The Omicron variant of SARS-CoV-2, the virus that causes COVID-19, was first identified in South Africa and was classified as a Variant of Concern by both WHO and CDC in November 2021. The first Omicron case to be sequenced in the US was identified in California on December 1 and the first reported death due to Omicron in the US was on December 20 in Texas. According to GISAID, in the last 30 days, the United States only sequenced about 2.56% of COVID cases (compare this to 9.8% in the UK, 6% in Australia, 18% in Denmark, and 17% in Israel), which would explain why we’re late to the game in addressing Omicron.
In under three weeks, Omicron has become the dominant variant in the US.
In the US, Omicron went from making up 12.6% of new COVID cases two weeks ago (week ending 12/11/32) to making up 73% of cases last week (reported 12/18/21). That’s an increase of more than 400% in one week. By comparison, the Delta doubled about once a week, going from around 3% of cases in mid-June to 41% of cases by early July and 62% of cases by mid-July. Omicron became the dominant variant in the US in less than half the amount of time that Delta did.
Nearly everyone (vaccinated or not, previously infected or not) who is exposed to Omicron is likely to become infected; vaccines will still prevent many infections, hospitalizations, and deaths, just not as many as with previous variants.
A study in South Africa found that during the current Omicron wave, two doses of the Pfizer vaccine provided “70% protection against severe complications of COVID-19 requiring hospitalisation, and 33% protection against COVID-19 infection.” In addition, researchers at Imperial College London estimate that the reinfection risk for Omicron is 5.4 times higher than for Delta, meaning that folks with previous COVID infections are likely to have limited protection.
Monoclonal antibody treatment (MAB) has saved the lives of many patients infected with other variants; it appears to be less effective against Omicron.
Two preprints, one published by German researchers on December 7, and another, a collaboration between American, Italian, Swiss, and Australian researchers, published on December 14, both suggest that due to Omicron’s 37 mutations in the Spike protein, 15 of which are in the receptor binding domain (RBD), it is able to evade our currently-available monoclonal antibody drugs. As William Haseltine explains in his write-up of the December 14 preprint: “Of the eight approved or authorized antibodies, all but sotrovimab completely or almost completely lost their neutralizing activity against the Omicron pseudovirus,” and “sotrovimab…retained neutralizing activity, but at a significant reduction.”
Omicron spreads more easily in households than Delta does, making it more likely that people will infect their loved ones this winter.
Data collected in UK households suggests that the secondary attack rate (chance that an index case in a household will infect someone else) for Omicron is 21.6%, compared to 10.8% for Delta.
Children may be at higher risk of contracting Omicron and being hospitalized, compared to previous variants.
A South African study found that “Despite very low absolute incidence, preliminary data suggests that children have a 20% higher risk of hospital admission in Omicron-led fourth wave in South Africa, relative to the D614G-led first wave.” And in England, hospital admissions for children over the last week are at an all-time high of 396.
This morning, the Washington Post reported that pediatric hospitals around the country are filling up; over the past three days, approximately 800 children per day were admitted for COVID infections.
Even mild infections can have severe consequences, like Long COVID and MIS-C. Those infected with Omicron who develop mild infections may still face long-term health complications due to Long COVID and/or MIS-C, and many of these patients in the US will go without proper diagnosis and treatment. Ed Yong has documented for The Atlantic how even health care workers have been dismissed and denied treatment for Long COVID. And yes, children also get Long COVID.
Now that you know more about Omicron, what should you do?
Wear a highly-protective mask, like an N95 or KN95. Beware of fakes. Do not order from a website like Amazon, which does not vet its suppliers. Project N95 is a trustworthy supplier of masks. For more on how to buy a quality mask online, see this NY Times piece and also this one. If you are not able to purchase an N95 or KN95 mask, layer a cloth mask over a surgical mask for a tight fit. Always make sure your mask covers your nose, mouth, and chin, with no gaps at the top or around the sides.
