SARS-CoV-2 Update 2/10/23

In 2022, multiple new Omicron variants BA.1, BA.2, BA.4, and BA.5 assaulted the world’s population of humans and other animals. By the time multiple companies made and tested Omicron BA.1 vaccines, BA.1 was no longer the dominant variant; in fact, it was no longer present. On August 31, 2022, the FDA allowed rapid introduction of an Omicron BA.5 bivalent vaccine. In 2023 our problems are being caused by XBB recombinant variants and BA.5 sub-variants BQ.1 and BQ.1.1. The Omicron BA.5 bivalent vaccine has had no effect on the immune evading BQ variants or XBB recombinant variants. In December the first highly infectious recombinant variant, XBB, began spreading around the world. The XBB variant XBB.1.5, has rapidly spread across the country and the world. Another new variant, CH.1.1 (BA. caused 5.9% of infections in the world from December 25 to January 14, 2023 and, from December 26 to January 1, 19.5% of infections in the United Kingdom. 

On January 13, the World Health Organization (WHO) updated its recommendations on mask wearing to specify that, given the global spread of COVID-19, masks should be worn “irrespective of the local epidemiological situation,” meaning that masks are now recommended for everyone, not just people in areas with high levels of transmission. 

Here are our 14-day moving average determinations for SARS-CoV-2 for the United States. 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.

XBB.1.5 Variant Continues to Dominate in the United States

During the week ending in 2/11/23, the CDC estimates that based on genomic surveillance, XBB.1.5 accounted for 74.7% of infections, followed by BQ.1.1 at 16.3%, BQ.1 at 5.1%, XBB at 1.9%, CH.1.1 at 1.3%, BN.1 at 0.8%, BA.5 at 0.3%, and BF.7 at 0.3%.  


BQ.1.1 has five spike mutations that are different from BA.5. Four of these mutations allow escape from immunity from monoclonal antibodies, any prior infection (including Omicron BA.5), or any vaccine to include the bivalent Omicron BA.5 vaccine. Infections are still occurring in our clinic in patients that received the Omicron BA.5 bivalent vaccine. The XBB recombinant isolate XBB.1.5  has rapidly become the dominant infection in the USA. It took 28 days to become the cause of 40% of infections in the USA. As of 1/14/23, XBB.1.5 now causes over 80% of infections in Regions 1 and 2. 

The “Omicron family feud” is a phrase coined by Dr. Raj Rajnarayanan to describe what’s going on between the Omicron BQ variants, BQ.1, BQ,1.1 (and other BQ variants) and XBB.1.5 (and other XBB variants). In the USA in regions 1 and 2, XBB.1.5 has won the feud. A new variant of BA2.75, CH.1.1, is now 4.9% of SARS-CoV-2 isolates in the world. It has the Delta mutation, P681R, which should raise a   red flag. According to Saito et al, the P681R mutation, “facilitates cleavage of the spike protein and enhances viral fusogenicity [the ability of the virus to fuse to human cell membranes]….and pathogenicity [lethality].”  

XBB.1.5 Proportion of Sequenced Isolates in the USA


BQ. 1 and BQ.1.1 Totaled Proportion of Sequenced Isolates in the USA


Percent of isolates identified as XBB.1.5 by Region

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SARS-CoV-2 infections per day in the United States have increased for the second time in 6 weeks. There is still widespread underreporting by states, a failure to capture all positive home tests, and a decreased PCR screening program in most states. Deaths per day in the United States have increased by 147 deaths per day. Many states are not reporting deaths or infections in a timely manner. The number of infections per day is expected to increase in the next four weeks due to a lack of mask use in schools, businesses, and airports; a failure of adequate building ventilation; lack of social distancing; and low rates of bivalent booster uptake. XBB, an Omicron recombinant variant first identified in India, caused a major outbreak in Singapore. XBB is the first recombinant variant combining spike protein sequences from two other Omicron BA.2 variants, that has spread aggressively around the world. New mutations of XBB, specifically XBB.1.5 have rapidly crowded out other variants in the USA. Current vaccines, monoclonal antibodies and prior infections will not protect you from getting an XBB.1.5 infection. A more detailed description of XBB variant mutations and epidemiology can be found on page 17 of the UK Health Security Agency Technical Briefing from November 25

