BA.2.38 sublineage with S:S247N, S:Y248S, S:K444N (29 seq, mainly India)

[silcn]

Proposal for a sublineage of BA.2.38
Earliest sequence: 2022-05-31 (India)
Countries detected: India (23 seq), US-WA (3), Denmark (2), Australia (1)

Defining mutations:
S:S247N, Y248S, K444N
nuc:G22225A

Yet another Indian lineage with recent emergence and spread to multiple continents. BA.2.38 with S:K444N was previously pointed out by @Sinickle in #746, but BA.2.38 with 444N doesn't seem to have much of an advantage over BA.2.38 without 444N which is probably why it hasn't been proposed for designation. This lineage seems to have grown quite rapidly after acquiring S:247N and S:248S, although it's too early to plot a growth advantage. That pair of mutations is in the same location as the insertions seen in BA.2.52 and #806, and BA.2 lineages with S:248 mutations have often shown a growth advantage.

Lineage is shown in yellow above. The yellow sequence near the bottom is also part of this lineage, but it's poor quality and Usher misplaces it.

https://nextstrain.org/fetch/github.com/silcn/subtreeAuspice1/raw/main/auspice/subtreeAuspice1_genome_340d_b8ee30.json?branchLabel=Spike%20mutations&c=gt-S_247&label=nuc%20mutations:G22225A

EPI_ISLs

EPI_ISL_13299674
EPI_ISL_13302198
EPI_ISL_13311009
EPI_ISL_13337549
EPI_ISL_13346711
EPI_ISL_13346714
EPI_ISL_13346715
EPI_ISL_13346784
EPI_ISL_13356325
EPI_ISL_13356332
EPI_ISL_13356357
EPI_ISL_13373040
EPI_ISL_13373193
EPI_ISL_13373294
EPI_ISL_13400946
EPI_ISL_13409381
EPI_ISL_13409409
EPI_ISL_13422074
EPI_ISL_13446517
EPI_ISL_13446519
EPI_ISL_13493456
EPI_ISL_13493525
EPI_ISL_13502379
EPI_ISL_13502531
EPI_ISL_13502533
EPI_ISL_13502539
EPI_ISL_13502541
EPI_ISL_13502542
EPI_ISL_13502551

Cov-spectrum: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=BA.2*+%26+S%3A247N+%26+S%3A248S+%26+22225A&

[c19850727]

There's another cluster mainly from Brazil featuring S:Y248SAVD. ~40 sequences at the moment.

Also #740 as well.

[FedeGueli]

@Sinickle spotted this sublineage too and we were monitoring it since. Good catch @silcn
I can comfirm that S:248S (and also S:64R) seems the mutation most beneficial to BA.2( there is also an unproposed sublineage in Germany with 248S and a couple with 64R) although none of the mentioned looks able to compete with BA.5

[FedeGueli]

edited
on usher tree i found 58 seqs as today.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_29ee4_2edfe0.json?c=pango_lineage_usher&label=nuc%20mutations:G22302A,A22305C

Now it has been exported to Singapore and Japan too.

It shows early, but significant signs of growth advantage vs BA.5 baseline

https://cov-spectrum.org/explore/India/AllSamples/Past2M/variants?aaMutations=M%3A3N&nucMutations=12160A&aaMutations1=s%3A248s%2Cs%3A247n%2Cs%3A417t%2Cs%3A444n&pangoLineage1=ba.2*&analysisMode=CompareToBaseline&

I think it is worth a fast designation to complete the picture of High trasmissible BA.2 sublineages emerged in India.

@corneliusroemer @InfrPopGen @chrisruis @AngieHinrichs @thomaspeacock

[karyakarte]

@FedeGueli In our latest sequencing run (Run 60, 89 samples), BA.2.38 number 30, BA.2 number 15, and BA.2.74,75,76 number 27 together. These 27 would have been counted as BA.2.

[FedeGueli]

Thx @karyakarte for sharing these results.
I think a fast designation of this sublineage could help to identify further what lineages are behind BA.2.38 and BA.2. I think i will split later the issue i opened on indian BA.2 sublineages and i will propose every lineage of interest circulating there cause my view is that the mayority of them are part of a relevant epidemiological event ongoing in India where we are seeing the global dominant strain (BA.5) kept at the bay and so they all match the pango designation rules.

@InfrPopGen @chrisruis @thomaspeacock @corneliusroemer @AngieHinrichs

[karyakarte]

Thanks @FedeGueli most of the samples were collected between 22nd and 29th June. What you say reflects in the above-mentioned run we have BA.4 = 3, BA.5 = 1, BA.5.2 = 4, BA.5.2.1 = 1 (Confirmed by IBDC).

[FedeGueli]

thx @chrisruis for designating this.

[chrisruis]

Thanks @silcn We've added this as BA.2.38.1 to start on the branch with G22302A (S:S247N) and A22305C (S:Y248S)