Get your booster vaccine as soon as possible. Per CDC, everyone 16+ should receive a booster shot. If you are not yet fully vaccinated, get vaccinated, and encourage friends and family to do the same. Everyone age 5+ can be vaccinated. LA County residents can go here to find information on where to get vaccinated. US residents can text your ZIP code to 438829 or call 1-800-232-0233 to find vaccine locations near you.
Gather outdoors and keep distance between you and people from outside your household. Because COVID is airborne, when people gather indoors, the virus builds up in the air, making it more likely for people to get infected. Think about it like cigarette smoke. If you allowed someone to smoke inside your house, the smoke would stay in the air, even hours later, making your indoor air unsafe to breathe. If you had a backyard barbecue and the same person went to the far corner of your yard (away from other people) to smoke, the chances of you breathing that smoke would be significantly lower.
If you must gather indoors, make sure everyone masks and that the space is well-ventilated. Open windows and use HEPA air purifiers whenever possible. Don’t have an air purifier? You can make a simple but effective one using HVAC filters and a box fan.
Test before and after you gather. If hosting a gathering, you can ask your guests to take a rapid antigen test at home on the day of the event. These tests, like Abbott’s Binax and Quidel’s Quickvue, don’t catch 100% of infections, but they will catch many. There are some tests (made by Applied DNA Sciences, Meridian Bioscience and Tide Laboratories) that the FDA has said cannot identify the Omicron variant, so take care to avoid those.
Avoid gathering with unvaccinated people. Make it clear to friends and family that gathering with you is a privilege, not a right. Vaccine-hesitant loved ones may find the motivation they need to get vaccinated if they realize that’s the only way that they’ll be seeing you.
Get your flu shot. COVID isn’t the only thing putting people in the hospital this winter, and it’s possible to be infected with both flu and COVID. A flu shot is the best defense against the flu.
If you develop COVID symptoms or flu-like symptoms: get tested for COVID-19. If you test negative for COVID, you may have the flu. If you believe you have the flu and have tested negative for COVID, you should request a prescription from your doctor for Tamiflu within the first 72 hours.
It’s time for our next 14-day moving average determinations for SARS-CoV-2 for the United States and my thoughts on vaccines 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 are accelerating at a rapid rate in the United States and many other countries including the United Kingdom, France, Germany, and Italy. This is caused by the Delta variants and the Omicron variant of concern. Omicron is at least four times as infectious as the already highly infectious Delta variants. UK scientists have found that the household secondary attack rate for Omicron is 21.6%, compared to 10.7% with Delta, meaning people infected with Omicron are twice as likely to infect household members as they would be if infected with Delta. They also estimate a “three- to eight-fold increased risk of reinfection with the Omicron variant.”
I would expect the Omicron variant to continue to mutate just like Delta. There are already two Omicron variants, BA.1 and BA.2. We expect to see additional Omicron variants as this isolate spreads rapidly around the USA and the World. As of 12/18/21 the Omicron variant, which was first seen in South Africa on 11/08/21, is now in 40 states, Puerto Rico and the District of Columbia. It has also been identified in at least 70 countries.
Omicron has 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. That’s 33 days ago and still no word from the FDA on approval. No deaths occurred in their study in the treatment group. We are averaging over 1,000 deaths per day in the USA and Russia. If the drug were available and just 90% effective in preventing deaths, each country could prevent over 900 deaths per day. If the FDA takes another 30 days for approval and drug distribution doesn’t occur rapidly then that’s at least 27,000 additional deaths in each country that could have been prevented. For now only masking (N95 rated masks, please!), social distancing and vaccination will have any effect on these variants.
In the United States, SARS-CoV-2 deaths have increased for the second time in six 14-day periods. There were 113 more deaths per day than in the last 14-day period. In the last 14 days, the number of infections has increased by 41,127 infections per day compared to the preceding 14-day period. Our infections per day have increased for the third time over the last 14 weeks.With travel and multiple holidays and events occurring in the next 60 days, we expect the infections to continue to increase. Unless people get vaccinated and get their third dose of the vaccine, we will see further spread of Delta variants like AY4.2 and an increase in deaths particularly in people with risk factors and over the age of 55. Anyone over the age of 5 years can now get vaccinated in the United States at no cost. This should get done immediately.
