COVID-19

SARS-CoV-2 Update

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 12/22/21 the Omicron variant, which was first seen in South Africa on 11/08/21, is now in all 50 states, Puerto Rico and the District of Columbia. As of 1/14/22 Omicron has been identified on all seven continents and in at least 117 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. 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. Fresno County covers 6,011 square miles with a population of 999,101. Four CVS pharmacies in Fresno County are the only listed pharmacies. We obtained PAXLOVIDTM from the Salinas CVS pharmacy and successfully treated two patients in the last two weeks.

In the PAXLOVIDTM study, no deaths occurred in the treatment group. We are averaging over 1,000 deaths per day in the USA and Russia.  If PAXLOVIDTM is widely available and just 90% effective in preventing deaths, each country could prevent over 900 deaths per day. If Molnupiravir is widely available and just 50% effective in preventing deaths and hospitalizations, each country could prevent over 450 deaths per day. If drug distribution doesn’t occur rapidly then that’s at least 27,000 additional deaths in each country that could have been prevented in the next 30 days. For now only masking (N95 rated masks, please!), social distancing and vaccination will have any effect on these variants. Furthermore, we do not believe that a 5-day quarantine or isolation period is sufficient for any COVID-19 infection. The Taiwanese CDC agrees with both our recommendations on quarantine period and masking. In fact, the Taiwanese CDC has recommended N95 masking since the beginning of the pandemic (and made these masks universally available to their population). Taiwan has one of the lowest death rates per million during the course of the pandemic (see graph below). 

In the United States as of 1/14/22, SARS-CoV-2 deaths have increased for the fifth time in ten 14-day periods. There were 357 more deaths per day than in the last 14-day period. In November 2021, SARS-CoV-2 was the third most common cause of death in the United States. 

In the last 14 days, the number of infections has increased by 451,915 infections per day compared to the preceding 14-day period. Our infections per day have increased for the fifth time over the last 14 weeks. With additional travel, holidays and events occurring in the next 30 days, we expect the infections to continue to increase. Unless people get vaccinated, including their third dose of the vaccine, we will see further spread of the Omicron variants and increase in deaths in people who are not vaccinated, have waning immunity, the immunocompromised population and others with risk factors particularly those older than over the age of 64. SARS-CoV-2 is now in the top ten most common causes of death for children. Anyone over the age of 5 years can now get vaccinated in the United States at no cost. This should get done immediately. 

The 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 caused a doubling of new infections every 1.3 days in Gauteng, South Africa. In just 67 days, as of 1/14/22, Omicron has been found on seven continents, in 117 countries and all 50 states in the United States. Unlike Delta variants in South Africa, Omicron was 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 like PAXLOVIDTM, 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. Per CDC data ending in 1/8/22, the Delta variant still accounts for 1.7% of new infections in the United States, while Omicron accounts for 98.3%. It’s worth noting that in the last 30 days, according to GISAID, the United States has only sequenced 0.885% of cases. 

On 1/14/22, the United States had 827,132 new infections with three states (Tennessee, Alabama, and Iowa) failing to report. There were also 2,303 deaths, with five other states failing to report deaths (Wyoming, Alaska, Connecticut, Missouri and Oklahoma). Florida continues to consistently under-report daily infections and deaths. The number of hospitalized patients has been increasing in many areas, and now 25,636 patients are seriously or critically ill; that number was 15,602 two weeks ago. The number of critically ill patients has increased by 10,034 in the last 14 days, while at least 25,181 new deaths occurred. The number of critically ill patients has increased for the fourth time in thirteen 14-day periods and a large number of patients are still dying each day (average 1,799/day). 

As of 1/14/22, we have had 872,086 deaths and 66,209,535 SARS-CoV-2 infections in the United States. We have had 10,513,035 new infections in the last 14 days, a new record. We are adding an average of 5,256,517 infections every seven days. For the pandemic in the United States we are averaging one death for every 75.9 infections reported or over 13,172 deaths for each one million infections. As of 1/14/22, thirty-five states have had greater than 500,000 total infections, and 36 states have had greater than 5,000 total deaths. Fourteen states (Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York, and California) have had greater than 60,000 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%. On 11/20/21 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 1/14/22, in the United States, 20.00% of the population has had a documented SARS-CoV-2 infection. In the last 14 months, 16.30% of our country became infected with SARS-CoV-2. In the last 2 weeks 3.32% of the country became infected. On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. In the last 13 months, there were 629,755 new deaths from SARS-CoV-2. For ten of those months, vaccines have been available to all adults. During these ten months, 267,413 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 1/14/24, California was ranked 44th in infection percentage at 16.79% and 13.16% of Californians were infected in the last 13 months. As of 1/14/22 44 states have greater than 16% of their population infected. Twenty-six states have had greater than 20% of their population infected, which is not a list that you’d like to be on in 2022. Rhode Island was at 28.51% (ranked #1), North Dakota was at 25.22% (ranked #2), Alaska was at 23.55% (ranked #3), Florida was at 23.46% (ranked #4)  and Utah was at 23.40% (ranked #5) of their population infected. Forty-eight states and the District of Columbia now have greater than 12% of their population infected. Only two states have less than 12% of their population infected: Maine (11.86%) and Hawaii (11.30%). Maine, Hawaii  and the US Virgin Islands still remain the safest places to visit in the United States. Hawaii had its first patient with an Omicron (B.1.1.529) SARS-CoV-2 infection six 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 and Arizona have the eighth highest COVID-19 deaths per million in the world. New Jersey is tied at ninth with Louisiana and Alabama, New York is at tenth, followed by  Arkansas at 11th, Massachusetts at 12th and Rhode Island at 13th and Florida at 14th. The United States as a whole ranks 19th in the world for deaths per million population (2,611 deaths per million). California ranks 37th in the USA (and 40th in the world). If we look at the death rates per million in South Korea (122), Iceland (128), Japan (146), and Israel (890), 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 1,517 per million, compared to 252 per million in Norway and 310 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 populationRank in USARanked within World
Mississippi3,570  1st8th
New Jersey  3,3734th9th tied
Louisiana3,2565th9th tied
New York 3,1926th10th
Alabama3,3943rd9th tied
Arizona3,4442nd8th
Massachusetts3,03811th12th tied
Rhode Island  2,997  15th13th tied
Arkansas3,1198th11th
Florida2,93717th14th
California1,972 37th40th
USA2,61119th
Peru6,0371st
Bosnia-Herzegovina  4,2293rd
North Macedonia  3,8806th
Hungary4,1814th
Montenegro3,9245th
Bulgaria4,6602nd
Gibraltar2,96913th
Czechia3,4288th
Brazil2,88914th
San Marino3.02612th
Georgia3,6197th
Sweden1,51757th
Israel89089th
Canada81994th
Finland310134th
Norway252137th
Japan146154th
Iceland128159th
South Korea122162nd

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. This drug is now approved. We have successfully treated two patients with this drug. In my opinion, this agent, if more widely available, could 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):

Omicron cases sequenced as of 1/16/22:

Source: GISAID

Map of Omicron sequenced transmissions:

Source: GISAID

Delta cases sequenced as of 1/16/22: 

Source: GISAID

Map of Delta sequenced transmissions:

