@CorneliusRoemer Evaluating the rate of increase of spectra worldwide with these mutations shows very clear, steady log growth, currently estimated at +105% week/week over BA.5
This phase of the pandemic is different than we've seen in the past, with the same advantageous mutations popping up all over instead of saltation (leaping) evolution. @shay_fleishon has a great, detailed thread
Instead of keeping track of a half dozen or more different variants with different names seems cumbersome for communications and evaluation. Logical grouping of similar evolutions makes sense at this point. Since it is a group, a different naming system seemed appropriate
It's hard to say at this point. I'm confident it won't be near the size of the January Omicron wave, but it could reach or surpass BA.5 wave peak. Difficult to estimate the amount of herd resistance to Pentagon in the population.
So which lineages are included in Pentagon?
BQ.1.1
BN.1
XBB
BA.2.75.2*
And a number of others with small sequence counts.
Variant soup
This particular model does not consider effects of background forces (shift to fall weather, behavioral changes, vaccine uptake etc).
Influx of cold weather pushing more people indoors could shift the upswing a bit earlier, mainly in northern states
Regardless, the arrival of #Pentagon variants will be the main driver of case increases from their significant transmission advantages
All the highlighted variants below are Pentagon, with 5 or more key escape mutations. The immune evasion even from BA.5 infection is impressive on all of them. Small numbers=more Immune evasion
An additional escape mutation is now being included in all of the Pentagon Variants. #Pentagon or #Hexagon, either name, they are the same set of variants
Largest spike AA evolutionary jumps from 2020-2024, plotted:
BA.1 Omiron's top spot was followed closely by JN.1 Pirola, and both stand well above the rest over the past 4 years.
Viewed from a different lens of total AA spike divergence from the current lineages, JN.1 takes the top spot. This is branch to branch distance. Also note BA.2 divergence from BA.1.
Divergence is not necessarily a direct predictor of impact to caseloads. A lot depends on the diversity of population antibody protection when the evolution occurs. BA.1 easily holds that title because of the lack of antibody diversity at arrival.
The cost of preventing a pandemic is far lower than the cost of dealing with a pandemic. The current response to H5N1 in bovine needs to be dramatically increased. 1) Federal funds for compensation of lost profits on H5N1 farms (increases cooperation) 2) Abundant sequencing of..
H5N1 positive cows and mammals on or near outbreak farms 3) Ramp up testing of farms and farm animals 4) Detailed sequencing metadata: date, location, etc. 5) Guarantee privacy on any humans with symptoms, test, trace, isolate, seq any positives 6) Guarantee immunity for...
...migrant workers on milk farms to encourage cooporation 7) If no temporary ban, require testing on all raw milk lots 8) Improved safe cattle transfer. Require testing of mixed milk lot from farm and cow before transfer 9) Survalence testing of other cattle
FLiRT is the clever nickname for two mutations on the spike protein of the highly mutated variant "Pirola", that accounts for >99% of all Covid right now.
F->L at position 456 and R->T at 346.
Both escape mutations were present last year, but never on Pirola.
The two mutations are like makeup and lipstick to disguise the virus a bit more to sneak past some of your antibodies from prior infection and vaccination. And she wears it well.
And what is "Pirola"? That's the name I coined for this highly mutated variant. This level of sudden mutation has only happened twice; Omicron, and Pirola. Pirola had even more new mutations than Omicron did when it evolved. A big jump like that definitely deserves a name.
It's apparently been 4 months since the first sample collection date, and it still hasnt been detected in any other country that does sequencing.
When Pirola first appeared, there were sequences spotted all over the world within a week or two of first detection.
2/
BA.2.86 already was as fast as the fastest variants out there, and the L455S mutation supercharged it to JN.1. This JN.1 background is going to be a very big hill to climb for a variant that hasn't managed a foothold outside of SA yet in a number of months. Pirola in SA: