Tag: Monterey

COVID-19

SARS-CoV-2 Update

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 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. 

CDC
CDC

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

CDC

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

CDC

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.”

VariantSublineage ofSpike MutationsGlobal SequencesUK Sequences
BF.7BA.5.2.1R346T9,809 (1,752 from Belgium)663
BQ.1.1BA.5N460KK444TR346T326(20 countries)60
BJ.1BA.513 non- synonymous spike mutations, 7 in RBD and including4 predicted immune escape locations123 (10 countries, most cases in India)1
BS.1BA.2.3.2R346TL452RN460KG476S25 (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. 

Monterey County Health Department

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

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). 

 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 

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 Professor Marc Johnson, molecular virologist @SolidEvidence on Twitter and 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.

LocationTotal Infections as of 10/21/22New Infections on 10/21/22Total DeathsNew Deaths on 10/21/22% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask MandateCurrently in Lockdown
World632,432,678(4,347,443 new infections in 14 days).349,3516,581,530(21,965 new deaths in last 14 days)1,1898.11%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  NoNo
USA99,055,537(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)NoNo
Brazil34,822,174(ranked #4) 64,917 new infections in the last 14 days. 3,400687,581(ranked #2; 732 new deaths in 14 days)3716.16%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)NoNo
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.43.17%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)NoNo
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)NoNo
California, USA11,332,345(ranked #14 in the world; 39,798 new infections in the last 14 days).99896,721 (ranked #20 in world)
303 new deaths in the last 14 days		1428.65%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)NoNo
Mexico7,106018(ranked #19) 4,587 new infections in 14 days).453330,321(ranked #5)181 new deaths in 14 days)155.40%NoNo
South Africa4,025,375(ranked #37; 4,587 new infections in 14 days).416102,257 (ranked #18) 63 new deaths in 14 days)116.62%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)NoNo
Canada4,314,718(ranked #33) 43,827 new infections in 14 days).3,06746,025(ranked #25)631  new deaths in the last 14 days4911.23% NoNo
Poland6,333,591 (ranked #21; 22,629  new infections in 14 days). 1,170118,015 (ranked #15)272 new deaths in the last 14 days2416.78%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 NoNo
Russia21,354,915(ranked #10), 190,973 new infections in 14 days).9,761 (ranked #8)389,359(ranked #4)1,368 new deaths in 14 days9314.64%NoNo
Peru4,152,019(ranked #32, 3,858 new infections in 14 days). 314216,877(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)NoNo
Iran7,555,694(ranked #17; 4,672 new infections in last 14 days)139144,540(ranked #12) 69 new deaths in the last 14 days48.78%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)NoNo
Spain13,488,015(ranked #12;   46,047 new infections in 14 days).3,630114,858 (ranked #16)390 new deaths in 14 days3128.87%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)NoNo
France36,524,605 (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.8155.69%  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) recombinantNoNo
Germany35,172,693(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 20441.93%
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) recombinantNoNo
South Korea25,244,255 (ranked #6 310,499 new infections in 14 days).24,709(ranked #8)28,952 (ranked #37) 338 new deaths in 14 days3049.18%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)NoNo
Vietnam11,496,354 (ranked #13; 10,933 new infections in 14 days).58243,159 (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)NoNo
Netherlands8,494,705 (ranked #16; 33,354 new infections in 14 days).95222,683 (ranked #41)549.35%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) recombinantNoNo
Denmark3,131,149(ranked #40) 12,835 new infections in 14 days. 6527,248 (ranked #79 126 new deaths in the last 14 days)1353.66%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) recombinantNoNo




Taiwan7,379,205(ranked #18)569,950 new infections in 14 days37,265 (ranked #3)12,206 (ranked #59 937 new deaths in the last 14 days)
7830.89%
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)NoNo
Japan21,926,231(ranked #9)463,493 new infections in the last 14 days31,593(ranked #5)46,152(ranked #25)
831 new deaths in the last 14 days		6717.45%
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.2*BA.5*NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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 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.

CDC

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. 

NY Times

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, PAXLOVIDTM, 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 PAXLOVIDTM 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 PAXLOVIDTM 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 PAXLOVIDTM 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 PAXLOVIDTM 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. 

