“the summer wave of FLiRT variants is here”

by r.j. sigmund 

FLiRT variants

no one seems to be talking about it, but Covid is worse than ever, even if it’s not as deadly . . . among the CDC’s “early indicators“, “test positivity”, or the percentage of tests for Covid that were positive, rose to 16.3% during the week ending July 27th, up from 14.3% the prior week, and up from 3.4% nine weeks ago . . . test positivity is now the highest it’s been in 2 1/2 years . . . at the same time, Covid cases accounted for 2.2% of hospital emergency room patients, up from 1.9% of emergency patients during the week ending July 13th, and up from 0.4% nine weeks earlier . . . the CDC’s map on that shows a wide range; hospitals in Florida are seeing 4.1% of emergency rooms patients for Covid. while just 1.4% of hospital emergency room visits in Ohio are for the virus . . . furthermore, in data that is two weeks older, the CDC reports that the Covid hospitalization rate rose to 3.1 per 100,000 population during the week ending July 13th, up from an upwardly revised 3.0 per 100,000 the prior week, and up from 1.1 per 100,000 during the week ending May 11th…

meanwhile, Covid accounted for 1.5% of all US deaths during the week ending July 27th, after the 1.1% figure they reported for deaths last week was revised up to 1.2% . . . as recently as three weeks ao, they had reported Covid deaths at 0.6% of all deaths, but that too was revised higher, to 0.8% . . . so by that metric, Covid deaths have nearly doubled . . . however, the CDC’s confirmed Covid deaths graph, which lags current data by 3 weeks, shows there were 421 US deaths from Covid during the week ending July 6th, up from an upwardly revised 383 deaths during the week ending June 29th, and up from an upwardly revised 404 US Covid deaths during the week ending June 22nd . . .

the CDC’s Covid metric for viral activity in wastewater was higher this week, and the downtick that they had reported last week was revised away, so the national viral activity graph now shows 13 consecutive increases, with the reading for the week ending July 27 at 7.28, up from 6.52 for the week ending July 20th, and up from 6.18 for the week ending July 13th . . . the viral activity level for all US regions continued to rise, with the level for the West rising from 10.40 for the week ending July 20th to 11.24 for the week ending July 27th, and the level for the South rising from 8.88 for the week ending July 20th to 10.67 for the week ending July 27th . . . in addition, Biobot also reports an increase in the concentration of the Covid virus in US sewer water, but that the rate of increase has slowed…we’ll again copy/paste the Covid relevant paragraphs from this week’s Biobot report below…

• Biobot’s national wastewater network showed very low national concentrations of influenza A & B and RSV during week 30, while the rate of SARS-CoV-2 concentration increase began to slow. The Northeast is the only region that experienced an increase in SARS-CoV-2 concentrations in week 30, with all other regions holding steady. These trends might signal that we are nearing the peak of the summer surge. Nationally, major clinical metrics remained low for influenza and RSV in week 29, while metrics for COVID-19 remained elevated.  
• Wastewater data show that COVID-19 activity and community viral load slightly increased during week 30, but that the rate of increase has slowed. It is too early to tell if we are at or near the peak for this summer surge. The national average SARS-CoV-2 wastewater concentration is now 620 copies per mL.
• SARS-CoV-2 wastewater concentrations held steady in the South during week 30, currently at 564 copies per mL. Georgia and Tennessee are the two Southern states in COVID-NET. In good news, Georgia continued to experience a decrease in the COVID-19 hospitalization rate in week 29, while Tennessee held steady. Overall, the hospitalizations rates in both states are low.
• COVID-19: SARS-CoV-2 wastewater concentrations held steady in the Midwest during week 30, currently at 694 copies per mL. Michigan, Minnesota, and Ohio are Midwestern states in COVID-NET. In week 29, the hospitalization rates in Minnesota decreased while rates in Michigan and Ohio held steady. Hospitalization rates remained low overall in these states.
• SARS-CoV-2 wastewater concentrations continued to increase in the Northeast during week 30, currently at 808 copies per mL. In week 29, the Northeastern states in COVID-NET, Connecticut, Maryland, and New York, all experienced decreases in COVID-19 hospitalization rates, which remained low overall.
•   During week 30, SARS-CoV-2 wastewater concentrations held steady in the West, currently at 516 copies per mL. California, Colorado, New Mexico, Oregon, and Utah are Western states in COVID-NET. California finally experienced a big decline in hospitalization rates, which are now down from 5 per 100,000 persons in week 28 to 2.9 per 100,000 persons in week 29. Hospitalizations rates also decreased in Colorado and Oregon, and held steady in New Mexico and Utah in week 29.

the CDC’s variant proportions page was updated this week, and shows that Omicron KP.3.1.1, which was first listed on this page two weeks ago, has already become the most common variant circulating, accounting for 27.8% of the virus samples sequenced during the July 21st to August 3rd period, up from 14.4% of the national total during the July 7th to July 20th period, and up from 7.2% of the total during the period before that (before the July 20th variants report, the KP.3.1.1 mutation had been aggregated with the totals for its parent KP.3; i believe that KP.3.1.1 differs from KP.3 because it lost one of its spike protein mutations, which apparently made it more infectious) . . . the KP.3 variant itself, which is a descendant of JN.1.11.1 and had been the top dog for 8 weeks, is now the 2nd most common Covid mutant circulating, accounting for 20.1% of US Covid infections during the two week period ending August 3rd, down from a downwardly revised 23.8% share of the total during the July 7th to July 20th period, and down from 23.3% of the total during the two week period before that . . . the LB.1 variant, a direct descendant of the original JN.1, is now the 3rd most common Covid variant out there, accounting for 16.0% of US Covid infections during the July 21st to August 3rd period, down from an upwardly revised 17.7% share of the total during the July 7th to July 20th period, and also down from 17.7% of the total during the two week period before that . . . meanwhile, the KP.2.3 variant, a daughter of the KP.2 variant, which had been the 3rd most common variant two weeks ago, is now the fourth most common mutation circulating, at 14.8% of the virus samples sequenced during the July 21st to August 3rd period, down from 15.0% of the national total during the July 7th to July 20th period, but up from 14.0% of the total during the period before that . . . the KP.2 variant, which is also an offspring of JN.1.11.1, and which had been aggregated with KP.2.3 before two weeks ago, remains the fifth most common Covid variant circulating, at 5.7% of the total during the period ending  August 3rd, down from 8.0% during the period ending July 20th, and from 9.3% during the two weeks before that . . . (NB: it occurs to me that it’s important to note that when i report the proportion of a variant is down, that doesn’t mean it’s actually receding; because the total number of infections is growing rapidly, all these variants are likely still growing, but because KP.3.1.1 is growing so much faster, the share of 100% for the others is smaller)….

i also want to note the LP.1 variant, which is an offspring of KP.1.1.3, because it has also increased, from 3.7% of our national sample two weeks ago to 4.5% of the total currently . . . LP.1 has an additional mutation (S:S31del) in addition to the substitutions present in KP.2 and KP.3 that designate them as FLiRT variants (distinguished by a substitution of F for L at position 456 and R for T at position 346 on the virus spike protein), and both LP.1 and KP.2.3 exhibited higher infectivity and more robust immune resistance than KP.2 . . . that’s relevant because the new vaccine that’s under development is being designed to target KP.2 . . . so i asked Microsoft’s AI gadget about that, and about the new dominant KP.3.1.1 strain . . . a copy of my questions and the responses that i received is pasted below..