Proposal for a Potential BA.2.x with Spike S704L (2.2k Seqs), and Its Potential sublineage with Additional Spike L452Q (240 Seqs)

[c19850727]

Description

Potential sublineage of: BA.2
Earliest sequence: 2021/12/06 (India)
Most recent sequence: 2022/3/25 (UK, Belgium, Denmark)
Mutation on top of BA.2: S:S704L (it's interesting that BA.1 also has a sublineage with S:S704L, which appears to have some growth advantage over original BA.1 in Brazil)
Countries circulating: India, UK, US, Belgium, Denmark, Germany, etc.

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants/international-comparison?aaMutations=S%3A704L&pangoLineage=BA.2*&nucMutations1=A2832G%2CG4184A%2CG10986A%2CA29510C

Evidence

Usher tree (BA.2+S:S704L in yellow color, and BA.2+S:S704L+S:L452Q in blue color):

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31cfc_5d5e70.json?c=gt-S_452,704&l=radial&label=nuc%20mutations:C241T,T670G,C2790T,C3037T,G4184A,C4321T,C9344T,A9424G,C9534T,C9866T,C10029T,C10198T,G10447A,C10449A,C12880T,C14408T,C15714T,C17410T,A18163G,C19955T,A20055G,C21618T,T22200G,G22578A,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,G22813T,T22882G,G22992A,C22995A,A23013C,A23040G,A23055G,A23063T,T23075C,A23403G,C23525T,T23599G,C23604A,C23854A,G23948T,A24424T,T24469A,C25000T,C25416T,C25584T,C26060T,C26270T,C26577G,G26709A,C26858T,A27259C,G27382C,A27383T,T27384C,C27807T,A28271T,C28311T,G28881A,G28882A,G28883C,A29510C

Genomes:

BA.2+S704L.csv

[c19850727]

I'd also like to propose a potential sublineage of #499 predominantly found in Canada and the US, with an additional Spike L452Q.

Potential sublineage of: #499
Earliest sequence: 2022/1/20 (Canada-AB
Most recent sequence: 2022/3/22 (US-NJ)
Mutation on top of BA.2: S:S704L, S:L452Q
Countries circulating: predominantly US and Canada

Evidence:

Usher tree:

Comparison between BA.2, BA.2+S:S704L, and BA.2+S:S704L+S:L452Q, in North America in recent 3 month:

Genomes:

BA.2+L452Q.csv

[FedeGueli]

Looking at covspectrum relative growth advantage of BA.2+S:704L,452Qin New York (the only one with sufficient sequences for a minimun estimate) is around +42% vs BA.2

https://cov-spectrum.org/explore/United%20States/AllSamples/from=2022-02-01&to=2022-04-01/variants?pangoLineage=BA.2*&aaMutations1=S%3A704L%2CS%3A452Q&pangoLineage1=BA.2*&analysisMode=CompareToBaseline

But it seems on the rise as share of total BA.2 seqs everywhere it popped up

[corneliusroemer]

The 704 one is definitely worth designating immediately. There's also a BA.1 sublineage with it: BA.1.9

[silcn]

But it seems on the rise as share of total BA.2 seqs everywhere it popped up

... but not in Canada where it appears to have originally arisen, so I think it's too early to declare this as having a significant advantage. The USA branch has an additional two silent mutations T15009C and C21721T but those shouldn't cause it to behave differently. There is a Canadian sequence from 2022-01-27 in this branch that predates all the USA ones (earliest being 2022-02-09), so it looks like it was imported to the USA in late Jan/early Feb, and then maybe took off by chance in NY in early March when case numbers were very low.

[FedeGueli]

But it seems on the rise as share of total BA.2 seqs everywhere it popped up

... but not in Canada where it appears to have originally arisen, so I think it's too early to declare this as having a significant advantage. The USA branch has an additional two silent mutations T15009C and C21721T but those shouldn't cause it to behave differently. There is a Canadian sequence from 2022-01-27 in this branch that predates all the USA ones (earliest being 2022-02-09), so it looks like it was imported to the USA in late Jan/early Feb, and then maybe took off by chance in NY in early March when case numbers were very low.

yes true! thank you very much i was meaning in the other states of united states

[RajLABN]

Just saw this.. I will close mine

[FedeGueli]

306 sequences now 277 in Usa for BA.2 with S:452Q, S_704L

[corneliusroemer]

Thanks @c19850727 this has been included in v1.3 as BA.2.12 and BA.2.12.1

[animesh-workplace]

Which one is BA.2.12 - S:452Q or S704L?

[FedeGueli]

BA.2.12 is S:704L BA.2.12.1 is S:704L + S:452Q
@animesh-workplace

[c19850727]

Just found there are 2 sequences of potential BA.1*+BA.2.12.1 recombinant, with likely breakpoint bwtween 10448 and 12879 (which is interestingly very similar to XE).
Genomes: EPI_ISL_12595963, EPI_ISL_12612080.
Private mutations: C7564T, A23440G