Monterey County Public Health

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:

  1. Facility/Provider Name for Registration
  2. Provider Type (Hospital, Pharmacy, Etc)
  3. Shipping Address
  4. Contact Name(s)
  5. Contact Email(s)
  6. 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

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.

LocationTotal Infections as of 8/12/22New Infections on 8/12/22Total DeathsNew Deaths on 8/12/22% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask MandateCurrently in Lockdown
World593,948,648(13,178,472 new infections in 14 days).792,5726,451,858(34,360 new deaths in last 14 days)2,2417.61%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)NoNo
USA94,643,632(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)NoNo
Brazil34,148,131(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)29215.82%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)NoNo
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.683.14%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)NoNo
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)NoNo
California, USA10,896,796(ranked #14 in the world;  198618 new infections in the last 14 days).13,30694,319 (ranked #20 in world)
615 new deaths in the last 14 days		5027.57%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)NoNo
Mexico6,903,862(ranked #18) 192,015 new infections in 14 days).13,313(ranked #12)328,596(ranked #5)1,071 new deaths in 214 days)715.23%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)NoNo
South Africa4,007,925(ranked #33; 3,370 new infections in 14 days).313101,982 (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)NoNo
Canada4,109,931(ranked #33) 87,572 new infections in 14 days).3,60343,583(ranked #24)3710.69% 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)NoNo
Poland6,113,840 (ranked #21; 48,508 new infections in 14 days). 4,223116,751 (ranked #15)1416.19%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 NoNo
Russia18,824,282(ranked #9), 247,309 new infections in 14 days).27,810383,011(ranked #4 in world)5712.88%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)NoNo
Peru4,013,831(ranked #34, 118,345 new infections in 14 days). 10,882214,890(ranked #6)7211.82%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)NoNo
Iran7,465,579(ranked #17; 88,785 new infections in last 14 days)6,404142,806(ranked #12)548.65%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)


NoNo
Spain13,294,139(ranked #12;   67,560 new infections in 14 days).4,528(ranked #22)111,667 (ranked #16)11028.41%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)NoNo
France34,191,919 (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		7452.13%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) recombinantNoNo
Germany31,535,343(ranked #5; 682,031 new infections in 14 days.).45,859 (ranked #4)145,698 (ranked #11)
1,726 new deaths in 14 days		13737.38%
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) recombinantNoNo
South Korea21,111,840 (ranked #8 1,491,323 new infections in 14 days).128,671(ranked #2)25,499 (ranked #37) 5841.10%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)NoNo
Vietnam11,362,540 (ranked #13; 586,056 new infections in 14 days).2,19243,096 (ranked #25)111.45%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)NoNo
Netherlands8,362,564 (ranked #16; 31,241 new infections in 14 days).1,88222,542 (ranked #41)448.57%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) recombinantNoNo
Denmark3,076,642 (ranked #40) 16,658 new infections in 14 days1,3236,792 (ranked #80)1252.72%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) recombinantNoNo




Taiwan4,846,477(ranked #24)
300,841 new infections in 14 days		21,965 (ranked #10)9,373 (ranked #67)
3120.27%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)NoNo
Japan15,086,304(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		21412.00%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.2*BA.5*NoNo

What Our Team Is Reading This Week

COVID-19

Monterey County California SARS-CoV-2 update 9/06-9/19/20

davidcwrightmd

In the last 14 days (September 6 – September 19, 2020), 9,289 RT-PCR assays for SARS-CoV-2 (COVID-19) were performed and 996 were positive for an average of 10.60% positive tests per day. We have had 9 deaths in 14 days, an average of 0.643 deaths per day. We have now had a total of 9,467 infections in our county; 10.52% of these infections have occurred in the last 14 days of the pandemic. At our current rate of new infections, 71 per day for the last 14 days, we will reach 10,000 total infections in 8 days. 41 new patients were hospitalized in the last 14 days bringing the total to 549; 7.46% of the total hospitalizations have occurred in the last 14 days. Our hospitalization rate is averaging 2.93 patients per day for the last 14 days. To date, 67 of the 549 patients have died (12.20%). We are not controlling the infection in Monterey County. If our rate of hospitalizations and death rate remain constant, we will reach a total of 100 COVID-19 deaths in our county between 11/3/20 and 11/09/20. If we can get the number of infections down below 1% to 3% per day, we might have a chance to control the pandemic and the deaths per day in our county. 

