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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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GQ.1 (CH.1.1.3.1) sublineage with S:G213E (19 seqs in New Zealand) #343

Closed HynnSpylor closed 1 year ago

HynnSpylor commented 1 year ago

Defining mutations: GQ.1>T6634C, C14183T(ORF1b:T239I), C27532A (ORF7a:H47N)>G22200A (S:G213E), C28831A GISAID query: G18025T, C24358T, C28831A Earliest seq: 2023-04-21 (New Zealand, EPI_ISL_17739724) Most recent seq: 2023-06-24 (New Zealand, EPI_ISL_17961699) Countries detected: New Zealand (19)

Usher Tree: QQ截图20230706181542

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a921_68f230.json?c=gt-S_213

It is first spotted in https://github.com/cov-lineages/pango-designation/issues/1872 S:213 is G in BA.2.75 lineages (including CH) while E in XBB lineages. Based on S:S486P, the branch gets one more XBB mutation.

Genomes: EPI_ISL_17739197, EPI_ISL_17739382, EPI_ISL_17739724, EPI_ISL_17740162, EPI_ISL_17740383, EPI_ISL_17961670, EPI_ISL_17961699, EPI_ISL_17961717, EPI_ISL_17961783, EPI_ISL_17961788, EPI_ISL_17961831, EPI_ISL_17961842, EPI_ISL_17961870, EPI_ISL_17961885, EPI_ISL_17962022, EPI_ISL_17962200, EPI_ISL_17962241, EPI_ISL_17962245, EPI_ISL_17962415

FedeGueli commented 1 year ago

Local prevalence of GQ.1 is significant around 3-4% good ypu proposed this onw

Sinickle commented 1 year ago

Seems to me to be a really important one to watch. CH.1.1.3 with S:213E has 14 sequences as well -- so this is the second time the lineage acquired the mutation successfully.