.1093/cid/ciac512
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins (Preprint) https://doi.org/10.1101/2021.08.10.455737
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows (Medical Express) https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID (eBioMedicine) https://doi.org/10.1016/j.ebiom.2022.104129
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters (Nature Communications) https://doi.org/10.1038/s41467-022-30195-w
Persistent 129Xe MRI Pulmonary and CT Vascular Abnormalities in Symptomatic Individuals with Post-Acute COVID-19 Syndrome (Radiology) https://doi.org/10.1148/radiol.220492
ACE2-independent infection of T lymphocytes by SARS-CoV-2 (Signal Transduction and Targeted Therapy) https://doi.org/10.1038/s41392-022-00919-x
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae (Preprint) https://doi.org/10.1101/2022.06.14.22276401
SARS-CoV-2 is detected in the gastrointestinal tract of asymptomatic endoscopy patients but is unlikely to pose a significant risk to healthcare personnel (Gastro Hep Adv) https://doi.org/10.1016/j.gastha.2022.06.002
Long COVID symptoms in SARS-CoV-2-positive children aged 0–14 years and matched controls in Denmark (LongCOVIDKidsDK): a national, cross-sectional study (Child & Adolescent Health) https://doi.org/10.1016/S2352-4642(22)00154-7
Age and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines (Nature Communications) https://doi.org/10.1038/s41467-022-31401-5
COVID-19 positive patients at higher risk of developing neurodegenerative disorders, new study shows https://medicalxpress.com/news/2022-06-covid-positive-patients-higher-neurodegenerative.html
Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors (Biophysics and Computational Biology) https://doi.org/10.1073/pnas.2119761119
Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2 (The Lancet) https://doi.org/10.1016/S0140-6736(22)00941-2
Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum (Cell) https://doi.org/10.1016/j.cell.2022.06.005
Immunomodulatory treatment in postural tachycardia syndrome: A case series (European Journal of Neurology) https://doi.org/10.1111/ene.14711
Long COVID-19 Liver Manifestation in Children (JPGN) https://journals.lww.com/jpgn/abstract/9900/long_covid_19_liver_manifestation_in_children.84.aspx
Cross-reactive immunity against the SARS-CoV-2 Omicron variant is low in pediatric patients with prior COVID-19 or MIS-C (Nature Communications) https://doi.org/10.1038/s41467-022-30649-1
C.D.C. Dismisses Airborne Transmission of Monkeypox. Some Experts Disagree. (NY Times) https://www.nytimes.com/2022/06/10/health/monkeypox-airborne.html
Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes (Science Immunology) https://doi.org/10.1126/sciimmunol.abq2427
SARS-CoV-2 Infection and Persistence Throughout the Human Body and Brain (National Institutes of Health) https://videocast.nih.gov/watch=45296?jwsource=twi
Long COVID is associated with extensive in-vivo neuroinflammation on [18F]DPA-714 PET (Preprint) https://doi.org/10.1101/2022.06.02.22275916
Unexpected worsening of progressive multifocal leucoencephalopathy following COVID-19 pneumonia (Journal of Neurovirology) https://doi.org/10.1007%2Fs13365-021-00980-2
Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5 (Preprint) https://doi.org/10.1101/2022.05.26.493539
During the Omicron Wave, Death Rates Soared for Older People (NY Times with CDC data) https://www.nytimes.com/2022/05/31/health/omicron-deaths-age-65-elderly.html
PD-1 blockade counteracts post–COVID-19 immune abnormalities and stimulates the anti–SARS-CoV-2 immune response (JCI Insight) https://insight.jci.org/articles/view/146701
Adverse effects of immune-checkpoint inhibitors: epidemiology, management and surveillance (Nature Reviews Clinical Oncology) https://doi.org/10.1038/s41571-019-0218-0
Herpesvirus infections and post-COVID-19 manifestations: a pilot observational study (Observational Research) https://doi.org/10.1007/s00296-022-05146-9
An early warning system for emerging SARS-CoV-2 variants (Nature Medicine) https://doi.org/10.1038/s41591-022-01836-w
