BA.2 in India with 8 spike mutations [14 sequences]

[Sinickle]

This was noticed by @ryhisner when it was just 2 sequences due to its unusual mutation profile, but there are now 9 sequences, found so far in the Indian states of Maharashtra and Telangana.

Earliest sequence: June 6
Second sequence: June 23

The main reason for proposing this sublineage is the unusual spike profile.

Mutations beyond BA.2 are present in 3+ sequences, and 100% of them that don't have the region dropped out:

Gene	Mutation
ORF1a	P1640H
S	W64R, G75V, S:138-144del, S:242-243del, R493Q, T572N, D843G, Q1113R

Notably, there is some difficult with identifying what mutations are present, due to dropout. Just looking at the spike mutations..

• The only one that has S:137-144 present has S:138-144del.

• Of the 2 that have S:241-243 present, one of them has S:242del, and both have S:243del.

• 3/6 that have S:440 present have S:440N, the other 3 have S:440K.

• One of them with S:440K has S:S443L and S:K444R.

• 3/3 of them with S:493 have S:493Q

• 2/8 that have S:526 present, have S:G526R. One of these has S:V327P.

Cov-Spectrum Query

EPI_ISL IDs: EPI_ISL_13988810, EPI_ISL_13422063, EPI_ISL_13988950, EPI_ISL_13611346, EPI_ISL_13988817, EPI_ISL_13847300, EPI_ISL_13847296, EPI_ISL_13988940, EPI_ISL_13988781

I would like to additionally thank @chaoran-chen, for creating collections on cov-spectrum, which has made it very easy to throw these odd sequences onto a list and be alerted if any more sequences like them show up!

Edit: With new samples coming in, it appears that the S:138-144 del is legitimate, as well as the S:242-243del.

[ryhisner]

Two more sequences of this uploaded today from India, Telangana, Hyderabad.

EPI_ISL_14196487
EPI_ISL_14196544

These are higher quality than most previous ones, and both have S:138-144del and S:242-243, so these deletions are very likely shared by the other sequences, which didn't have coverage in this area. Both have ORF1a:A3730V, not found in any of the previous sequences, and ORF1a:3675-3677del, which was in just one previous sequence. Below is the spike profile from all 11 sequences as they appear on NextClade, with the two newest ones at the bottom.

Usher puts these two in an entirely different tree from all the others, but that's due to the very low coverage of the others. They clearly belong together.

Subtree #1 (with 9 of the 11 sequences): https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_14e50_95a990--9-of-11.json

Subtree #2 (with 2 most recent sequences): https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/subtreeAuspice1_genome_428ba_95c510--2-New.json

[Sinickle]

EPI_ISL_14502420 -- US sequence from 8/4. No new spike mutations.

[chrisruis]

Thanks @Sinickle As we're not seeing too many new sequences from this, will close for now

[Sinickle]

August 4
EPI_ISL_14502420
First US sequence.
I'm finding 14 seqs total now, globally.