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

Richard Neher
Biozentrum, University of Basel

slides at


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

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

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

Genomic analysis as complement to contact tracing

A European cluster in summer 2020

A European cluster in summer 2020

What's next?

  • Social distancing is very effective
    → we can suppress the outbreak if we want!
  • Many Asian and European countries have successfully suppressed the virus while re-opening
  • What role does seasonality have?
    (indoor vs outdoor activities)

Seasonal incidence of influenza viruses

Data by the US CDC

2009 pandemic influenza -- UK

By Dave Farrance - wikipedia

Human corona viruses have pronounced seasonal prevalence (Sweden)

  • Respiratory virus incl seasonal CoVs show seasonality
  • Forcing through human behavior (indoor/outdoor activities).
  • Control of the virus might be harder in temperate winter
  • Absolute effect of seasonality unknown
Neher et al