COVID-19

Monterey County California SARS-CoV-2 Update

davidcwrightmd

In the last 14 days (August 23-September 5, 2020), 10,812 RT-PCR assays for SARS-CoV-2 (COVID-19) were performed and 1,146 were positive for an average of 10.60% positive tests per day. We have had 6 deaths in 14 days or an average of 0.428 deaths per day. We have now had a total of 8,439 infections in our county; 14.3% of these infections have occurred in the last 14 days of the pandemic.  77 new patients were hospitalized in the last 14 days, bringing the total to 507; 15.18% of the total hospitalized patients have occurred in the last 14 days. To date 58 of the 507 patients have died (11.43%). We are not controlling the infection in Monterey County and our hospitalization rate is averaging 5.5 patients per day the last 14 days.  If we can get the number of infections down below 1 to 3% per day we might have a chance to control the pandemic in our county. 

COVID-19

COVID-19 Update (6/11/20)

davidcwrightmd

By our way of counting, this is Day 161 of the COVID-19 pandemic. To date, we have neither a vaccine nor a widely available drug to effectively treat or prevent this infection. Our first USA case was identified in Washington State on Day 21 of the pandemic. In those next 140 days (20 weeks) the United States, as of 6/08/20, had 2,007,499 known COVID-19 PCR positive infected patients and 112,469 deaths, giving us a death rate of 5.6%. We had 18,905 new cases and 16,923 people in serious or critical condition on that day. That was the twentieth consecutive day that we’ve had over 16,900 people in serious or critical condition in the United States. We have 1,315,537 more COVID-19 positive infected patients than any other country in the world. The five countries other than the United States with the most cases (Brazil, Russia, Spain, the United Kingdom, and India) have a total of 1,991,945 cases combined, which is 15,544 fewer cases than in the United States. 

Four rapidly expanding “hot spot” countries on 6/07/20 are India with 257,486 infections and 10,864 new infections, Peru with 186,515 infections and 4,757 new infections, Russia with 467,673 infections and 8,849 new infections and Brazil with 691,962 infections and 18,375 new infections. 

Our Updated COVID-19 Projections

The University of Washington’s Institute of Health Metrics (IHME) said on 4/28/20 that we would have a total of 74,000 deaths in the USA by August 5, 2020. In contrast to this, we analyzed the case and death data using our two methods again on 5/22/20.  We estimated that we would reach 2,000,000 infected patients by June 7th (in 15.4 days, 369 hours or 2.2 weeks) and have between 17,710 and 20,513 new deaths for a total number of deaths between 115,357 and 118,156. The actual numbers by the morning of June 8th were 2,007,499 and 112,469 deaths (Worldometers). We use the Worldometers numbers rather than the Johns Hopkins numbers because Worldometers includes Veteran deaths in VA facilities, deaths in the US Military, deaths in Federal Prisons, and deaths in the Navajo Nation. 

Our estimates of the number of COVID-19 deaths on June 7th were higher than the actual deaths by 2,888 deaths or 2.57%. We think this overestimation of the number of deaths might be because of hyperimmune plasma use, Remdesivir use, use of both or possibly better critical care at US hospitals. Other possibilities might be decreasing virulence of COVID-19 or flaws in our predicted models of deaths. Our modeling of the number of infected patients was off by 0.37% or 7,499 additional infections.

All of our past predictions from 4/28/20, 5/03/20, 5/08/20 and 5/22/20 for time to reach 2,000,000 infections and the estimate of the number of deaths are listed in the following chart:

A month ago, the University of Washington re-projected the number of deaths by August 4, 2020 to be 134,475. When we checked their website on 5/23/20, they had revised this number to 143,357.

