search

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
Other
1.05k stars 98 forks source link

AY.32 definition from #209 fails to include huge Sri Lanka branch #289

Closed FedeGueli closed 3 years ago

FedeGueli commented 3 years ago

AY.32,as described in issue #209 is a "bi-headed" large lineage from South Africa and Sri Lanka (plus Maldives), the defining mutation should be T572I Actually defining mutations fail to assign it correctly at least in Sri Lanka Tree: (neher lab) Schermata 2021-10-23 alle 11 12 14

https://nextstrain.org/groups/neherlab/ncov/asia-sri-lanka?branchLabel=aa&c=pango_lineage&d=tree,entropy,frequencies&label=spike_mutations:T572I&p=full&r=division&tl=pango_lineage

tree (aicbu)

Schermata 2021-10-23 alle 11 16 48 Schermata 2021-10-23 alle 11 16 56

https://nextstrain.org/community/aicbu/ncov/srilanka?branchLabel=aa&c=pango_lineage_local&tl=pango_lineage_local

While in Africa the algorithm apparently learned to assign this lineage correctly Schermata 2021-10-23 alle 11 38 39

In Sri Lanka this didnt happen Schermata 2021-10-23 alle 11 38 54

Actually searching for AY.32 in CovidSpectrum no AY.32 sequence is found in Sri Lanka, while this lineage accounts for at least 14% of the viruses circulating Schermata 2021-10-23 alle 18 14 57

FedeGueli commented 3 years ago

Now designated as AY.104. @chrisruis https://www.pango.network/summary-of-designated-ay-lineages/

Commit: https://github.com/cov-lineages/pango-designation/commit/c3c5c8d3b1eba7056f612ba5dda486a90de78b63