Covid coverage includes the most common variants

This week’s Covid coverage includes the most common variants … currently circulating

– by r. j. Sigmund

Briefly, since the CDC’s Covid demographic metrics continue to recede, albeit slowly. Among the “early indicators” “test positivity”, or the percentage of tests for Covid that were positive, fell to 4.8% during the week ending November 2nd, down from 5.0% positive during the week ending October 26th, while Covid cases accounted for 0.5% of hospital emergency room patients during the week ending November 2nd, down from 0.6% of emergency patients during the week ending October 26th. In hospital data that is two weeks older, the CDC reports that the US Covid hospitalization rate fell to 2.0 per 100,000 population during the week ending October 19th, down from an unrevised 2.4 per 100,000 during the week ending October 12th.

The CDC also reported that Covid accounted for 1.2% of all US deaths during the week ending November 2nd, up from an unrevised 1.1% Covid death rate during the week ending October 26th. but down from 1.4% of deaths that were due to Covid for the week ending October 19th. Meanwhile, the CDC’s provisional Covid deaths graph, which lags current data by 3 weeks, shows there were 759 US deaths from Covid during the week ending October 12th, down from an upwardly revised 935 Covid deaths during the week ending October 5th, and down from an upwardly revised 997 Covid deaths during the week ending September 28th. That graph shows no sign of an uptick in the incomplete provisional figures for subsequent weeks.

CDC’s readings for viral activity in wastewater were again higher in the Midwest this week, and lower everywhere else. The national “viral activity level” fell to 1.95 for the week ending November 2nd, down from an upwardly revised 2.04 for the week ending October 26th, and down from an upwardly revised 2.07 for the week ending October 19th. The viral activity level in the Midwest rose from a barely revised 2.25 for the week ending October 26th to 2.50 for the week ending November 2nd, while the viral activity level in the West fell from an upwardly revised 2.16 for the week ending October 26th to 2.14 during the week ending November 2nd. At the same time, the viral activity level metric in the South fell from an upwardly revised 1.93 for the week ending October 26th to 1.82 for the week ending November 2nd, and the viral activity level in the Northeast fell from an unrevised 1.18 for the week ending October 26th to 1.02 for the week ending November 2nd.

This was the week that the CDC reports on the proportions of Covid variants that are currently circulating, and it continues to indicate that the Omicron KP.3.1.1 variant is still dominant in the US, but that the recombinant XEC variant continued to rapidly make inroads against it and the other variants that are still circulating.

The KP.3.1.1 variant, which became the most common Covid variant circulating at the end of July, accounted for 52% of the virus samples sequenced during the October 27th through November 9th period, down from 57% of the national total during the October 13th through October 26th period, and down from a slightly revised 56% of US Covid infections during the September 29th through October 12th period, but up from 50% of the total during the two week period before that. The KP.3.1.1 variant is an offspring of KP.3 (see below) that has a mutation in the spike protein that enhances its transmissibility and immune evasion capabilities, which gives it an effective reproduction number (Rₑ) that’s significantly higher than its parent or that of any of the other variants that were circulating this summer, except for the recently emerged XEC variant. Like most every other variant currently circulating, KP.3.1.1 has the FLiRT mutations, characterized by replacements of phenylalanine (F) with leucine (L) at position 456 and arginine (R) with threonine (T) at position 346 on the virus’s spike protein, which eliminate binding sites for antibodies on that protein that would otherwise neutralize the Covid virus, which is why they became dominant and caused this summer’s wave of Covid infections. Since KP.3.1.1 is closely related to the KP.2 variant that the new vaccine was designed to target, the vaccine is expected to provide reasonable protection against it. It’s been reported that “early studies indicate that the updated vaccines are effective in reducing severe illness, hospitalization, and death caused by KP.3.1.1.” Notice that they don’t say you won’t contract the KP.3.1.1 virus if you’re vaccinated, just that the resulting illness will be less severe.

The recently emerged recombinant XEC variant continues to be the 2nd most common Covid mutant circulating in the US, accounting for 28% of US Covid infections during the October 27th through November 9th period, up from an unrevised 17% of the national Covid virus total during the October 13th through October 26th period, and up from 9% of the national total during the September 29th through October 12th period. The XEC variant is a recombinant of two Covid virus variants that had previously been circulating concurrently: the KS.1.1 variant and the KP.3.3 variant, both of which are descendants of JN.1, the strain that was dominant last winter. KS.1.1 evolved from JN.1.13 through JN.1.13.1.1, to KS.1, while the KP.3.3 variant evolved from KP.3, which is an offspring of JN.1.11.1. Since both of those strains had the FLiRT mutations, XEC also does, but in the recombination underlying its emergence, it picked up the FLuQE mutation from KP.3.3, wherein the amino acid glutamine (Q) is mutated to glutamic acid (E) on the spike protein, making it more efficient in binding to human cells, and other mutations that increased its infectiousness and its ability to evade antibodies and vaccines. XEC’s advantage might also originate with the relatively rare T22N mutation (inherited from KS.1.1) combined with Q493E (from KP.3.3) in the spike protein; however, little is known about the effects of the T22N mutation on how well the virus can replicate or spread between people.

Japanese researchers report that  the reproduction number of XEC is greater than that of KP.3.1.1, which means it will eventually become the dominant strain globally, and that its increase in infectivity is due to one of the two spike protein mutations (S:F59S) characteristic of XEC.

Meanwhile, the MC.1 strain, which the CDC first listed as a separate virus four weeks ago, is now the third most common variant circulating, at 6% of the national Covid total during the October 27th through November 9th period, up from 5% of the national Covid virus total during the October 13th through October 26th period, and up from 3% of the national total during the September 29th through October 12th period. MC.1 is an offspring of KP.3.1.1 and hence shares its enhanced transmissibility and immune evasion capabilities, but it also “has unique mutations in its spike protein”, which “might affect how efficiently the virus can enter cells and evade the immune system” and it “may be better at evading immune responses, even in individuals who have been previously infected or vaccinated.” while i’ve been unable to determine what those “unique mutations” are, it’s obvious that early analysis is proving out, since the proportion of MC.1 continues to increase, while the proportion of its parent has slipped a bit

The KP.2.3 variant, a direct offspring of the KP.2 variant that the new vaccine was designed for, has slipped to the fourth most common Covid mutant circulating, accounting for 3% of US Covid infections during the two week period ending November 9th, down from an unrevised 5% share of the total during the October 13th through October 26th period, and down from a downwardly revised 4% of the total during the two week period before that. The KP.2.3 variant “acquired a deletion at the 31st position in S (Ser31del)” in addition to the FLiRT substitutions, which gave it “higher pseudo virus infectivity and more robust immune resistance than KP.2.” The proportion of KP.2.3 had been running in the upper teens this past summer, so it appears to be on its way out now.