Source: GISAID

B.1.640 cases sequenced as of 1/16/22:

Source: GISAID

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 1/14/22New Infections on 1/14/22Total DeathsNew Deaths on 1/14/22% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World324,182,263(25,715,028 new infections in 14 days; a new record for the pandemic for 14 days).3,233,8685,547,390(94,398 new deaths in last 14 days)7,8524.16%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 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)NoNo
USA66,209,535
(ranked #1) 10,513,035 new infections in the last 14 days; new record for the pandemic for 14 days).
827,132
(ranked #1)
872,086
(ranked #1)25,181 new deaths in the last 14 days.
2,30320.00%
(3.32% increase in 14 days, new record for the pandemic for a 14 day period). 
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 (South Africa November 2021)B.1.640.1 (Congo/France)NoNo
Brazil22,927,203(ranked #3)   111,376620,847(ranked #2)23810.67%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)NoNo
India36,850,962(ranked #2)268,833485,780(ranked #3)4302.63%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)NoNo
United Kingdom12,937,886(ranked #4; was #6 twenty weeks ago; increased by 2,128,529 infections in 2 weeks; a new pandemic record for 14 days).99,652151,612 (ranked #7 in world)27022.01%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)NoNo
California, USA5,363,784(ranked #12 in the world;  1,241,751 new infections; a new pandemic record for 14 days).118,32477,928 (ranked #20 in world)13116.79%(3.12% increase in 14 days)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)NoNo
Mexico4,257,740(ranked #16; 288,054 new infections in 14 days).43,523300,912(ranked #5)1483.24%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 Africa3,552,043(ranked #18; 275,514  new infections in 14 days).


Exponential growth of Omicron occurred in South Africa. Children under 5 were infected.Quadrupling of daily infections over four days.
5,235
11,754 on 12/31/21
16,055 on 12/3/21,11,535 on 12/2/21,8,561 on 12/1/21,4,373 on 11/30/21,789 on 11/19/21339 on 11/5/21
9 (ranked #17)845.72%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)NoNo
Canada2,717,982(ranked #22, was 26th two weeks ago; 534,455 new infections in 14 days, a new pandemic record for 14 days).29,23131,317(ranked #29)1277.10% (2.23 % increase in two weeks, a new pandemic record for 14 days).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
Poland4,281,482(ranked #14)16,047101,841 (ranked #15)42311.33%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 + BA.3 (South Africa November 2021)NoNo
Turkey10,339,097(ranked #7, 865,547 new infections in 14 days, a new pandemic record for 14 days).67,85784,445 (ranked #19)16712.05%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 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)NoNo
Russia10,747,125(ranked #6)23,820319,911(ranked #4 in world)7397.35%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
Argentina6,932,972(ranked #11; 1,278,504 new infections in 14 days, a new pandemic record for 14 days).139,853117,901 (ranked #13 in world)9315.12% (2.78 % increase in two weeks, a new pandemic record for 14 days).B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gama/P.1 (Brazil)Delta/B.1.617.2 (India)Lambda/C.37 (Peru)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)NoNo
Colombia5,157,440(ranked #13, 318,469 new infections in 14 days.)34,923130,731 (ranked #11 in world)10610.58%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)NoNo
Peru2,296,831(ranked #23, 215,958 new infections in 14 days). 39,080203,302(ranked #6)477.46%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
Indonesia4,269,740(ranked #15)850144,163 (ranked #8)81.53%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.1.640.1 (Congo/France)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)
NoNo
Iran6,217,320(ranked 12th; was 12th  twenty weeks ago)2,539132,026 (ranked #10)247.25%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
Spain8,093,036(ranked 9th;   1,798,291 new infections in 14 days, a new pandemic record for 14 days).162,50690,759 (ranked #18)13917.29% (3.84% increase in two weeks, a new pandemic record for 14 days). 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
France13,569,675 (ranked #5)329,371126,721 (ranked #12)19120.71Delta/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)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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 12/22/21 the Omicron variant, which was first seen in South Africa on 11/08/21, is now in all 50 states, Puerto Rico and the District of Columbia. It has also been identified in at least 92 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. 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. Fresno County covers 6,011 square miles with a population of 999,101. Four CVS pharmacies in Fresno County are the only listed pharmacies.

In the PAXLOVIDTM study no deaths occurred in the treatment group. We are averaging over 1,000 deaths per day in the USA and Russia.  If PAXLOVIDTM is widely available and just 90% effective in preventing deaths, each country could prevent over 900 deaths per day. If Molnupiravir is widely available and just 50% effective in preventing deaths and hospitalizations, each country could prevent over 450 deaths per day. If drug distribution doesn’t occur rapidly then that’s at least 27,000 additional deaths in each country that could have been prevented in the next 30 days. For now only masking (N95 rated masks, please!), social distancing and vaccination will have any effect on these variants. Furthermore, we do not believe that a 5-day quarantine or isolation period is sufficient for any COVID-19 infection. The Taiwanese CDC agrees with both our recommendations on quarantine period and masking. In fact, the Taiwanese CDC has recommended N95 masking since the beginning of the pandemic (and made these masks universally available to their population). Taiwan has one of the lowest death rates per million during the course of the pandemic (see graph below). 

In the United States as of 12/31/21, SARS-CoV-2 deaths have increased for the third time in seven 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 160,999 infections per day compared to the preceding 14-day period. Our infections per day have increased for the fourth 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 was causing a doubling of new infections every 1.3 days in Gauteng, South Africa. In just 54 days, as of 12/31/21, 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. Per CDC data ending in 12/25/21, the Delta variant still accounts for 41.1% of new infections in the United States, while Omicron accounts for 58.6%. It’s worth noting that in the last 30 days, according to GISAID, the United States has only sequenced 2.23% of cases. 

