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
Massachusetts2,7447th10th tied
Rhode Island  2,720   9th10th tied
Arkansas2,807 8th10th tied
California1,840 35th36th
Bosnia-Herzegovina  3,6023rd
North Macedonia  3,4584th
San Marino2,70410th
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
(ranked #1) 1,015853 new infections in the last 14 days)
(ranked #1)
(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