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
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:
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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