A new variant, B.1.1.529 (Omicron), was first seen in South Africa on 11/8/21 with multiple new mutations, deletions and an insertion that is causing a doubling of new infections every 1.3 days in Gauteng, South Africa. In just 40 days, as of 12/17/21, Omicron has been found in 70 countries and 40 states in the United States. Unlike Delta variants in South Africa, Omicron is infecting and hospitalizing patients in all age groups but particularly children under five years of age and adults greater than 60 years of age. Increased vaccinations, vaccines against new mutants, drugs against 3C-like protease, increased mask usage and social distancing, which are part of the Biden SARS-CoV-2 plan, are all necessary to continue to stop further spread of mutants and reduce infections, hospitalizations, and deaths. The Delta variants still account for 97% of new infections in the United States. Omicron accounted for 3% of infections by 12/11/21.
On 12/17/21, the United States had 163,707 new infections with two states failing to report (Iowa and Maryland). There were also 1,653 deaths (with five other states failing to report deaths). Florida continues to consistently under-report daily infections and deaths. The number of hospitalized patients has been increasing in many areas, and now 15,602 patients are seriously or critically ill; that number was 13,714 two weeks ago. The number of critically ill patients has increased by 1,888 in the last 14 days, while at least 18,603 new deaths occurred. The number of critically ill patients has increased for the third time in twelve 14-day periods and a large number of patients are still dying each day (average 1,329/day).
As of 12/17/21, we have had 826,719 deaths and 51,510,281 SARS-CoV-2 infections in the United States. We have had 1,932,232 new infections in the last 14 days. We are adding an average of 966,166 infections every seven days. For the pandemic in the United States we are averaging one death for every 62.3 infections reported or over 16,050 deaths for each one million infections. As of 12/17/21, thirty-one states have had greater than 500,000 total infections, and 36 states have had greater than 5,000 total deaths. Eleven states (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 50,000 deaths.
On 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota, 9.18% of the population was infected (ranked #1), and in South Dakota, 8.03% of the population was infected (ranked #2). As of 12/17/21, in the United States, 15.45% of the population has had a documented SARS-CoV-2 infection. In the last 13 months, 11.75% 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 13 months, there were 566,388 new deaths from SARS-CoV-2. For ten of those months, vaccines have been available to all adults. During these ten months, 221,946 people have died of SARS-CoV-2 infections. Many of these hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.
As of 12/17/21, California was ranked 42nd in infection percentage at 12.80% and10.04% of Californians were infected in the last 13 months. And now let’s look at the top 27 infected states, all greater than 16%, which is not a list that you’d like to be on in 2021. North Dakota was at 22.17% (ranked #1), Alaska was at 20.39% (ranked #2), Tennessee was at 19.71% (ranked #3), Rhode Island was at 19.70% (ranked #4), South Dakota was at 19.62% (ranked #5), Wyoming 19.60% (ranked #6), , Utah at 19.26% (ranked #7), Iowa was at 18.93% (ranked #8), Kentucky was at 18.48% (ranked #9), Arizona was at 18.28% (ranked #10), Montana was at 18.22% (ranked #11), South Carolina was at 18.18% (ranked #12), Wisconsin was at 18.10% (ranked #13), Arkansas was at 17.97% (ranked #14), Florida was at 17.59% (ranked #15), Indiana was at 17.55% (ranked#16), Mississippi was at 17.55% (ranked #17), Idaho was at 17.53% (ranked #18), West Virginia was at 17.49% (ranked #19), Alabama was at 17.47% (ranked #20), Oklahoma was at 17.30% (ranked #21), Minnesota was at 17.15% (ranked#22), Kansas was at 16.93%(ranked #23), Nebraska was at 16.27% (ranked #24), Louisiana was at 16.79% (ranked #25), Delaware was at 16.74%(ranked #26) and Michigan at 16.01% of the population infected (ranked #27). Forty-two states now have greater than 12% of their population infected. Only one state has less than 7% of their population infected: Hawaii (6.43%). Hawaii and the US Virgin Islands still remain the safest places in the United States. Hawaii had its first patient with an Omicron (B.1.1.529) SARS-CoV-2 infection two weeks ago.
