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
New York 2,8624th8th
Rhode Island  2,665   8th10th
Arkansas2,505 9th11th
California1,739 33rd34th
Bosnia-Herzegovina  3,2012nd
North Macedonia  3,1473rd
Brazil2,769 9th
San Marino2,64610th
Sweden1,452 43rd
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
(ranked #1) 1,926,987 new infections in the last 14 days)
(ranked #1)
(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