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, SARS-CoV-2 therapeutic agents and mutant viruses. We use the WORLDOMETERS aggregators data set to make any projections since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

SARS-CoV-2 infections per day in the United States have decreased for the first time in two weeks; however, there is still widespread underreporting by states, a failure to capture positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have decreased by 31 deaths per day. The number of infections have decreased by 19,061 infections per day.  The CDC estimates that BA.2.12.1 accounted for 0.2% of isolates, BA.2 accounted for 0%, BA.5 accounted for 88.7%, BA.4 accounted for 3.6%, BA.4.6 accounted for 7.5%, and B.1.1.529 accounted for 0% in the week ending August 27.

CDC

We frequently hear messaging from health officials and politicians that Omicron is “mild,” especially compared to the Delta variant, and as a result, many of our patients believe that they no longer need to wear their masks. This is a dangerous misconception. SARS-CoV-2 still remains a highly transmissible, airborne virus. The following graph, based on CDC data from April 2, 2022, shows that Omicron deaths in people over 65 are much higher than Delta deaths in the same age group. In fact, the peak of Omicron deaths in people over 65 years of age is 163% higher than the Delta peak. The death rate from Omicron is only lower than Delta in the populations between 12 and 64 years of age. Until we have more data on these newer mutants of SARS-CoV-2, we will not know the lethality of each variant. It may take months to measure objective differences in the death rates of new circulating variants. We recommend that all of our patients and family members continue to wear N95 masks in all enclosed spaces.

NY Times

In patients treated with Paxlovid for five days who have persistent symptoms and continued positivity, we feel that clinicians should consider giving a second course of Paxlovid for five days. Boucau et al have demonstrated that in a study of seven patients with recurrent symptoms, “High viral loads (median 6.1 log10 copies/mL) were detected after rebound for a median of 17 days after initial diagnosis. Three had culturable virus for up to 16 days after initial diagnosis.” This was not due to resistance-associated mutations of the virus, suggesting that the course of therapy may be inadequate in this group of persistently infected patients. 

The Omicron variant has continued to mutate just like Delta. There are now 276 Omicron sub-variants (an increase of 46 in the last two weeks) that have been assigned Pango lineages, including 123 sub-lineages of BA.2 (an increase of 7 in two weeks), one sub-lineage of BA.3, 15 sub-lineages of BA.4 (an increase of one in two weeks), and 45 sub-lineages of BA.5 (an increase of 21 in two weeks). The BF lineage (new ten weeks ago) now has 21 sublineages, an increase of 10 in two weeks. The BE lineage (also new ten weeks ago), with BE.1 first detected in South Africa, Austria and England, now has 7 sublineages, an increase of 3 in two weeks. There are also new lineages from ten weeks ago: BC.1 (Japan), BC.2 (Peru),BD.1 (UK), BG.1 (Peru), BG.2 (US, Denmark, Canada), BG.3 (Peru), BG.4 (Israel). In the last two weeks, the BG lineage has expanded to include BG.5 (USA) and BG.6 (Peru). Lastly, two new sublineages were added in the past two weeks: BH.1 (India) and BK.1 (USA and Canada). 

In Monterey County, as of 8/28/22, 0.5% of 0-4 year-olds and 39.4% of 5-11 year-olds have received the first two doses of vaccine, while 72.9% of 12-17 year-olds have received two doses. Only 53.4% of Monterey County residents have received a third dose of the vaccine. On June 17, The FDA authorized both the Pfizer and Moderna vaccines for use in children ages 6 months to four years. We believe children under 5 should be vaccinated as soon as possible. We would anticipate, with the start of school on August 5 and the low vaccination rates in our county, that we’ll have a marked increase in the number of infected patients. All Monterey County residents should get up to date on COVID-19 vaccinations as soon as possible. 

Monterey County Health Department

On 8/26/22, the United States had 63,798 documented new infections. There were also 312 deaths. Twenty-four states did not report their infections, and 28 states didn’t report their deaths. In the United States the number of hospitalized patients has decreased slightly in many areas and was 38,630 on August 27, a decrease of 9% compared to the previous 14 days. Now there are 3,992 patients who are seriously or critically ill; that number was 4,490 two weeks ago. The number of critically ill patients has decreased by 498 in the last 14 days, while at least 6,692 new deaths occurred. The number of critically ill patients has decreased for the second time in twenty-six 14-day periods. Patients are still dying each day (average 478/day). Omicron BA.4, BA.4.6 (a new USA variant) and BA.5 variants causing infections should continue to increase and critically ill patients may increase. Deaths usually lag two to four weeks behind exponential increase in infections. Past infections with a BA.1 or BA.2 variant will not prevent infections with BA.4, BA.4.6 or BA.5. 

