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Repository for suggesting new lineages that should be added to the current scheme
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Issue in Pango v.3.1.7 2021-07-09 to classify the VOC Delta B.1.617.2 #163

Closed paolaresende closed 2 years ago

paolaresende commented 3 years ago

Please,

I would like to inform a possible error in the current version of Pango v.3.1.7 2021-07-09. Some lineages have been classified as the VOC Delta B.1.617.2, but they do not share the signatures of this lineage.

In this file three genomes that I could identify this issue gisaid_hcov-19_2021_07_27_13_Delta.txt

Bellow the lineage report lineage_report.txt

These genomes were previously classified by PLEARN-v1.2.13 15/06/2021 as: hCoV-19/Dominican_Republic/33905/2021 | B.1.311 hCoV-19/Dominican_Republic/33906/2021 | B.1.623 hCoV-19/Dominican_Republic/33911/2021 | B.1.621

Thanks for the brilliant work that the Pango team has done!

Cheers, Paola Resende

ha-ruiz75 commented 3 years ago

Hello, all.

I have also observed this in sequences belonging to the B.1.621 lineage with >90% coverage. Their mutation profile contains spike mutation R346K, E484K, N501Y, P681H so we are certain they do not belong in the B.1.617.2 lineage.

rmcolq commented 2 years ago

I believe this issue is now resolved. With the above changes, the 3 example sequences come back as none (scorpio disagrees with AY.33 call), and B.1.621