XBB.1.5.20 with S:Q954Y [29 sequences, Canada]

[Outpfmance]

Description Sub-lineage of:XBB.1.5.20 Earliest sequences:2023-3-24,Canada EPI_ISL_17462154 Latest sequences:2023-4-2,Canada EPI_ISL_17500101/17500102 Countries:Canada(22) Number of Sequences:22 GISAID query:Spike_Q954Y,T17124C,A19326G,T23018C,C9532T Cov-spectrum: https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-03-01%26to%3D2023-04-22/variants?aaMutations=s%3A954Y&nextcladePangoLineage=XBB.1.5.20& Nextstrain: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_27dfe_377050.json?f_userOrOld=uploaded%20sample Nextclade:

Evidence This is a particular branch that replaces one of Omicron's defining mutations, Q954H. It is well known that S:Q954H and S:N969K make S2 in this region more positively charged than pre-Omicron lineages. Does this property change when one of them changes? I think this is a branch that needs to be looked at and tracked. Sequences: EPI_ISL_17412758
EPI_ISL_17462154
EPI_ISL_17462155
EPI_ISL_17462158
EPI_ISL_17462160
EPI_ISL_17499741
EPI_ISL_17499809
EPI_ISL_17499811
EPI_ISL_17499812
EPI_ISL_17499857
EPI_ISL_17499860
EPI_ISL_17499863
EPI_ISL_17500043
EPI_ISL_17500044
EPI_ISL_17500045
EPI_ISL_17500047
EPI_ISL_17500050
EPI_ISL_17500051
EPI_ISL_17500052
EPI_ISL_17500056
EPI_ISL_17500101
EPI_ISL_17500102

[ryhisner]

I've seen a few S:H954L sequences lately as well. I wonder if there are some weak S2 antibodies to Q954H causing this (possible) trend.

Huh, it turns out nine recent S:H954L sequences are from a branch of EG.1 (XBB.1.9.2 + S:Q613H) spread across four European countries, though 6/9 are from Italy.

[Outpfmance]

29 sequences now. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1bf99_a6b9d0.json?f_userOrOld=uploaded%20sample&label=id:node_4700458

[Outpfmance]

@ryhisner I open a issue for this. #1968

[Memorablea]

68 NOW

[DailyCovidCases]

This branch is dead, please close this issue