Potential BA.2.75*/BQ.1* recombinant sublineage with S:D111N, ORF1ab:T1828N, ORF3a:S195P (65 seq., 7 countries)

[agamedilab]

Proposal for a potential BA.2.75*/BQ.1*recombinant sublineage
Earliest sequence: 22.12.2022 (Singapore)
Countries detected: Singapore, Malaysia, USA, England, Austria

This is another potiential BA.2.75*/BQ.1* recombinant sublineage defined by S:D111N, ORF1ab:T1828N, ORF3a:S195P. Nextclade identifies the sequences as XBP or XBS while usher places them within BA.2.75. 42 seq. as of 11.03.23.

Gisaid query: C5748A, T13324C, G21893A, C22747T, T25975C

Defining Mutations:
nuc unique C5748A, T13324C, G21893A, C22747T, T25975C
nuc homoplasies C11124T, C23595T
ORF1ab unique T1828N
ORF1ab homoplasies A3620V
S unique D111N
S homoplasies T678I
ORF3a unique S195P

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_dbfc_ceedb0.json?c=gt-S_678,111

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=M%3AD3N%2CS%3A346T%2CN%3AE136D%2CS%3AK444T%2CS%3AL452R%2CS%3AF486V%2CS%3AD111N%2CS%3AT678I&

EPI_ISL_16976933, EPI_ISL_16977008, EPI_ISL_17178366, EPI_ISL_17179291, EPI_ISL_17182593, EPI_ISL_17182494, EPI_ISL_17182489, EPI_ISL_16415291, EPI_ISL_16352127, EPI_ISL_17045324, EPI_ISL_16980144, EPI_ISL_16676426, EPI_ISL_17007764, EPI_ISL_17178366, EPI_ISL_16952041, EPI_ISL_16978835, EPI_ISL_17032398, EPI_ISL_17032492

OQ426072.1, OQ515811.1, OQ445271.1, OX443241.1, OX438343.1, OX437448.1, OX437448.1, OX439491.1, OX440851.1, OX439497.1, OX440876.1, OX441983.1

[agamedilab]

48 as of 20.03.23.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_358eb_85d2d0.json?c=gt-S_111

Small subclade defined by ORF1ab: T749A, P7013L, R7014H, R7014S (11 seq., England) maybe worth proposing on its own.

ORF1b:P2612L
ORF1b:R2613N

[agamedilab]

65 as of 28.03.23.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2b400_2ac0a0.json?c=gt-S_111

[InfrPopGen]

Thanks for submitting. We've added lineage XCA with 41 newly designated sequences, and 0 updated. Defining mutations C5748A (ORF1a:T1828N), C11124T (ORF1a:A3620V), T25975C (ORF3a:S195P), G21893A (S:D111N), C23595T (S:T678I), T13324C, C22747T (following G18583A (ORF1b:V1706I)).