SARS-CoV-2 genomics update
Trevor Bedford
Fred Hutchinson Cancer Center / Howard Hughes Medical Institute
21 Nov 2023
Viruses and Vaccines Seminar Series
Brotman Baty Institute
Slides at: bedford.io/talks
Recent wave in the US peaked in September
This wave was at least partially driven by spread of EG.5.1
EG.5.1 is XBB.1.5 (current vaccine strain) with spike mutations 52H and 456L
Data from CDC,
Model from Figgins and Bedford. 2022. medRxiv.
As is now common, we saw repeated parallel evolution for 456L
Due to epistatic interaction, 456L unlocked mutation at 455F
455F has grown from 1% to 60% global frequency in 5 months
BA.2.86 emerged as "saltational" variant with ~30 spike mutations and was first detected in August
Figure from Neher, Roemer, nextstrain.org,
Citation Khan et al. 2023. medRxiv.
Initially BA.2.86 increased slowly in frequency
However, JN.1 sublineage picked up spike 455F and has been spreading rapidly
JN.1 currently the fasted growing lineage that we're tracking
Acknowledgements
SARS-CoV-2 genomic epi: Data producers from all over the world, GISAID and the Nextstrain team
Bedford Lab:
John Huddleston,
James Hadfield,
Katie Kistler,
Thomas Sibley,
Jover Lee,
Cassia Wagner,
Miguel Paredes,
Nicola Müller,
Marlin Figgins,
Victor Lin,
Jennifer Chang,
Allison Li,
Eslam Abousamra,
Donna Modrell,
Cécile Tran Kiem