Troubling Variant News from the UK

The latest UK Health Security Agency Technical Briefing, published February 10, reports that variants XBB.1.5 and CH.1.1, along with their sublineages, have a growth advantage over previously dominant variants, are likely responsible for the current increase in cases in the UK, and “will continue to increase overall transmission as they become more prevalent.” In addition, they state that, based on their data, vaccine effectiveness against CH.1.1 and XBB.1.5 may be reduced compared to BQ.1. From this, we can conclude, as we have previously, that vaccination alone is not enough to protect people from being infected with these newer SARS-CoV-2 variants. 

Another new variant, XBF, which is a recombinant of BA.5 and CJ.1 (which is a descendant of BA.2.75) has also shown up in low proportions in the UKHSA’s signal monitoring. More troubling is that, per GISAID, XBF currently accounts for more than 15% of sequences in Australia. We’ll be watching carefully to see which isolate will eventually supplant XBB.1.5. At this stage, it’s unclear whether it will be a mutation of XBB.1.5, another recombinant like XBF, or something else. 

Yet another piece of bad news from UKHSA concerns molnupiravir, one of two oral antiviral medications approved in the U.S. for the treatment of COVID-19. This drug works by causing a large number of random mutations in the virus, which hinder its replication. That also means that molnupiravir leaves a particular “signature” of mutations that can be observed through viral sequencing. The Technical Briefing references a new preprint out of the London-based Francis Crick Institute which contains analysis of more than 13 million SARS-CoV-2 sequences in global databases. The researchers observed “a set of long phylogenetic branches that exhibit a high number of transition mutations.” In other words, on the SARS-CoV-2 family tree, there are some variants that are very different from their parents. They also observed that the number of these long branches (with more mutations between variant and sub-variant) increased in 2022, after the introduction of molnupiravir, and that the variants on those branches were more common in countries where molnupiravir was in use. In addition, they noted that the patterns of mutations among these variants were “highly similar to that in patients known to be treated with molnupiravir.” They conclude that there have been some cases in which “viruses with a large number of molnupiravir-induced substitutions have been transmitted to other individuals.” This analysis was compelling enough that the UKHSA’s Variant Technical Group is recommending further investigation into the impact of molnupiravir treatment on the evolution of the virus, especially in the case of chronic infections and infections in immunocompromised people. 

In our clinic, we only treat patients with Paxlovid because of our concerns about the potential of developing new resistant variants on molnupiravir therapy, particularly in our immunocompromised patients. If additional information develops about the mutation problem with molnupiravir, then the drug may need to be pulled off the market. 

UK Health Security Agency
UK Health Security Agency

For a more detailed picture of COVID variant evolution in the United States, we recommend checking out the dashboard put together by Raj Rajnarayanan, Assistant Dean of Research and Associate Professor at NYITCOM at Arkansas State University. 

To understand the true impact of these variants, it’s helpful to examine their evolution. Two virologists collaborated on Twitter to create the figure below, which Professor Johnson titled “Convergent Evolution on Steroids.”  It shows the key mutations present in many of the currently-circulating Omicron subvariants and demonstrates that mutation at site 346 is becoming more and more common. 

From Daniele Focosi, M.D., Ph.D. @dfocosi on Twitter, February 3, 2023

Past infections with a BA.1, BA.2 or BA.5 variants will not prevent infections with any of the newer variants. Monoclonal antibodies are no longer effective against newer BQ variants, XBB variants and other spike protein mutated variants. The last remaining monoclonal antibody, bebtelovimab, was removed from use by the FDA on 12/2/22. Paxlovid was only 89% effective in the original clinical trials against SARS-CoV-2. If resistance develops this winter to oral Paxlovid, we will have more Paxlovid failures and increased hospitalizations and deaths.

