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BA.5.2.48 sublineage with N:Q241K circulating in China 2223 sequences as 16/02/23 #1478

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FedeGueli opened this issue Dec 27, 2022 · 11 comments
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@FedeGueli
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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
Schermata 2022-12-27 alle 16 18 08

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
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This lineage seems to be a sublineage of #1471

@FedeGueli
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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 FedeGueli changed the title BA.5.2 + N:Q241K lineage circulating in China 18 sequences BA.5.2 + N:Q241K lineage circulating in China 30 sequences Dec 27, 2022
@FedeGueli
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30 sequences now, big upload from Singapore this evening

@FedeGueli FedeGueli changed the title BA.5.2 + N:Q241K lineage circulating in China 30 sequences BA.5.2 + N:Q241K lineage circulating in China 36 sequences Dec 28, 2022
@FedeGueli
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36 as today, its designation should be happen ONLY after a decision will be taken on #1471

@FedeGueli FedeGueli changed the title BA.5.2 + N:Q241K lineage circulating in China 36 sequences BA.5.2 + N:Q241K lineage circulating in China 71 sequences Jan 2, 2023
@FedeGueli
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this is the bigger sublineage of #1471 now at 71 sequences. It should be designated just after the parent.

@FedeGueli FedeGueli changed the title BA.5.2 + N:Q241K lineage circulating in China 71 sequences BA.5.2 + N:Q241K lineage circulating in China 71 sequences as 01/01/23 Jan 2, 2023
@FedeGueli FedeGueli changed the title BA.5.2 + N:Q241K lineage circulating in China 71 sequences as 01/01/23 BA.5.2 sublienage of #1471 1ith N:Q241K circulating in China 71 sequences as 01/01/23 Jan 2, 2023
@FedeGueli FedeGueli changed the title BA.5.2 sublienage of #1471 1ith N:Q241K circulating in China 71 sequences as 01/01/23 BA.5.2 sublienage of #1471 with N:Q241K circulating in China 71 sequences as 01/01/23 Jan 2, 2023
@FedeGueli FedeGueli changed the title BA.5.2 sublienage of #1471 with N:Q241K circulating in China 71 sequences as 01/01/23 BA.5.2.48 sublineage with N:Q241K circulating in China 165 sequences as 06/01/23 Jan 6, 2023
@FedeGueli
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FedeGueli commented Jan 6, 2023

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

@xz-keg
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xz-keg commented Jan 9, 2023

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 FedeGueli changed the title BA.5.2.48 sublineage with N:Q241K circulating in China 165 sequences as 06/01/23 BA.5.2.48 sublineage with N:Q241K circulating in China 329 sequences as 17/01/23 Jan 17, 2023
@FedeGueli FedeGueli changed the title BA.5.2.48 sublineage with N:Q241K circulating in China 329 sequences as 17/01/23 BA.5.2.48 sublineage with N:Q241K circulating in China 830sequences as 21/01/23 Jan 21, 2023
@FedeGueli
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With the last upload from Shandong this represents around half of BA.5.2.48 sequences

@wending-lee
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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 FedeGueli changed the title BA.5.2.48 sublineage with N:Q241K circulating in China 830sequences as 21/01/23 BA.5.2.48 sublineage with N:Q241K circulating in China 2223 sequences as 16/02/23 Feb 16, 2023
@FedeGueli
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2233 seqs as today

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

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