Perspectives on SARS-CoV-2 evolution


Trevor Bedford (@trvrb)
Associate Professor, Fred Hutchinson Cancer Research Center
18 Mar 2021
SXSW 2021
Slides at:

Over 800k SARS-CoV-2 genomes shared to GISAID and evolution tracked in real-time at

Spike protein is critical for cell invasion by the virus and is the primary target for human immune response

Spike mutations 484K and 501Y appearing repeatedly

Emergence of 501Y.V1 (B.1.1.7) in the UK

Up to December, my expectation was evolution as seen in seasonal coronaviruses with flu B-like rates of evolution

Rapid spike S1 amino acid evolution in SARS-CoV-2

It's possible evolution of SARS-CoV-2 will slow down, but I wouldn't count on it

  1. Flu H3N2 rates of evolution suggest vaccine updates every 1-2 years
  2. Flu H3N2 infects 5-10% of the US every year
  3. Similar levels of SARS-CoV-2 circulation possible (though mRNA vaccines are amazing)

Importance of predictive modeling of SARS-CoV-2 evolution

  1. Forecasting evolution in seasonal influenza has seen some success
  2. Huge amount of data available for SARS-CoV-2

Given flu-like evolution, my general speculation looks like

  1. Infections of previously vaccinated / infected individuals are likely to be milder
  2. A winter "COVID" season with significant SARS-CoV-2 circulation but lower levels COVID-19 disease
  3. Voluntary yearly COVID vaccine for people who are interested in increased protection from circulating viruses
  4. Depending on level of circulation/disease continued push for case finding / contact tracing, but I'd hope to avoid societal restrictions

Continued improvements to sequencing throughput of common viral infections can provide early warning system for emerging pandemic threats


SARS-CoV-2 genomic epi: Data producers from all over the world, GISAID and the Nextstrain team

Bedford Lab: Alli Black, John Huddleston, James Hadfield, Katie Kistler, Louise Moncla, Maya Lewinsohn, Thomas Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin, Cassia Wagner, Miguel Paredes, Nicola Müller, Marlin Figgins, Eli Harkins