Sublineage of BW.1 with S:V486A (30 seq)

[ryhisner]

Description

Sub-lineage of: BW.1
Earliest sequence: 2022-9-24, Mexico, Yucatan — EPI_ISL_15310350
Most recent sequence: 2022-11-7, Denmark — EPI_ISL_15757637; Austria, EPI_ISL_15758143, EPI_ISL_15758252
Countries circulating: Mexico (12), Austria (3), USA (3), Denmark (1), England (1), Chile (1)
Number of Sequences: 21
GISAID Query: Spike_K444T, Spike_N460K, Spike_F486A, NSP16_T140I
CovSpectrum Query: Nextcladepangolineage:BW.1* & S:V486A
Substitutions on top of BW.1:
Spike: V486A
Nucleotide: T23019C, G29044A

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BW.1%20%2B%20V486A%20-%20subtreeAuspice1_genome_2b8e1_36cca0.json

Evidence
Like BW.1, it appears that this lineage originated in Mexico. It is just now starting to spread internationally, with two sequences uploaded from Austria and one from Denmark yesterday, all three with collection dates of November 7. It has also been detected in England. Sequences from Mexico tend to have much longer delays than elsewhere, so I expect more sequences of this lineage to be uploaded before long from Mexico. Austria and Denmark are the quickest at sequencing, so it is likely present in other European countries as well.

One sequence from Mexico also has S:F157L.

According to the Bloom Lab RBD Heat Map tool, A486 has a slight advantage over F486 in terms of ACE2 affinity and a moderate advantage in terms of RBD expression.

Genomes

Genomes

EPI_ISL_15310350, EPI_ISL_15513565, EPI_ISL_15528594, EPI_ISL_15546675, EPI_ISL_15671257, EPI_ISL_15671324, EPI_ISL_15671326, EPI_ISL_15671327, EPI_ISL_15671340, EPI_ISL_15671365, EPI_ISL_15671371, EPI_ISL_15671378, EPI_ISL_15671382, EPI_ISL_15695745, EPI_ISL_15703314, EPI_ISL_15707354, EPI_ISL_15754275, EPI_ISL_15757637, EPI_ISL_15758143, EPI_ISL_15758252, EPI_ISL_15758556

[FedeGueli]

Great catch Ryan i was noticing an increased growth of BW.1 in the last two weeks, maybe unrelated with this but i think it is worth to rapidly designate this one to be sure it is not anything of special or either something to monitor closely .

@corneliusroemer @InfrPopGen

[FedeGueli]

Just in the last ten days it was first spotted in Usa, Austria, Chile, Switzerland, Denmark suggesting or a likely high prevalence in motherland Mexico or being fast or at least faster than BW.1 or maybe but to me is unlikely it got the right network ( the one with more intenrational links first before the parental lineage BW.1)

[FedeGueli]

@corneliusroemer the one u designated yesterday was 486S i think this deserves a designation too.

[JosetteSchoenma]

3 were found in the Netherlands in Amsterdam. The GISAID query now finds 29.

[FedeGueli]

NOW 30 WITH THE LAST FROM ENGLAND

[FedeGueli]

two new sequences from Scotland and England bringing the total count to 32

[FedeGueli]

@corneliusroemer is it the same youn
designated BW.1.1 with S:486S?

[corneliusroemer]

Usher doesn't give the correct amino acid if there's >1 mutation in a codon, yeah!