There is, then, every reason at both the population and individual level to expect that vaccination will strongly decrease the chances of a more dangerous coronavirus strain taking hold. If we’d had them earlier and were able to deploy them quickly and widely enough, we never would have seen the Delta variant in the first place. If we keep deploying them now, we will keep worse variants from even being able to form. Anyone who tells you that vaccines will make things worse is at best deeply misinformed and at worst lying to you for profit.
Thanks for posting that article! Encouraging to see some data about how vaccines can reduce the formation of new variants
The claim is that vaccination is somehow self-defeating, since all we would be doing is putting more selection pressure on the virus to escape vaccine-derived immunity. Why doesn’t that just lead to disaster?
To address a key point that comes up right at the start: no, we have not actually been seeing more dangerous variants occurring since vaccination became more common. It’s easy to see the rise of the Delta variant this year and jump to the “after, therefore because” fallacy. But it wasn’t even “after” to start with: the Delta variant was first detected in India back in October of last year. This is before anyone was getting vaccinated. The Delta variant is by far the dominant one in the world, crowding out all the others, and it did not come as a result of vaccination.
But that said, the idea of vaccines affecting coronavirus evolution is not a ridiculous question, and it’s worth thinking about to understand more about viral evolution and the effect of our own immune systems.
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The more chances you give the coronavirus to reproduce, the more mutations it will explore. Its proofreading system for reproduction is pretty good but not perfect, and that’s where the mutations come from. It’s a numbers game all the way. The virus is not thinking about how to evade vaccine-induced immunity; it’s throwing stuff randomly against every available wall in every available direction, and whatever sticks gets a chance to go on throwing some more. Remember, an unvaccinated person is still mounting an antibody defense against the virus - they’re just having to do it from scratch, rather than having a pre-primed leg up like someone who’s been vaccinated. The longer these infections go on inside human bodies, the more bets the virus gets to put down on the table. The good news is that so far, there is not much evidence that the virus is doing much evasion inside a given person during the course of normal infection.
So one key way to cut down on the odds of a nasty mutant popping up is to just keep the virus from reproducing so much . Cut down on the number of people it infects. When it does infect people, cut down on the amount of time it spends reproducing inside the body. These countermeasures are exactly what a mass vaccination program does . Fewer people get infected in the first place, and when they do get infected, their disease course tends in the great majority of cases to be shorter and milder. A nasty variant is almost certainly going to come up by accident, so let’s not have so many accidents going on constantly around the clock, around the world.
But back to the earlier discussion: what if the vaccines are still putting direct pressure on the virus? Aren’t we selecting for exactly the things we fear the most? The answer to that is counterintuitive. Take a look, for example, at this preprint from July. The authors looked over 1.8 million coronavirus genomes from infections around the world, and compared that background data set to specific breakthrough infection sequences in vaccinated patients. What they find is that the genomic sequences from the breakthrough infection patients are significantly less diverse than what’s seen in the wild. The authors believe that this shows that " COVID-19 vaccines are fundamentally restricting the evolutionary and antigenic escape pathways accessible to SARS-CoV-2 ", and that’s the flip side of the above argument. You are putting pressure on the virus to escape the immune attack, but at the same time you are cutting sharply back on the pathways it can use to get there. Remember, a true vaccine-evading mutant is going to need a set of several mutations (off the existing variants) all at the same time. The vaccine-induced immune response looks like it’s knocking down a lot of these intermediate-step mutations before they can keep on throwing off subsequent mutations on top of the first ones. These pathways are choked off before they can even get explored, and this “evolutionary smothering” is something that you don’t see so dramatically when you’re doing those in vitro experiments with specifically targeted small molecules mentioned at the top of this post. A broad antibody and T-cell response is a different thing altogether.
That was one of the points I was trying to make (albiet much less eloquently) in exchange with @dsterncardinale on this prior post:
The only point I was making there was that widespread vaccination imposes selective pressure on the target virus, and delta has the characteristics we’d expect to be selected for by a largely vaccinated host population.
Delta would also be selected for within a largely unvaccinated population (as it was in India when it first arose), wouldn’t it? Because Delta is so infectious, it outcompetes other variants?
Depends on its intrahost competitiveness. In a population that is largely susceptible, getting from host to host is trivial, and individual hosts sometimes have more than 1 variant present, so the most successful variants are going to be the ones that can “win” against all the other circulating variants when they coinfect a single host. I’m not sure delta is any worse when it comes to intrahost competition, but it’s definitely better at interhost competition, i.e. it is more transmissible, which is what you select for with widespread vaccination, which probably explains why it’s the most successful strain at this stage of the pandemic.
I slightly disagree with Derek here. Its true that the more people are vaccinated, the lesser the number of susceptible hosts available for the virus to transmit between, hence, reducing the number of opportunities for the virus to accumulate more immunity-related adaptive mutations. However, I think this holds mostly when the virus’s mutation rate is relatively low as seen in SARS-CoV-2. Viruses, like HIV and influenza, with a higher mutation rates would relatively easily produce vaccine-resistant strains which can be selected for during vaccination campaigns.
Even for SARS-CoV-2, I think its still possible for vaccine-resistant strains to emerge via mutations and increase in frequency due to selection. However, considering the mutation rate alone, I think this is quite unlikely.