SARS-CoV-2 Evolution will Accelerate

SARS-CoV-2 is known to be a seasonal virus because the amount of viral transmission depends critically on the temperature. There are higher loads of viral inoculum that are transmitted greater distances when it's cold and absolute humidity is lower, and people are more likely to gather inside together for warmth.

https://www.frontiersin.org/articles/10.3389/fpubh.2021.650493/full

This is true of all strains, and we are entering autumn with a higher case count than we had last year. Also, last winter, Alpha was dominant nearly entirely alone, and it's not antigenically very distant from the original S protein. Instead, today, we now have many antigenically distant strains and variants of concern(VoCs). Check the dot plot for cross-immunoreactivity between strains in the following article.

https://www.sciencemag.org/news/2021/08/new-sars-cov-2-variants-have-changed-pandemic-what-will-virus-do-next

Through those two factors, we should see new domestic highs in case counts, probably by a lot. The US set a record for daily cases of ~320k, even exceeding that of last winter, ~300k, on Friday. The moving average is not as high and Fridays are always peaks due to reporting delays, but it's a strong indicator.

https://origin-coronavirus.jhu.edu/data/new-cases

But this is an even worse set-up because of recombination. Our vaccines are not effective enough at preventing infection by VoCs, and infection with one strain will confer less protection against other strains. It is highly likely that individuals will be co-infected with multiple strains, most likely VoCs, and SARS-CoV-2 has already shown that its primary current evolutionary pathway is recombination. Recombination will become multiplicatively more probable as case counts rise and antigenic drift continues. It's a snowball effect with little to bound it beyond the available pool of existing haplotypes and SARS-CoV-2's evolution and transmission rates.

A higher rate of infection combined with a higher rate of recombination is likely to produce strains that are significantly more dangerous than current variants of concern. It's less probable that we will exceed death counts from last winter due to a higher number of epitopes recognized by T-cells, thanks to vaccination and more convalescents, but it's eminently plausible if a variant of high concern emerges.

Though it depends on the strains that emerge from this winter's recombination events, my base case expectation is accelerating evolution of SARS-CoV-2 from here on out because we will not get R below 1 for a sufficient number of strains.

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