We don’t usually project out 2 months for total infections and deaths, but if we did, using our methodologies, in our new projections over the next 58 days we would predict that by August 4, 2020 inclusive in the United States we will have 3,264,069 COVID-19 infected patients and a total of between 165,307 and 182,836 deaths. If the death rate (now 5.60%) decreases further, these estimates of the number of deaths will be too high.

State of California

As of 6/07/20, the State of California has 131,319 total infections, 2,279 new infections, 4,653 total deaths. On 6/07/20, California reported 4,506 hospitalized COVID-19 patients (on that day) and 1,301 patients in the ICU. If California were a country, it would rank 18th in total number of cases in the world (above China) and 14th in total deaths (above Mexico). It would rank 4th in the world in ICU patients (between Brazil and Iran). 

Click to enlarge images.

Monterey County

As of 6/07/20, Monterey County has 763 total  COVID-19 infections, 12 new infections and 11 total deaths (3 new deaths since our last report on 5/24/20). An unknown number of deaths (< 11 according to CPHD) have been reported at a skilled nursing home in Salinas (Windsor The Ridge Rehabilitation Center).  COVID-19 infections in Healthcare workers at two other skilled nursing facilities in the cities of Monterey and Soledad have been reported to CPHD. Two infected State prison employees have been reported in a state prison in Soledad.

We have expanding numbers of infections in eight zip codes 93901 (Salinas, 54 total infections), 93905 (Salinas, 233 total infections), 93906 (Salinas, 144 total infections), 93907 (North County, 31 total infections), 93926 (Gonzales, 28 total infections), 93927 (Greenfield, 67 total infections), 93960 (Soledad, 49 total infections) and 93930 (King City, 63 total infections). We continue to have new infections and deaths in our county that are not occurring in our neighboring agricultural counties Santa Cruz and San Benito Counties. We have five times the number of deaths that Santa Cruz and San Benito County have. We are not yet seeing infections in Pacific Grove, Carmel, Pebble Beach, Carmel Highlands or Carmel Valley.  The differences in total infections  in parts of our county compared to these other counties, valleys and cities have not been explained by public health officials.

Recommended Reading

Coronavirus in prisons: See which area of the San Joaquin Valley is the most impacted https://www.fresnobee.com/news/local/article243315226.html 

Protest held at Avenal State Prison after COVID-19 outbreak inside facility https://abc30.com/protest-avenal-state-prison-covid-19/6235421/ 

Chicago coronavirus: Autopsy shows Chicago infant died of COVID-19 in March, ME says https://abc7chicago.com/illinois-coronavirus-cases-chicago-update/6241173/ 

Uncategorized

COVID-19 Update (5/24/20)

davidcwrightmd

In this post:

  • The United States still leads the world in COVID-19 cases and deaths.
  • We have no effective available oral treatment or preventative drugs, vaccines or hyperimmune intravenous immunoglobulin for COVID-19. Potential therapies are probably 6 to 9 months away. 
  • Despite the data, in the United States our political leaders , federal agencies, and many state public health officials have decided to open back up our country. 
  • In California, although ICU numbers have been stable the last 7 days, COVID-19 cases and deaths are still on the rise. The majority of reported cases (50.8%) are in the 18-49 age group. 
  • We examine the 1918 flu pandemic’s impact on different age groups and compare it with this year’s COVID-19 data in California, concluding that closing schools early was wise and reopening in August would be deadly. 
  • We continue to recommend staying home whenever possible, wearing a mask in public, and staying 6 feet apart from people outside your household. We outline suggestions for businesses and organizations seeking to reopen more safely, highlighting the dangers of congregating in buildings with poor ventilation (which is most buildings).
  • In Monterey County, agricultural workers, health care workers, and first responders are among the occupations most impacted by COVID-19. More than half of COVID-19 patients in the county have no known pre-existing medical condition. 
  • The incomplete nature of the data collected from California’s skilled nursing homes is problematic.  
  • Based on our modeling, we expect to have 2 million COVID-19 infections and 115,357 deaths in the United States by June 7. 
  • By August 4, 2020, at our current rate of new COVID-19 infections and deaths, we anticipate 3,337,190 COVID-19 infected patients and a total of 192,613 deaths. 

