– 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.