A Deeper Dive into U.S. COVID Data

On 1/27/23, the United States had 12,107 documented new infections. There were also 159 deaths. Thirty-nine states did not report their infections, and 38 states and the District of Columbia didn’t report their deaths. In the United States on 2/09/23 the number of hospitalized patients (29,299)  has decreased  (-13.83% compared to the previous 14 days) and was 34,015 on January 27. On 1/27/23 there were 3,608 patients who were seriously or critically ill (a 17.03% decrease); that number was 4,349 two weeks ago. The number of critically ill patients has decreased by 741 in the last 14 days, while at least 7,743 new deaths occurred. Patients are still dying each day (average 553/day). 

As of 2/10/23, we have had 1,139,979 deaths and 104,760,445 SARS-CoV-2 infections in the United States. We have had 653,533 new infections in the last 14 days. We are adding an average of 326,767 new infections every seven days. For the pandemic in the United States we are averaging one death for every 91.89 infections or over 10,882 deaths for each one million infections. As of 2//23, thirty-nine states have had greater than 500,000 total infections, and 38 states and Puerto Rico have had greater than 5,000 total deaths. Forty-six states have had greater than 2,000 deaths. Only Vermont has had less than a thousand deaths (901 deaths). Now 11 states have over 4,000 deaths per million population: Mississippi (4,444), Arizona (4,525), Alabama (4,261), West Virginia (4,410), New Mexico (4,293), Tennessee (4,234), Arkansas (4,281), Michigan (4,186),  New Jersey (4,038), Kentucky (4,015) and Louisiana (4,006). 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. Nine states have had greater than 40,000 deaths: Florida (85,710 deaths), Texas (93,364 deaths), New York (76,800 deaths), Pennsylvania (49,921 deaths), Georgia (42,161 deaths), Ohio (41,535 deaths), Illinois (41,263 deaths), Michigan (41,809), and  California (100,345 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 (27 months), there were 872,878 new deaths from SARS-CoV-2. For twenty-three of those months, vaccines have been available to all adults. During these twenty-three months, 567,780 people have died of SARS-CoV-2 infections. Clearly, a vaccine-only approach is not working anywhere, especially not in the United States. In addition to getting more people vaccinated, most of the hospitalizations and deaths could have been prevented by proper masking (N95 or better), social distancing, and treatment with oral antiviral agents like Paxlovid. We recommend all of these precautions and treatments to every patient in our clinic, and we have only lost one patient to COVID in 3 years. 

As of 2/10/23, California was ranked 31st in the USA in infection percentage at 30.39%. In California, 26.42% of the people were infected in the last 22 months. As of 2/10/23, 33 states have had greater than 30% of their population infected. Fifty states, the District of Columbia and Puerto Rico have greater than 20% of their population infected.                   

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FDA-Approved Oral Drug Treatments for SARS-CoV-2

Pfizer has developed PAXLOVID™, an oral reversible inhibitor of C3-like protease of SARS-CoV-2. The drug inhibits this key enzyme that is crucial for virus production. The compound, also called Compound 6 (PF-07321332), is part of the drug combination PAXLOVID™ (PF-07321332; ritonavir), which 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 showed 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 was approved on 12/23/21. PAXLOVID™ one year later is widely available at major pharmaceutical chains and smaller independent drug stores throughout the USA. We have  been able to obtain PAXLOVID™ for any patient desiring treatment. We have only had one  drug failure and death from SARS-CoV-2 during 2022. That death occurred in an octogenarian male in the fourth quarter of 2022.

