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BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 2022-08-19) #963

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agamedilab opened this issue Aug 18, 2022 · 3 comments · Fixed by #966
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BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 2022-08-19) #963

agamedilab opened this issue Aug 18, 2022 · 3 comments · Fixed by #966
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BA.2.75.2

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@agamedilab
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Proposal for a sublineage of BA.2.75
Earliest sequence: 04.07.2022 (India)
Countries detected: India, Chile, England, Singapore, Spain, Germany

Defining mutation:
S:R346T
S:F486S
S:D1199N

This variant is defined by S:R346T, S:F486S, S:D1199N and was first detected in India. Now it is present in 6 countries across 3 continents (expansion into Germany with todays GISAID upload). 11 seq on Usher as of 18.08.22. Sequences carrying S:D1199N where mentioned by @RajLABN in #918. However the proposed sublineage is apparently distinct from those mentioned in #961 (i.e. #918, #957, #944). Sequence quality is fine but the sublineage currently clusters with a bunch of lower quality sequences with a lot of dropouts (see below).

grafik
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_39c1_e48170.json?branchLabel=aa%20mutations&c=gt-S_346,486

grafik

grafik
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AR346T%2CS%3AF486S%2CS%3AD1199N&pangoLineage=BA.2.75*&

EPI_ISL_14290506
EPI_ISL_14307810
EPI_ISL_14441071
EPI_ISL_14458978
EPI_ISL_14480635
EPI_ISL_14480645
EPI_ISL_14517967
EPI_ISL_14519683
EPI_ISL_14521272
@agamedilab agamedilab mentioned this issue Aug 18, 2022
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@agamedilab
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Expansion into South Korea, Australia, USA with yesterdays uploads. 17 seq. on usher as of 19.08.22.

grafik
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b34e_f2bbe0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C5192T,T23019C,G25157A

@agamedilab agamedilab changed the title BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (11 seq. India, Chile, England, Singapore, Spain, Germany) BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 17.08.22) Aug 19, 2022
@corneliusroemer corneliusroemer changed the title BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 17.08.22) BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 2022-08-19) Aug 19, 2022
@corneliusroemer
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I independently noticed this lineage when reviewing new uploads of BA.2.75

It is an independent lineage not obviously related to any other of the big circulating branches - so I think this is ready for designation - especially considering the Spike profile and rapid growth internationally.

Nucleotide mutations on top of BA.2.75:
C5192T, G22599C, T23019C, G25157A

@corneliusroemer corneliusroemer mentioned this issue Aug 19, 2022
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corneliusroemer added a commit that referenced this issue Aug 19, 2022
@corneliusroemer
Added new lineage BA.2.75.2 from #963 with 10 new designations
ba6e625 
Resolves #963
Defining mutations: C5192T,G22599C,T23019C,G25157A
corneliusroemer added a commit that referenced this issue Aug 19, 2022
@corneliusroemer
Merge pull request #966 from cov-lineages/issue-963
934b67d 
Added new lineage BA.2.75.2 from #963 with 10 new designations
@agamedilab
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many thanks! If you have time I would be very happy if a label / milestone could be added to this issue. All the best! @corneliusroemer @InfrPopGen

@corneliusroemer corneliusroemer added this to the BA.2.75.2 milestone Aug 19, 2022
@cvejris cvejris mentioned this issue Aug 31, 2022
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Added new lineage BA.2.75.2 from #963 with 10 new designations cov-lineages/pango-designation
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@corneliusroemer @thomasppeacock @agamedilab