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Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a Sublineage of BA.5.2.1 with ORF1a:I880V in Brazil [130 as of 2022-08-29] #956

Closed alex-ranieri closed 2 years ago

alex-ranieri commented 2 years ago

By Alex Ranieri and Gabriela Ribeiro (Butantan Network for Pandemic Alert of SARS-CoV-2 Variants, São Paulo).

Description

We've noticed that the same mutation occurring on BA.4 #954 and BA.5.1 #955

Sub-lineage of: BA.5.2.1 Countries circulating: 106 in Brazil (Mainly in São Paulo State), 1 in Israel, 2 in United States Earliest sequence: 2022-05-20 (Israel - EPI_ISL_13111005) Most recent sequence: 2022-07-26 (Brazil - EPI_ISL_14279054) Cov-spectrum: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF1a%3AI880V&pangoLineage=BA.5.2.1& Number of Sequences: 109 on GISAID (as of 2022-08-16) Genomes: EPI_ISL_13111005, EPI_ISL_13562260-13562261, EPI_ISL_13576695, EPI_ISL_13994835, EPI_ISL_13994849-13994851, EPI_ISL_13994867, EPI_ISL_13994874-13994875, EPI_ISL_14049000, EPI_ISL_14109314-14109316, EPI_ISL_14109318-14109331, EPI_ISL_14109336-14109349, EPI_ISL_14109351-14109352, EPI_ISL_14109354, EPI_ISL_14109356-14109357, EPI_ISL_14109487, EPI_ISL_14109531-14109535, EPI_ISL_14109537-14109538, EPI_ISL_14109541-14109543, EPI_ISL_14109698-14109699, EPI_ISL_14109702, EPI_ISL_14109706-14109708, EPI_ISL_14109711, EPI_ISL_14109715, EPI_ISL_14109719, EPI_ISL_14187905, EPI_ISL_14278709, EPI_ISL_14278711-14278712, EPI_ISL_14278714-14278715, EPI_ISL_14278718-14278721, EPI_ISL_14278726-14278727, EPI_ISL_14278730, EPI_ISL_14278733-14278745, EPI_ISL_14278752-14278754, EPI_ISL_14278756-14278760, EPI_ISL_14279021, EPI_ISL_14279044-14279045, EPI_ISL_14279048-14279049, EPI_ISL_14279054, EPI_ISL_14336292

USHER Tree

tree

https://nextstrain.org/fetch/repositorio.butantan.gov.br/bitstream/butantan/3982/13/BA.5.2.1_ORF1a_I880V.json?branchLabel=aa%20mutations&c=pango_lineage&label=nuc%20mutations:A27038G

growth
alex-ranieri commented 2 years ago

Seven more genomes: EPI_ISL_14464198 EPI_ISL_14464199 EPI_ISL_14464212 EPI_ISL_14464216 EPI_ISL_14464223 EPI_ISL_14464240 EPI_ISL_14464245

alex-ranieri commented 2 years ago

14 more genomes EPI_ISL_14583960 EPI_ISL_14583987 EPI_ISL_14583999 EPI_ISL_14584044 EPI_ISL_14584045 EPI_ISL_14584049 EPI_ISL_14584051 EPI_ISL_14584053 EPI_ISL_14584054 EPI_ISL_14584055 EPI_ISL_14584056 EPI_ISL_14584058 EPI_ISL_14584059 EPI_ISL_14584060

InfrPopGen commented 2 years ago

Within this proposed clade, there appears to be a sub-clade of 19 sequences which have reversion ORF1a:V880I (nt:G2903A); these are off Internal node 14282453 on the 31st August tree. I suspect these should not really be there, and may move away in a future tree build. Also, few of the members of the sub-clade are from Brazil, whereas all those in the parent clade are (at least at the moment).

corneliusroemer commented 2 years ago

To me this looks like ORF1a:I880V is an artefact here - it pops up in two many backgrounds.

It seems to pop up only in certain countries - and the onset is not monophyletic and can be very abrupt. Possibly related to a switch in primer schemes.

image

It seems that these sequences are limited to one sequencing lab: Butantan. Looking at that lab's sequences, there seems to be a general issue with reversions to reference. For example S:440 is reverted to reference in almost all the sequences suggested here - indicative of bioinformatics pipeline errors.

Almost all the recent ORF1a:I880V are from the Butantan lab - whereas other labs in Brazil don't see this mutation.

Overall, this makes it pretty clear that the mutation is an artefact. I should have realized this when three lineages from one location from one lab in different phylo backgrounds were proposed https://github.com/cov-lineages/pango-designation/issues/955 https://github.com/cov-lineages/pango-designation/issues/954 #956 - this by itself is very indicative of artefacts - but back then I didn't look closely enough.

As a result, I will close this issue. And I also propose that we should withdraw BA.5.1.13 from the proposals above.