On 12/31/21, the United States had 443,677 new infections with twenty-two states and the District of Columbia failing to report. There were also 716 deaths (with 27 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 12/31/21, we have had 846,905 deaths and 55,696,500 SARS-CoV-2 infections in the United States. We have had 4,186,219 new infections in the last 14 days. We are adding an average of 2,093,110 infections every seven days. For the pandemic in the United States we are averaging one death for every 65.3 infections reported or over 15,206 deaths for each one million infections. As of 12/31/21, thirty-four states have had greater than 500,000 total infections, and 36 states have had greater than 5,000 total deaths. Thirteen states (Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York, and California) have had greater than 60,000 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 604,574 new deaths from SARS-CoV-2. For ten of those months, vaccines have been available to all adults. During these ten months, 242,232 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 12/31/21, California was ranked 43rd in infection percentage at 13.57% and 10.04% of Californians were infected in the last 13 months. As of 12/31/21 42 states have greater than 16% of their population infected. Five states have greater than 20% of their population, which is not a list that you’d like to be on in 2021. North Dakota was at 22.85% (ranked #1), Rhode Island was at 21.81% (ranked #2), Tennessee was at 20,89% (ranked #3), Alaska was at 20.72% (ranked #4)  and South Dakota was at 20.25% (ranked #5) of their population infected. Forty-four states and the District of Columbia now have greater than 12% of their population infected. Only one state has less than 8% of their population infected: Hawaii (7.97%). 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 four 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 seventh highest COVID-19 deaths per million in the world. New Jersey is 8th, New York, Louisiana and Arizona would be tied at the 9th highest number of deaths per million in the world, followed by  Arkansa at 12th, Arizona, Massachusetts and Rhode Island tied at 13th and Florida at 14th. The United States as a whole ranks 21st in the world for deaths per million population (2,559 deaths per million). California ranks 36th in the USA (and 37th in the world). If we look at the death rates per million in South Korea (108), Iceland (107), Japan (146), and Israel (884), 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 1,498 per million, compared to 238 per million in Norway and 282 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 populationRank in USARanked within World
Mississippi3,511  1st7th
New Jersey  3,2694th8th
Louisiana3,2245th9th tied
New York 3,0856th9th tied
Alabama3,3562nd9th tied
Arizona3,3293rd9th tied
Massachusetts2,94111th13th tied
Rhode Island  2,894  15th13th tied
Arkansas3,031 8th12th
Florida2,90913th14th
California1,920 35th36th
USA2,55921st
Peru6,0221st
Bosnia-Herzegovina  4,1363rd
North Macedonia  3,8216th
Hungary4,0724th
Montenegro3,8215th
Bulgaria4,5062nd
Gibraltar2,96912th
Czechia3,3678th
Brazil2,88214th
San Marino2,93613th
Georgia3,2618th
Sweden1,49857th
Israel88487th
Canada79394th
Finland282135th
Norway238138th
Japan146154th
Iceland107164th
South Korea108163rd

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):

Source: World Health Organization

Omicron cases sequenced as of 1/2/22:

Source: GISAID

Delta cases sequenced as of 1/2/22: 

Source: GISAID

Map of Delta sequenced transmissions:

Source: GISAID

B.1.640 cases sequenced as of 1/2/22:

Source: GISAID

Gamma cases sequenced as of 1/2/22:

Source: GISAID

Mu cases sequenced as of 1/2/22:

Source: GISAID

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 12/31/21New Infections on 12/31/21Total DeathsNew Deaths on 12/31/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World288,467,234(14,507,440 new infections in 14 days).1,638,2365,452,992(92,274 new deaths in last 14 days)5,9443.70%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)NoNo
USA55,510,281
(ranked #1) 4,182,219 new infections in the last 14 days)
443,677
(ranked #1)
846,905
(ranked #1)20,186 new deaths in the last 14 days)
71616.68%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)NoNo
Brazil22,287,521(ranked #3)   10,282619,109(ranked #2)8510.37%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)NoNo
India34,861,579(ranked #2)22,775481,486(ranked #3)4062.49%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)NoNo
United Kingdom12,937,886(ranked #4; was #6 eighteen weeks ago)189.846148,624 (ranked #7 in world)20318.90%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)NoNo
California, USA5,363,784(ranked #13 in world)39,04378,739 (ranked #20 in world)4913.67%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)NoNo
Mexico3,969,686(ranked #16)8,024 299,285(ranked #5)1533.03%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)NoNo
South Africa3,276,529(ranked #18)




Exponential growth of Omicron occurring in South Africa. Children under 5 are infected.Quadrupling of daily infections in last four days.
11,754 on 12/31/21

16,055 on 12/3/21,11,535 on 12/2/21,8,561 on 12/1/21,4,373 on 11/30/21,789 on 11/19/21339 on 11/5/21
91,145 (ranked #17)845.72%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)NoNo
Canada2,183,527(ranked #26)41,21730,319(ranked #29)124.87%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)NoNo
Poland4,108,215(ranked #15)13,61397,054 (ranked #15)63810.87%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)NoNo
Turkey9,482,550(ranked #7)40,78682,361 (ranked #19)16311.06%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)NoNo
Russia10,499,982(ranked #5)20,638308,860(ranked #4 in world)9127.19%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)NoNo
Argentina5,654,468(ranked #12)47,663117,169 (ranked #13 in world)2312.34%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)NoNo
Colombia5,157,440(ranked #13)1,803129,942 (ranked #11 in world)419.97%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 (South Africa November 2021)NoNo
Peru2,296,831(ranked #23)4,577202,690(ranked #6)376.82%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 (South Africa November 2021)NoNo
Indonesia4,262,720(ranked #14)180144,094 (ranked #8)=61.53%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)NoNo
Iran6,194,401(ranked 10th; was 12th eighteen weeks ago)1,703131,606 (ranked #10)347.23%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 (South Africa November 2021)NoNo
Spain6,294,745(ranked 9th) ———-89,405 (ranked #18)——-13.45%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 South Africa November 2021)B.1.640 (Congo/France)NoNo

What Our Team Is Reading This Week

COVID-19

What You Should Know about Omicron

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. 

Source: CDC https://covid.cdc.gov/covid-data-tracker/#variant-proportions  

In Los Angeles County, new COVID infections per day (8,000+) are now over triple what they were a week ago.

Source: https://twitter.com/lapublichealth 

In December, Monterey County has seen a spike in cases for all age groups, but especially for children 12-17. 

Source: 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 

Statewide, this past weekend, California averaged 2,456 more new cases per day than the previous weekend. 

*Includes weekend cases—average 6,301 new cases per day. Source: https://www.cdph.ca.gov/Programs/OPA/Pages/NR21-360.aspx 

*Includes weekend cases—average 8,757 new cases per day, an increase of 2,456. Source: https://www.cdph.ca.gov/Programs/OPA/Pages/NR21-351.aspx 

In the United States, as of 12/23/21, cases, deaths, and hospitalizations are trending upward.

Cases are up 55% over the last 14 days, deaths are up 7%, and hospitalizations are up 10%. 

Source: NY Times https://www.nytimes.com/interactive/2021/us/covid-cases.html 

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. 

Source: https://twitter.com/Antonio_Caramia/status/1474428188398862339/photo/1 

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?

  1. 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. 
  1. 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.
  1. 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. 
  1. 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
  1. 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. 
  1. 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. 
  1. 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. 
  1. 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. 

COVID-19

SARS-CoV-2 Update

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% and 10.04% 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 populationRank in USARanked within World
Mississippi3,479  1st5th
New Jersey  3,2283rd9th tied
Louisiana3,2105th10th
New York 3,0336th9th tied
Alabama3,3332nd7th
Arizona3,2274th9th tied
Massachusetts2,87011th14th tied
Rhode Island  2,824  13th14th tied
Arkansas2,959 7th11th
Florida2,8969th12th
California1,920 35th36th
USA2,49520th
Peru6,0071st
Bosnia-Herzegovina  4,0363rd
North Macedonia  3,7416th
Hungary3,8994th
Montenegro3,7765th
Bulgaria4,3562nd
Gibraltar2,96910th
Czechia3,2647th
Brazil2,87513th
San Marino2,76214th
Georgia3,2618th
Sweden1,49156th
Israel88287th
Canada78594th
Finland260135th
Norway219139th
Japan146153rd
Iceland105163rd
South Korea89167th

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):

Omicron cases sequenced as of 12/17/21:

Source: GISAID

Delta cases sequenced as of 12/17/21: 

Source: GISAID

Map of Delta sequenced transmissions:

Source: GISAID

B.1.640 cases sequenced as of 12/17/21:

