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Repository for suggesting new lineages that should be added to the current scheme
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Diverged descendant of B.1 with multiple VOC-like mutations and deletions. #54

Closed evogytis closed 3 years ago

evogytis commented 3 years ago

New lineage proposal by Gytis Dudas, Guy Baele, Ingrida Olendraitė, Daniel Naumovas

Description Sub-lineage of: B.1 Earliest sequence: 2021-02-26 (hCoV-19/France/ARA-210013001901/2021) Most recent sequence: 2021-04-06 (hCoV-19/USA/WV-WVU-WV064773/2021) Countries circulating: Lithuania (definitely), France (likely), Belgium (likely), United Kingdom (likely), Germany (possible)

Genomes of this lineage initially attracted attention in Lithuania due to having the S:E484K mutation, high numbers of unique mutations in nextclade QC and (incorrect) classification as pango lineage B.1.177.57. Earliest French genome is a travel case coming from Cameroon. We reached out to submitters of other genomes and confirmed that three additional genomes on GISAID are also travel cases arriving from Cameroon. Lithuanian cases are related to travel from France and potentially Belgium, not Cameroon.

Genomes (Note some genomes are missing characteristic deletions or have excessive number of missing sites) lineage_proposal.txt

Numerous mutations present in this lineage have been observed in other VOCs (lineage in question marked XXXX, mutations unique to it in this plot marked in red):

VOC-like_muts

N:A220V shared with B.1.177 is the likely reason for this lineage's pango lineage misclassification. Another putative Cameroonian lineage (#44) shares some of these mutations (E484K, T1027I) in common. Distantly related genomes from Cameroon on GISAID also share at least one more synonymous mutation (C15324T).

Evidence (Proposed lineage at the bottom, dashed outline, only showing sites different from reference in proposed lineage and shared by at least two proposed lineage genomes) defining-mutations

chrisruis commented 3 years ago

Hi @evogytis thanks for submitting this, we've added this as lineage B.1.620. Its included in v1.1.16

babarlelephant commented 3 years ago

Hi, did you notice the (mis-assigned?) sublineage of B.1.523 having E484K, N440K plus all the deletions (ORF1a:S3675-, S:69-, S:143-) ? It doesn't look the same as Cameroon/B.1.619 E484K, N440K @evogytis

evogytis commented 3 years ago

@babarlelephant I had not, no. It doesn't have the S:241- deletion but the degree of convergence is is still quite striking.