XBB.1* Sublineage with S:L335S, S:R403K, S:S486P, ORF1a:T403I, ORF1b:S2212I (15 seq, 4 continents, May 16—1 seq from Congo)

[ryhisner]

Description (Transferring this from the other page now that it's >10 seq & in four continents)

Sub-lineage of: XBB.1* (Possibly XBB.1.28, but I'm not certain)
Earliest sequence: 2023-3-27, France — EPI_ISL_17480623
Most recent sequence: 2023-4-24, France
Countries circulating: France (2), China (1), USA (1)
Number of Sequences: 4
GISAID AA Query: Spike_L335S, Spike_F486P, Spike_R403K
GISAID Nucleotide Query: G22770A, T22566C, T23018C
CovSpectrum Query: Nextcladepangolineage:
Substitutions on top of XBB.1:
Spike: L335S, R403K, S486P
ORF1a: T403I (NSP2_T223I)
ORF1b: S2212I (NSP15_S161I)
Nucleotide: C1473T, G20102T, G22770A, T22566C, T23018C

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1_L335S_R403K_S486P_4seq.json

Evidence
There are only four sequences at this point, but they are spread across three continents, with sequences from China, USA, and France. Short description of additional mutations on each sub-branch:

• USA sequence—S:G476S, ORF1b:V1402I (NSP13_V479I) + synonymous nuc mutations G12331A, C17850T, C25276T, and C29416G

• France sequence 1 — synonymous nuc mutations G12331A, C17850T, C25276T, and C29416G

• France sequence 2—ORF6:L35H, ORF1a:R24C, ORF1a:A117T, ORF1a:E1293D, ORF1a:P1497T

• China sequence—S:K478R, ORF1a:L397F, ORF1b:I829V, ORF1b:Y1200H plus synonymous nuc mutations C17850T, C25276T, and C29416G

Genomes

Genomes

EPI_ISL_17480623, EPI_ISL_17593232, EPI_ISL_17615418, EPI_ISL_17618380

[ryhisner]

There are now three sequences in this lineage with S:K478R. Only 13 sequences seem to show up on GISAID, but there are clearly 15 different ones on the Usher tree.

[HynnSpylor]

one more seq with S: K478R from Netherlands

[HynnSpylor]

one new seq from Singapore

[ryhisner]

The sequence from Singapore today has travel history to Ghana. I think there's a good chance this variant originated in Africa somewhere. EPI_ISL_17694854

[FedeGueli]

@InfrPopGen @corneliusroemer ping you here for fast review of this one, very likely it is widely bigger than shown by sequence count

[ryhisner]

Democratic Republic of Congo (DRC) uploaded 14 sequences today, and 13 of them are XBB.1.41. Only one has a month and day listed, and it is from May 4. I think this is pretty good evidence that XBB.1.41 is dominant in DRC and possibly surrounding countries as well.

The DRC sequences are scattered widely about the XBB.1.41 Usher tree.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_27a6_78da80.json?c=gt-S_335&label=id:node_6658034