As of 8/26/22, we have had 1,068,843 deaths and 95,970,007 SARS-CoV-2 infections in the United States. We have had 1,326,375 new infections in the last 14 days. We are adding an average of 663,188 infections every seven days. For the pandemic in the United States we are averaging one death for every 89.78 infections or over 11,137 deaths for each one million infections. As of 8/26/22, thirty-eight states have had greater than 500,000 total infections, and 37 states have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths, and 42 states have greater than 2,000 deaths per million population. Vermont, at 1,153 deaths per million, and Hawaii, 1,133 deaths per million, are the states with the lowest death rates. Eighteen states (Alabama, Virginia, Missouri, North Carolina, Indiana, Tennessee, Massachusetts, Ohio, Michigan, Georgia, Illinois, New Jersey, Pennsylvania, Florida, Texas, New York, Arizona and California) have had greater than 20,000 deaths. Four states have had greater than 70,000 deaths: Florida (79,568 deaths), Texas (90,539 deaths), New York (71,422 deaths), and  California (94,959 deaths, 20th most deaths in the world). 

On 11/20/20, there were 260,331 (cumulative) deaths in the US from SARS-CoV-2. Since 11/20/20 (21 months), there were 808,712 new deaths from SARS-CoV-2. For seventeen of those months, vaccines have been available to all adults. During these seventeen months, 497,746 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 8/26/22, California was ranked 32nd in the USA in infection percentage at 27.97%. In California, 24.0% of people were infected in the last 19 months. As of 8/26/22, 41 states have had greater than 25% of their population infected. No state has less than 20% of their population infected. 

Worldwide, average deaths per day are 2,399 for the last 14 days, which is a 55 deaths-per-day decrease over the previous 14 days. The United States accounts for 19.92% (478 per day) of all deaths per day in the world over the last two weeks. Worldwide infections per day were 774,366. The United States accounts for 12.23% of those infections (or 94,741 infections per day). 

Watching World Data

Over the next few months, we’ll be paying close attention to correlations between the SARS-CoV-2 data, the number of isolates identified in various countries and states, and the non-pharmaceutical interventions (like mask mandates and lockdowns) put in place by state and national governments. Data on infections, deaths, and percent of population infected was compiled from Worldometers. Data for this table for SARS-CoV-2 Isolates Currently Known in Location was compiled from GISAID and the CDC. It’s worth noting that GISAID provided more data than the CDC.