The table below shows that if we rank the US states with the highest death rates per million population within the world rankings, we see that Mississippi has the fifth highest COVID-19 deaths per million in the world. New York, New Jersey and Arizona would be tied at the 9th highest number of deaths per million in the world, followed by Louisiana at 10th, Arkansa at 11th, Arizona, Florida at 12th, Massachusetts and Rhode Island tied at 14th. The United States as a whole ranks 20th in the world for deaths per million population (2,495 deaths per million). California ranks 35th in the USA (and 36th in the world). If we look at the death rates per million in South Korea (89), Iceland (105), Japan (146), and Israel (882), they suggest that treatment outcomes are somehow different in these four countries. The same phenomenon can be seen in Scandinavia, where the death rate in Sweden is 1,491 per million, compared to 219 per million in Norway and 260 per million in Finland. The United States should take a closer look at how countries with low death rates (like South Korea, Iceland, Japan, Finland, and Norway) are preventing COVID-19 infections and treating COVID-19 patients.
State or Country
COVID-19 Deaths per million population
Rank in USA
Ranked within World
Mississippi
3,479
1st
5th
New Jersey
3,228
3rd
9th tied
Louisiana
3,210
5th
10th
New York
3,033
6th
9th tied
Alabama
3,333
2nd
7th
Arizona
3,227
4th
9th tied
Massachusetts
2,870
11th
14th tied
Rhode Island
2,824
13th
14th tied
Arkansas
2,959
7th
11th
Florida
2,896
9th
12th
California
1,920
35th
36th
USA
2,495
20th
Peru
6,007
1st
Bosnia-Herzegovina
4,036
3rd
North Macedonia
3,741
6th
Hungary
3,899
4th
Montenegro
3,776
5th
Bulgaria
4,356
2nd
Gibraltar
2,969
10th
Czechia
3,264
7th
Brazil
2,875
13th
San Marino
2,762
14th
Georgia
3,261
8th
Sweden
1,491
56th
Israel
882
87th
Canada
785
94th
Finland
260
135th
Norway
219
139th
Japan
146
153rd
Iceland
105
163rd
South Korea
89
167th
A New Drug for SARS-CoV-2 Treatment
Pfizer has developed a reversible inhibitor of C3-like protease of SARS-CoV-2. The drug inhibits this key enzyme that is crucial for virus production. The compound, called Compound 6, 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. I had anticipated that the drug would be approved in the next 7 days. In my opinion, this agent, if approved, will markedly alter the course of every coronavirus infection throughout the world.
The Threat of SARS-CoV-2 Variants
In response to the need for “easy-to-pronounce and non-stigmatising labels,” at the end of May, the World Health Organization assigned a letter from the Greek alphabet to each SARS-CoV-2 variant. GISAID, Nextstrain, and Pango will continue to use the previously established nomenclature. For our purposes, we’ll be referring to each variant by both its Greek alphabet letter and the Pango nomenclature.
The WHO has sorted variants into two categories: Variants of Concern (VOC) and Variants of Interest (VOI). The criteria for Variants of Concern are as follows:
Increase in transmissibility or detrimental change in COVID-19 epidemiology; or
Increase in virulence or change in clinical disease presentation; or
Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.
The WHO categorizes the following five variants as Variants of Concern (VOC):
Source: World Health Organization
The criteria for Variants of Interest (VOI) are as follows:
has been identified to cause community transmission/multiple COVID-19 cases/clusters, or has been detected in multiple countries; OR
is otherwise assessed to be a VOI by WHO in consultation with the WHO SARS-CoV-2 Virus Evolution Working Group.
