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Non-recombinant: XAU #348

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szhan opened this issue Feb 25, 2025 · 2 comments
Open

Non-recombinant: XAU #348

szhan opened this issue Feb 25, 2025 · 2 comments

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@szhan
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szhan commented Feb 25, 2025 •
edited by jeromekelleher
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cov-lineages/pango-designation#894

ktmeaton/ncov-recombinant#103

Below is info collated from the pango-designation issues by the RecombinHunt authors.

It is detected as a recombinant by RecombinHunt-GISAID and RecombinHunt-Nexstrain.

method left_parent right_parent left_breakpoint right_breakpoint
pango-designation BA.1.1* BA.2.9* 2834 4184
RecombinHunt-GISAID BA.1.1.2 BA.2.9 2835 2836
RecombinHunt-Nextstrain BA.1.1.9 BA.2.9 3037 3038

Discussion started in #285.

Quoting Yan: "No clear recombination, and no reversions etc on the nearby branches. Unless there is a deletion we are missing, I suppose."

Copying image from Yan.
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@szhan szhan mentioned this issue Feb 25, 2025
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What are the pango parents and breakpoints? (and ground truth?)

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szhan commented Feb 25, 2025

What are the pango parents and breakpoints? (and ground truth?)

Updated above.

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@jeromekelleher @szhan