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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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Proposal to withdraw lineage BA.5.1.16 due to defining mutations being sketchy #1040

Closed corneliusroemer closed 1 year ago

corneliusroemer commented 1 year ago

Looking at BA.5.1.16 I investigated the two defining mutations: A2969G, G27470A

G27470A is very close to the BA.5.1 defining mutation T27438C (32 bases away), it has almost never been seen in Japan until BA.5.1 showed up. It is also extremely rare worldwide over the whole pandemic. This suggests purifying selection and that the mutation may be an artefact.

A2969G has a very artefacty signature looking at covSpectrum: it suddenly popped up in Ireland when Delta appeared and just as suddenly disappeared again. Just before, it suddenly appeared and disappeared in Germany.

image

It also very suddenly appeared and disappeared in Russia. Suggestive of bioinformatics issue that was then resolved.

image

Here I'm not 100% convinced that this can't be real but I have my doubts.

AngieHinrichs commented 1 year ago

I'm not so sure this isn't real. While this one is seen mostly in Japan, it has also been observed in several other countries. Here it is colored by country, and you can see multiple countries with evidence of local transmission:

image

Also, I don't see any reversions on 27470 or 2969 on that branch, which we might see if other mutations were pulling sequences in despite disagreeing on 27470 or 2969.

corneliusroemer commented 1 year ago

Thanks for looking at this! It's comforting that we may have some real here.

I should learn how to read the huge Usher tree live with taxonium instead of making slow one-off Usher trees via usher.bio

So the best warning sign remains unusual clustering across geographic boundaries. I feel like we might actually turn this into a metric that could help spot artefacty parts of the tree!

On Mon, Sep 5, 2022, 23:07 Angie Hinrichs @.***> wrote:

I'm not so sure this isn't real. While this one is seen mostly in Japan, it has also been observed in several other countries. Here it is colored by country, and you can see multiple countries with evidence of local transmission: [image: image] https://user-images.githubusercontent.com/186983/188511894-eeed58d3-49ca-458e-9c2a-ea4fa24e0d78.png Also, I don't see any reversions on 27470 or 2969 on that branch, which we might see if other mutations were pulling sequences in despite disagreeing on 27470 or 2969.

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