Antigenic drift of SARS-CoV-2 and vaccine distribution in 2021: NextStrain mapping emergence and spread of variants

Nextstrain plays a critical role tracking the spread of SARS-CoV-2, and is open-sourcing the data to increase epidemiological understanding and improve public health responses. Trevor Bedford, a scientist at the Fred Hutchinson Cancer Research Institute who studies the spread and evolution of viruses, co-developed Nextstrain. Trevor and his team just posted their analysis of vaccine distribution in 2021 and antigenic drift of SARS-CoV-2 (read the full thread by @trvrb on twitter). From Trevor: “In the near-term, vaccine efficacy will likely not be reduced but it is important to continue tracking mutations and updating as we learn more.”

With #COVID19 vaccine efficacy of ~95%, I'm looking forward to vaccine distribution in 2021 bringing the pandemic under control. However, I'm concerned that we'll see antigenic drift of SARS-CoV-2 and may need to update the strain used in the vaccine with some regularity. 1/18
— Trevor Bedford (@trvrb) December 19, 2020

There has been an open question to the degree to which SARS-CoV-2 will behave like influenza and require vaccine updates. However, emerging evidence suggests that antigenic drift is likely. 4/18
— Trevor Bedford (@trvrb) December 19, 2020

First off, we have new studies on antigenic drift in seasonal coronaviruses. Katie Kistler and I have shown abundant adaptive evolution in the spike proteins of viruses OC43 and 229E consistent with antigenic drift (https://t.co/CGeN6dQJsP). 5/18 pic.twitter.com/dGknZQgsP1
— Trevor Bedford (@trvrb) December 19, 2020

For SARS-CoV-2, we only expect antigenic variants to spread once enough people have been infected to give these variants a transmission advantage gained by the ability to reinfect some portion of individuals immune to the original variant. 7/18
— Trevor Bedford (@trvrb) December 19, 2020

At this point, many countries have had perhaps 10% to 20% of their population infected (https://t.co/UWF8rNlOLS), and so we expect some weak evolutionary pressure for antigenic drift. 8/18 pic.twitter.com/J1VUfRQQSI
— Trevor Bedford (@trvrb) December 19, 2020

Independent emergence and spread of variants is suggestive of natural selection where in addition to N501Y we see for example S477N emerging independently in Europe (https://t.co/CWq7c2h4bf) and in Australia (https://t.co/Gyfu4PAcgX). 13/18 pic.twitter.com/oEPfSWEQyK
— Trevor Bedford (@trvrb) December 19, 2020

All this said, I'm not concerned that these variants will significantly reduce vaccine efficacy in the 2021 rollout. Most circulating SARS-CoV-2 viruses do not have any mutations in the spike receptor binding domain (https://t.co/TZt5BqhSzk). 15/18 pic.twitter.com/NmgHrotaiJ
— Trevor Bedford (@trvrb) December 19, 2020

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