Real-time tracking of SARS-CoV-2 evolution and spread

Richard Neher
Biozentrum & SIB, University of Basel

slides at

Data summarized by Ian MacKay
Data summarized by Ian MacKay
Data summarized by Ian MacKay
Data summarized by Ian MacKay
Data summarized by Ian MacKay
by Trevor Bedford
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
→ the closest to "real-time" we have experienced so far...
Figure by James Hadfield/Emma Hodcroft
Mutations accumulate constantly, but most of them are irrelevant and rare.
The genome accumulates about two mutations a month...
Diversified into multiple global variants. Groups 20A/B/C have taken over.

Genomic analysis as complement to contact tracing

Swiss sequences on August 31, most sequencing by Tanja Stadler's group at ETH, D-BSSE

A European cluster in summer 2020

What's next?

Seasonal incidence of influenza viruses

Data by the US CDC

2009 pandemic influenza -- US

2009 pandemic influenza -- UK

By Dave Farrance - wikipedia

2009 pandemic influenza -- Germany

by Trevor Bedford

Human corona viruses have pronounced seasonal prevalence (Sweden)

  • Most respiratory virus including established CoVs show seasonality
  • Little direct evidence; absolute effect of seasonality unknown
  • But expect control of the virus to be harder in winter
Neher et al

Potential transition to an endemic seasonal virus


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