SARS-CoV-2 Omicron Variant is as Deadly as Previous Waves After Adjusting for Vaccinations, Demographics, and Comorbidities (Preprint) https://doi.org/10.21203/rs.3.rs-1601788/v1
Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1 (Preprint) https://www.medrxiv.org/content/10.1101/2022.04.25.22274187v1
COVID-19 Associated Hepatitis in Children (CAH-C) during the second wave of SARS-CoV-2 infections in Central India: Is it a complication or transient phenomenon. (Preprint) https://doi.org/10.1101/2021.07.23.21260716
Liver and Gastrointestinal Involvement in Patients With COVID-19: A Retrospective Study https://www.cureus.com/articles/90062-liver-and-gastrointestinal-involvement-in-patients-with-covid-19-a-retrospective-study
Cortical Grey Matter Volume Loss links to Neurological Sequelae in post COVID-19 “Long Haulers” (Preprint) https://doi.org/10.21203/rs.3.rs-1582065/v1
Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike (Cell) https://doi.org/10.1016/j.cell.2022.04.035
Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages https://www.krisp.org.za/manuscripts/MEDRXIV-2022-274406v1-deOliveira.pdf
Molecular consequences of SARS-CoV-2 liver tropism (Nature Metabolism) https://doi.org/10.1038/s42255-022-00552-6
China CDC shares latest COVID-19 data (GISAID) https://www.gisaid.org/resources/gisaid-in-the-news/china-shares-latest-11-apr-2022/#c920
Persistent COVID-19 symptoms in a community study of 606,434 people in England (Nature) https://www.nature.com/articles/s41467-022-29521-z
Brain Inflammation and Intracellular α-Synuclein Aggregates in Macaques after SARS-CoV-2 Infection (Viruses) https://www.mdpi.com/1999-4915/14/4/776
Antibody Resistance of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages (Preprint) https://www.biorxiv.org/content/10.1101/2022.04.07.487489v1
Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2 (Nature Medicine) https://www.nature.com/articles/s41591-022-01816-0
Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain (Preprint) https://www.biorxiv.org/content/10.1101/2022.01.07.475453v1
Risks of deep vein thrombosis, pulmonary embolism, and bleeding after covid-19: nationwide self-controlled cases series and matched cohort study (BMJ) https://www.bmj.com/content/377/bmj-2021-069590
SARS-CoV-2 Infection Induces Ferroptosis of Sinoatrial Node Pacemaker Cells (Circulation Research) https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.121.320518
SARS-CoV-2 variants of concern and variants under investigation in England (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1063424/Tech-Briefing-39-25March2022_FINAL.pdf
Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine (Preprint) https://doi.org/10.1101/2022.03.24.485633
COVID-19-Associated Encephalitis: Two Case Reports https://www.cureus.com/articles/86903-covid-19-associated-encephalitis-two-case-reports
First evidence that an emerging mammalian alphacoronavirus is able to infect an avian species (Transboundary and Emerging Diseases) https://doi.org/10.1111/tbed.14535
SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses (The Lancet) https://doi.org/10.1016/S0140-6736(22)00383-X
Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination (Preprint) https://www.medrxiv.org/content/10.1101/2022.03.09.22272113v1
Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France (Preprint) https://www.medrxiv.org/content/10.1101/2022.03.03.22271812v1.full
Mandatory masking in schools reduced COVID-19 cases during Delta surge (NIH press release) https://www.nih.gov/news-events/news-releases/mandatory-masking-schools-reduced-covid-19-cases-during-delta-surge
School Masking Policies and Secondary SARS-CoV-2 Transmission (Pediatrics) https://publications.aap.org/pediatrics/article/doi/10.1542/peds.2022-056687/185379/School-Masking-Policies-and-Secondary-SARS-CoV-2
Transmission of SARS-CoV-2 delta variant (AY.127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study (The Lancet) https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00326-9/fulltext
