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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 broaden AY.41 definition to ORF1b:1257V, S:1167V, ORF1b:1643V , as already proposed in #237, plus Orf1b:K82R #440

Closed FedeGueli closed 2 years ago

FedeGueli commented 2 years ago

Proposal to broaden AY.41 definition to ORF1b:1257V, S:1167V, ORF1b:1643V + Orf1B:K82R as proposed by @corneliusroemer in #237 . This would comprise the proposed sublineage in #436

Before trying to reconstruct the designation history of this large clade it would be better first looking at the TREE Schermata 2022-02-15 alle 01 19 15

In #237 @c19850727 proposed 4 sublineages. The 4th lineage has been proposed with the following mutations: ORF1b:A1643V, then S:G1167V, then G9220A, then ORF1b:K82R, then G7936T, then ORF1b:I1257V, then ORF1a:K669N, then ORF1a:G519S and S:S477I, then S:A262S then ORF1b:P218S but it has been designating AY.41 starting with G1820A (Orf1a:G519S) and G22992T (S:S477I) As @corneliusroemer immediately noted in this comment it was too deep in the branch: in fact he identified a common branch between the newly designated AY.41 and the future AY.103, at the time still undesignated, starting with ORF1b:1257V. Then in USA it acquired nuc:24208T and then it has been designated AY.103 independently from #237, instead in Croatia it acquired S:1167V, ORF1b:1643V then G9220A, then ORF1b:K82R and then, as shown here , it has been divided in two main branch : one designated AY.41 starting with G1820A (Orf1a:G519S) and G22992T (S:S477I) but comprising ORF1a:G519S, Orf1a:K669N and ORF1b:P218S too and the other defined by nuc: G26840T then ORF3a:G18V (G25445T), Orf3a:T151I(C25844T) that has kept circulating till week 5-2022 in Germany and has been proposed in #436 .

Schermata 2022-02-15 alle 01 03 55

So i propose to broaden AY:41 starting with ORF1b:1257V, S:1167V, ORF1b:1643V and ORF1b:K82R Number of sequences : 10821 List of sequences: contributors (4).csv Countries : Slovenia 2388 seqs, Croatia 2866seqs, Germany 1970 seqs , Poland 396, Switzerland 300+, Denmark 300+.

Actually this sublineage is assigned in this way: B.1.617.2 (43.64%) AY.41 (32.68%) AY.103 (13.03%) AY.125 (4.27%) AY.46.6 (2.03%) AY.122 (1.33%) AY.102 (0.44%) AY.91 (0.41%) AY.126 (0.31%) AY.4.7 (0.26%) AY.131 (0.15%) AY.43 (0.14%) AY.25.3 (0.12%) AY.127 (0.12%) AY.111 (0.09%)

So the current definition of AY.41 catches just 1/3 of the sequences belonging to the parental broader lineage. COV-SPECTRUM

cc @AngieHinrichs

FedeGueli commented 2 years ago

This lineage kept circulating in Germany and Slovenia through week 5/2022 and one sequence is from.w10/2022 in USA I think the broadening of AY.41 definition still makes sense , it circulated widely in western europe and made its way to 2022. More It is a sibling lineage of AY.103 that gave birth to some putative recombinant seqs in USA. To track potential recombination events it will be helpful to broaden the definition also in light of masses moving from east to west due to the invasion of Ukraine What do you think @chrisruis ?

FedeGueli commented 2 years ago

@InfrPopGen I was seeing you are working on designation of past delta sublineages, if you have time to look at this. It is quite clear from the initial @corneliusroemer analysis mentioned above. I understand that is far from important, but otherwise i ll close this issue.

chrisruis commented 2 years ago

I'll close this for now as AY.41 hasn't been seen much recently