Proposal for a Sublineage of BA.2.13 with Spike T941S

[ryhisner]

Description

Sub-lineage of: BA.2.13
Earliest sequence: 2022-4-9 (USA, Florida)
Most recent sequence: 2022-6-19 (USA, Nebraska)
Countries circulating: Mostly the US (315 of 333 according to GISAID)
Number of Sequences: 375 in the Usher tree; 333 in GISAID search for L452M + T941S 

Substitutions on top of BA.13

Spike: T941S

Nucleotide: A24383T, C16954T



USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_b285_4d78c0%20-%20BA.2.13%20%2B%20T941S.json
Evidence
Relative weekly growth advantage (20%) via CovSpectrum over BA.2.13* in the last three months in the US:
https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?pangoLineage=BA.2.13*&aaMutations1=S%3AT941S&pangoLineage1=BA.2.13*&analysisMode=CompareToBaseline&

Relative weekly growth advantage (16%) via CovSpectrum over S:L452Q + S:S704L in the last three months in the US:

https://cov-spectrum.org/explore/United%20States/AllSamples/Past2M/variants?aaMutations=S%3AL452Q%2CS%3AS704L&aaMutations1=S%3AL452Q%2CS%3AS704L%2CS%3AV1264L%2CN%3AT282I&analysisMode=CompareToBaseline&

Genomes
GISAID_hcov-19_ids_2022_06_23_21_46 - L452M + T941S GISAID search results.csv

[FedeGueli]

Hi @ryhisner i got an error in the usher tree you linked.

[ryhisner]

Thanks for telling me, @FedeGueli. I have to run right now, but I'll fix it as soon as I can.

[AngieHinrichs]

I removed some extra stuff from the end of the link above, this seems to work:

https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_b285_4d78c0%20-%20BA.2.13%20%2B%20T941S.json

[ryhisner]

Quick update on this. There are now 482 members of this lineage on the Usher tree, though I suspect that's an undercount as I found several others the clearly belong there but were instead placed in a weird tree with a bunch of garbage sequences (by Curative and such).
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_371d3_919f02022-7-2.json

Weekly growth advantage in the United States relative to BA.2.13 without S:T941S over the past three months (using a more precise nucleotide CovSpectrum query) has increased to 37% with CI of 31%-43%. https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?variantQuery=A23767G+%26+C22792T+%26+%21A24383T&variantQuery1=A23767G+%26+C22792T+%26+A24383T&analysisMode=CompareToBaseline&
Worldwide, the same comparison returns a weekly growth advantage of 51% with CI of 46%-57%.
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?variantQuery=A23767G+%26+C22792T+%26+%21A24383T&variantQuery1=A23767G+%26+C22792T+%26+A24383T&analysisMode=CompareToBaseline&

Relative to BA.2.12.1 in the United States over the past 3 months, this proposed lineage has a 17% growth advantage, one point higher than when it was first proposed, and now the confidence intervals have tightened to 12-22%. https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?variantQuery=S%3AL452Q+%26+S%3AS704L&variantQuery1=A23767G+%26+C22792T+%26+A24383T&analysisMode=CompareToBaseline&

[AngieHinrichs]

I found several others the clearly belong there but were instead placed in a weird tree with a bunch of garbage sequences

@ryhisner can you send some example names/IDs? I might be able to clean that up a bit.

[InfrPopGen]

Thanks for submitting. We've added lineage BA.2.13.1 with 415 newly designated sequences, and 25 updated designations from BA.2, and 2 updated from BA.2.13. Defining mutation(s) A24383T (S:T941S).