Non-recombinant: XN

[szhan]

Pango designation issue: cov-lineages/pango-designation#480

Edge case in sc2rf, usually not detected as recombinant: ktmeaton/ncov-recombinant#137

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

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

This is a nice example of a clean case of non-recombinant as per sc2ts.

method	left_parent	right_parent	left_breakpoint	right_breakpoint
pango-designation	BA.1*	BA.2*	2833	4184

Copying image from Yan here #285:

[jeromekelleher]

Copied from original issue:

Looking at the pango designation issue for XN, it looks like there's only 3 mutations on the far left that make it look like a recombinant, C241T, A2832G, and C3037T.

A2832G occurs above our well supported BA.2 internal node, and I have a feeling that 241 and 3037 are highly recurrent. So I think there's good support here for XN not really being recombinant.