is this the smoking gun for leaky vaccines driving viral evolution to hotter strains?

delta variant AY.4 Y145H warrants more investigation

there’s a new kid in town in the UK, and his name is AY.4, a sub variant of delta that’s taken over the UK and is propagating though the US.

i’m not sure just where scott is getting this 8% figure, but according to the UK variants of concern REPORT, AY.4 IS now delta. it’s not a sub-strain. it IS the strain.

the Y145H spike mutation seems new though and i suspect this is the 8% he’s referencing. this would imply we’re really looking for a sub-sub variant.

(if anyone knows where that data comes from, please let me know)

this mutation appears to have not yet shown up in much of the US. AY.4 is far less of delta overall there.

Nathan Grubaugh @NathanGrubaugh

🧬10/14 Connecticut #SARSCoV2 variant surveillance @CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed 👑Delta - 99.7% (321/322 sequenced) Sublineage leaderboard 27% = AY.4 25% = B.1.617.2 22% = AY.25 9% = AY.3 3% = AY.26 short 🧵 | Report 👉 covidtrackerct.com/variant-survei…

covidtrackerct.comConnecticut SARS-CoV-2 variant surveillance – Report 2021-10-14In collaboration with the Connecticut Department of Public Health, the Centers for Disease Control and Prevention, Yale University, Jackson Laboratories, and diagnostic laboratories across the stat…

there are quite a few things we can take away here:

first, after all this time, scott still does not know how to read this data and the difference between day of report and day of actual incidence.

he has also not learned what sample rate is and how it works. he’s using raw case numbers.

cases are actually down in the UK from this time last year. testing is up 3.6X while cases are only up 2.5X. that implies that on a testing adjusted basis, cases are actually down about 30% YoY.

cases are up in the last month, even (and especially) on a sample rate adjusted basis, but this is also seasonally expected. they did the same thing this time last year..

amazing that after all this time, ideas like controlling for testing rates and seasonality are still absent from the discussion.

so it’s not a major smoking gun.

it’s seasonally expected, lower than last year, and we know these vaccines do not stop spread and may actually be making it worse and that viruses tend to evolve to be more contagious and less harmful. it’s how pandemics peter out.

but the second thing we can take away is this: scott is not looking at the interesting part of the question.

the interesting part of the question is this: is this AY sub variant more virulent/lethal than the previous variants and is this new mutation making it even more so? because that would be extremely interesting and deeply counter to expectation.

harming the host is maladaptive to genetic propagation for viruses, so much so that seeing it happen is like seeing water flow uphill. it should always make you ask: “what is driving this?”

and something looks to be driving evolution back towards greater lethality. i discuss this in detail HERE.

you can see it in the data and there is some interesting timing alignment here. AY.4 has been dominant throughout this rise, but prevalence on some of these intra-subvariant mutations has not.

this seems like it might be the pond in which we need to go fishing.

Y145H started spreading in july (or, more to the point, its spread became noticeable in july.) this is also where CFR really started to rise. now, some of this was age bracket driven, but even adjusted for that, CFR has tripled since june in the UK.

that’s wildly unexpected as a natural phenomenon. but it’s exactly what one would suspect if you had leaky vaccines that provided protection against severe cases. that breeds for hotter strains. it not only grants them an evolutionary future that would otherwise be impossible, but it actually selects for them preferentially. this was known and knowable. detailed discussion HERE.

when i spoke recently about this vaccine mediated evolution (VME) and what a disaster it might be were it occurring, one of the striking features was that CFR was rising in the unvaxxed just as it was in the vaxxed (though on different scales). this seems to rule out all manner of first and second order post vaccine effects as the primary driver of enhanced virulence. everyone is experiencing it.

that points to virus, not inoculum.

and the vaccines clearly ARE providing protection against covid death. (though perhaps not protection overall in terms of all cause mortality which leads to a whole set of interesting questions about 2nd and 3rd order after-effects)

but the question is: are they still making everyone worse off?

getting 50% protection from a tripling in virulence caused by the vaccines is still a net loser for the vaccinated. and it’s savage for the unvaccinated. everyone loses. and this evolution is ongoing.

one of the (reasonable) questions many asked about my VME theory was this: so is there genetic evidence we can point to? where is the smoking gun?

well, perhaps here it is.

i have not yet seen data on the AY.4 Y145H sub lineage CFR, but THAT number, not its relative contagion, is what we need to be most aggressively looking at because if it (or some other sub variant) is a big jump up from prior strains then it’s a bit like finding the higgs boson and this theory has made a prediction that panned out.

a drop in contagiousness at the same time would be doubly damning and represent quite strong evidence that evolution is being played silly buggers with by some outside force, but this might also just be a greater number of those with immunity from recovery (which IS sterilizing) having effect. this needs more investigation as well.

hospitalizations and deaths are roughly 1/3 higher in UK than this time last year on what looks to be a lower actual case count. it’s far higher than that in much of the US north though sample rate adjusted cases look higher there too.

something is driving that and it’s interesting that the high contagion in the US seems associated with much lower AY subvariant prevalence.

establishing what is going on here should be the all hands on deck mission of global public health right now.

none of us want to be living in the world where we leaky-vaxxed ourselves into a second pandemic by reversing the evolution of one that was about to go endemic and harmless.

that’s a terrible place to be.

but if that IS where we are, we need to know, and we need to know right now.

and this looks a bit suspicious. CFR is way up for delta and the reversal and rise looks conspicuously correlated to when “vaccine fade” really gets going 3-4 months post dose 3.

it’s also interesting that AY went from tiny to dominant in delta right as the vaccination campaign was at its peak, though perhaps also interesting that it has been slower to do so in the US.

if these are just coincidences, they certainly are provocative ones…

fear a truth may be unpleasant is no excuse not to seek it. too much is at stake.

and so the search goes on.