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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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BQ.1.1 with additional spike Y144del, K182E, P251L and G446R (64 seqs as of 2023-03-07) #1713

Closed c19850727 closed 1 year ago

c19850727 commented 1 year ago

First spotted by @oliasdave . Many thanks!

Description

Sublineage of: BQ.1.1 (sibling to BQ.1.1.38 on Usher). Earliest sequence: 2022/12/30 (UK-England) Most recent sequence: 2023/02/18 (UK-England) Countries circulating: UK (45/46), Ireland (1/46) Mutations on top of BQ.1.1: C22314T (S:P251L) > A28834G > A22106G (S:K182E), T23716C > G2281A > C8950T > G22898C (S:G446R), T25959C It's convergent to BQ.1.1.39 (#1385 ) in terms of spike changes, but should be unrelated. GISAID and Cov-spectrum query: G2281A, C8950T, T25959C

Evidence

Usher tree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_bf4f_f72260.json?c=gt-nuc_22898&label=id:node_6017558

Relative growth advantage With only 36 sequences available on Cov-spectrum, it has a growth advantage of ~70% over BQ.1.1 in last 2 months in the UK, and almost the same as XBB.1.5 (wide confidence interval) image

image

Genomes:

EPI_ISL_16441667, EPI_ISL_16496148, EPI_ISL_16496508, EPI_ISL_16525084, EPI_ISL_16535976, EPI_ISL_16535995, EPI_ISL_16536059, EPI_ISL_16584034, EPI_ISL_16613017, EPI_ISL_16613064, EPI_ISL_16645503, EPI_ISL_16722034, EPI_ISL_16722057, EPI_ISL_16808821, EPI_ISL_16810360, EPI_ISL_16810397, EPI_ISL_16829143, EPI_ISL_16924910, EPI_ISL_16937825, EPI_ISL_16952259, EPI_ISL_16954876, EPI_ISL_16978780, EPI_ISL_16978875, EPI_ISL_16978903, EPI_ISL_16978918, EPI_ISL_16985742, EPI_ISL_16985812, EPI_ISL_17007852, EPI_ISL_17016502, EPI_ISL_17016548, EPI_ISL_17016592, EPI_ISL_17016595, EPI_ISL_17016626, EPI_ISL_17016636, EPI_ISL_17016727, EPI_ISL_17016739, EPI_ISL_17016790, EPI_ISL_17017225, EPI_ISL_17026965, EPI_ISL_17032412, EPI_ISL_17032447, EPI_ISL_17032457, EPI_ISL_17032462, EPI_ISL_17032645, EPI_ISL_17063145, EPI_ISL_17063443

c19850727 commented 1 year ago

I am also to propose a recombinant related to #1713.

Description

Recombinant between: XBB.1.5* and #1713 Earliest sequence: 2023/02/16 (UK-England) Most recent sequence: 2023/02/16 (UK-England) Countries circulating: UK-England (2/2) Potential breakpoint: between NSP14 and spike NTD (19327-22305) Potential BQ.1.1 donor: #1713 Potential XBB.1.5 donor: XBB.1.5 with C5055T, C5301T, C5812T. Mutation profile: image GISAID and Cov-spectrum query: C5055T, C5301T, C5812T, T25959C

Evidence

Usher tree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_db88_311b0.json?c=gt-nuc_5055&label=id:node_7436070

Genomes:

England/PHEC-YYERMZS/2023 England/PHEC-YYERMAW/2023 Not yet on GISAID though.

InfrPopGen commented 1 year ago

Thanks for submitting. We've added lineage BQ.1.1.71 with 26 newly designated sequences, and 0 updated. Defining mutations G22898C (S:G446R), T25959C (following GC8950T). It might be good to create a dedicated issue for the recombinant, so we can keep an eye on it (and then this issue can be closed).

FedeGueli commented 1 year ago

It scores quite high in collection24, even if there is some bias from High sequencing intensity in UK

c19850727 commented 1 year ago

Thanks @InfrPopGen ! I'll close this issue and make a separate proposal for the recombinant.

FedeGueli commented 1 year ago

BQ.1.1.71 appears as today the fastest non recombinant sublineage on earth so in the group just back the leading lineages : https://cov-spectrum.org/collections/24

FedeGueli commented 1 year ago

cc @corneliusroemer someone noticed that S:G446R is not shown on the nextclade tree of BQ.1.1.71

c19850727 commented 1 year ago

I double checked BQ.1.1.71 and found 46 out of 64 genomes currently on GISAID also have S:Y144del. And those 18 genomes without Y144del are all from one lab (PHEC).

FedeGueli commented 1 year ago

I double checked BQ.1.1.71 and found 46 out of 64 genomes currently on GISAID also have S:Y144del. And those 18 genomes without Y144del are all from one lab (PHEC).

Oh yes @c19850727 sorry for not saying that before, when i checked Nextclade tree this lineage has as unique defining mutation S144del!

Maybe worth correcting the original post, you know maybe some scientists could get fooled pseudovirusing that.

FedeGueli commented 1 year ago

3 english sequences of this one added further S:Y248H , that is a residue in which mutations are known to benefit a lot on BQ.1 . all sampled in March 23:EPI_ISL_17153501, EPI_ISL_17153506, EPI_ISL_17153712, @c19850727 @thomasppeacock maybe worth flagging.

c19850727 commented 1 year ago

Yes @FedeGueli I am also monitoring it. There are 9 with S:Y248H in total. Will propose it once it grows further.

FedeGueli commented 1 year ago

Yes @FedeGueli I am also monitoring it. There are 9 with S:Y248H in total. Will propose it once it grows further.

Sorrry i dint read this msg! i ve proposed it : https://github.com/cov-lineages/pango-designation/issues/1739 i will edit it crediting you!