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:

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

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

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


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