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Proposal to withdraw lineage XBC.1.6.1 due to the defining mutation ORF1b:N498I being likely an artifact #1948

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oobb45729 opened this issue Apr 23, 2023 · 1 comment
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Proposal to withdraw lineage XBC.1.6.1 due to the defining mutation ORF1b:N498I being likely an artifact #1948

oobb45729 opened this issue Apr 23, 2023 · 1 comment

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@oobb45729
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1
https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?variantQuery=ORF1b%3AN498I&
2
https://cov-spectrum.org/explore/Australia/AllSamples/AllTimes/variants?variantQuery=ORF1b%3AN498I&
corneliusroemer added a commit that referenced this issue Apr 23, 2023
@corneliusroemer
Change defining mutation for XBC.1.6.1 from ORF1b:N498I to ORF8:P36L
b33756e 
In #1948, @oobb45729 raised that ORF1b:N498I seems to
be an artefact in sequences from Australia-SA

This does look to be the case, it is very homoplasic in XBC.1.6

Redefining XBC.1.6.1 to be defined by ORF8:P36L fixes this issue

@AngieHinrichs may want to apply branch specific masking on 14960
for XBC.1.6, or maybe even mask 14960 altogether given it's an
artefact in a lot of Australia-SA sequences
@corneliusroemer
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Resolved in b33756e

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@corneliusroemer @oobb45729