Potential New BA.2.x lineage with S:G257S + ORF1ab:P2287S circulating in Puerto Rico with spillover into multiple US states and Europe (251 seqs as of 6/5/2022)

[arodzh-sudo]

Description

Potential sublineage of BA.2 monitored by the Puerto Rico Public Health Laboratory
Earliest sequence: 2022/03/07 from Puerto Rico
Most recent sequence: 2022/05/03 from UK/Scotland and Canada
Mutation on top of BA.2: ORF1ab:P2287S + S:G257S
Countries circulating: Puerto Rico, United States, Canada and UK (Scotland)

Country	Number of sequences
United States	110 (113 seqs, 3 seqs from Puerto Rico were uploaded as North America / USA)
United Kingdom	3
Canada	1
Division	Number of sequences
Puerto Rico	61 (64 seqs, 3 seqs from Puerto Rico were uploaded as North America / USA)
New York	9
Pennsylvania	9
Florida	4
Michigan	3
New Jersey	3
Scotland	3
South Carolina	3
Connecticut	2
Illinois	2
Virginia	2
California	1
Colorado	1
Georgia	1
Louisiana	1
Massachusetts	1
Minnesota	1
Nevada	1
North Carolina	1
Ontario	1
Rhode Island	1
Texas	1
Utah	1
Wisconsin	1

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2aa3c_e52df0.json?branchLabel=aa%20mutations&c=gt-ORF1ab_2287

Cov-spectrum query:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF1a%3AP2287S%2CS%3AG257S&pangoLineage=BA.2*&

Also, interestingly enough a group of BA.2.12.1 sequences, mostly from USA, are also picking up the S:G257S mutation:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2aa3c_e52df0.json?branchLabel=Spike%20mutations&c=pango_lineage

Estimates from cov-spectrum suggest a relative growth advantage of ~37% over a BA.2 baseline:

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=BA.2*&aaMutations1=ORF1a%3AP2287S%2CS%3AG257S&pangoLineage1=BA.2*&analysisMode=CompareToBaseline&

List of genomes:

contributors-ORF1abP2287S-SD257S.csv

[arodzh-sudo]

UPDATE: 64 additional sequences with the most recent sequences from 5/15/2022 and circulating in additional countries: Australia, Chile, Japan, Portugal and Denmark.

contributors-ORF1abP2287S-SD257S.csv

We are also monitoring an additional new potential BA.2.x lineage with S:Q613H, ORF1a:P1054L, ORF8:S69T possibly from Puerto Rico (65 seqs, ~30% in Puerto Rico).

Potential sublineage of: BA.2
Earliest sequence: 2022/03/24 from Puerto Rico
Most recent sequence: 2022/05/13 from USA / Oregon
Mutation on top of BA.2: ORF1a:P1054L, + S:Q613H + ORF8:S69T
Countries circulating: Puerto Rico, United States, France and UK

Country	Number of sequences
United States	63
France	1
United Kingdom	1
Division	Number of sequences
Puerto Rico	19
New York	9
Oregon	7
Florida	6
Massachusetts	5
North Carolina	4
Maryland	3
New Jersey	2
Pennsylvania	2
Washington	2
Colorado	1
England	1
Grand Est	1
Indiana	1
Rhode Island	1
Texas	1

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_db95_da38d0.json?branchLabel=aa%20mutations&c=gt-nuc_3426,23401,29473

Cov-spectrum query:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF1a%3AP1054L%2CS%3AQ613H%2CORF8%3AS69T&pangoLineage=BA.2*&aaMutations1=ORF1a%3AP2287S%2CS%3AG257S&pangoLineage1=BA.2*&

Estimates from cov-spectrum suggest a relative growth advantage of ~47% over a BA.2 baseline

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=BA.2*&aaMutations1=ORF1a%3AP1054L%2CS%3AQ613H%2CORF8%3AS69T&pangoLineage1=BA.2*&analysisMode=CompareToBaseline&

List of genomes:
contributors-ORF1aP1054L-SQ613H-ORF8S69T.csv

UPDATE: 32 new sequences as of 6/5/2022 from multiple US states

[arodzh-sudo]

@InfrPopGen @AngieHinrichs @chrisruis could you take a quick look at this? In Puerto Rico we have a low sequencing rate at about ~0.015% of positive cases sequenced. We think this small clade might be significant based on the aforementioned. Thanks.

[chrisruis]

Thanks @arodzh-sudo We've added this as BA.2.73 to start on the branch with G22331A (S:G257S)