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Repository for suggesting new lineages that should be added to the current scheme
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HT.2 (XBB.1.5.49.2) with ORF1a:M3752I (nsp6_M183I) and S:T478R (22 seqs, 4 countries) #2275

Closed NkRMnZr closed 1 year ago

NkRMnZr commented 1 year ago

Taken from Branch 7 of multitask sars-cov-2-variants/lineage-proposals#451

Defining Mutations: HT.2 > G11521T(ORF1a:M3752I/nsp6_M183I), C15960T > C22995G(S:T478R) Query: G11521T, C21714T, C22995G Earliest seq: 2023-07-05 (EPI_ISL_17985212, Basque, Spain) Latest seq: 2023-08-13 (EPI_ISL_18222970, California, USA) Sampled Countries: USA (10: CA/7; HI; NY; OR), Spain (5), France (1), Mexico (1)

Genomes: `EPI_ISL_17985212, EPI_ISL_18044159, EPI_ISL_18049081, EPI_ISL_18060664, EPI_ISL_18072611, EPI_ISL_18073902, EPI_ISL_18094328, EPI_ISL_18095035, EPI_ISL_18108081, EPI_ISL_18121993, EPI_ISL_18137298, EPI_ISL_18222421, EPI_ISL_18222538, EPI_ISL_18222711, EPI_ISL_18222970, EPI_ISL_18233893, EPI_ISL_18238034`

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_91dd_c5ddf0.json?f_userOrOld=uploaded%20sample&label=id:node_7171398 image

corneliusroemer commented 1 year ago

Too small and doesn't have novel RBD haplotype either

FedeGueli commented 1 year ago

@corneliusroemer i dont think closing things in two days helps a lot. It was choosen cause we saw a high homoplasy level of 478R on XBB.1.5.49 especially in Mexico we tracked them all for a while. Backbone is not that fast but this one likely for its geographical spread wasnt that slow either. I am not saying we should designate everything but tracking for a bit more what has been selected after a good work of tracking could be more sensitive and maybe also give more fruit. Also likely you dint notice that this got mutations at 261 and 583 in the follow up branches. but ok.

FedeGueli commented 12 months ago

19 now