Source: GISAID

Gamma cases sequenced as of 12/17/21:

Source: GISAID

Mu cases sequenced as of 12/17/21:

Source: GISAID

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 12/17/21New Infections on 12/17/21Total DeathsNew Deaths on 12/17/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World273,960,234(8,798,529 new infections in 14 days).730,0905,360,728(102,682 new deaths in last 14 days;7,2973.51%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)NoNo
USA51,510,281
(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)
1,65315.45%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)NoNo
Brazil22,209,020(ranked #3)   4,079617,647(ranked #2)12610.34%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)NoNo
India34,732,592(ranked #2)6,543476,897(ranked #3)382.48%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)NoNo
United Kingdom11,190,354(ranked #4; was #6 sixrteen weeks ago)93,045147,048(ranked #7 in world)11116.35%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)NoNo
California, USA5,067,329(ranked #14 in world)9,12575,935(ranked #20 in world)11312.82%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)NoNo
Mexico3,927,265(ranked #15)2,627 297,356(ranked #4)1693.00%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)NoNo
South Africa3,276,529(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 12/17/21,16,055 on 12/3/21,11,535 on 12/2/21,8,561 on 12/1/21,4,373 on 11/30/21,789 on 11/19/21339 on 11/5/2190,297355.42%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)NoNo
Canada1,864,891(ranked #27)6,89230,624124.87%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)Yes, except Alberta ProvinceNo
Poland3,923,472(ranked #16)20,02790,87256610.38%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)NoNo
Turkey9,136,565(ranked #6)18,14180,05319010.66%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)NoNo
Russia10,159,389(ranked #5)27,743295,104(ranked #5 in world)1,0806.95%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)NoNo
Argentina5,382,290(ranked #11)5,648116,8921811.75%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)NoNo
Colombia5,103,269(ranked #13)1,803129,345509.87%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,269,180(ranked #23)——–202,076(ranked #6)——-6.71%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)NoNo
Indonesia4,260,148(ranked #14)291143,98671.53%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)NoNo
Iran6,157,650(ranked 9th; was 12th sixteen weeks ago)2,196130,992467.20%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain5,455,527(ranked 10th) 33,35988,7084111.66%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 South Africa November 2021)B.1.640 (Congo/France)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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% and 9.74% 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 populationRank in USARanked within World
Mississippi3,460    1st6th
New Jersey  3,2013rd7th tied
Louisiana3,1894th7th tied
New York 2,9946th9th tied
Alabama3,2982nd7th tied
Arizona3,0775th9th 
Massachusetts2,82811th12th tied
Rhode Island  2,776   12th12th tied
Arkansas2,883 8th12th tied
Florida2,8709th11th
California1,898 35th35th
USA2,42120th
Peru5,9881st
Bosnia-Herzegovina  3,9023rd
North Macedonia  3,6965th
Hungary3,6496th
Montenegro3,6964th
Bulgaria4,1852nd
Gibraltar2,94010th
Czechia3,1227th
Brazil2,86611th
San Marino2,73312th
Georgia3,0818th
Sweden1,48656th
Israel87986th
Canada77894th
Finland245136th
Norway199141st
Japan146153rd
Iceland102163rd
South Korea73169th
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):

Source: World Health Organization

Omicron cases sequenced as of 12/4/21:

Source: GISAID

Delta cases sequenced as of 12/4/21: 

Source: GISAID

B.1.640 cases sequenced as of 12/4/21:

Source: GISAID

Map of Delta sequenced transmissions:

Source: GISAID

Gamma cases sequenced as of 12/4/21:

Source: GISAID

Mu cases sequenced as of 12/4/21:

Source: GISAID

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 12/03/21New Infections on 12/03/21Total DeathsNew Deaths on 12/03/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World265,161,705(8,234,681 new infections in 14 days; an increase of 1,142,190 infections from the preceding 14 days)705,5745,258,046(102,708 deaths in 14 days; an increase of 5,145 deaths from the preceding 14 days).7,9153.40%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)NoNo
USA49,878,049
(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)
1,35214.94%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)NoNo
Brazil22,129,409(ranked #3)   10,627615,454(ranked #2)2,22910.30%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)NoNo
India34,624,360(ranked #2)8,603470,530(ranked #3)4152.47%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)NoNo
United Kingdom10,349,647(ranked #4; was #6 fourteen weeks ago)50,584145,424 (ranked #7 in world)14315.17%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)NoNo
California, USA4,978,179(ranked #14 in world)8,54775,013 (ranked #20 in world)9012.59%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)NoNo
Mexico3,894,364(ranked #15)3,146 294,715(ranked #4)2872.97%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)NoNo
South Africa3,004,203(ranked #18)
Exponential growth of Omicron occurring in South Africa. Children under 5 are infected.Quadrupling of daily infections in last four days.
16,055 on 12/3/21,11,535 on 12/2/21,8,561 on 12/1/21,4,373 on 11/30/21,789 on 11/19/21339 on 11/5/2189,940254.97%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)NoNo
Canada1,802,359(ranked #26)3,48729,757204.71%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)Yes, except Alberta ProvinceNo
Poland3,67,452(ranked #16)26,96585,1264709.58%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)NoNo
Turkey8,861,386(ranked #6)21,49577,41718710.34%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)NoNo
Russia9,736,037(ranked #5)32,930278,857(ranked #5 in world)1,2176.66%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)NoNo
Argentina5,337,692(ranked #10)2,382116,6394211.65%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)NoNo
Colombia5,076,378(ranked #13)2,299128,685509.82%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,241,027(ranked #22)1,606201,326(ranked #6)446.665%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)NoNo
Indonesia4,257,243(ranked #14)245143,85881.53%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)NoNo
Iran6,069,559(ranked 8th; was 12th fourteen weeks ago)3,603130,066787.16%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain5,202,858(ranked 11th) 13,73888,1593711.12%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 South Africa November 2021)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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 decreased for the third time in eighteen 14-day periods. There were 306 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 8,080 infections per day compared to the preceding 14-day period. Our infections per day have decreased for the fouth time over the last 14 weeks. This trend will continue. Increased vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan continue to stop the further spread of mutants and reduce infections, hospitalizations, and deaths. On 11/05/21, the United States had 84,846 new infections with one state failing to report (Iowa). There were also 1,345 deaths (with seven other states failing to report deaths). Florida continues to consistently under-report daily infections and deaths. Florida and five other states failed to report their deaths. The number of hospitalized patients is decreasing in many areas and only 11,535 patients are seriously or critically ill; that number was 14,232 two weeks ago. The number of critically ill patients has decreased by 2,697 in the last 14 days, while at least 18,952 new deaths occurred. The number of critically ill patients has decreased for the fifth time in nine 14-day periods but a large number of patients are still dying each day (average 1,354/day). 