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 2/10/23New Infections on 2/10/23Total DeathsNew Deaths on 2/10/23% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask MandateCurrently in Lockdown
World677,294,111(2,779,648 new infections in the last 14 days with an average of 198,546 infections per day).135,5096,780755(52,474 new deaths in the last 14 days with an average of 3,748 deaths per day.)8888.68%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)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)BF.7BJ.1XBB (new recombinant India)BQ.1BQ.1.1BS.1BN.1XBB.1XBB.1.5CH.1.1  NoNo
USA104,760,445(ranked #1) 653,533 new infections in the last 14 days with an average of 46,681 infections/day
12,107(ranked #7)
39 states failed to report infections on 2/10/23.
1,139,979(ranked #1) 7,743 new deaths reported in the last 14 days or an average of 553 deaths/ day. 159
38 states failed to report deaths on 2/10/23.
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)BA.4.6 (USA 7/22)BF.7BJ.1XBB (new recombinant India)BQ.1BQ.1.1BN.1XBB.1XBB.1.5CH.1.1NoNo
Brazil36,930,339(ranked #5) 124,372 new infections in the last 14 days. 12,716 (ranked#5)697,662(ranked #2; 1,777 new deaths in the last 14 days)4217.14%
India 44,682,530(ranked #2).
530,739(ranked #3) 3.17%
Unchanged in 8 weeks
United Kingdom
24,293,752(ranked #9) 34,506 new infections in the last 2 weeks.204,898 (ranked #7) 1,669 new deaths in the last 2 weeks35.46%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, USA12,011,521(ranked #12 in the world; 50,447 new infections in the last 14 days).1,459100,345 (ranked #20 in world; 452  new deaths in the last 14 days2230.39%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)BQ.1BQ.1.1BN.1XBBXBB.1XBB.1.5CH.1.1NoNo
Mexico7,400,848(ranked #19) 47,218 new infections in 14 days).– 332,850(ranked #5) 834 new deaths in the last 14 days)5.62%NoNo
South Africa4,057,211(ranked #38; 1,927 new infections in the last 14 days).102,595 (ranked #18) no new deaths in the last 14 days).6.67%

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
Canada4,560,962(ranked #34) 21,733 new infections in 14 days).50,629(ranked #24) 494  new deaths in the last 14 days.11.88% NoNo
Russia22,047,525 (ranked #10), 77,539 new infections in 14 days).12,392 (ranked #6)395,484(ranked #4)582 new deaths in 14 days3715.12%NoNo
Peru4,483,236(ranked #35, 2,408 new infections in 14 days). 200219,229(ranked #6) 500 new deaths in the last 14 days.113.31%NoNo
Spain13,748,918(ranked #12; 37,667 new infections in 14 days).1,119 (ranked #13)118,876 (ranked #16) 542 new deaths in 14 days.3629.42%
France39,,559,127 (ranked #3)3,336 (ranked #9)164,537 (ranked #10) 457  new deaths in 14 days.4460.31%  a 0.07% increase in 14 days.NoNo
Germany37,739,472(ranked #4; 167,840 new infections in 14 days.)13,420 (ranked #4)166,763 (ranked #9)1,322 new deaths in 14 days. 10345.19%0.20% increase in 14 daysNoNo
South Korea30,325,483 (ranked #7; 218,129 new infections in 14 days).13,504(ranked #3)33,697 (ranked #34) 365 new deaths in 14 days.1759.07%0.42% increase in 14 daysNoNo
Netherlands8,586,372 (ranked #17; 4,951 new infections in 14 days).39622,992 (ranked #41)49.88%NoNo
Taiwan9,773,627(ranked #16); 345,147  new infections in 14 days16,964 (ranked #2)16,964 (ranked #56; 760 new deaths in the last 14 days)
1.45% of population has been infected in the last 14 days
Japan32,908,240(ranked #6)543,390 new infections in the last 14 days28,615(ranked #1)70,377(ranked #20)
3,327 new deaths in the last 14 days for an average of 238  deaths per day.
0.43-% of the population infected in the last 14 days.
Australia11,330,342(ranked #14) 34,876 new infections in 14 days.2,491 (ranked #10)19,070(ranked #49) 455 new deaths in 14 days.3543.46% 
0.14-% of the population infected in last 14 days.
Hong Kong2,880,518(ranked# 41) 62,811 new infections in the last 14 days.25013,412 (ranked#60)132 new deaths in the last 14 days.537.88%
0.15% of the population infected in the last 14 days.

What Our Team Is Reading This Week