This Weeks Covid spiel includes current details on variant proportions
– by R.J. Sigmund
Most of the demographic indicators of this summer’s Covid wave continued to recede rapidly in this week’s reports, and wastewater levels of the virus, the most definitive indicator of infections, have fallen to “low.” Among the CDC’s “early indicators” “test positivity”, or the percentage of tests for Covid that were positive, fell to 7.7% during the week ending October 5th, down from 9.5% positive during the week ending September 28th, which had not been reported a week ago,
Test positivity was last reported at 11.6% during the week ending September 21st, down from 13.4% during the week ending September 14th, so we’ve had a significant decrease in positive tests. Mean while, Covid cases accounted for 0.8% of hospital emergency room patients during the week ending October 5th, down from an unrevised 1.1% of emergency patients during the week ending September 28th, and down from 1.4% of emergency patients during the week ending September 21st. In hospital data that is two weeks older, the CDC reports the US Covid hospitalization rate fell to 3.6 per 100,000 population during the week ending September 21st, down from an upwardly revised 4.3 per 100,000 during the week ending September 14th, which is now higher than the unrevised 4.0 per 100,000 shown for the week ending September 7th….
At the same time, the CDC reported that Covid accounted for 1.9% of all US deaths during the week ending October 5th, unchanged from the 1.9% Covid death rate reported for the week ending September 28th. which had been down from 2.0% for the week ending September 21st, and down from the 2.3% deaths due to Covid for the week ending September 14th. Meanwhile, the CDC’s provisional Covid deaths graph, which lags current data by 3 weeks, shows there were 1,157 US deaths from Covid during the week ending September 14th, little changed from the upwardly revised 1,159 Covid deaths during the week ending September 7th, but down from the upwardly revised 1,306 Covid deaths during the week ending August 31st, which was the highest Covid death toll of the now receding wave.
The CDC’s national reading for viral activity in wastewater has now fallen to LOW, and their metric is also lower in all four major CDC regions for the consecutive week. The national “viral activity level” metric fell
to 2.77 for the week ending October 5th, down from a slightly revised 3.88 for the week ending September 28th, down from a barely revised 5.22 for the week ending September 21st, and down from 6.60 for the week ending September 14th, which was revised sharply lower.
The viral activity level in the West fell from a downwardly revised 4.51 for the week ending September 28th to 3.41 during the week ending October 5th; the viral activity level in the Midwest fell from an upwardly revised 4.25 for the week ending September 28th to 2.89 for the week ending October 5th; the viral activity level metric in the South fell from an upwardly revised 3.95 for the week ending September 28th to 2.91 for the week ending October 5th, and the viral activity level for the Northeast fell from an upwardly revised 2.54 for the week ending September 28th to 1.07 for the week ending October 5th. That 1.07 viral activity level for the Northeast, whatever it means, is the lowest number reported for any region since May 24th, 2023.
Biobot has resumed weekly reports on concentrations of the major infectious viruses (Covid, influenza, and RSV) in US wastewater, but they’re quite sketchy and not accompanied by any data that i could find. However, by blowing up the tiny static graph that accompanies this week’s report, I can estimate that the national average wastewater concentration of the Covid virus has fallen to about 320 copies per mL during the week ending October 7th from about 350 copies per mL during the week ending September 30th, and that’s it’s down from the recent peak of around 800 copies per mL five weeks ago. I don’t know what’s up with Biobot, or if they will ever resume publishing useful reports.
This was the week that the CDC reports on the proportions of Covid variants that are currently circulating, and it shows that the Omicron KP.3.1.1 variant has continued to increase its dominance, while the new recombinant XEC variant continues to expand its presence, while still only accounting for a relatively small proportion of the total. KP.3.1.1, which became the most common variant circulating ten weeks ago, accounted for 57.2% of the virus samples sequenced during the September 29th through October 12th period, up from a downwardly revised 52.6% of US Covid infections during the September 15th to September 28th, up from 41.2% of the national Covid virus total during the September 1st to September 14th period, and up from 33.9% 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 currently circulating, except for the new emerged XEC. Like most every other variant currently circulating, KP.3.1.1 has the FLiRT mutations, characterized by a substitution of F for L at position 456 and R for T at position 346 on the 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 our current 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 KP.3.1.1 if you’re vaccinated, just that it will be less severe.
The new XEC variant is now the 2nd most common Covid mutant circulating in the US, even though it only first appeared in Germany in August, accounting for 10.7% of US Covid infections during the September 29th to October 12th period, up from a downwardly revised 5.3% of the national Covid virus total during the September 15th to September 28th period, and up from 2.3% of the national total during the September 1st to September 14th 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, picked up those parts of the KS.1.1 and KP.3.3 variants that increased its infectiousness and its ability to evade antibodies and vaccines.
since i went thru the trouble to research these other Covid variants, and since the post title here refers to them, i’ll just add some details on the rest of them as a comment here:
the KP.2.3 variant, a direct offspring of the KP.2 variant that the new vaccine was designed for, has slipped to the 3rd most common Covid mutant circulating, accounting for 7.8% of US Covid infections during the two week period ending October 12th, down from an upwardly revised 10.4% share of the total during the September 15th to September 28th period, and down from 12.1% 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 pseudovirus infectivity and more robust immune resistance than KP.2″…
the LB.1 variant, a direct descendant of the originally dominant JN.1, is now the fourth most common Covid variant circulating, accounting for 5.8% of US Covid infections during the September 29th through October 12th period, down from a downwardly revised 8.3% share of the total during the the September 15th to September 28th period period, and down from 9.9% of Covid infections during the two week period before that…the LB.1 variant is “similar to the FLiRT variants but has an additional mutation (S:S31del)”, (note that’s the same deletion at the 31st position in S that KP.2.3 has)…since the neutralization titers of the new vaccine are slightly lower against LB.1 compared to KP.2, “the vaccine might be somewhat less effective against LB.1 than KP.2, but it should still offer significant protection..”
