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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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KP.2.3 + S:S31del branch with N:H145Y + S:K679R + ORF1a:T2016K (207 in 9 countries) + Branch with S:G184S (13) and a Branch with ORF1a:S944L + S:E1202G (21) #2732

Open Fearuncle opened 4 weeks ago

Fearuncle commented 4 weeks ago

from: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1603 image tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_43792_cbe980.json?f_userOrOld=uploaded%20sample

Query: C6312A, T19449C, A23598G, C28706T

Query with S:G184S: G22112A,C28706T, C6312A

Query with S:E1202G and ORF1a:S944L: C3096T, A25167G, C28706T

Over-There-Is commented 3 weeks ago

There is a subbranch with S:G184S. I think it's also worth tracking.

FedeGueli commented 3 weeks ago

There is a subbranch with S:G184S. I think it's also worth tracking.

query: G22112A,C28706T, C6312A Samples:11

Please @Fearuncle add this to the title ad the man proposal

Over-There-Is commented 2 weeks ago

EPI_ISL_19280116 imported from Peru

Fearuncle commented 2 weeks ago

9 with ORF1a:S944L + S:E1202G image

Fearuncle commented 4 days ago

Passed 200 seq.

FedeGueli commented 4 days ago

9 with ORF1a:S944L + S:E1202G (C3096T, A25167G, C28706T)

This is a canadian cluster >> scoring high for growth advantage but worth keeping it tracked if it starts emerging elsewhere. @ryhisner any idea if S:E1202G could mean something? it is the same residue of the double nuc (silent 1201 + 1202K) we saw multiple times

ryhisner commented 4 days ago

Fede, you're thinking of S:Q1201K, which often has a silent mutation in S:L1200. But Q1201K also shows up pretty frequently without that second nuc mutation (which creates a suboptimal TRS motif), so I think it must have a function apart from its TRS implications. I don't know what it would be though. I don't think this region is an antibody target, but it's hard to be sure.

image
FedeGueli commented 3 days ago

Fede, you're thinking of S:Q1201K, which often has a silent mutation in S:L1200. But Q1201K also shows up pretty frequently without that second nuc mutation (which creates a suboptimal TRS motif), so I think it must have a function apart from its TRS implications. I don't know what it would be though. I don't think this region is an antibody target, but it's hard to be sure. image

Yeah sorry i miss recalled it as 1202 it is obviously 1201! and 1200 as silent. thank you very much!