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mpxv-lineages / lineage-designation

Official place for proposals and details around monkeypox virus lineage designations
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Proposal for B.1.20 sublineage OPG117:S297L #2 #40

Open ammaraziz opened 3 months ago

ammaraziz commented 3 months ago

Second proposal for a sublineage of B.1.20. The proposed sublineage is found in USA from public data but soon there will be more from Australia.

Screenshot from 2024-06-03 14-20-17

https://nextstrain.org/mpox/lineage-B.1?branchLabel=aa&c=gt-OPG117_297&gmax=98406&gmin=96049

Mutations

OPG117:S297L

New sequences from Australia sit in the lower branch of B.1.20+OPG117:S297L which is defined by only nucleotides G23100A, C50572T, C176642T

This one is a tad tricky as there's a clear sub-sub-lineage within the proposed B.1.20+OPG117:S297L, which I will call B.1.20 + OPG117:S297L + OPG029:R108C

image

Unsure if B.1.20 + OPG117:S297L + OPG029:R108C should be designated a new sublineage alongside the above sublineage. It does not meet the criteria of has spread internationally

corneliusroemer commented 3 months ago

Thanks for the issues @ammaraziz! Could you send me those sequences from Australia? Just the fasta is fine, no need for any metadata! You can either post them here or send via email/Slack. Would be helpful for designation purposes.

Using a single defining mutation should be ok here as it is part of a not so huge polytomy - in contrast to the original B.1 outbreak where using just one SNP is asking for ambiguity in tree building/lineage definition.

It would be amazing if I could see the sequences - while I trust you, it's always good to make decisions based on data :)