search

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
Other
1.04k stars 98 forks source link

Danish BA.2 (+C22792T) lineage with S:W64L [700 seq] #512

Closed corneliusroemer closed 2 years ago

corneliusroemer commented 2 years ago

I think it would be worth designating a BA.2 sublineage with S:W64L as it could have a growth advantage. It's early to tell, but the mutation popped up in both South Africa and Denmark recently (one needs to see whether this is the same lineage). It's not a mutation that has been observed much before (only some 600 sequences over the pandemic outside of BA.2).

image image
corneliusroemer commented 2 years ago

Issue #533 is for the South African lineage

This issue is for the Danish one, they are independent.

corneliusroemer commented 2 years ago

S:W64L has arisen at least twice in BA.2

This proposal is for the Danish lineage.

It's on the global BA.2 branch (9866 mutated) and has the extra syn mut C22792T, so it's well separated from the SA lineage.

image

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_e701_1fdc30.json?c=userOrOld&label=nuc%20mutations:G21753T

Usher is very clean. This should be easy to designate.

It's travelled a bit around the world already.

image

https://cov-spectrum.org/explore/South%20Africa/AllSamples/Past6M/variants/international-comparison?aaMutations=S%3A64L&nucMutations=9866%2CC22792T&pangoLineage=BA.2*&

chrisruis commented 2 years ago

Thanks @corneliusroemer It looks like the increase in this clade as a proportion of BA.2+C22792T in Denmark may have plateaued, difficult to tell at this stage. However, given the similar increase in the #533 clade in South Africa, agree these 2 clades warrant a designation. We've added this as BA.2.14