Tracking and interpreting novel SARS-CoV-2 variants

Richard Neher
Biozentrum & SIB, University of Basel

slides at

by Trevor Bedford
by Trevor Bedford

Available data on Jan 26 2020

Early genomes differed by only a few mutations, suggesting very recent emergence

VoCs have more mutations than expected...


VoCs and VoIs: rapid converging evolution by Emma Hodcroft

VoCs partially escape neutralizing antibodies and transmit faster

Althaus et al, 2021, Wall et al, Lancet

Nextstrain builds for different countries

  • Started as part of the surveillance effort in Switzerland
  • Most European countries -- updated twice a week
  • Heavy focus on sequences from the last 4 weeks (but still subsampled in many cases)
  • Administrative divisions for some countries
  • Variant specific builds via CoVariants

Similarities to influenza virus evolution

Klingen et al, Trends in MicroBio, 2018


Trevor Bedford and his lab -- terrific collaboration since 2014

especially James Hadfield, Emma Hodcroft, Ivan Aksamentov, Moira Zuber, and Tom Sibley

Allie Greaney and Jesse Bloom for discussion of the dms data

Data we analyze are contributed by scientists from all over the world

Data are shared and curated by GISAID