The WHO categorizes the following six variants as Variants of Interest (VOI):
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 12/17/21
New Infections on 12/17/21
Total Deaths
New Deaths on 12/17/21
% of Pop.Infected
SARS-CoV-2 Isolates Currently Known in Location
National/ State Mask Mandate?
Currently in Lockdown?
World
273,960,234(8,798,529 new infections in 14 days).
730,090
5,360,728(102,682 new deaths in last 14 days;
7,297
3.51%
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 (South Africa November 2021)B.1.640 (Congo/France)
No
No
USA
51,510,281 (ranked #1) 1,932,232 new infections in the last 14 days)
163,707 (ranked #1)
826,719 (ranked #1)18,603 new deaths in the last 14 days)
1,653
15.45%
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)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 (South Africa November 2021)B.1.640 (Congo/France)
No
No
Brazil
22,209,020(ranked #3)
4,079
617,647(ranked #2)
126
10.34%
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 (South Africa November 2021)
No
No
India
34,732,592(ranked #2)
6,543
476,897(ranked #3)
38
2.48%
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 (South Africa November 2021)B.1.640 (Congo/France)
No
No
United Kingdom
11,190,354(ranked #4; was #6 sixrteen weeks ago)
93,045
147,048(ranked #7 in world)
111
16.35%
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 (South Africa November 2021)B.1.640 (Congo/France)
No
No
California, USA
5,067,329(ranked #14 in world)
9,125
75,935(ranked #20 in world)
113
12.82%
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 (South Africa November 2021)
No
No
Mexico
3,927,265(ranked #15)
2,627
297,356(ranked #4)
169
3.00%
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 (South Africa November 2021)
No
No
South Africa
3,276,529(ranked #18) Exponential growth of Omicron occurring in South Africa. Children under 5 are infected.Quadrupling of daily infections in last four days.
20,713 on 12/17/21,16,055on 12/3/21,11,535 on 12/2/21,8,561on 12/1/21,4,373on 11/30/21,789on 11/19/21339on 11/5/21
90,297
35
5.42%
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 South Africa, November 2021)B.1.640 (Congo/France)
No
No
Canada
1,864,891(ranked #27)
6,892
30,624
12
4.87%
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 (South Africa November 2021)B.1.640 (Congo/France)
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 (South Africa November 2021)
No
No
Turkey
9,136,565(ranked #6)
18,141
80,053
190
10.66%
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)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 (South Africa November 2021)
No
No
Russia
10,159,389(ranked #5)
27,743
295,104(ranked #5 in world)
1,080
6.95%
B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)R1(Japan) B.1.640 (Congo/France)Omicron/B.1.1.529 (South Africa November 2021)
No
No
Argentina
5,382,290(ranked #11)
5,648
116,892
18
11.75%
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 (South Africa November 2021)
B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Eta/B.1.525 (Nigeria/UK)Theta/P.3 (Philippines) Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)B.1.640 (Congo/France)Omicron/B.1.1.529 (South Africa November 2021)
Neutralising antibody titres as predictors of protection against SARS-CoV-2 variants and the impact of boosting: a meta-analysis (The Lancet) https://doi.org/10.1016/S2666-5247(21)00267-6
“Vaccination reduces the risk of delta variant infection and accelerates viral clearance. Nonetheless, fully vaccinated individuals with breakthrough infections have peak viral load similar to unvaccinated cases and can efficiently transmit infection in household settings, including to fully vaccinated contacts. Host–virus interactions early in infection may shape the entire viral trajectory.”
Pediatric COVID-19 Cases in Counties With and Without School Mask Requirements — United States, July 1–September 4, 2021 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7039e3
Association Between K–12 School Mask Policies and School-Associated COVID-19 Outbreaks — Maricopa and Pima Counties, Arizona, July–August 2021 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7039e1
Decreased Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food During the COVID-19 Pandemic — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2017–2020 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7038a4
Starr, T.N., Czudnochowski, N., Liu, Z. et al. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 597, 97–102 (2021). https://doi.org/10.1038/s41586-021-03807-6
It’s time for our next 14-day moving average determinations for SARS-CoV-2 for the United States and my thoughts on vaccines 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.
