Are leaky vaccines driving delta variant evolution and making it more deadly?

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assessing the england data on variants and vaccines. the pieces are coming together.

one of the great fears in any vaccination campaign is that the vaccine can wind up becoming the driver viral evolution and making the virus more dangerous. this is a special concern around imperfect (so called “leaky”) vaccines that are non-sterilizing. such vaccines do not stop spread or contagion of the virus. this means the virus will have lots of chances to replicate.

when you combine this with a vaccine that reduces severity of cases and prevents deaths in the vaccinated, it’s a bit of a perfect storm. you get full spread but break the evolutionary gradient towards mildness that viruses tend to follow (and that protects humanity from them).

all a virus wants is to replicate. “make a copy of me and pass it on.” that’s the biological imperative of the selfish gene. excel at it, you win. fail, you disappear. simple as that.

killing or harming the host is maladaptive to viral spread. it’s like burning down your own house with your car in the garage. now you have nowhere to live and no way to get around. that’s not a recipe for reproductive fitness.

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this is a property of the world, not of the viruses themselves. so it applies to all of them, evolved and lab hotwired alike.

so viruses evolve to become less, not more virulent. they do not want to kill you. ideally, they’d like to help you. figure out how to be a useful symbiote, and you get a huge boost in propagation. (mitochondria were probably bacteria that were so useful, all our cells incorporated them.) so seeing case fatality rate (CFR) rise in a variant of a virus is like watching water flow uphill. it’s not supposed to do that and when it does, you need to suspect some external force acting on it.

and we’re seeing water flow uphill here.

i started with the england variants of concern (VoC) data. it’s the best quality and the best broken out. (the US data is just plain broken. it’s being deliberately scrubbed to prevent analysis like this.) because this data is always aggregated from feb to current period, it does not provide good temporal snapshots, but this can be fixed by subtracting the penultimate report from the current one etc. you subtract report 22’s totals from report 23 and you get just what happened in the last 2 weeks (it used to be a weekly report, now it’s bi-weekly)

what we see is not what one would expect from a virus. none of the other variants (pre vaccine) worked like this. none saw CFR rise like this. and no jump from major variant to variant saw a statistically significant rise in deadliness.

this IS however what one would expect if a virus were undergoing vaccine mediated evolution (as mareks disease did in chickens) and selecting for hotter strains because vaccinated people can carry and spread them and not die.

experienced CFR on delta is nearly 7X what it was in the beginning of june and has been galloping since the middle of july.

(note that pretty much all this data has a large artifact in it from the 21 june report (VoC 17). there was a “data-dump” in it where they caught up on a bolus of past data. it’s an artifact, not a signal. best to ignore it. i suspect the curve from mid june to mid july was smooth.)


put simply: this is not good.

delta is rapidly approaching alpha (1.1%) in terms of CFR whereas it used to be 90% lower. (it also means that the reports on delta CFR in these VoC updates are FAR too low because they are a blend of all cases and deaths back to feb, so they are averaging in the low CFR past and are slow to respond to current dynamics)

this is consistent with, but not proof of vaccines mediated evolution. to get there, we need to do better.

so now we need to start ruling things out and validating this claim to see if it’s meaningful.

first, it’s not a simpson’s paradox in age data. CFR is rising in over and under 50’s. it’s not mix shift alone. CFR in over 50’s is up 2.5X. it’s up 4-7X in under 50’s.

we’re at about a 3X rise in CFR overall in delta since the summer once we adjust for shifts in age. not as worrying as 7, but still worrying.