As of 11/05/21, we have had 774,673 deaths and 47,280,449 SARS-CoV-2 infections in the United States. We have had 1,015,853 new infections in the last 14 days. We are adding an average of 507,926 infections every seven days. For the pandemic in the United States we are averaging one death for every 61 infections reported or over 16,385 deaths for each one million infections. As of 11/05/21, thirty-one states have had greater than 500,000 total infections, and 34 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 11/05/21, in the United States, 14.17% of the population has had a documented SARS-CoV-2 infection. In the last 12 months, over 10% 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 11 months, there were 514,342 new deaths from SARS-CoV-2. For nearly six of those months, vaccines have been available to all adults. During these six months, 179,762 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 11/5/21, California was ranked 41st in infection percentage at 12.23% and 9.46% of Californians were infected in the last 12 months. And now let’s look at the top 20 infected states, which is not a list that you’d like to be on in 2021. North Dakota was at 19.80% (ranked #1),Tennessee was at 18.84% (ranked #2), Alaska was at 18.70% (ranked #3), Wyoming 18.19% (ranked #4),  South Dakota was at 17.74% (ranked #5), South Carolina was at 17.52% (ranked #6), Utah at 17.48% (ranked #7), Florida was at 17.24% (ranked #8), Rhode Island was at 17.09% (ranked #9), Arkansas was at 17.08% (ranked #10),  Alabama was at 17.03% (ranked #11), Mississippi was at 17.02% (ranked #12),  Montana was at 16.88% (ranked #13), Iowa was at 16.81% (ranked #14), Kentucky was at 16.80% (ranked #15), Idaho was at 16.56% (ranked #16), Louisiana was at 16.38% (ranked #17), Oklahoma was at 16.38% (ranked #18), Arizona was at 16.25% (ranked #19) and Georgia was at 15.45% of the population infected (ranked #20). Forty-one states now have greater than 12% of their population infected. Only two states have less than 6% of their population infected: Hawaii (5.99%) and Vermont is at (5.94%). Hawaii, Vermont, and the US Virgin Islands still remain the safest places in the United States. 

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, Louisiana, Arizona,  Alabama would be tied at the 7th highest number of deaths per million in the world, followed by  Massachusetts, Georgia, Rhode Island, Arkansas, South Dakota, and South Carolina tied at 10th. 

The United States as a whole ranks 16th in the world for deaths per million population (2,322 deaths per million). California ranks 41st in the USA (and 35th in the world). If we look at the death rates per million in South Korea (57), Iceland (99), Japan (145), and Israel (870), 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 1,475 per million, compared to 168 per million in Norway and 213 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 populationRank in USARanked within World
Mississippi3,220     1st5th
New Jersey  3,1593rd7th tied
Louisiana3,1444th7th tied
New York 2,9495th7th tied
Alabama3,2202nd7th tied
Arizona2,8616th8th 
Massachusetts2,7447th10th tied
Rhode Island  2,720   9th10th tied
Arkansas2,807 8th10th tied
Florida2,8038th9th
California1,840 35th36th
USA2,32216th
Peru5,9651st
Bosnia-Herzegovina  3,6023rd
North Macedonia  3,4584th
Hungary3,3296th
Montenegro3,4075th
Bulgaria3,6262nd
Gibraltar2,9107th
Czechia2,8828th
Brazil2,8389th
San Marino2,70410th
Sweden1,47554th
Israel87085th
Canada76381st
Finland213136th
Norway168144th
Japan145150th
Iceland99161st
South Korea57175th

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 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 is applying for an Emergency Use Authorization for this drug. The data still needs to be submitted to the FDA for review and approval. I would anticipate that the drug would be approved in less than 45 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 four variants as Variants of Concern (VOC):

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):

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 11/05/21New Infections on 11/05/21Total DeathsNew Deaths on 11/05/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World243,714,456(6,120,077 new infections in 14 days; an increase of 379,882 infections from the preceding 14 days)506,2635,053,433(199,408 deaths in 14 days; an increase of 4,185 new deaths from the preceding 14 days).7,7113.20%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)NoNo
USA47,280,449
(ranked #1) 1,015853 new infections in the last 14 days)
84,846
(ranked #1)
774,673
(ranked #1)18,952 new deaths in the last 14 days)
1,34514.17%B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)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)NoNo
Brazil21,862,458(ranked #3)   13,321609,112(ranked #2)39710.18%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)NoNo
India34,344,087(ranked #2)11,689460,268(ranked #3)3932.45%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)NoNo
United Kingdom9,241,916(ranked #4; was #6 ten weeks ago)34,029141,58819313.51%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)NoNo
California, USA4,836,074(ranked #12 in world)8,10672,70710512.23%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) NoNo
Mexico3,818,216(ranked #15)3,763289,131(ranked #4)2442.92%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)NoNo
South Africa2,923,393(ranked #18)38989,295444.84%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)NoNo
Canada1,727,686(ranked #26)2,53529,132174.52%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)Yes, except Alberta ProvinceNo
Poland3,076,518(ranked #16)15,90477,5471528.14%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)NoNo
Turkey8,178,901(ranked #6)28,19371,7241099.53%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)NoNo
Russia8,714,595(ranked #5)40,735244,447(ranked #5)1,1925.96%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)NoNo
Argentina5,295,260(ranked #9)1,271116,0832811.57%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)NoNo
Colombia5,010,982(ranked #11)1,975127,456399.70%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,205,486(ranked #21)1,062200,373(ranked #6)236.56%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)NoNo
Indonesia4,247,320(ranked #14)518143,519191.53%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)NoNo
Iran5,973,457(ranked 8th; was 12th ten weeks ago)8,633127,0531326.98%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain5,025,639(ranked 10th) 3,09387,5042710.79%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)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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.

n the United States, SARS-CoV-2 deaths have decreased for the second time in seventeen 14-day periods. There were 282 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 24,140 infections per day compared to the preceding 14-day period. Our infections per day have decreased for the third time over the last 14 weeks. This trend will continue. Increased vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan continue to stop the further spread of mutants and reduce infections, hospitalizations, and deaths. On 10/22/21, the United States had 82,483 new infections with one state failing to report (Iowa). There were also 1,610 deaths (with seven other states failing to report deaths). Florida continues to consistently under-report daily infections and deaths. The number of hospitalized patients is decreasing in many areas and only 14,232 patients are seriously or critically ill; that number was 17,497 two weeks ago. The number of critically ill patients has decreased by 3,265 in the last 14 days, while at least 23,244 new deaths occurred. The number of critically ill patients has decreased for the fourth time in eight 14-day periods but a large number of patients are still dying each day (average 1,660/day). 