In the United States, SARS-CoV-2 deaths have increased for the first time in five 14-day periods. There were 43 more deaths per day than in the last 14-day period. In the last 14 days, the number of infections has increased by 8,237 infections per day compared to the preceding 14-day period. Our infections per day have increased for the second time over the last 12 weeks. With travel and multiple holidays and events occurring in the next 60 days, I expect the infections to continue to increase. Unless people get vaccinated and get their third dose of the vaccine we will see further spread of Delta variants like AY4.2 and an increase in deaths particularly in people with risk factors and over the age of 55. Anyone over the age of 5 years can now get vaccinated in the United States at no cost. This should get done immediately.
A new variant, B.1.1.529 (Omicron), was first seen in South Africa on 11/8/21 with multiple new mutations, deletions and an insertion that is causing a doubling of new infections every 1.3 days in Gauteng, South Africa. In just 26 days, as of 12/03/21, Omicron has been found in 42 countries and 12 states in the United States.Unlike Delta variants in South Africa, Omicron is infecting and hospitalizing patients in all age groups but particularly children under five years of age and adults greater than 60 years of age. Increased vaccinations, vaccines against new mutants, drugs against 3C-like protease, increased mask usage and social distancing, which are part of the Biden SARS-CoV-2 plan, are all necessary to continue to stop further spread of mutants and reduce infections, hospitalizations, and deaths. The Delta variants still account for 99% of new infections in the United States. On 12/03/21, the United States had 147,434 new infections with one state failing to report (Iowa). There were also 1,352 deaths (with six other states failing to report deaths). Florida continues to consistently under-report daily infections and deaths. The number of hospitalized patients had been decreasing in many areas but now 13,714 patients are seriously or critically ill; that number was 11,767 two weeks ago. The number of critically ill patients has increased by 1,947 in the last 14 days, while at least 17,018 new deaths occurred. The number of critically ill patients has increased for the second time in eleven 14-day periods and a large number of patients are still dying each day (average 1,216/day).
As of 12/03/21, we have had 808,116 deaths and 49,378,049 SARS-CoV-2 infections in the United States. We have had 1,356,453 new infections in the last 14 days. We are adding an average of 678,227 infections every seven days. For the pandemic in the United States we are averaging one death for every 60.4 infections reported or over 16,533 deaths for each one million infections. As of 12/03/21, thirty-one states have had greater than 500,000 total infections, and 35 states have had greater than 5,000 total deaths. Eleven states (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 50,000 deaths.
On 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota 9.18% of the population was infected (ranked #1), and in South Dakota 8.03% of the population was infected (ranked #2). As of 12/03/21, in the United States, 14.94% of the population has had a documented SARS-CoV-2 infection. In the last 12.5 months, over 11% 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 12 months, there were 547,885 new deaths from SARS-CoV-2. For nearly nine of those months, vaccines have been available to all adults. During these nine months, 203,345 people have died of SARS-CoV-2 infections. Many of these hospitalizations and deaths could have been prevented by vaccination, proper masking, and social distancing.
