R. J. Sigmund

September 29, 2024

The major Covid demographic metrics we track continued to trend lower this past week, but we have a new recombinant mutant out there that is multiplying quite rapidly and is forecast to become the dominant strain, probably just in time for the annual winter holidays infection wave.

Among the CDC’s “early indicators” “test positivity”, or the percentage of tests for Covid that were positive, fell to 11.6% during the week ending September 21st, down from 13.4% positive during the week ending September 14th, which had not been reported a week ago, test positivity was last reported at 14.9% during the week ending September 7th. Meanwhile, Covid cases accounted for 1.4% of hospital emergency room patients during the week ending September 21st, down from an unrevised 1.7% of emergency patients during the week ending   September 14th down from 2.1% of emergency patients during the week ending September 7th.

In hospital data that is two weeks older, the CDC reports that the US Covid hospitalization rate fell to 4.0 per 100,000 population during the week ending September 7th, down from an unrevised 4.1 per 100,000 during the week ending August 31st, and down from 4.3 per 100,000 during the week ending August 24th. At the same time, the CDC reported that Covid accounted for 2.1% of all US deaths during the week ending September 21st, down from 2.3%deaths due to Covid indicated for the week ending September  14th, which was the same proportion of deaths due to Covid we saw during the week ending September 7th. Meanwhile, the CDC’s provisional Covid deaths graph, which lags current data by 3 weeks, shows there were 1,239 US deaths from Covid during the week ending August 31st, up from the upwardly revised 1,176 Covid deaths during the week ending August 24th, and up from an upwardly revised 1,035 US Covid deaths during the week ending August 17th . . . the August 31 death toll was the highest since March 2nd, but only half the number of Covid deaths seen during the week ending January 13th, when last winter’s Covid wave peaked out….

The CDC’s national reading for viral activity in wastewater remains HIGH, but it’s lower in all four major CDC regions for the 2nd consecutive week . . . the metric known as the national viral activity level fell to 5.29 for the week ending September 21st, down from a downwardly revised 6.78 for the week ending September 14th, and down from 7.49 during the week ending September 7th. Whatever that number means, it had been as high as 8.21 during the week ending August 24th, and as low as 1.34 during the week ending May 4th. 

Regionally, the viral activity level in the Midwest is now the highest*, even as it fell from a downwardly revised 7.51 for the week ending September 14th to 5.81 for the week ending September 21st. Meanwhile, the viral activity level in the West fell from a downwardly revised 10.75 during the week ending September 7th, and from a downwardly revised 8.61 for the week ending September 14th, to 5.65 for the week ending September 21st, while the viral activity level metric in the South fell from a downwardly revised 6.69 for the week ending September 14th to 5.28 for the week ending September 21st…lastly, the viral activity level for the Northeast fell from an upwardly revised 4.35 for the week ending September 14th to 3.39 for the week ending September 21st…

This was the week that the CDC updated its variant proportions page, and it includes for the first time a new variant which has been raising concern in health circles globally, because it appears to be far more infectious and immune evasive than anything else out there…the XEC variant was first detected in Germany in August and quickly spread throughout Europe, but hadn’t been mentioned as being present in the US until a week ago, when it was reported to have spread to half of the US states . . . since Saturday’s CDC update shows it’s already accounting for 6.0% of US Covid infections, it’s reasonable to figure it has penetrated everywhere.

The XEC variant is a recombinant of two Covid virus variants that had 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 are among the now dominant FLiRT variants (so-called because they have a substitution of F for L at position 456 and R for T at position 346 on the spike protein), XEC also includes those characteristic substitutions, which eliminate binding sites for antibodies on that protein that would otherwise neutralize the Covid virus, which is why they’ve become dominant, while the older strains have waned…. recombination of similar viruses happen more often than one would think when they infect the same individual, but most of those are no more viable than the contributing strains, and more often less so…XEC appears to have gotten lucky, picking up those parts of KS.1.1 and KP.3.3 that increased its infectiousness and its ability to evade antibodies…

At any rate, XEC still just accounts for 6% of our infections currently, while Omicron KP.3.1.1, which became the most common variant circulating two months ago, has continued to increase. It accounted for 58.7% of the virus samples sequenced during the September 15th to September 28th period, up from an upwardly revised 50.2% of US Covid infections during the September 1st to September 14th period, up from 37.7% of the national Covid virus total during the August 18th to August 31st period, and up from 29.0% 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, (now except for XEC)… since KP.3.1.1 is closely related to the KP.2 variant that the new vaccine is designed to target, the vaccine was 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…

Meanwhile, the KP.2.3 variant, a direct offspring of the KP.2 variant that the new vaccine was designed for, continues to be the 2nd most common Covid mutant circulating, and accounted for 9.4% of US Covid infections during the two week period ending September 28th, down from a barely revised 12.0% share of the total during the September 1st to September 14th period, and down from 13.3% 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, continues as the third most common Covid variant circulating, accounting for 7.9% of US Covid infections during the September 15th to  September 28th period, down from a downwardly revised 10.5% share of the total during the September 1st to September 14th period, and down from 11.7% of the total 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 holding on as the 4th most common variant circulating…it accounted for 7.1% of the virus samples sequenced during the September 15th to September 28th period, down from 10.1% of the national total during the September 1st to September 14th period, and down from 12.2% of the total during the period before that…KP.3 is one of the original FLiRT mutations, 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…

The previously discussed XEC variant has moved into the 5th most common slot in its first appearance on the CDC’s list…it accounted for 6.0% of the virus samples sequenced during the September 15th to September 28th period, up from 2.5% of the total during the September 1st to September 14th period, and up from 0.9% of the total during the period before that…its prevalence varies widely, from accounting for 3.1% of infections in CDC region 5 (the Great Lakes states) to 12.7% of the infections in region 9 (CA, NV, & AZ), where it has knocked KP3.1.1 down to 49.5%

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 6th most common variant circulating, but it only accounted for 2.5% of US Covid infections during the September 1st to September 14th period, down from an upwardly revised 3.6% share of the total during the the September 1st to September 24th period, and down from an upwardly revised 7.0% 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.