By our way of counting, this is Day 145 of the COVID-19 pandemic. To date, we have neither a vaccine nor a widely-available drug to effectively treat or prevent this infection. Our first USA case was identified in Washington State on Day 21 of the pandemic. In those next 124 days (17.7 weeks) the United States, as of 5/22/20, had 1,645,099 known COVID-19 PCR positive infected patients and 97,647 deaths, giving us a still rising death rate of 5.94%. We had 24,197 new cases and 17,109 people in serious or critical condition on that day. That was the fourth day in a row that we’ve had over 17,000 people in serious or critical condition in the United States. We have 1,314,204 more COVID-19 positive infected patients than any other country in the world. The five countries other than the US with the most cases (Brazil, Russia, Spain, the United Kingdom, and Italy) have a total of 1,422,095 cases combined, which is 223,004 fewer cases than in the United States. 

Four rapidly expanding “hot spot” countries are India with 118,226 infections and 6,198 new infections on 5/21/20, Peru with 108,769 infections and 4,749 new infections, Russia had 317,554 infections and 8,849 new infections on   5/21/20, and Brazil had 310,921 infections and 17,564 new infections. Today we’ll focus our discussion on the State of California and Monterey County.

State of California

As of 5/21/20, the State of California has 88,488 total infections, 3,624 new infections, 3,624 total deaths and 110 new deaths. On 5/21/20, California had more new deaths than any other state, with the exception of New York and was 7th in total deaths in the United States, having just surpassed Connecticut’s deaths. On 5/21/20, California reported 4,735 hospitalized COVID-19 patients (on that day) and 1,310 patients in the ICU. If California were a country, it would rank 13th in total number of cases in the world (above China) and 17th in total deaths (between Russia and India). It would rank 10th in new deaths in the world on 5/21/20. It would rank 7th in the world in ICU patients (between Spain and the UK). As of 5/21/20, California reported conducting 1,421,127 COVID-19 tests, which represents 3.57% of California’s population of 39.78 million. However, we know that some people have been tested more than once, so in fact, less that 3.57% of the population has been tested for COVID-19. 

So what can these numbers suggest to us about what public policies would be prudent at this time for California? Here’s what we think:

Keep School Buildings Closed to Protect Youth and the Elderly

From the beginning of the pandemic, it was messaged to us by public health officials and politicians alike that COVID-19 disproportionately affects folks 65 and over and those with underlying health conditions, leading young healthy folks to believe that they would not be infected or become seriously ill. This made it more difficult for young working people to accept the stay-at-home order as the new way of life, and many are counting down the days, hours, and minutes until they can return to work in person, get their hair and nails done, and return to their local bars, restaurants, gyms, and sporting events. 

However, if we look at the data on which age groups are most affected by COVID-19, we see a much different picture. In California, as of 5/21/20, the age group with the largest number of confirmed infections is people 18-49 years of age, with 44,953 infections, compared to 21,461 people 50-64 and 17,864 people 65 and up. The 0-17 age group has 4,049 cases. (Incidentally, the 0-17 age group is also the least-tested group.) We know that 7,908 of those 65+ folks are residents in skilled nursing facilities are infected with COVID-19, so when you take those folks out of the equation, there are only 9,956 other people over the age of 65 infected in California. Deaths in skilled nursing facilities make up 39.5% of the COVID-19 deaths in California. The point is that people over 65 who are not in skilled nursing facilities are not getting infected at the same rate as younger people. Now, it might be a coincidence, but we can’t help noticing that the two age groups that we have essentially mandated stay home since mid-March (school-aged children and senior citizens) have the lowest numbers of infections. Perhaps preventing infections is not as complicated as folks are making it out to be. 

A standard Influenza respiratory epidemic has a U-shaped death curve (see dotted line 1911-1917 curve below), meaning that you have very young and very old people dying. What happened in the 1918 Influenza pandemic is that they had a W-shaped curve (see solid line below). The peak in the middle happened to be people between the ages of 20 and 40.

