BA.5.2.48 sublineage with N:Q241K circulating in China 2223 sequences as 16/02/23

[FedeGueli]

This lineage was spotted first by Yunlong Richard Cao,

Defining mutations :
BA.5.2 ( > C27513T > C27012T > G12310A > C16616A (Orf1b:1050N)) then C2710T > C8626T > C11824T > T17208C > N:Q241K (C28994A )

Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_1acf9_b0ad20.json?c=userOrOld&label=id:node_7080113

Gisaid Query: N_Q241K,NSP13_T127N,M_D3N

Sequences : 18

EPI_ISL_16259462, EPI_ISL_16259469, EPI_ISL_16259474, EPI_ISL_16259481, EPI_ISL_16259506, EPI_ISL_16283958, EPI_ISL_16283962, EPI_ISL_16283966, EPI_ISL_16283969, EPI_ISL_16283971, EPI_ISL_16283985-16283987, EPI_ISL_16283993, EPI_ISL_16284002-16284003, EPI_ISL_16284007, EPI_ISL_16286992,

[AnonymousUserUse]

This lineage seems to be a sublineage of https://github.com/cov-lineages/pango-designation/issues/1471

[FedeGueli]

This lineage seems to be a sublineage of #1471

thx for noticing i will wait for the decision of @corneliusroemer and @InfrPopGen if designate or not 1471 from T17208C.

[FedeGueli]

30 sequences now, big upload from Singapore this evening

[FedeGueli]

36 as today, its designation should be happen ONLY after a decision will be taken on #1471

[FedeGueli]

this is the bigger sublineage of #1471 now at 71 sequences. It should be designated just after the parent.

[FedeGueli]

This is the biggest sublineage of the recently designated BA.5.2.48 dominating in China, accounting for nearly half of the sequences assigned to the parental lineage.

@InfrPopGen @thomasppeacock @corneliusroemer

[aviczhl2]

175 now, Italy and New Zealand.

Italy EPI_ISL_16431224. EPI_ISL_16431225 New Zealand EPI_ISL_16436171

Travel history unknown, are they locally transmitted?

[FedeGueli]

With the last upload from Shandong this represents around half of BA.5.2.48 sequences

[wending-lee]

Confirmed in wastewater. This mutation has been detected most prevalent (77 out of 88 samples, detection threshold at >100 reads) in wastewater samples collected in the recent two months in southern China. We've been monitoring novel mutations that have not been assigned to any lineages, the most prevalent nuc mutations with >50% in wastewater samples are: C28994A(0.875), C5628T(0.864), A28370T(0.807), C16887T(0.727), G21987A(0.557), T26773C(0.534).

[FedeGueli]

2233 seqs as today

[corneliusroemer]

Yep, this is a clear one to designated. Will assign myself