Update Omicron clade definitions to be robust to BA.4 and BA.5 by trvrb · Pull Request #913 · nextstrain/ncov (original) (raw)
Including BA.4 and BA.5 sequences can alter tree topology and change clade placement. These clade updates should make existing 21K, 21L and 21M clades robust to these tree topology changes. Existing non-artifactual genomes should receive the same clade label as previously. For the moment, this groups BA.4 and BA.5 into 21L along with BA.2. This was chosen to be robust to stochastic differences in phylogenetic reconstruction.
For whatever reason 10449A is fully congruent with Omicron clades in GISAID builds but not in GenBank builds. Swapping to 18163G makes things consistent across the board.
Although 18163G occurs on the branch leading to 21M, including it here for 21K and 21L helps to keep clades from becoming "inverted".
This was referenced
Apr 14, 2022
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