From 1918 Influenza: the Mother of All Pandemics (Emerging Infectious Diseases) https://wwwnc.cdc.gov/eid/article/12/1/05-0979_article 

If we look at the data from the 2020 COVID-19 pandemic in California, plotted by age group, we can see some similarities and some key differences from the 1918 pandemic. By closing schools and telling older people to stay home in California, we’ve decreased the number of COVID-19 cases in both groups, effectively losing the left arm of the W and flattening out the right arm from the 1918 Influenza graph.

Thanks to early implementation in California of non-essential business closures, school closures, stay-at-home policies, social distancing, and use of masks, we’ve been able to avoid some of the hardships that folks experienced in the 1918 Influenza pandemic.

However, social distancing is not possible in schools–period. Getting children to wear masks safely and wash their hands with soap and warm water before touching their faces, their food, or their classmates is impossible. We won’t even go into how difficult it would be to keep student bathrooms sanitary. Moreover, large class sizes and inadequate ventilation systems (both of which are the norm in California public schools) are not conducive to safe social distancing. In order to make classrooms workable for social distancing, California schools would likely have to triple their teaching staffs, expand facilities, and spend millions of dollars updating air conditioning systems and adding HEPA filter systems. Furthermore, we’ve already been told that school budget cuts are inevitable at this point. Therefore, from our perspective, the only solution for safely educating our children during the next two years of this epidemic would be distance learning. Many school districts are currently surveying parents to collect their input on plans for the upcoming school year. Parents would be prudent to request that their districts offer distance learning for students of all ages.

Wear a Mask in Public

All people should wear masks in public at all times. There is very compelling scientific evidence that masks decrease the incidence of respiratory infections by preventing people’s respiratory droplets from circulating in shared air. We can see correlations between mandated mask-wearing policies and lower numbers of COVID-19 infections and deaths in countries across Asia like Japan, Vietnam, and Taiwan. There are certainly other factors in play that have helped these nations control the spread of COVID-19, like having more socially-distant ways of greeting people, better early education campaigns for COVID-19, prior experience with the SARS epidemic, increased travel restrictions, experimental pharmaceutical interventions (like Japan’s favipiravir) and better contact tracing. However, it’s worth noting that in some countries where most of these factors were not present, masks have been a game-changer, keeping cases and deaths relatively low. Take, for example, the Czech Republic, which mandated face masks in public in late March (along with closing borders, prohibiting public gatherings, and shuttering non-essential businesses). With a population of approximately 10 million, as of 5/23/20, Czechia (as it is also known) had 8,890 total reported cases of COVID-19 and just 314 total deaths. That’s 830 cases per million people and 29 deaths per million, and constitutes a death rate of about 3.5%. In Portugal, whose population is also around 10 million, masks in public were recommended but not required back in April. As of 5/23/20, Portugal had 30,471 total reported cases and 1,302 total deaths. That’s 2,987 cases per million people and 128 deaths per million, for a death rate of 4.3%. Even if we rewind to May 1, before Portugal began partially reopening businesses, we see it had a total of 24,987 cases and 1,007 deaths (death rate 4%), which is 2,450 cases per million and 99 deaths per million. Compare this to Czechia on May 1 with 7,737 total cases and 240 deaths (death rate 3.1%) That’s 722 cases per million and 22 deaths per million. This is not to say we think that mandated mask wearing is solely responsible for the differences in Portugal and Czechia’s numbers, but it certainly couldn’t hurt. 

Avoid Gathering in Enclosed Spaces, Regardless of Restriction Easing

Biologist Erin Bromage from the University of Massachusetts Dartmouth makes some valid points about infection risk in her blog post published on May 6, which was inspired by Jonathan Kay’s April 23 piece in Quillette on COVID-19 superspreader events. We won’t go into detail on the specifics of superspreader events in our post today, but we do have a few things to say about what you can do to stay safe as cities begin to reopen selected businesses and public spaces. 

The keys to preventing transmission of infection are personal protective equipment, washing hands with soap and warm water, and adequate ventilation. Unfortunately, most businesses and public buildings, like schools (see above), restaurants, bars, gyms, and salons (and even many doctor’s offices and hospitals) do not have the HEPA filtered air systems that are required to prevent the spread of COVID-19 and other viruses like influenza. Sanitizing surfaces, erecting barriers, setting up fans, and opening windows will not resolve the air issues in these locations. The reality is, there are few safe buildings when it comes to COVID-19. 