As of 12/03/21, California was ranked 41st in infection percentage at 12.50% and9.74% of Californians were infected in the last 12 months. And now let’s look at the top 26 infected states (all greater than 16%, which is not a list that you’d like to be on in 2021. North Dakota was at 21.53% (ranked #1), Alaska was at 20.03% (ranked #2), Tennessee was at 19.37% (ranked #3), Wyoming 19.37% (ranked #4), South Dakota was at 19.02% (ranked #5), Utah at 18.77% (ranked #6), South Carolina was at 17.90% (ranked #10), Rhode Island was at 18.39% (ranked #7), Montana was at 17.98% (ranked #9), Iowa was at 18.08% (ranked #8), Florida was at 17.43% (ranked #14), Arkansas was at 17.63% (ranked #12), Kentucky was at 17.79% (ranked #11), Alabama was at 17.28% (ranked #16), Mississippi was at 17.32% (ranked #15), Idaho was at 17.27% (ranked #17), Arizona was at 17.43% (ranked #13) Oklahoma was at 16.94% (ranked #19), Louisiana was at 16.622% (ranked #21), Wisconsin was at 17.13% (ranked #18), West Virginia was at 16.66% (ranked #20), Indiana was at 16.61% (ranked#22), Kansas was at 16.28%(ranked #23), Minnesota was at 16.24% (ranked#25) and Nebraska at 16.22% of the population infected (ranked #2). Forty-two states now have greater than 12% of their population infected. Only one state has less than 7% of their population infected: Hawaii (6.21%). Hawaii, Vermont, and the US Virgin Islands still remain the safest places in the United States. Although Hawaii has just had its first patient with an Omicron (B.1.1.529) SARS-CoV-2 infection.
The table below shows that if we rank the US states with the highest death rates per million population within the world rankings, we see that Mississippi has the sixth highest COVID-19 deaths per million in the world. Alabama, New Jersey and Louisiana would be tied at the 7th highest number of deaths per million in the world, followed by Arizona, NewYork tied at 9th, Florida at 11th, Arkansas, Massachusetts and Rhode Island tied at 12th. The United States as a whole ranks 20th in the world for deaths per million population (2,390 deaths per million). California ranks 35th in the USA (and 36th in the world). If we look at the death rates per million in South Korea (73), Iceland (102), Japan (146), and Israel (879), they suggest that treatment outcomes are somehow different in these four countries. The same phenomenon can be seen in Scandinavia, where the death rate in Sweden is 1,486 per million, compared to 199 per million in Norway and 245 per million in Finland. The United States should take a closer look at how countries with low death rates (like South Korea, Iceland, Japan, Finland, and Norway) are preventing COVID-19 infections and treating COVID-19 patients.
State or Country
COVID-19 Deaths per million population
Rank in USA
Ranked within World
Mississippi
3,460
1st
6th
New Jersey
3,201
3rd
7th tied
Louisiana
3,189
4th
7th tied
New York
2,994
6th
9th tied
Alabama
3,298
2nd
7th tied
Arizona
3,077
5th
9th
Massachusetts
2,828
11th
12th tied
Rhode Island
2,776
12th
12th tied
Arkansas
2,883
8th
12th tied
Florida
2,870
9th
11th
California
1,898
35th
35th
USA
2,421
20th
Peru
5,988
1st
Bosnia-Herzegovina
3,902
3rd
North Macedonia
3,696
5th
Hungary
3,649
6th
Montenegro
3,696
4th
Bulgaria
4,185
2nd
Gibraltar
2,940
10th
Czechia
3,122
7th
Brazil
2,866
11th
San Marino
2,733
12th
Georgia
3,081
8th
Sweden
1,486
56th
Israel
879
86th
Canada
778
94th
Finland
245
136th
Norway
199
141st
Japan
146
153rd
Iceland
102
163rd
South Korea
73
169th
Data from Worldometers
A New Drug for SARS-CoV-2 Treatment
Pfizer has developed a reversible inhibitor of C3-like protease of SARS-CoV-2. The drug inhibits this key enzyme that is crucial for virus production. The compound, called Compound 6, 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. I would anticipate that the drug would be approved in the next 21 days. In my opinion, this agent, if approved, will markedly alter the course of every coronavirus infection throughout the world.
The Threat of SARS-CoV-2 Variants
In response to the need for “easy-to-pronounce and non-stigmatising labels,” at the end of May, the World Health Organization assigned a letter from the Greek alphabet to each SARS-CoV-2 variant. GISAID, Nextstrain, and Pango will continue to use the previously established nomenclature. For our purposes, we’ll be referring to each variant by both its Greek alphabet letter and the Pango nomenclature.
