BA.2 sublineage with S:N148T (202 seq, ~9% of BA.2 in Ontario, Canada)

[silcn]

Proposal for a sublineage of BA.2
Earliest sequence: 2022-01-09 (Canada)
Latest sequence: 2022-03-30 (Canada)

Countries detected: Canada (172, all Ontario), USA (30, across 13 states)

Defining mutations: N:D348H and then S:N148T, nuc:C28498T

This lineage currently makes up about 9% of BA.2* (7% of all sequences) in Ontario. Cov-spectrum shows a preliminary estimate of 24% growth advantage over BA.2* in Ontario. The growth advantage across Canada as a whole is misleading because Ontario makes up a higher proportion of recent sequences.

Cov-spectrum query: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=A22005C%2CC28498T%2CG29315C&pangoLineage=BA.2*&variantQuery1=BA.2*+%26+A22005C+%26+C28498T+%26+G29315C&

[corneliusroemer]

Looks interesting. Would be great if you could include a link to the Usher tree. Thanks!

It's interesting how it's growing in the US, too

First mutation seems to have been ORF9b:T72I = C28498T, then N, then S

The ORF9b lineage has ~1k sequences worldwide, first sequenced in Denmark.

Good growth in Ontario, I agree

Here's an Usher link
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_194c0_2084f0.json?c=country&label=nuc%20mutations:A22005C,C28498T

[corneliusroemer]

Interestingly, S:148T had slight growth advantages in both Alpha and Delta

Both times around 1% per day

[chrisruis]

Thanks @silcn We've added this as BA.2.20 to start on the branch with A22005C (S:N148T) and C28498T (synonymous)

[venkataduvvuri]

Hello Chris

Is BA.2.20 lineage or sub-lineage? What is the best practice to use lineage or sub-lineage terminology? I appreciate your reply.

Thank you
Venkata

[chrisruis]

Hi Venkata, I'd refer to individual Pango labels like BA.2.20 as lineages

[venkataduvvuri]

Thank you, Chris.