nextclade
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Spike only sequences from VOC alpha aren't assigned the 20I (Alpha) but 20B
The presence of recombinant lineage XA
with Alpha spike in a non-alpha background attracts Spike only Alpha sequences.
Unsure how to handle this, but as a stop-gap solution we could remove recombinant lineages from the reference tree.
Since I've implemented only the stop-gap solution, I'll reopen and label with hard problem
.