Tracking variants turned out to be crucial
Emergence and dominance of VoCs
VoCs have more mutations than expected...
nextstrain
VoCs have been replacing other strains quickly
S-gene positivity in the UK
Althaus et al, 2021, PHE Technical Briefing
Global
South America
How do we tell early on whether a variant is concerning?
How unusual are the patterns of convergent evolution?
SARS-CoV-2 variants can become dominant without advantage
Hodcroft et al
High case numbers in Spain and high travel volume spread the variant
Hodcroft et al
Travel driven variant dispersal and displacement
- High incidence differential and high travel volume can shift variant distribution
- Travel associated activities and behavior further increases impact
- Onward spread in traveling demographics can be higher
Mutational signatures
Number of amino acid changes in the S1 domain
Prominent deletions the spike NTD
Common convergent deletion in NSP6
Growth measures and fitness scores
Recent growth rate
Fitness based on mutational effects by Obermeyer et al
- Within browser alignment and phylogenetic placement
- Calls mutations relative to the reference
- Assigns clades
- Calculates QC metrics
SARS-CoV-2 acknowledgements
- Emma Hodcroft (now in Bern)
- Moira Zuber (Basel)
- IƱaki Comas and Fernando Gonzalez-Candelas, Valencia
- Martina Reichmuth and Christian Althaus (Bern)
- Tanja Stadler, Sarah Nadeau, Tim Vaughan at ETH
- Alberto Hernando and David Matteo at Kido Dynamics
- Jesse Bloom, Katherine Crawford at Fred Hutch
- David Veesler, Alex Walls, Davide Corti, John Bowen at UW
Acknowledgments
Trevor Bedford and his lab -- terrific collaboration since 2014
especially James Hadfield, Emma Hodcroft, Ivan Aksamentov, Moira Zuber, John Huddleston, and Tom Sibley
Data we analyze are contributed by scientists from all over the world
Data are shared and curated by GISAID