Real-time tracking of SARS-CoV-2 using Nextstrain

Richard Neher
Biozentrum & SIB, University of Basel

slides at

by Trevor Bedford
by Trevor Bedford

Sequences record the spread of pathogens

images by Trevor Bedford

Tracking diversity and spread of SARS-CoV-2 in Nextstrain

Available data on Jan 26

Early genomes differed by only a few mutations, suggesting very recent emergence
Summer 2020: Mutations accumulate constantly, but most of them are irrelevant and rare.
In the second half of 2020, Variants of Concern emerged.
The genome accumulates about two mutations a month... but some variants are more diverged
Diversification into multiple clades/variants distributed across Europe.
Variants are rising and falling in frequency.

Why molecular surveillance of novel variants?

  • Epidemiological investigations
  • Molecular correlates of changing patterns in spread and disease
  • Early warning signals
  • Changes in transmissibility or presentation
  • Immune-escape variants and effects on vaccine efficacy
  • Essential input for future vaccine strain selection process


Trevor Bedford and his lab -- terrific collaboration since 2014

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

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

Data are shared and curated by GISAID