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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 for a new B.1.617.2 sublineage with N:P207S, Orf1b:K469N circulating in Belgium #271

Closed FedeGueli closed 3 years ago

FedeGueli commented 3 years ago

Looking at 20I Nextstrain clade i spotted a couple of still undesignated sublineages:

The first one is a relatively small clade circulating in Belgium (407 sequences) and Netherlands (161 sequences) since may 2021 with key mutations Orf1b:K469N and N:P207S plus synonymous T6496C,G14874T Schermata 2021-10-19 alle 23 23 41 https://nextstrain.org/groups/neherlab/ncov/belgium?branchLabel=aa&c=gt-nuc_6469,14874&d=tree,entropy,frequencies&p=full&r=division&tl=pango_lineage

It is around 3% in Belgium according to covspectrum.ethz.ch: Schermata 2021-10-19 alle 23 28 56

2% cumulative prevalence in Belgium on Outbreak.info: Schermata 2021-10-19 alle 23 30 02

Looking at the same tree it is quite clear that a clade (the one starting with N950D) is still mistakenly not assigned to AY.9: Schermata 2021-10-19 alle 23 33 08

Here the sequences if it could help: Schermata 2021-10-19 alle 23 36 26

FedeGueli commented 3 years ago

This has been designated as AY.66 starting with T6496C According to new designations from https://www.pango.network/summary-of-designated-ay-lineages/ Tree: Schermata 2021-11-01 alle 20 50 32

cc @chrisruis

corneliusroemer commented 3 years ago

Thanks @FedeGueli you should include the commit message of the designation to improve trackability like this https://github.com/cov-lineages/pango-designation/commit/1478ff2e39eedfcfad874c88cd8deede256e4e62

you can find the commit by using github search for say AY.66

FedeGueli commented 3 years ago

Hi @corneliusroemer thank you, i wasnt able to find the commit of the others issues i matched with new AY.s on mobile, Now i found them using Pc thank you very much