Dear Users,
I have encountered too many cases of recombinant in the column of clade while using Nextclade
and I realized a new column of Pango lineage (Nextclade) that gives me XJ, XH, XF, XD as pango lineages. I am totally confused about this. Any support in interpreting these data is appreciated.
Regards
Hi @Mature,
You can read more about the Nextclade Pango lineage assignments here:
https://docs.nextstrain.org/projects/nextclade/en/latest/user/algorithm/nextclade-pango.html
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Further to Jover’s answer, these annotations are Nextclade’s attempt to assign Pango lineages to SARS-CoV-2 lineages. The lineage definitions are identical to what pangolin uses, but the algorithm is different.
XJ etc are recombinants. You can read more about the Pango lineage nomenclature for example here: Phylogenetic Assignment of Named Global Outbreak Lineages - Wikipedia