BA.2.75.1 Sublineage with S:R346T, S:V445A, ORF10:A28V, ORF1a:L1160F (135 Seq, Jan 6) + Sublineage with S:G482R, ORF1a:S1510F (31 seq—Jan 6)

[ryhisner]

Description

Sub-lineage of: BA.2.75.1
Earliest sequence: 2022-9-2, USA, New York — EPI_ISL_14914703
Most recent sequence: 2022-12-18, South Korea — EPI_ISL_16412866, EPI_ISL_16413667, EPI_ISL_16413721, EPI_ISL_16413725, EPI_ISL_16413776
Countries circulating: South Korea (105), USA (28), Mexico (1), New Zealand (1)
Number of Sequences: 135
GISAID Query: Spike_D574V, Spike_V445A, Spike_R346T + Nucleotide: C25276A
CovSpectrum Query: Nextcladepangolineage:BA.2.75.1* & S:V445A & C25276A
Substitutions on top of BA.2.75.1:
Spike: R346T, V445A,
ORF10: A28V
ORF1a: L1130F
Nucleotide: C3653T, C7564T, T13527C, G22599C, T22896C, C25276A, C25339T, C29640T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BA.2.75.1%20%2B%20R346T%2C%20V445A%2C%20ORF10A28V%2C%20ORF1aL1130F%20-%20asubtreeAuspice1_genome_17125_88d2a0.json

Evidence
Nextclade calls this a sublineage of BL.1, but Usher puts it in a separate sublineage of BA.2.75.1 with the synonymous nucleotide mutation C25276A, followed by S:R346T, S:V445A, & ORF10:A28V, and then by ORF1a:L1130F (which only one sequence possessing the other three mutations lacks, possibly due to a sequencing issue). This lineage has been around for a while but has only grown much in the past month or so. The smaller sublineage with S:G482R seems to be growing more quickly than the lineage as a whole, with 17 of its 31 sequences having been uploaded in the past seven days, all from South Korea.

Another South Korean sublineage with N:Q242H has only recently appeared, with all 38 if its sequences uploaded in the past 20 days.

Genomes for Larger Lineage

Genomes

EPI_ISL_14914703, EPI_ISL_15277378, EPI_ISL_15358874, EPI_ISL_15391779, EPI_ISL_15391784, EPI_ISL_15458258, EPI_ISL_15483399, EPI_ISL_15532429, EPI_ISL_15534750, EPI_ISL_15535013, EPI_ISL_15609562, EPI_ISL_15666211, EPI_ISL_15666216, EPI_ISL_15672628, EPI_ISL_15719301, EPI_ISL_15778756, EPI_ISL_15807428, EPI_ISL_15812992, EPI_ISL_15818610, EPI_ISL_15818612, EPI_ISL_15849050, EPI_ISL_15861195, EPI_ISL_15890498, EPI_ISL_15906277, EPI_ISL_15944830, EPI_ISL_15946424, EPI_ISL_15946602, EPI_ISL_15961386, EPI_ISL_15975938, EPI_ISL_15979770, EPI_ISL_15979772, EPI_ISL_15979826, EPI_ISL_15980061, EPI_ISL_15980278-15980279, EPI_ISL_16010640, EPI_ISL_16022540, EPI_ISL_16047725, EPI_ISL_16091696, EPI_ISL_16105177, EPI_ISL_16105844, EPI_ISL_16135064, EPI_ISL_16135235, EPI_ISL_16135500, EPI_ISL_16135736, EPI_ISL_16136005, EPI_ISL_16136202-16136209, EPI_ISL_16136233, EPI_ISL_16136263, EPI_ISL_16136321, EPI_ISL_16136511, EPI_ISL_16136531, EPI_ISL_16136537, EPI_ISL_16137131, EPI_ISL_16137181, EPI_ISL_16137211, EPI_ISL_16191963, EPI_ISL_16191995, EPI_ISL_16192119, EPI_ISL_16206781, EPI_ISL_16222657, EPI_ISL_16265243, EPI_ISL_16314650, EPI_ISL_16333661, EPI_ISL_16334062, EPI_ISL_16336341, EPI_ISL_16336417, EPI_ISL_16336577, EPI_ISL_16336592, EPI_ISL_16336650, EPI_ISL_16336777, EPI_ISL_16337769, EPI_ISL_16337779, EPI_ISL_16337825, EPI_ISL_16337883, EPI_ISL_16337929, EPI_ISL_16337945, EPI_ISL_16337989, EPI_ISL_16338056, EPI_ISL_16338123, EPI_ISL_16338223, EPI_ISL_16338254, EPI_ISL_16338953, EPI_ISL_16339221, EPI_ISL_16339260, EPI_ISL_16339350, EPI_ISL_16339592, EPI_ISL_16339660, EPI_ISL_16339762, EPI_ISL_16340145, EPI_ISL_16340153, EPI_ISL_16340318, EPI_ISL_16340341, EPI_ISL_16340533, EPI_ISL_16340607, EPI_ISL_16340714, EPI_ISL_16340857, EPI_ISL_16341112, EPI_ISL_16341147, EPI_ISL_16341260-16341262, EPI_ISL_16341517, EPI_ISL_16341534, EPI_ISL_16341939, EPI_ISL_16341953, EPI_ISL_16341978, EPI_ISL_16342040, EPI_ISL_16342120, EPI_ISL_16372233, EPI_ISL_16379284, EPI_ISL_16379290, EPI_ISL_16379297, EPI_ISL_16412866, EPI_ISL_16413667, EPI_ISL_16413721, EPI_ISL_16413725, EPI_ISL_16413776, EPI_ISL_16417253, EPI_ISL_16417289, EPI_ISL_16417312-16417313, EPI_ISL_16417373, EPI_ISL_16418951, EPI_ISL_16419003, EPI_ISL_16419086, EPI_ISL_16419094, EPI_ISL_16419167

Genomes for S:G482R Sublineage

Genomes

EPI_ISL_15979826, EPI_ISL_15980061, EPI_ISL_16135064, EPI_ISL_16135500, EPI_ISL_16135736, EPI_ISL_16136202-16136209, EPI_ISL_16191995, EPI_ISL_16334062, EPI_ISL_16336341, EPI_ISL_16336592, EPI_ISL_16336650, EPI_ISL_16337769, EPI_ISL_16337929, EPI_ISL_16338123, EPI_ISL_16339221, EPI_ISL_16339260, EPI_ISL_16340318, EPI_ISL_16340607, EPI_ISL_16340714, EPI_ISL_16379297, EPI_ISL_16413667, EPI_ISL_16417373, EPI_ISL_16418951, EPI_ISL_16419167