As of 10/22/21, we have had 755,721 deaths and 46,246,596 SARS-CoV-2 infections in the United States. We have had 1,128,976 new infections in the last 14 days. We are adding an average of 564,488 infections every seven days. For the pandemic in the United States we are averaging one death for every 61 infections reported or over 16,341 deaths for each one million infections. As of 10/22/21, thirty-one states have had greater than 500,000 total infections, and 33 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 10/22/21, in the United States, 13.87% of the population has had a documented SARS-CoV-2 infection. In the last 11 months, over 10% 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 11 months, there were 495,390 new deaths from SARS-CoV-2. For nearly five of those months, vaccines have been available to all adults. During these five months, 160,810 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 10/22/21, California was ranked 40th in infection percentage at 12.03% and 9.25% of Californians were infected in the last 11 months. And now let’s look at the top 20 infected states, which is not a list that you’d like to be on in 2021. North Dakota was at 18.90% (ranked #1),Tennessee was at 18.63% (ranked #2), Alaska was at 17.50% (ranked #3), Wyoming 17.30% (ranked #4),  South Carolina was at 17.30% (ranked #5), South Dakota was at 17.21% (ranked #6), Florida was at 17.14% (ranked #7), Arkansas was at 16.88% (ranked #8),  Mississippi was at 16.83% (ranked #9), Utah at 16.80% (ranked #10), Rhode Island was at 16.80% (ranked #11), Alabama was at 16.69% (ranked #12), Kentucky was at 16.43% (ranked #13), Iowa was at 16.31% (ranked #14), Louisiana was at 16.25% (ranked #15), Oklahoma was at 16.14% (ranked #16), Montana was at 15.95% (ranked #17), Idaho was at 15.90% (ranked #18), Arizona was at 15.73% (ranked #19) and Georgia was at 15.30% of the population infected (ranked #20). Thirty-six states now have greater than 12% of their population infected. Only one state has less than 6% of their population infected: Hawaii (5.85%). Vermont is at (6.14%). Hawaii, Vermont, and the US Virgin Islands still remain the safest places in the United States. 

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 fourth highest COVID-19 deaths per million in the world. New York would be 6th. New Jersey, Louisiana, and Alabama would be tied at the 7th highest number of deaths per million in the world, followed by Arizona (8th) and Massachusetts, Rhode Island, Arkansas, and Florida tied at 10th. 

The United States as a whole ranks 34th in the world for deaths per million population (2,266 deaths per million). California ranks 35th in the USA (and 34th in the world). If we look at the death rates per million in South Korea (53), Iceland (96), Japan (144), and Israel (862), they suggest that treatment outcomes are somehow different in these three countries. The same phenomenon can be seen in Scandinavia, where the death rate in Sweden is 1,469 per million, compared to 163 per million in Norway and 212 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 populationRank in USARanked within World
Mississippi3,357     1st4th
New Jersey  3,1333rd7th tied
Louisiana3,1114th7th tied
New York 2,9155th6th
Alabama3,1362nd7th tied
Arizona2,8616th8th 
Massachusetts2,7447th10th tied
Rhode Island  2,711   10th10th tied
Arkansas2,735 8th10th tied
Florida2,7299th10th tied
California1,810 35th34th
USA2,26620th
Peru5,9581st
Bosnia-Herzegovina  3,4792nd
North Macedonia  3,3693rd
Hungary3,1676th
Montenegro3,2754th
Bulgaria3,2755th
Gibraltar2,9107th
Czechia2,8518th
Brazil2,8219th
San Marino2,67510th
Sweden1,460952nd
Israel86283rd
Canada75391st
Finland212136th
Norway163147th
Japan144149th
Iceland96160th
South Korea53175th

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 four variants as Variants of Concern (VOC):

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):

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 10/22/21New Infections on10/22/21Total DeathsNew Deaths on 10/22/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World243,714,456(5,740,195 new infections in 14 days; a decrease of 368,066 infections from the preceding 14 days)458,9504,953,025(96,223 deaths in 14 days; a decrease of 9,990 new deaths from the preceding 14 days).7,8053.12%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)NoNo
USA46,264,596
(ranked #1) 1,128,976 new infections in the last 14 days)
82,483
(ranked #1)
755,721
(ranked #1)23,244 new deaths in the last 14 days)
1,61013.87%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)NoNo
Brazil21,711,843(ranked #3)   14,502605,211(ranked #2)44710.12%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)NoNo
India34,158,772(ranked #2)16,331453,742(ranked #3)6662.44%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)NoNo
United Kingdom8,689,949(ranked #4; was #6 eight weeks ago)49,298139,32618012.71%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)NoNo
California, USA4,755,586(ranked #12 in world)6,96671,52511912.03%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) NoNo
Mexico3,772,556(ranked #15)4,798285,669(ranked #4)3222.85%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)NoNo
South Africa2,918,8883(ranked #17)51788,891564.84%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)NoNo
Canada1,695,914(ranked #27)2,74528,729624.44%B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Yes, except Alberta ProvinceNo
Poland2,961,923(ranked #16)5,70676,359597.83%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)NoNo
Turkey7,800,796(ranked #6)28,19268,7002289.12%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)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Russia8,168,305(ranked #5)37,141228,453(ranked #5)1,0645.59%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)NoNo
Argentina5,278,910(ranked #9)1,385115,8192311.54%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)NoNo
Colombia4,988,021(ranked #11)1,772126,994359.66%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,194,132(ranked #21)1,043299,003(ranked #6)256.53%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)NoNo
Indonesia4,238,594(ranked #14)760143,153331.52%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)NoNo
Iran5,844,589(ranked 8th; was 12th eight weeks ago)11,064124,9281656.84%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain4,997,732(ranked 10th) 2,55687,1323010.68%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)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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 decreased for the first time in sixteen 14-day periods. There were 77 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 32,841 infections per day compared to the preceding 14-day period.Our infections per day have decreased for the second time in  over the last 14 weeks. THIS trend will continue. Increased vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan continue to stop the further spread of mutants and reduce infections, hospitalizations and deaths. On 10/08/21, the United States had 106,298 new infections with one state failing to report (Iowa). There were also 1,937 deaths (with seven other states failing to report deaths). Florida continues to consistently under-report daily infections and deaths. The number of hospitalized patients is decreasing in many areas and only 17,497 patients are seriously or critically ill; that number was 22.226 two weeks ago. The number of critically ill patients has decreased  by 5,172 in the last 14 days, while at least 27,184 new deaths occurred. The number of critically ill patients has decreased for the third time in seven 14-day periods but a large number of patients are still dying each day (average 1,942/day). 

As of 10/08/21, we have had 732,477 deaths and 45,135,620 SARS-CoV-2 infections in the United States. We have had 1,466,940 new infections in the last 14 days. We are adding an average of 733,470 infections every 7 days. For the pandemic in the United States we are averaging one death for every 62 infections reported or over 16,100 deaths for each one million infections. As of 10/04/21, twenty-nine states have had greater than 500,000 total infections, and 33 states have had greater than 5,000 total deaths. Ten states (Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York 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 10/04/21, in the United States, 13.53% of the population has had a documented SARS-CoV-2 infection. In the last 10 months, over 9% of our country became infected with SARS-CoV-2. 

As of 10/04/21, California was ranked 40th in infection percentage at 11.84%. Tennessee was at 18.29% (ranked #1), North Dakota was at 17.99% (ranked #2), Florida was at 16.98% (ranked #3), South Carolina was at 16.97% (ranked fourth), South Dakota was at 16.70% (ranked fifth), Arkansas was at 16.61% (ranked sixth),  Mississippi was at 16.60% (ranked seventh), Rhode Island was at 16.47% (ranked #8),  Alabama was at 16,44% (ranked #9), Wyoming was at 16.29% (ranked tenth), Utah at 16.22% (ranked eleventh) and Louisiana had 16.07% of the population infected (ranked twelfth). Thirty-six states now have greater than 12% of their population infected. Two states have less than 6% of their population infected: Vermont (5.64%) and Hawaii (5.72%). These two states and the US Virgin Islands still remain the safest place to travel.

