BQ.1.1.32 (S:M153I + Y144-) + S:S494P in England (16 sequences) + USA (2 sequences)

[rquiroga7]

Sub-lineage of: BQ.1.1.32
Earliest sequence: 2022-11-15
Most recent sequence: 2022-12-20
Countries circulating: England

The proposed lineage has S:494P, and seems to be growing fast. This seems to be a sublineage of BQ.1.1.32, since they have S:M153I, and S:Y144-. Also, two sequences from USA appear within same subtree. Interestingly, same combination of Spike mutations as I reported in issue #1483 (S:Y144- + S:S494P).

Genomes

USA/CA-CDC-LC0956282/2022|EPI_ISL_16206113|2022-12-05
USA/CA-CDC-LC0956284/2022|EPI_ISL_16206111|2022-12-05
England/PHEP-YYGDYTT/2022|2022-12-09
England/LSPA-3262C4F4/2022|2022-12-15
England/LSPA-325EFB35/2022|OX378388.1|2022-11-15
England/PHEC-YY8W8Z4/2022|2022-12-19
England/PHEC-YY81TMP/2022|2022-12-07
England/PHEC-YY8TMZH/2022|2022-11-30
England/PHEC-YY8WKAI/2022|2022-12-18
England/PHEC-YY8UH8E/2022|2022-12-20
England/LSPA-3262C4E5/2022|2022-12-16
England/LSPA-32634C88/2022|2022-12-19
England/LSPA-32634EBF/2022|2022-12-19
England/LSPA-3262C88F/2022|2022-12-16

Usher tree:

[silcn]

These don't have C913A, so they aren't BQ.1.1.22.

[AngieHinrichs]

I see that pangoLEARN really consistently calls the BQ.1.1 > S:M153I (G22021A) branch as BQ.1.1.22, although as @silcn points out, the sequences in this proposal do not have C913A so aren't fully BQ.1.1.22 as currently defined. However, BQ.1.1.22 was motivated not by the synonymous mutation C913A but by the deletion that accompanies it. From lineage_notes.txt:

BQ.1.1.22       Alias of B.1.1.529.5.3.1.1.1.1.1.1.22, Australia/England/Denmark, S:144- and C913A

I haven't looked at these sequences, but just speculating -- perhaps they also have the S:144- ? That would be invisible to UShER since it deals only with substitutions, not insertions/deletions.

[silcn]

The S:M153I branch does also have 144del, and it turns out it has already been proposed in #1402, so a decision should be made on that proposal before this one. There are lots of BQ.1.1*+S:144del lineages; BQ.1.1.22 is one and the S:M153I branch is another.

[rquiroga7]

I think you are right about issue #1402, this might be a sub-branch of M153I+S:144- that has also acquired S494P. Do you agree @silcn?

[silcn]

@rquiroga7 yes, that's what I was trying to say though I didn't explain it very clearly - since this is a sublineage of #1402, it needs to be designated before this one.

[FedeGueli]

@silcn @rquiroga7 in #1402 there are two lineages a bigger one with G22021A and a smaller one with G22021T

[rquiroga7]

Sorry, just noticed I missed ID of some of the genomes. Here are all:

USA/CA-CDC-LC0956282/2022|OQ080983.1|2022-12-05
USA/CA-CDC-LC0956284/2022|OQ080981.1|2022-12-05
England/PHEP-YYGDYTT/2022|2022-12-09
England/LSPA-3262C4F4/2022|2022-12-15
OX396335.1|2022-12-15
England/LSPA-325EFB35/2022|OX378388.1|2022-11-15
England/LSPA-32641A60/2022|2022-12-20
England/PHEC-YY8W8Z4/2022|2022-12-19
England/PHEC-YY81TMP/2022|2022-12-07
England/PHEC-YY8WKAI/2022|2022-12-18
England/PHEC-YY8UH8E/2022|2022-12-20
England/LSPA-32637B00/2022|2022-12-20
England/LSPA-32638B5A/2022|2022-12-20
England/QEUH-32638659/2022|2022-12-12
England/PHEC-YY8TMZH/2022|2022-11-30
England/LSPA-3262C4E5/2022|2022-12-16
England/LSPA-32634C88/2022|2022-12-19
England/LSPA-32634EBF/2022|2022-12-19
England/LSPA-3262C88F/2022|2022-12-16

[rquiroga7]

This seems to be a sublineage of BQ.1.1.32, designated today.

According to GISAID, in England, BQ.1.1.32 with no S:S494P mutations represented 0.14% of sequences sampled between 2022-12-01 and 2022-12-15, and also 0.14% of sequences sampled between 2022-12-15 and 2022-12-31.

Meanwhile, for the same time periods, BQ.1.1.32 + S:S494P went from 0.04% to 0.29% of sequences. This suggests that S:S494P gives this sublineage a fitness advantage.