the KP.3 variant, the parent of the KP.3.1.1 strain and an offspring of JN.1.11.1, with a 1.2 fold higher (Rₑ) number than its parent, is is now the 5th most common variant circulating…it accounted for 5.7% of the virus samples sequenced during the September 29th through October 12th period, down from 8.1% of the national total during the September 15th to September 28th period, and down from 12.2% of the total during the period before that…KP.3 is one of the original FLiRT mutants, and was the most prevalent Covid variant circulating when the decision was made to have the new vaccines target its sister KP.2 variant, which suggests that those making that decision felt that a vaccine targeting KP.2 would be more effective against both of them than one targeting KP.3 would be against KP.2…
a new Covid strain, MC.1, is now the 6th most common variant circulating, at 3.2% of the national Covid total during the week ending October 12th, up from 2.5% of the national Covid virus total during the September 15th to September 28th period, and up from 1.7% of the national total during the September 1st to September 14th period…perhaps i’m mischaracterizing it as “new”, since it is an offspring of KP.3.1.1 and hence shares its enhanced transmissibility and immune evasion capabilities…although there’s not much info available on it, MC.1 “has notable changes 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”….note that inclusion of this as a separate variant appears to be the reason that the proportions of KP.3.1.1 were revised lower this week..
Finally, the KP.2 variant, which is an offspring of JN.1.11.1 and which the new vaccines were designed for, is now the 7th most common variant circulating, accounting for 2.0% of US Covid infections during the September 29th through October 12th period, down from an upwardly revised 3.0% share of the total during the the September 15th to September 28th period, and down from an upwardly revised 5.0% of the total during the two week period before that…KP.2 has the FLiRT substitutions and an additional substitution in the non-S protein which enhances its viral fitness and effective reproduction number and, with KP.3. was expected to become the predominant variants worldwide before their offspring took over…
here’s this week’s update on the CDC’s Covid metrics as of the October 18th report…there was no new data on the variant proportions..
the demographic indicators for Covid were again down sharply, and with a mild Autumn forecast for most of the US, appear likely to recede further until the cold weather arrives and forces people indoors…among the CDC’s “early indicators” “test positivity”, or the percentage of tests for Covid that were positive, fell to 6.3% during the week ending October 12th, down from a downwardly revised 7.6% positive during the week ending October 5th, and down from a downwardly revised 9.4% during the week ending September 28th…positives had been coming up in over 18% of tests during the middle two weeks of August, so that’s down more than 65% in less than two months…meanwhile, Covid cases accounted for 0.7% of hospital emergency room patients during the week ending October 12th, down from an unrevised 0.8% of emergency patients during the week ending October 5th, and down from 1.1% of emergency patients during the week ending September 28th…
in hospital data that is two weeks older, the CDC reports that the US Covid hospitalization rate fell to 3.2 per 100,000 population during the week ending September 28th, down from an upwardly revised 3.7 per 100,000 during the week ending September 21st, and down from an unrevised 4.3 per 100,000 during the week ending September 14th…the Covid hospitalization rate for the current wave peaked at 4.9 per 100,000 during the week ending August 10th, quite a bit lower than the peak at 7.8 per 100,000 during the week after Christmas in this past winter’s wave…
the CDC also reported that Covid accounted for 1.5% of all US deaths during the week ending October 12th, down from the downwardly revised 1.8% Covid death rate reported for the week ending October 5th. and down from the 1.9% of deaths that were due to Covid for the week ending September 28th…meanwhile, the CDC’s provisional Covid deaths graph, which lags current data by 3 weeks, shows there were 997 US deaths from Covid during the week ending September 21st, down from the upwardly revised 1,186 Covid deaths during the week ending September 14th, and down from 1.173 Covid deaths during the week ending September 7th….in our current wave, Covid deaths peaked at 1,318 during the week ending August 31st; the week ending September 21st was the first drop below 1000 deaths in seven weeks…
the CDC’s national reading for viral activity in wastewater continues to be LOW, but while their “viral activity level” metric fell nationally, it rose sharply in the Northeast, so it appears that something is going on there…the national “viral activity level” fell to 2.27 for the week ending October 12th, down from a barely revised 2.76 for the week ending October 5th, also down from a barely revised 3.89 for the week ending September 28th, and down from an upwardly revised 5.27 for the week ending September 21st… however, the viral activity level in the Northeast more than doubled, from an upwardly revised 1.23 for the week ending October 5th to 2.59 during the week ending October 12th; there’s no apparent reason why that would have happened; it hasn’t been so cold as to drive people indoors, and the mix of Covid variants in the region is similar to those elsewhere, while the prevalence of the rapidly expanding new recombinant XEC variant a bit below the national average…meanwhile, the wastewater metric continues to fall elsewhere….the viral activity level in the West fell from an upwardly revised 3.67 for the week ending October 5th to 2.46 during the week ending October 12th; the viral activity level in the Midwest fell from a downwardly revised 2.66 for the week ending October 5th to 2.30 for the week ending October 12th; and the viral activity level metric in the South fell from an barely revised 2.92 for the week ending October 5th to 2.01 for the week ending October 12th..