BELIEVE IN EVOLUTION? HELL, I’VE SEEN IT DONE: Plasmodium falciparum evolving to escape malaria rapid diagnostics in Africa.

A major tool against malaria in Africa has been the use of rapid diagnostic tests, which have been part of the “test-treat-track” strategy in Ethiopia, the second most-populated country in Africa. But researchers studying blood samples from more than 12,000 individuals in Ethiopia now estimate these tests missed nearly 10% of malaria cases caused by the parasite Plasmodium falciparum, the most common cause of malaria cases and deaths.

The research, published in Nature Microbiology, showed that two genetic mutations to the parasite allow it to escape detection.

So if malaria can evolve to defeat a test, I have a thought: Could widespread vaccination be a mistake with Covid?

We know that the vaccine is imperfect, and lets people who have been vaccinated get infected. By definition, those are infections that are able to avoid the effect of the vaccine. If most people are vaccinated, then shouldn’t it be the case that after a bit, most cases of the virus everywhere will be vaccine resistant? And wouldn’t that leave people who are most vulnerable, like the old, the sick, and the obese, more vulnerable to the virus than if only the vulnerable people had been vaccinated all along?

Am I missing something here?

UPDATE: Via the comments, this from Derek Lowe: Vaccines Will Not Produce Worse Variants. However, I wasn’t suggesting that the vaccine will produce mutations. Rather, I was suggesting that widespread vaccination would apply selection pressure in favor of variants that are not blocked by the vaccine. Lots of interesting stuff in this piece, though. Excerpt, but you should read the whole thing:

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. It’s certainly true that if you want to induce resistant variations to some antiviral drug in the lab, you let them infect cells in culture while treating them with not-quite-adequate amounts of your proposed drug. You “passage” these into fresh cell cultures, often increasing the amount of the antiviral along the way as you do so, with the idea being that the viral particles that are infecting each new population of cells are the ones that have made it past the effects of the drug. This can go on for weeks or even months, depending on the organism, the drug, and how easy or hard it might be to stumble on effective resistance mutations, but at the end of it, you can produce a form of the virus that will laugh off what would be a killing dose against the original wild-type. . . .

That’s not so easy, because (for one thing) there are an enormous number of different antibodies involved (and an enormous number of T-cell recognition proteins). There are any number of ways to bind to a given protein target, and the adaptive immune system’s whole function is to be ready for all kinds of targets and to hit them in all kinds of ways. And there’s that constraint mentioned above: the virus still has to be able to function! Losing the entire Spike protein or mutating it completely beyond recognition would definitely evade vaccine-induced immunity, but it would also definitely produce a coronavirus that couldn’t infect human cells in the way it’s completely evolved to do. Coming up with a completely new infection route is (mutationally) extremely costly and complex, and not something that can be done “on the fly”. Various coronaviruses use different human cell surface proteins to do their attack, but these have gradually developed and diverged over evolutionary time (hundreds of thousands, or millions of years) through untold numbers of tiny steps.

But it can be done, in principle. And as with everything in evolution, if it gets done at all, it’ll get done by similarly untold numbers of individual mutants, and mutants on top of those mutants, until something appears that can both avoid being inactivated by the immune response and still infect cells and reproduce. There is no guarantee that such a virus can exist, and there is no guarantee that it can’t. Evaluating the number of possibilies is frankly beyond computation – we didn’t, for example, see the details of the Delta variant coming, and if you’d given someone that exact sequence last year, there’s no guarantee that they would have been able to predict how much more infectious it would be.

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.

So there’s the argument that my concerns are overstated.