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


Richard Neher
Biozentrum, University of Basel


slides at neherlab.org/202009_SNI.html

Acknowledgments

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

BBC
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
nextstrain.org/ncov/2020-01-26
→ 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

nextstrain.org/ncov, most sequencing by Tanja Stadler's group at ETH, D-BSSE

A European cluster in summer 2020

nextstrain.org/ncov

A predominantly GE/VD cluster

nextstrain.org/ncov

A predominantly ZH/BS/BL/BE cluster

nextstrain.org/ncov

What's next?

Weekly cases and deaths in Switzerland

What have we learned? What are the unknowns?

  • Social distancing is very effective
    → we can suppress the outbreak if we want!
  • Many Asian and European countries have largely re-opened
    → some now see consistent rise in cases
    → exponential increase
  • Test-Trace-Isolate-Quarantine is more effective and less disruptive at low case numbers
    → acceleration possible when TTIQ systems get overwhelmed
  • What role does seasonality have?
    → behavioral component: indoor vs outdoor activities
    → environmental component: less ventilation, drier air
    → interaction with other viruses

Influenza A pandemics of the last 120 years

slide by Trevor Bedford

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

Robert-Koch-Institut

1918 influenza --- UK

Taubenberger et al
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

Acknowledgments

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

Acknowledgments

  • Robert Dyrdak
  • Jan Albert
  • Valentin Druelle
  • Emma Hodcroft