Evolutionary dynamics of SARS-CoV-2


Trevor Bedford (@trvrb)
Associate Professor, Fred Hutchinson Cancer Research Center
26 Mar 2021
Pew Annual Meeting
Slides at: bedford.io/talks

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

SARS-CoV-2 lineages establish globally in February and March

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

Emergence of 501Y.V2 (B.1.351) in the South Africa

Emergence of 501Y.V3 (P.1) in the Brazil

Repeated convergent evolution across sites in spike

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

SARS-COV-2 spike S1 evolution similar to evolution of flu H3N2

501Y.V2 shows an ~8-fold drop in neutralization titer, equivalent to ~3 years of H3N2 evolution

Generally, I suspect we're looking at a data-rich version of the influenza strain selection process

  1. mRNA vaccines allow faster turnarounds and may push for more regional strategies
  2. Work directly from human serological data rather than naive animals
  3. Multiple valencies possible, clinical trials should be conducted now comparing regimens


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