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 third highest COVID-19 deaths per million in the world. New Jersey, Louisiana, Alabama and New York would be tied at the 6th highest number of deaths per million in the world, followed by Arizona, Massachusetts and Louisiana tied at 10th and Florida and Arkansas Arizona tied at 11th. 

The United States as a whole ranks 16th in the world for deaths per million population. California ranks 34th. If we look at the death rates per million in South Korea (50), Iceland (96), and Japan (142), they suggest that treatment outcomes are somehow different in these three countries. The same phenomenon can be seen in Scandinavia, where the death rate in Sweden is 1,452 per million, compared to 159 per million in Norway and 197 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 populationRank in USARanked within World
Mississippi3,297     1st3rd
New Jersey  3,1042nd6th
Louisiana3,0493rd6th
New York 2,8895th6th
Alabama3,0094th6th
Arizona2,7926th10th 
Massachusetts2,7207th10th
Rhode Island  2,694   8th10th
Arkansas2,588 10th11th
Florida2,6269th11th
California1,775 34th34th
USA2,11620th
Peru5,9491st
Bosnia-Herzegovina  3,3372nd
North Macedonia  3,1473rd
Hungary3,1445th
Montenegro3,1524th
Bulgaria3,1376th
Gibraltar2,8807th
Czechia2,8418th
Brazil2,800 9th
San Marino2,67510th
Sweden1,460 50th
Israel84582nd
Canada73990th
Finland197137th
Norway150146th
Japan142148th
Iceland96158th
South Korea50175th

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 four variants as Variants of Concern (VOC):

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):

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 10/08/21New Infections on 10/08/21Total DeathsNew Deaths on 10/08/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World237,974.261(6,108,627 new infections in 14 days; a decrease of 1,142,653 infections from the preceding 14 days)444,4164,856,802(106,213  deaths in 14 days; a decrease of 5,307 new deaths from the preceding 14 days).7,6273.05%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)NoNo
USA45,135,620
(ranked #1) 1,466,940 new infections in the last 14 days)
106,298
(ranked #1)
732,497
(ranked #1)27,184 new deaths in the last 14 days)
1,93713.53%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)NoNo
Brazil21,550,730(ranked #3)   18,172600,493(ranked #2)62810.04%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)NoNo
India33,934,335(ranked #2)19,870450,408(ranked #3)2482.42%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)NoNo
United Kingdom8,081,300(ranked #4; was #6 six weeks ago)36,060137,54112411.82%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)NoNo
California, USA4,680,659(ranked #13 in world)6,67670,14412611.84%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) NoNo
Mexico3,707,234(ranked #15)7,613281,121(ranked #4)5142.83%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)NoNo
South Africa2,910,681(ranked #17)92488,2361324.83%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)NoNo
Canada1,665,380(ranked #27)4,14728,186454.33%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)Yes, except Alberta ProvinceNo
Poland2,918,863(ranked #16)1,89575,834317.72%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)NoNo
Turkey7,387,537(ranked #6)30,20165,7781888.64%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)NoNo
Russia7,717,356(ranked #5)27,246214,485(ranked #5)9365.28%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)NoNo
Argentina5,265,058(ranked #9)753115,4442811.51%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)NoNo
Colombia4,969,113(ranked #11)1,607126,552359.63%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,183,025(ranked #21)919199,615(ranked #6)359.63%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)NoNo
Indonesia4,225,871(ranked #14)1,384142,560661.52%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)NoNo
Iran5,683,980(ranked 8th; was 12th six weeks ago)9,897122,1971856.65%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain4,973,619(ranked 10th) 2,30986,7787710.63%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)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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 fifth time in fifteen 14-day periods. There were 624 more deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 17,861 infections per day compared to the preceding 14-day period.Our infections per day have decreased for the first time in  over the last 12 weeks. We will see if this trend continues. Increased vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan will be necessary to stop the further spread of mutants and cause reductions in infections, hospitalizations and deaths. On 9/24/21, the United States had 131,007 new infections with one state failing to report (Iowa). There were also 2,019 deaths (with seven other states failing to report deaths). Florida continues to consistently under-report daily infections and deaths. The number of hospitalized patients is decreasing in some areas and only 22,669 patients are seriously or critically ill; that number was 25,748 two weeks ago. The number of critically ill patients has decreased  by 3,079 in the last 14 days, while at least 28,276 new deaths occurred. The number of critically ill patients has decreased for the second time in six 14-day periods but an increasingly large number of patients are still dying each day (average 2,019/day). 

As of 9/24/21, we have had 705,293 deaths and 43,668,680 SARS-CoV-2 infections in the United States. We have had 1,926,987 new infections in the last 14 days. We are adding an average of 963,494 infections every 7 days. For the pandemic in the United States we are averaging one death for every 62 infections reported or 16,151 deaths for each one million infections. As of 9/24/21, twenty-eight states have had greater than 500,000 total infections, and 33 states have had greater than 5,000 total deaths. Ten states (Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York 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 9/24/21, in the United States, 13.09% of the population has had a documented SARS-CoV-2 infection. In the last 10 months, over 9% of our country became infected with SARS-CoV-2. 

As of 9/24/21, California was ranked 38th in infection percentage at 11.60%. Tennessee was at 17.71% (ranked #1), North Dakota was at 16.86% (ranked #2), Florida was at 16.69% (ranked #3), South Carolina was at 16.34% (ranked fourth), Arkansas was at 16.27% (ranked fifth),  Mississippi was at 16.27% (ranked sixth), South Dakota was at 16.14% (ranked seventh), Rhode Island was at 16.11% (ranked #8),  Alabama was at 15.99% (ranked #9) and Louisiana had 15.80% of the population infected (ranked tenth). Thirty-four states now have greater than 12% of their population infected and 42 states have greater than 10% of their population infected. Two states have less than 6% of their population infected: Vermont (5.22%) and Hawaii (5.46%). Hawaii reported 403 new infections and nine new deaths on 9/24/21. Vermont reported 242 new infections and three deaths on 9/24/21. These two states and the US Virgin Islands still remain the safest place to travel.

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 third highest COVID-19 deaths per million in the world. New Jersey has the 5th highest number of deaths per million in the world, followed by Louisiana (7th), New York (8th), and Alabama (9th). Arizona, Massachusetts, and Rhode Island tie at 10th. The United States as a whole ranks 20th in the world for deaths per million population. California ranks 34th. If we look at the death rates per million in South Korea (47), Iceland (96), and Japan (138), they suggest that treatment outcomes are somehow different in these three countries. The same phenomenon can be seen in Scandinavia, where the death rate in Sweden is 1,452 per million, compared to 155 per million in Norway and 191 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 populationRank in USARanked within World
Mississippi3,167     1st3rd
New Jersey  3,0742nd5th
Louisiana2,9563rd7th
New York 2,8624th8th
Alabama2,8395th9th
Arizona2,7126th10th 
Massachusetts2,6907th10th
Rhode Island  2,665   8th10th
Arkansas2,505 9th11th
Florida2,47310th12th
California1,739 33rd34th
USA2,11620th
Peru5,9391st
Bosnia-Herzegovina  3,2012nd
North Macedonia  3,1473rd
Hungary3,1314th
Montenegro2,9995th
Bulgaria2,9676th
Gibraltar2,8807th
Czechia2,8378th
Brazil2,769 9th
San Marino2,64610th
Sweden1,452 43rd
Israel81682nd
Canada72489th
Finland191133rd
Norway155145th
Japan138147th
Iceland96156th
South Korea47173rd

