Vaccine Escape Mutations “Will Become a Major Mechanism of Transmission”, Say Researchers

When the vaccine rollout got underway, some scientists argued that mass vaccination would set up an evolutionary selection pressure in favour of vaccine-resistant strains, potentially prolonging the pandemic.

For example, Robert Malone and Peter Navarro wrote the following in the Washington Times:

The more people you vaccinate, the greater the number of vaccine-resistant mutations you are likely to get, the less durable the vaccines will become, ever more powerful vaccines will have to be developed, and individuals will be exposed to more and more risk … If the entire population has been trained via a universal vaccination strategy to have the same basic immune response, then once a viral escape mutant is selected, it will rapidly spread through the entire population

To avoid being locked into an arms race with the virus, they argued that only the most vulnerable should be vaccinated. They were calling, in other words, for focused protection.

However, many scientists were sceptical that this constituted a good enough reason to hold off on mass vaccination. After all, people were dying of Covid now, and the ‘arms race argument’ was in any case speculative.

It’s important to note: the premise of Malone and Navarro’s argument – that vaccination can drive viral evolution – is accepted by many of those who support the mass rollout of Covid vaccines. At a press conference in January, the UK’s Chief Scientific Adviser Patrick Vallance said the following:

The more you vaccinate, the more you put evolutionary pressure on the virus. So it’s true that, as you get up to very high levels of vaccination, the virus is then struggling to find out what to do, and that eventually will become an issue.

The part of Malone and Navarro’s argument that is in dispute, it seems, is that the ensuing arms race will prove unmanageable. For example, Vallance followed his comments above by saying, “the virus probably will mutate at that point, and that means that different vaccines will be needed in due course.”

So Malone and Vallance agree that mass vaccination can drive viral evolution, at least in principle. But is there any empirical evidence that this is happening with the Covid vaccines? Yes, according to a paper published in the Journal of Physical Chemistry Letters.

Rui Wang and colleagues analysed SARS-CoV-2 genetic sequence data from the first ten months of 2021, and identified one particular viral mutation that has vaccine escape properties. (This mutation goes by the catchy name “Y449S”.)

They tracked Y449S over time in 14 different countries with high vaccination rates, and found that its frequency was correlated the percentage of people vaccinated, as shown in the figure below.

Although the mutation’s absolute frequency remained relatively low in all countries, it became more prevalent as the percentage of people vaccinated went up. This constitutes preliminary evidence that it was selected for by the vaccine rollout.

Of course, we know that Y449S did not come to dominate in the population of Covid variants. Another mutation, Delta, turned out to be more evolutionarily successful. This suggests that vaccine escape was not the main force driving the SARS-CoV-2 evolution over the period in question.

However, the researchers conclude that once most people around the world have acquired antibodies from either vaccination or infection, vaccine and immune escape mutations “will become a major mechanism of transmission”.

Returning to Malone and Navarro’s argument, it all hinges on how manageable the ensuing arms race proves to be. Given that many scientists support the mass rollout of Covid vaccines, they must believe that it will be manageable. We’ll learn over the following months and years whether they’re right.