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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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JN.1.7* with S:704L cluster in Ireland (40) #1452

Closed krosa1910 closed 3 months ago

krosa1910 commented 5 months ago

Mutations on top of JN.1*: T9757C,C15960T, A21137G, C23673T Gisaid Inquiry: T22896A,A22629,C23673T,T9757 First Sequence: EPI_ISL_18984051 Dublin, Ireland 2024-02-06 Second Sequence: EPI_ISL_18994147 Dublin, Ireland 2024-02-28 Last Sequence: EPI_ISL_18994168 Dublin, Ireland 2024-03-13 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_3099f_bf7ce0.json?f_userOrOld=uploaded%20sample&label=id:node_5540100

Screenshot 2024-03-21 at 5 05 05 PM

Note: it reached 16/46 since the second sequence in Ireland, and while nearly all seqs are in Dublin, the capital, there is one sequence in Galway indicating possible spread, and we could expect it to go to UK or mainland Europe soon given its high prevalence now. Another thing is that it seemed to got some apparent gap issue that's fooling nextclade, usher seemed to ignore it already and just place them in a tree.

Screenshot 2024-03-21 at 5 06 49 PM
krosa1910 commented 5 months ago

S704L had been relatively successful in XBB, maybe the most successful S2 mutation. It is convergently gained by XBB.1.5.70.1, HV.1.6.1, JG.3 and GA.4. It also appeared in XDD.1 which is essentially JN.1 spike. jbloom lab once mentioned it as a mutation increasing ACE2 binding (on XBB basis, so don't put too much trust), so like T572I it could grow a bit within JN.1

FedeGueli commented 5 months ago

19 now

FedeGueli commented 3 months ago

40, but has decreased its growth, closing it