nextstrain/nextclade_data 2021-11-16

on GitHub

SARS-CoV-2

New dataset version (tag 2021-11-16T16:38:05Z)

Changes

• Reference tree: Recombinant pango lineages (= those starting with X) have been excluded in order to reduce clade misassignment noise, in particular for short sequences like just S. Only one recombinant has been designated so far (XA) and it broke up the branch leading up to Alpha exerting bad influence that warranted removal.
• QC rules: The lists of known, (likely) biological and thus acceptable frame shifts and stop codons have been extended. The ~20 most common frame shifts and ~40 most common stop codons on genes ORF3a/6/7a/7b/8 are now declared known. Common frame shifts and stops on ORF1a/b and S are not declared known since these are most likely sequencing artefacts and not biological.

Updates

• Reference tree: Data has been updated to sequences submitted to Genbank by mid November
• Reference tree: Pango lineages designated until 2021-11-04 have been sampled into the tree
• Sample sequences