The WHO has sorted variants into two categories: Variants of Concern (VOC) and Variants of Interest (VOI). The criteria for Variants of Concern are as follows:
Increase in transmissibility or detrimental change in COVID-19 epidemiology; or
Increase in virulence or change in clinical disease presentation; or
Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.
The WHO categorizes the following five variants as Variants of Concern (VOC):
Source: World Health Organization
The criteria for Variants of Interest (VOI) are as follows:
has been identified to cause community transmission/multiple COVID-19 cases/clusters, or has been detected in multiple countries; OR
is otherwise assessed to be a VOI by WHO in consultation with the WHO SARS-CoV-2 Virus Evolution Working Group.
The WHO categorizes the following six variants as Variants of Interest (VOI):
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 12/03/21
New Infections on 12/03/21
Total Deaths
New Deaths on 12/03/21
% of Pop.Infected
SARS-CoV-2 Isolates Currently Known in Location
National/ State Mask Mandate?
Currently in Lockdown?
World
265,161,705(8,234,681 new infections in 14 days; an increase of 1,142,190 infections from the preceding 14 days)
705,574
5,258,046(102,708 deaths in 14 days; an increase of 5,145 deaths from the preceding 14 days).
7,915
3.40%
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)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 (South Africa November 2021)
No
No
USA
49,878,049 (ranked #1) 1,356,453 new infections in the last 14 days)
147,434 (ranked #1)
808,116 (ranked #1)17,018 new deaths in the last 14 days)
1,352
14.94%
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)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 (South Africa November 2021)
No
No
Brazil
22,129,409(ranked #3)
10,627
615,454(ranked #2)
2,229
10.30%
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 (South Africa November 2021)
No
No
India
34,624,360(ranked #2)
8,603
470,530(ranked #3)
415
2.47%
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 (South Africa November 2021)
No
No
United Kingdom
10,349,647(ranked #4; was #6 fourteen weeks ago)
50,584
145,424 (ranked #7 in world)
143
15.17%
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 (South Africa November 2021)
No
No
California, USA
4,978,179(ranked #14 in world)
8,547
75,013 (ranked #20 in world)
90
12.59%
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 (South Africa November 2021)
No
No
Mexico
3,894,364(ranked #15)
3,146
294,715(ranked #4)
287
2.97%
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 (South Africa November 2021)
No
No
South Africa
3,004,203(ranked #18) Exponential growth of Omicron occurring in South Africa. Children under 5 are infected.Quadrupling of daily infections in last four days.
16,055on 12/3/21,11,535 on 12/2/21,8,561on 12/1/21,4,373on 11/30/21,789on 11/19/21339on 11/5/21
89,940
25
4.97%
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 South Africa, November 2021)
No
No
Canada
1,802,359(ranked #26)
3,487
29,757
20
4.71%
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 (South Africa November 2021)
Neutralising antibody titres as predictors of protection against SARS-CoV-2 variants and the impact of boosting: a meta-analysis (The Lancet) https://doi.org/10.1016/S2666-5247(21)00267-6
“Vaccination reduces the risk of delta variant infection and accelerates viral clearance. Nonetheless, fully vaccinated individuals with breakthrough infections have peak viral load similar to unvaccinated cases and can efficiently transmit infection in household settings, including to fully vaccinated contacts. Host–virus interactions early in infection may shape the entire viral trajectory.”
Pediatric COVID-19 Cases in Counties With and Without School Mask Requirements — United States, July 1–September 4, 2021 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7039e3
Association Between K–12 School Mask Policies and School-Associated COVID-19 Outbreaks — Maricopa and Pima Counties, Arizona, July–August 2021 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7039e1
Decreased Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food During the COVID-19 Pandemic — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2017–2020 (MMWR) http://dx.doi.org/10.15585/mmwr.mm7038a4
Starr, T.N., Czudnochowski, N., Liu, Z. et al. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 597, 97–102 (2021). https://doi.org/10.1038/s41586-021-03807-6
David C. Wright, M.D. 
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