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 four variants as Variants of Concern (VOC):

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):

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 9/24/21New Infections on 9/24/21Total DeathsNew Deaths on 9/24/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World231,865,634(7,251,280 new infections in 14 days; a decrease of 1,207,825 infections from the preceding 14 days)500,3184,750,589(121,520  deaths in 14 days; a decrease of 140,122 new deaths from the preceding 14 days).8,4742.97%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)NoNo
USA41,741,693
(ranked #1) 1,926,987 new infections in the last 14 days)
131,007
(ranked #1)
705,293
(ranked #1)28,276 new deaths in the last 14 days)
2,00413.09%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)NoNo
Brazil21,327,616(ranked #3)   19,438593,698(ranked #2)6809.94%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)NoNo
India33,623,072(ranked #2)29,580446,690(ranked #3)2912.40%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)NoNo
United Kingdom7,601,487(ranked #4; was #6 four weeks ago)35,953135,98318011.12%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)NoNo
California, USA4,591,516(ranked #13 in world)7,32768,72416411.62%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) NoNo
Mexico3,608,976(ranked #15)11,808274,139(ranked #4)7482.76%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)NoNo
South Africa2,894,342(ranked #17)2,26186,9673124.80%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)NoNo
Canada1,598,800(ranked #27)4,60027,620394.19%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)Yes, except Alberta ProvinceNo
Poland2,901,674(ranked #16)81375,551147.67%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)NoNo
Turkey6,987,494(ranked #6)27,19762,7452218.17%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)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Russia7,376,374(ranked #5)21,379                                               202,273(ranked #5)8285.05%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)NoNo
Argentina5,248,847(ranked #9)1,849114,82818311.48%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)NoNo
Colombia4,948,513(ranked #10)1,702126,069369.59%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,171,374(ranked #20)899199,182(ranked #6)266.47%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)NoNo
Indonesia4,204,116(ranked #13)2,557141,2581441.51%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)NoNo
Iran5,508,885(ranked 8th; was 12th four weeks ago)15,294118,7922846.45%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain4,946,601(ranked 11th) 2,74686,2294410.57%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)NoNo

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

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 fourth time in fifteen 14-day periods. There were 412 more deaths per day than in the last 14-day period. In the last 14 days, the number of infections has increased by 4,204 infections per day compared to the preceding 14-day period.  Our infections per day are continuing to rise again over the last 10 weeks, secondary to SARS-CoV-2 mutant Delta/B.1.617.2 and other variants like Mu/B.1.621. The opening of schools, places of worship, bars, restaurants, indoor dining and travel all will contribute to further spread of SARS-CoV-2 mutants, like the Delta, Delta plus, Lambda and the Colombian variant Mu/B.1.621 with continued rising numbers of infections, hospitalizations and deaths. Increased vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan will be necessary to stop the spread of mutants and cause reductions in infections, hospitalizations and deaths. On 8/27/21, the United States had 171,125 new infections with one state failing to report (Iowa). There were also 1,761 deaths (with seven other states failing to report deaths). Florida is a persistent reporting failure of daily infections and, particularly, deaths. The number of hospitalized patients is again increasing and 25,749 patients are seriously or critically ill, that number was 24,809 two weeks ago. The number of critically ill patients has increased by 949 in the last 14 days, while at least 19,526 new deaths occurred. The number of critically ill patients is increasing for the fifth time in five 14-day periods and an increasingly large number of patients are still dying each day (average 1,395/day). 

As of 9/10/21, we have had 677,017 deaths and 41,741,693 SARS-CoV-2 infections in the United States. We have had 2,177,039 new infections in the last 14 days. We are adding an average of 1,088,519 infections every 7 days. For the pandemic in the United States we are averaging one death for every 61 infections reported or 16,219 deaths for each one million infections. As of 8/27/21, twenty-seven states have had greater than 500,000 total infections, and 33 states have had greater than 5,000 total deaths. Ten states (Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York, and California) have had greater than 40,000 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 9/10/21, in the United States, 12.52% of the population has had a documented SARS-CoV-2 infection. In the last 9 months, over 8% of our country became infected with SARS-CoV-2. 

As of 9/10/21, California was ranked 36th in infection percentage at 11.32%. Tennessee was at 16.46% (ranked #1), Florida was at 16.08% (ranked #2), North Dakota was at 15.98% (ranked #3), Rhode Island was at 15.65% (ranked #4), Arkansas was at 15.64%(ranked fifth), Mississippi was at 15.466% (ranked sixth), South Dakota was at 15.460% (ranked seventh), Louisiana was at 15.32% (ranked eighth), South Carolina was at 15.22% (ranked ninth) and Alabama was at 15.11% of their population infected (ranked tenth). Thirty-two states now have greater than 12% of their population infected and 42 states have greater than 10% of their population infected. Two states have less than 5% of their population infected: Vermont (4.76%) and Hawaii (4.96%). Unfortunately Hawaii reported 747 new infections and 8 deaths on 9/10/21.

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 four variants as Variants of Concern (VOC):

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):

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 9/10/21New Infections on 9/10/21Total DeathsNew Deaths on 9/10/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World224,614,354(8,459,105 new infections in 14 days)595,8944,629,069(261,642 new deaths in 14 days)9,6552.88%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)NoNo
USA41,741,693
(ranked #1)
171,125
(ranked #1)
677,017
(ranked #1)
1,76112.52%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)NoNo
Brazil20,974,850(ranked #3)   15,951585,923(ranked #2)7189.78%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)NoNo
India33,200,877(ranked #2)37,873442,350(ranked #3)3042.57%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)NoNo
United Kingdom7,168,806(ranked #4; was #6 two weeks ago)37,873133,98814710.49%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)NoNo
California, USA4,345,068(ranked #13 in world)13,46366,62520311.32%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) NoNo
Mexico3,479,999(ranked #15)14,828266,150(ranked #4)7302.66%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)NoNo
South Africa2,848,925(ranked #17)5,88384,6082814.73%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)NoNo
Canada1,538,093(ranked #27)4,60427,170364.03%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)Yes, except Alberta ProvinceNo
Poland2,892,642(ranked #16)52875,41787.65%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)NoNo
Turkey6,613,976(ranked #7)23,56250,3842147.74%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)NoNo
Russia7,102,625(ranked #5)18,314                                               191,1657894.86%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)NoNo
Argentina5,221,809(ranked #9)2,816113,28218311.42%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)NoNo
Colombia4,926,772(ranked #10)1,772125,529499.56%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)NoNo
Peru2,159,306(ranked #18)813198,673(ranked #5)526.44%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)NoNo
Indonesia4,158,731(ranked #13)5,376138,4313151.50%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)NoNo
Iran5,258,913(ranked 8th; was 12th two weeks ago)21,114113,3804456.16%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)NoNo
Spain4,907,461(ranked 10th) 4,44085,2907210.49%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Kappa/B.1.617.1 (India)Mu/B.1.621 (Colombia)NoNo

What Our Team Is Reading This Week