So what are our recommendations for folks who are determined to dine out, get a haircut, join a yoga class, or attend a religious service as soon as their local governments allow it? 

Small businesses need to rethink how they provide services to their patrons. Restaurants, rather than looking for ways to make poorly-ventilated indoor dining rooms safer, should be focused on offering outdoor dining. Hairdressers, barbers, and nail technicians should consider making use of their parking lots to provide their services in the open air, or performing services for their clients in their backyards. Gym owners, likewise, could look for opportunities to move classes outdoors. 

Places of worship should continue to offer services online and should consider outdoor services, where people should wear masks and stay six feet apart. Drive-in services might also be possible for churches with large parking lots, leaving at least one parking space vacant between cars. Of course, some practices, like the distribution of wafers and grape juice or wine for communion, would remain high-risk, whether conducted indoors or outdoors. The bottom line is it’s not safe to be in a public place near people from outside your household who are eating, talking, or singing without wearing masks. 

If you’re going to be around people from outside your household and have the choice to do so outdoors rather than indoors, outdoors would be a significantly safer choice. This is not to say that it’s prudent to have a large backyard barbecue or any large gathering of people outdoors. It’s still best to limit gatherings to no more than 10 people. Stick to video chatting with friends and family who have high risk for exposure to COVID-19 (like essential workers). 

Monterey County

In Monterey County, 40% of the infections are in folks who work in agriculture and 9% of infections are in health care workers and first responders. In 210 (57%) of the cases, patients had no known pre-existing medical conditions. How are people getting infected? In Monterey County, 51% of reported cases are epidemiologically linked to a confirmed case, 43% of cases are community acquired, and 6% are travel-related. In theory, if a county is doing an excellent job of contact tracing, the percentage of community acquired cases would be very low–because cases would be quickly identified and folks could be quarantined before infecting others. The fact that 43% of the cases in our county are community acquired suggests we should be doing better case contact tracing and increase testing for everyone, but especially for essential workers, particularly those who come in close contact with the public. We ought to be testing all agricultural workers, health care workers, and first responders. 

In California, the state public health department reports infections and deaths in skilled nursing facilities. It’s worth noting that since April 23, on any given day, only between 81% and 95% of California’s skilled nursing facilities have reported their COVID-19 cases and deaths to the state health department.  On its website, California Department of Health lists data for COVID-19 infections and deaths for 16 of Monterey County’s skilled nursing facilities. Based on this data, one 103-bed facility, Windsor The Ridge Rehabilitation Center in Salinas (zip code 93906) has reported cases in health care workers and patients. They are also listed as having patient deaths. Because the state of California does not report specific numbers of deaths and cases in skilled nursing facilities unless the number is greater than 11, we do not know how many of the cases and deaths in our county are associated with this facility–the report says fewer than 11. We also reviewed the California Department of Health skilled nursing COVID-19 data base (May11, 2020) and found a total of nine Windsor facilities in California with COVID-19 cases. The site with the most infections was in Solano County where 25 healthcare workers and 60 patients were infected with fewer than 11 deaths. The Monterey County Health Department has not disclosed the number of cases or deaths in the Salinas skilled nursing facility in our county. This data should be made available to the public. In addition, if it has not already been done, all staff and patients at this facility should be tested for COVID-19 by PCR on a routine basis. The state of New York has mandated that each nursing home will test each healthcare provider twice a week for COVID-19. This seems a reasonable approach to any facility with any healthcare provider or patient infection. A more proactive approach would be to test all healthcare providers and patients in skilled nursing facilities. 

Our Updated COVID-19 Projections

The University of Washington’s Institute of Health Metrics (IHME) said on 4/28/20 that we would have a total of 74,000 deaths in the USA by August 5, 2020. In contrast to this, we analyzed the case and death data using our two methods again on 5/22/20.  We estimated that we will reach 2,000,000 infected patients by June 7th (in 15.4 days, 369 hours or 2.2 weeks) and have between 17,710 and 20,513 new deaths for a total number of deaths between 115,357 and 118,156.

