This is a transcribed Twitter thread from Trevor Bedford from March 2020 on Predicted antigenic drift of SARS-CoV-2.
A thread on #SARSCoV2 mutations and what they might mean for the #COVID19 vaccination and immunity, in which I predict it will take the virus a few years to mutate enough to significantly hinder a vaccine.
Predicted antigenic drift of SARS-CoV-2
I’m writing this thread because I have a bunch of mentions talking about 100s of “strains” and no ability to vaccinate against them. I want to clarify scientific usage of strain vs mutation. RNA viruses such as influenza mutate very rapidly. The molecular machinery they use to replicate in the body is highly error prone.
If you follow a transmission chain in which one person with flu infects another person and they infect another person and so on, you’ll find that the virus mutates about once every 10 days across its genome. Almost all of these mutations will have little to no effect on virus function. Evolution weeds out the mutations that “break” the virus and mutations that make a virus replicate better are extremely rare. For influenza, the major driver of evolution is immunity.
Mutations will occasionally appear that cause people’s existing immunity to no longer protect as well against a newly emerged mutant virus. This is why the strain used in the influenza vaccine needs to be updated by the @WHO every year. Here you can see evolution of influenza H3N2 over the past 12 years and the amount of “antigenic drift”, ie evolution relevant to vaccines and immunity. nextstrain.org/flu/seasonal/h… Importantly, this evolution takes takes place over years.
When pandemic swine flu emerged in 2009, it took the virus a solid 3 years before we saw any evidence at all of antigenic drift. nextstrain.org/flu/seasonal/h… If I had to guess, I would predict that #SARSCoV2 will behave similarly to existing seasonal coronaviruses in its ability to mutate to avoid vaccines and immunity. Here we see that seasonal coronaviruses may behave similarly to seasonal flu in which frequent mutations to spike protein (the protein targeted by immunity) are observed (microbiologyresearch.org/content/journa…, nature.com/articles/srep1…).
Here’s @firefoxx66‘s analysis of seasonal coronavirus OC43 where we see frequent mutations to spike protein. nextstrain.org/community/next… So, my prediction is that we should see occasional mutations to the spike protein of #SARSCoV2 that allow the virus to partially escape from vaccines or existing “herd” immunity, but that this process will most likely take years rather than months.
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