COVID-19 Variant Dashboard – USA by Raj Rajnarayanan https://public.tableau.com/app/profile/raj.rajnarayanan/viz/USAVariantDB/VariantDashboard
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 38 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1060337/Technical-Briefing-38-11March2022.pdf
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 37 (UK Health Security Agency) https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1057359/Technical-Briefing-37-25February2022.pdf
Engineered extracellular vesicles antagonize SARS-CoV-2 infection by inhibiting mTOR signaling (Biomaterials and Biosystems) https://www.sciencedirect.com/science/article/pii/S2666534422000046?via%3Dihub
Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study (Preprint) https://doi.org/10.21203/rs.3.rs-1385593/v1
Dynamics of the Delta and Omicron variants of SARS-CoV-2 in the United States: the battle of supremacy in the presence of vaccination, mask usage and antiviral treatment (Preprint) https://doi.org/10.21203/rs.3.rs-1420446/v1
Virological characteristics of SARS-CoV-2 BA.2 variant (Preprint) https://www.biorxiv.org/content/10.1101/2022.02.14.480335v1
Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households (Preprint) https://www.medrxiv.org/content/10.1101/2022.01.28.22270044v1
Waning 2-Dose and 3-Dose Effectiveness of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7107e2.htm?s_cid=mm7107e2_e&ACSTrackingID=USCDC_921-DM75599&ACSTrackingLabel=MMWR%20Early%20Release%20-%20Vol.%2071%2C%20February%2011%2C%202022&deliveryName=USCDC_921-DM75599
SARS-CoV-2 B.1.1.529 (Omicron) Variant Transmission Within Households — Four U.S. Jurisdictions, November 2021–February 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7109e1.htm?s_cid=mm7109e1_w
Pediatric Emergency Department Visits Before and During the COVID-19 Pandemic — United States, January 2019–January 2022 (MMWR) https://www.cdc.gov/mmwr/volumes/71/wr/mm7108e1.htm?s_cid=mm7108e1_w#F2_down
Birth Of The Omicron Family: BA.1, BA.2, BA.3. Each As Different As Alpha Is From Delta. (Forbes) https://www.forbes.com/sites/williamhaseltine/2022/01/26/birth-of-the-omicron-family-ba1-ba2-ba3-each-as-different-as-alpha-is-from-delta/?sh=403de4ee3da9
Take a look at SARS-CoV-2’s family tree. It’s full of surprises (NPR) https://www.npr.org/sections/goatsandsoda/2022/02/09/1047616658/take-a-look-at-sars-cov-2s-family-tree-its-full-of-surprises
SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 35 https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1050999/Technical-Briefing-35-28January2022.pdf
Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants (Nature) https://www.nature.com/articles/s41586-022-04466-x_reference.pdf
Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time (Preprint) https://www.medrxiv.org/content/10.1101/2022.01.14.22269235v1
Syncytin, envelope protein of human endogenous retrovirus (HERV): no longer ‘fossil’ in human genome (Animal Cells and Systems) https://doi.org/10.1080/19768354.2021.2019109
Host Chitinase 3-like-1 is a Universal Therapeutic Target for the Delta, Omicron and Other SARS-CoV-2 Viral Variants in COVID 19 (Preprint) https://www.biorxiv.org/content/10.1101/2022.01.21.477274v1
COVID-19 reinfections among naturally infected and vaccinated individuals (Nature) https://www.nature.com/articles/s41598-022-05325-5
Duration of Protection against Mild and Severe Disease by Covid-19 Vaccines (NEJM) https://www.nejm.org/doi/full/10.1056/NEJMoa2115481
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants (Preprint) https://www.medrxiv.org/content/10.1101/2022.01.25.22269794v1
COVID-19 and the Common Cold—Preexisting Coronavirus Antibodies May Hinder SARS-CoV-2 Immunity (JAMA) https://jamanetwork.com/journals/jama/fullarticle/2788621?guestAccessKey=0bbad800-e651-496b-8046-d124bbc63a5a&term=01262022&utm_source=silverchair&utm_medium=email&utm_campaign=article_alert-jama&utm_content=olf&utm_term=012622
Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant https://dash.harvard.edu/handle/1/37370587