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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Saltation of CH.1.1.18 with S:T323I, S:E484P, ORF8:L7S, N:A155V, N:T271I (13 seqs as of 2023-04-06 in 3 countries) #1747

Closed c19850727 closed 1 year ago

c19850727 commented 1 year ago

First spotted by @ryhisner , many thanks!

This proposed sublineage should be a sub-branch of CH.1.1 with S:K187T, an undesignated branch that currently has ~150 sequences, but it is (mis)placed at a sibling branch probably due to missing coverages.

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Description

Sublineage of: CH.1.1 Earliest sequence: 2023/02/07 (Germany-SH) Most recent sequence: 2023/02/20 (Germany-SH) Countries circulating: Switzerland (1/6), Germany (2/6), Oman (3/6) The 3 genomes from Oman have some detailed metadata, indicating one of which is from ILI sentinel surveillance sample, while the other two are from non-sentinel-surveillance in two different hospitals.

Mutations on top of CH.1.1: A9154G, C11674T > A2015G (ORF1a:M584V), C23086T > C25710T, C28737T (N:A155V) > C3486T (ORF1a:A1074V) > A22122C (S:K187T) > A5068G, C22530T (S:T323I), G23012C (S:A484P), C23380T, T27913C (ORF8:L7S), C28312T, C29085T (N:T271I)

GISAID and Cov-spectrum query: A2015G, C3486T, A5068G, A9154G

Evidence

Usher tree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_363cb_a8fae0.json?branchLabel=Spike%20mutations&c=gt-nuc_22122&label=id:node_8011844

Genomes:

EPI_ISL_17004806, EPI_ISL_17026462, EPI_ISL_17026466, EPI_ISL_17026483, EPI_ISL_17071908, EPI_ISL_17076001

Mydtlwn commented 1 year ago

S:K187T mutation was mentioned by @silcn and @oobb45729 in #1380

ryhisner commented 1 year ago

I believe K187T creates a potential glycan site: N-F-T.

And these all have ORF9b:L10F (C28312T) as well! I know @fedegueli has often voiced his suspicion that ORF9b:L10F confers a real advantage over ORF9b:P10L.

AnonymousUserUse commented 1 year ago

Maybe this branch should be designated first: A9154G, C11674T > A2015G (ORF1a:M584V), C23086T > C25710T, C28737T (N:A155V) > C3486T (ORF1a:A1074V) > A22122C (S:K187T). And then the further 7 mutations on the top are only mini-saltation.

c19850727 commented 1 year ago

12 sequences in total now. 5 more from Oman and 1 from India-KL. Those 5 from Oman are among a batch of 60 uploaded today, and are all very recently swabbed.

corneliusroemer commented 1 year ago

Parent is designated CH.1.1.18. I suspect the tree is wrong and the parent is 187T.

c19850727 commented 1 year ago

It seems it's no longer growing. Close the issue for now.