HK.20.1 with S:S704L in England (22 seqs, 2 countries)

FedeGueli commented 10 months ago

I noticed a while back a stepwise evolved HK.20.1 (Flip+S:G482R) that got S:S704L, now it is 18 and worth tracking it publicly. Looking at the tree it is possible to spot 3/4 independent acquisition of S:S704L by HK.20.1 all very recent ( cc @angiehinrichs the tree seems solid here)

Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2d1d5_9e5d10.json?c=gt-S_704&gmax=25384&gmin=21563&label=id:node_3468979

Despite not being big it has already got two/three sub-branches defined by spike mutations as S:V705I on the top , or S:K444M on the bottom:

Defining mutations: HK.20.1 > > C17502T > C28214T > C19803T > T23398C > C7834T, Orf1b:I1675T(T18488C), C19290T > S:S704L (C23673T)

Query: T18488C, C19290T ,C23673T

Samples: 19 First : England 2023-11-13 Last : England 023-12-24

IDs: EPI_ISL_18525477, EPI_ISL_18545581, EPI_ISL_18578093, EPI_ISL_18598905, EPI_ISL_18598931, EPI_ISL_18606211, EPI_ISL_18641385, EPI_ISL_18652416, EPI_ISL_18688185-18688186, EPI_ISL_18694599, EPI_ISL_18694612, EPI_ISL_18712636, EPI_ISL_18712645, EPI_ISL_18717916, EPI_ISL_18717932, EPI_ISL_18717942, EPI_ISL_18717965, EPI_ISL_18720990,

Mydtlwn commented 10 months ago

this is interesting!

FedeGueli commented 10 months ago

this is interesting!

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=T18488C%2CC19290T%2CC23673T&analysisMode=CompareToBaseline&

FedeGueli commented 9 months ago

too slow to track

sars-cov-2-variants / lineage-proposals

HK.20.1 with S:S704L in England (22 seqs, 2 countries) #1266