Closed c19850727 closed 1 year ago
I am also to propose a recombinant related to #1713.
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:
GISAID and Cov-spectrum query: C5055T, C5301T, C5812T, T25959C
England/PHEC-YYERMZS/2023 England/PHEC-YYERMAW/2023 Not yet on GISAID though.
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).
It scores quite high in collection24, even if there is some bias from High sequencing intensity in UK
Thanks @InfrPopGen ! I'll close this issue and make a separate proposal for the recombinant.
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
cc @corneliusroemer someone noticed that S:G446R is not shown on the nextclade tree of BQ.1.1.71
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).
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.
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.
Yes @FedeGueli I am also monitoring it. There are 9 with S:Y248H in total. Will propose it once it grows further.
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!
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:
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](https://user-images.githubusercontent.com/86835836/222336351-2d2221ab-fab1-4b67-a73d-205bc58ca5fd.png)
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