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Proposal to split B.1.1.529 to incorporate a newly characterised sibling lineage #361

rambaut opened this issue Dec 6, 2021 · 6 comments


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rambaut commented Dec 6, 2021

In the last few days a number of genomes have been uploaded by South Africa, Australia and Canada that whilst having many of the defining mutations of B.1.1.529 (Omicron) do not have the full set and also have a number of their own unique mutations. This was first described in Issue #359

The mutations are as follows:
Omicron_BA 1_BA 2_mutations

where the yellow column gives the mutations unique to the new 'BA.2' lineage, blue column the mutations unique to the original 'BA.1' lineage of Omicron and the green column those shared by both - i.e. inferred to have arisen prior to the split.

A CSV version of this table is available here: Omicron_BA.1_BA.2_mutations.csv

Here we propose expanding the breadth of the B.1.1.529 lineage to include all of these variants. Then 2 sub-lineages created - BA.1 for the original globally-distributed lineage and BA.2 for the new outlier lineage. The names BA.1 and BA.2 follows the Pango convention to avoid more than three numerical fields, an alias is made for the parent lineage.

A couple of observations -

Both sub-lineages (and thus we assume the common ancestor) carry almost all the spike RBD mutations first noted for Omicron and both furin cleaveage adjacent mutations. They both have the NSP6 deletion seen in other VOCs.

The new sub-lineage (putative BA.2) does not carry the spike:69/70del deletion and will thus not be detectable by SGTF (S-gene target failure).

Pangolin currently assign the outlier lineage as B.1.1.529 but Scorpio will give the additional label 'Probable Omicron' because the outlier lineage is missing many of the original defining mutations.

@rambaut rambaut added the urgent Proposal flagged for urgent review (provide explanation) label Dec 6, 2021
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rambaut commented Dec 7, 2021

Current set of genomes in the 'outlier' lineage:


(removed QLD2584 as @bioinforME confirms a resampling of the same case, below).

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Hi rambaut, good to see this outlier lineage is supported by more sequences and looking forward to a new (sub)lineage assignment. "Probable" Omicron is casting doubt on the quality of the sequences, which is not the case.

Just to mention sequence QLD2584 is a re-swab of the same patient as QLD2568. We accidentally uploaded it and have already requested to remove from GISAID.

Chenwei Wang


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@cov-lineages cov-lineages locked as resolved and limited conversation to collaborators Dec 7, 2021
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Now added as lineages BA.1 and BA.2 in v1.2.106

@cov-lineages cov-lineages deleted a comment from FedeGueli Dec 7, 2021
@chrisruis chrisruis added this to the BA.1 BA.2 milestone Dec 7, 2021
@chrisruis chrisruis added designated and removed urgent Proposal flagged for urgent review (provide explanation) labels Dec 7, 2021
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rambaut commented Dec 7, 2021

Hi Andrew, In addition to this finding, there are some B.1.1.529 lineages that do not have the N440K and K417N mutation (336 entries in GISAID) and form a separate clade when analysed with other sequences that do contain these mutations.

Removing this comment - only because it is off-topic for this issue (a separate issue could be created)

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rambaut commented Dec 7, 2021

Updated the table of mutations, above, to reflect some corrections and additions by @AngieHinrichs

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