Potential BA.1*/BA.2 Recombinant with Likely Breakpoint at NSP3/NSP4 (9 Seqs in Japan, Canada and India)

[c19850727]

Description

Recombinant between: BA.1* & BA.2
Earliest sequence: 2022/1/20 (Japan ex-India)
Most recent sequence: 2022/3/4 (India-Maharashtra)
Countries circulating: India (3 seqs in Gurajat and 2 seqs in Maharashtra), Japan (1 seq from imported case with travel history to India)
Likely breakpoint: between 6518 and 9343 (NSP3 or NSP4).
Conserved Nuc mutations (those in red frames are likely from the donor from the BA.1 side):

Cov-spectrum query: A2832G, C25416T, T22792C, T5386G, G5924A, 29510C

Evidence

Usher tree:

(The neighboring branch is XL.)
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3207_a713c0.json?c=gt-nuc_25416&label=nuc%20mutations:T22792C

Genomes:

Accession	Virus name
EPI_ISL_10495221	hCoV-19/Japan/IC-4679/2022
EPI_ISL_10523603	hCoV-19/India/RJ-SMS-ICMR-INSACOG-TS-11049/2022
EPI_ISL_10675556	hCoV-19/India/RJ-SMS-ICMR-INSACOG-TS-9433/2022
EPI_ISL_10675557	hCoV-19/India/RJ-SMS-ICMR-INSACOG-TS-9434/2022
EPI_ISL_11664674	hCoV-19/India/MH-KasturbaMCGM-ICMR-INSACOG-WG3600/2022
EPI_ISL_11664669	hCoV-19/India/MH-KasturbaMCGM-ICMR-INSACOG-WG3595/2022

[c19850727]

9 sequences as of 2022-04-10, and newly found in India-Rajastan and Canada.

[thomasppeacock]

I think this is a recombinant that is worth assigning even though it doesnt hit the minimum sequence numbers due to:

1. Mainly being focussed in a country with medium volumes of sequencing
2. found in 2 non-contiguous Indian states.
3. found twice in other countries (with travel history for at least one)
   All of this suggests this recombinant is much more widespread than it appears and an assignment will help both domestic and international surveillence pick this up.

[c19850727]

I came across a few other potential BA.1+BA.2 recombinants, mainly from India, and also among imported cases from Japan, Canada, etc.

Those potential recombinants all have similar breakpoints like #522; they also have the conserved mutation 25416T (many of them also have 22792C), but they don't cluster on Usher tree.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_424a9_8ecd00.json?c=country&gt=nuc.25416T,22792C&label=nuc%20mutations:T4321C&tl=country

[c19850727]

Just found from @corneliusroemer 's other proposals that C25416T is a common BA.2 mutation in India and a few other regions. Problem solved I suppose.

[learithe]

We saw a sequence that belongs in this group in late February in Sydney. EPI_ISL_11993540 hCoV-19/Australia/NSW-ICPMR-23049/2022

[chrisruis]

Thanks @c19850727 We've added this as XU

[AngieHinrichs]

Just wanted to note briefly that the two Canada sequences turned up by the cov-spectrum query also have quite a few other mutations that distinguish them from the India, Japan & Australia sequences, and are placed a lot farther out on the branch of miscellaneous BA.1/BA.2 recombinants in the UShER tree. And I see @chrisruis didn't include the Canada sequences in the designated sequences, so, good. :)

[JosetteSchoenma]

XU