Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Non-recombinant: XAN #353

Open
szhan opened this issue Feb 25, 2025 · 1 comment
Open

Non-recombinant: XAN #353

szhan opened this issue Feb 25, 2025 · 1 comment

Comments

@szhan
Copy link
Collaborator

szhan commented Feb 25, 2025 •
edited by jeromekelleher
Loading

cov-lineages/pango-designation#771

ktmeaton/ncov-recombinant#109

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

method left_parent right_parent left_breakpoint right_breakpoint
pango-designation BA.2* BA.5.1 17822 21766

Discussion started #285.

Quoting Yan: "Slightly less sure, with multiple recurrent/reversion mutations, but XAV and XAN may not be recombinants."

Coping image from Yan.
Image
@szhan szhan changed the title Non-recombinant: XAV Non-recombinant: XAN Feb 25, 2025
@szhan szhan mentioned this issue Feb 25, 2025
Open
@szhan
Copy link
Collaborator Author

szhan commented Feb 25, 2025 •
edited
Loading

It is detected a recombinant by both RecombinHunt-GISAID and RecombinHunt-Nextstrain.

method left_parent right_parent left_breakpoint right_breakpoint
RecombinHunt-GISAID BJ.1 BA.5.1.23 9866 9867
RecombinHunt-Nextstrain BA.2 BA.5.1.23 9866 9867

N.B. I checked again with SupplementaryNotes2_RH_gisaid_sarscov2_detail.html. The breakpoint intervals are way off compared to the ground truth.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@szhan