All of our predictions from 4/28/20, 5/03/20, 5/08/20 and 5/22/20 for time to reach 2,000,000 infections and the estimate of the number of deaths are listed in the following chart:

A few weeks ago, the University of Washington re-projected the number of deaths by August 4, 2020 to be 134,475. When we checked their website on 5/23/20, they had revised this number to 143,357. (Musical chairs, anyone?)

We don’t usually project out 2 months for total infections and deaths, but if we did, using our methodologies, we would predict that by August 4, 2020 in the United States we will have 3,337,190 COVID-19 infected patients and a total of between 192,613 and 199,229 deaths. If the death rate (now 5.94%) increases, these estimates of the number of deaths will be too low.

On 5/01/20, the FDA finally approved Gilead’s Remdesivir for intravenous treatment of COVID-19 infected patients. Since we initially recommended approval of this drug, another 97,600 Americans have died. Gilead is donating a large amount of drug for free. Unfortunately, it now appears that the government will be involved in the distribution of the drug, which means that university medical centers, hospitals in rural counties, and outpatient clinics like ours will probably not have the opportunity to treat our patients with Remdesivir. If it were up to us, this drug would be sold through normal drug distribution channels. Hopefully use of Remdesivir and/or plasma therapy will alter reported deaths in the next two months. We’re not optimistic based on the United States government’s performance during the first 145 days of the COVID-19 pandemic.  

We have no effective available oral treatment or preventative drugs, vaccines or hyperimmune intravenous immunoglobulin for COVID-19. Potential therapies are probably 6 to 9 months away. In the United States our political leaders (the President and most Governors) and federal agencies (HHS, CDC) and many state public health officials have decided to open back up our country. Viruses (COVID-19, Influenza and perhaps measles) will have many more potential victims this year.

Please think globally and act locally.

Recommended Reading

We Cannot Return to Campus This Fall https://thebolditalic.com/we-cannot-return-to-campus-this-fall-1ad91b8a65e0

1918 Influenza: the Mother of All Pandemics (Emerging Infectious Diseases) https://wwwnc.cdc.gov/eid/article/12/1/05-0979_article 

American Pandemic: The Lost Worlds of the 1918 Influenza Epidemic by Nancy K. Bristow https://www.goodreads.com/book/show/13540533-american-pandemic

The Great Influenza: The Story of the Deadliest Pandemic in History by John M. Barry https://www.goodreads.com/book/show/29036.The_Great_Influenza?ac=1&from_search=true&qid=9DWUInOM10&rank=1

The Complex Question of Reopening Schools (The New Yorker) https://www.newyorker.com/magazine/2020/06/01/the-complex-question-of-reopening-schools 

Public Health Experts Say Many States Are Opening Too Soon To Do So Safely (NPR) https://www.npr.org/2020/05/09/853052174/public-health-experts-say-many-states-are-opening-too-soon-to-do-so-safely 

This Japanese Island Lifted Its Coronavirus Lockdown Too Soon and Became a Warning to the World (Time) https://time.com/5826918/hokkaido-coronavirus-lockdown/ 

Tired Of Wearing A Face Mask In Public? New Research Underscores Why You Still Need To (Forbes) https://www.forbes.com/sites/brucelee/2020/05/14/here-is-more-evidence-for-face-mask-use-with-covid-19-coronavirus/#30c0654b1060 

The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission (PNAS) https://www.pnas.org/content/early/2020/05/12/2006874117 

Hearts and masks: Czech-Vietnamese solidarity during coronavirus https://www.aljazeera.com/indepth/features/hearts-masks-czech-vietnamese-solidarity-coronavirus-200407101254028.html 

California is publicly sharing incomplete data on coronavirus outbreaks at nursing homes (SF Chronicle) https://www.sfchronicle.com/bayarea/article/California-s-method-of-reporting-coronavirus-15258007.php 

2019 Novel Coronavirus (2019-NCoV) – Local Data (Monterey County Public Health) https://www.co.monterey.ca.us/government/departments-a-h/health/diseases/2019-novel-coronavirus-covid-19/2019-novel-coronavirus-2019-ncov-local-data-10219