search

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
Other
1.05k stars 98 forks source link

Early Delta sub-lineage with reversion Orf7A:V82A plus N:183T, ORF1b:2432I #302

Closed corneliusroemer closed 2 years ago

corneliusroemer commented 3 years ago

Zach Hensel noticed that the Polish lineage #301 has a reversion at Orf7A:82 comment.

It turns out there are a number of independent occurrences of that reversion within Delta.

One that seems particularly persistent is one with N:183T, ORF1b:2432I on top that was at times big in Israel and is currently growing in Belgium and Denmark. It was apparently first sequenced in Sweden in 2021-21 then Finland, Germany, Belgium in 2021-22. What's odd is that in almost all these countries the lineage disappeared only to come back now. Artefact?

Denmark: image

Belgium: image

Israel: image https://nextstrain.org/groups/neherlab/ncov/israel?branchLabel=aa&c=gt-ORF7a_82&r=division

orf7a82reversion.txt

Worldwide there are ~1k sequences that are mislabelled all over the place by pangoLEARN

image

https://cov-spectrum.ethz.ch/explore/World/AllSamples/Past6M/variants?aaMutations=N%3AS183T%2CORF1b%3A2432I&pangoLineage=B.1.617.2*

aineniamh commented 2 years ago

Closing this as it is a stale issue.