LocationTotal Infections as of 8/26/22New Infections on 8/26/22Total DeathsNew Deaths on 8/26/22% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask MandateCurrently in Lockdown
World604,789,766(10,841,118 new infections in 14 days).689,1946,485,447(33,589 new deaths in last 14 days)1,9277.75%B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Delta/B.1.617.2 (India)BV-1 (Texas, USA)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Theta/P.3 (Philippines) Mu/B.1.621 (Colombia)C.1.2 (South Africa 2% of isolates in July 2021)R1 (Japan)Omicron/B.1.1.529 + BA.1 + BA.2 + BA.3 (South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)Four new recombinants 12/31 to 3/22)BA.2.12.1 (USA)BA.4 (South Africa)BA.5 (South Africa)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)  NoNo
USA95,970,007(ranked #1) 1,326,375 new infections in the last 14 days.
63,798(ranked #3)
24 states failed to report infections on 8/26/22.
1,068,843(ranked #1) 6,692  new deaths reported in the last 14 days. 312
30 states failed to report deaths on 8/26/22.
26.72%*
*Not updated for 8 weeks by Worldometer.
B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Iota/B.1.526 (USA-NYC)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)BV-1 (Texas, USA)Theta/P.3 (Philippines) Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)R1(Japan)         Omicron/B.1.1.529 + BA.1 + BA.2 (South Africa November 2021)B.1.640.1 (Congo/France)Recombinant Delta AY.119.2- Omicron BA.1.1 (Tennessee, USA 12/31/21)\BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)BA.4.6 (USA 7/22)NoNo
Brazil34,368,909(ranked #4) 220,778 new infections in the last 14 days. 18,270 (ranked #8)683,464(ranked #2; 2,147 new deaths in 14 days)13615.92%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Zeta/P.2 (Brazil)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)NoNo
India 44,398,696(ranked #2); 159,324 new infections in 2 weeks.9,520 (ranked #12)
527,597(ranked #3) 631 new deaths in 2 weeks.413.15%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Eta/B.1.525 (Nigeria/UK)APTK India VOI 32421Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Iota/B.1.526 (USA-NYC) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India)NoNo
United Kingdom
23,492,875(ranked #6) 72,049 new infections in 2 weeks.187,761 (ranked #7) 1,674 new deaths in 2 weeks34.22%B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)C.1.2 (South Africa)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)XD (AY.4/BA.1) recombinantXF (Delta/BA.1) recombinantXE (BA.1/BA.2) recombinantBA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)NoNo
California, USA11,052,866(ranked #14 in the world;  156,070 new infections in the last 14 days).11,37494,959 (ranked #20 in world)
640 new deaths in the last 14 days
5527.97%B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Gamma/P.1 (Brazil)Epsilon/B.1.427 + B.1.429 (USA)*Zeta/P.2 (Brazil)Delta/B.1.617.2 (India)Theta/P.3 (Philippines) Kappa/B.1.617.1 (India)Lambda/C.37 (Peru) Mu/B.1.621 (Colombia) Omicron/B.1.1.529 + BA.1 (South Africa November 2021)BA.2BA.2.12.1 (United States)BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)BA.2.75 (India 7/22)NoNo
Mexico7,001,590(ranked #18) 7,728 new infections in 14 days).7,281(ranked #16)329,289(ranked #5)693 new deaths in 214 days)645.31%B2 lineageAlpha/B.1.1.7 (UK)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)NoNo
South Africa4,010,632(ranked #36; 2,607 new infections in 14 days).247102,084 (ranked #18) 6.58%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)       C.1.2 (South Africa, July 2021)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)BA.2BA.4 (South Africa 11/21)BA.5 (South Africa 11/21)NoNo
Canada4,158,491(ranked #33) 48,560 new infections in 14 days).3,27043,797(ranked #24)3910.81% B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Epsilon/B.1.427 + B.1.429 (USA)*Gamma/P.1 (Brazil)Delta/B.1.617.2 (India)Kappa/B.1.617.1 (India)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)NoNo
Poland6,162,662 (ranked #21; 48,822 new infections in 14 days). 3,847117,007 (ranked #15)4016.32%B2 lineageAlpha/B.1.1.7 (UK)Eta/B.1.525 (Nigeria/UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 + (South Africa November 2021),Omicron/B.1.1.529 +BA.3 NoNo
Russia19,311,973(ranked #9), 487,691 new infections in 14 days).46,452 (ranked #4)383,910(ranked #4)899 new deaths in 14 days8113.22%B2 lineageAlpha/B.1.1.7 (UK)Beta/B.1.351 (SA)Delta/B.1.617.2 (India)R1 (Japan) B.1.640.1 (Congo/France)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)NoNo
Peru4,094,652(ranked #34, 80,821 new infections in 14 days). 3,286215,566(ranked #6)4212.05%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Gamma/P.1 (Brazil)Iota/B.1.526 (USA-NYC)Lambda/C.37 (Peru)Mu/B.1.621 (Colombia)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)NoNo
Iran7,520,993(ranked #17; 55,414 new infections in last 14 days)2,019143,647(ranked #12)358.71%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India)Beta/B.1.351 (SA)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)


NoNo
Spain13,332,976(ranked #12;   38,737 new infections in 14 days).3,064(ranked #26)112,454 (ranked #16)787 new deaths in 14 days7028.49%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)Omicron/B.1.1.529 + BA.1 (South Africa November 2021)B.1.640.1 (Congo/France)NoNo
France34,446,854 (ranked #3; 254,935 new infections in the last 14 days).18,116 153,857 (ranked #10)
793 new deaths in 14 days
5152.52%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)B.1.640.1 (Congo/France)B.1.640.2 (Cameroon/France)GKA (AY.4/BA.1) recombinantNoNo
Germany32,041,348(ranked #5; 506,005 new infections in 14 days.).33,226 (ranked #5)147,104 (ranked #11)
1,406 new deaths in 14 days
10137.98%
B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinantNoNo
South Korea22,802,985 (ranked #7 1,691,145 new infections in 14 days).101,064(ranked #2)26,413 (ranked #37) 8144.39%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)NoNo
Vietnam11,399,400 (ranked #13; 36,860 new infections in 14 days).3,19543,110 (ranked #25)11.48%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)NoNo
Netherlands8,381,009 (ranked #16; 18.445 new infections in 14 days).1,15622,594 (ranked #41)248.68%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinantNoNo
Denmark3,089,118 (ranked #40) 12,476 new infections in 14 days6806,893 (ranked #79)552.93%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)GKA (AY.4/BA.1) recombinantNoNo




Taiwan5,168,949(ranked #23)
322,462 new infections in 14 days
26,713 (ranked #6)9,773 (ranked #65)
4521.61%B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)NoNo
Japan17,983,797(ranked #10)
2,897,493 new infections in the last 14 days
227,139(ranked #1)38,197(ranked #27)
3,660 new deaths in the last 14 days
31014.31%
2.31% of population has been infected in the last 14 days
B2 lineageAlpha/B.1.1.7 (UK)Delta/B.1.617.2 (India) Delta/B.1.617.2 (India) Omicron/B.1.1.529 South Africa November 2021)BA.2*BA.5*NoNo

What Our Team Is Reading This Week