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Repository for suggesting new lineages that should be added to the current scheme
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XBB.2.3 sublineage with S:E654K and possible S:K478T reversion (65 seqs in 9 countries) #2241

Closed HynnSpylor closed 1 year ago

HynnSpylor commented 1 year ago

*Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/731 @ryhisner has noticed it and the parent lineage is tracked by @aviczhl2 in #1945. Thx a lot!

Defining mutations: XBB.2.3> C5622T (ORF1a:P1786L)> C7303A> C10776T (ORF1a:P3504L), C22624T, G23522A (S:E654K) GISAID query: C7303A, C10776T, G23522A Earliest seq: 2023-06-20 (Maharashtra, India- EPI_ISL_18052802) Most recent seq: 2023-08-24 (Maharashtra, India- EPI_ISL_18209977) Countries detected: India (24, including 1 detected in US International Airport), US (1)

Usher Tree: QQ截图20230901220922

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_10b57_1ed5f0.json?c=gt-S_654

It is a branch with S:G184V ( proposed but undesignated in https://github.com/cov-lineages/pango-designation/issues/1945) but without another defining mutation of XBB.2.3.2 (ORF1a:R2159W), hence it is not classified as XBB.2.3.2

Another notable feature is the almost seqs are possible S:K478T reversion. If we show the S:478 on neighbored branches, the other branch are not the concentrative reversion. Moreover, if we query the other samples updated in the same batch on GISAID, the samples outside the branch are all showing the S:T478X mutation. Therefore, I suggest the reversion is possibly true instead of artefacts. QQ截图20230901221055

*The branch accounts for >30% of samples updated in MH, India today, and over half of them are collected in last 10 days.

Genomes: EPI_ISL_18052798, EPI_ISL_18052802, EPI_ISL_18120273, EPI_ISL_18120276, EPI_ISL_18125007, EPI_ISL_18126472, EPI_ISL_18209930-18209931, EPI_ISL_18209936, EPI_ISL_18209945, EPI_ISL_18209947-18209948, EPI_ISL_18209950-18209951, EPI_ISL_18209954, EPI_ISL_18209959, EPI_ISL_18209961, EPI_ISL_18209967, EPI_ISL_18209969, EPI_ISL_18209973, EPI_ISL_18209976-18209977, EPI_ISL_18209980-18209981, EPI_ISL_18209983

HynnSpylor commented 1 year ago

1 more seq in Australia

HynnSpylor commented 1 year ago

today +3, Ireland, France and UK (England).

HynnSpylor commented 1 year ago

54 seqs now and it has a ~35% prevalence in MH, India.

HynnSpylor commented 1 year ago

62 seqs now

FedeGueli commented 1 year ago

65 now

FedeGueli commented 1 year ago

85 now @corneliusroemer this one even if likely not able to compete with HK.3 represents 30% of samples (5/15 so...) collected in MH, India. Dr Karyakarte confirmed us XBB.2.3 is still on the lead there. I think could be a good idea to deisngate this one. Not urgent.