Nested recombinants: XE/XH

[szhan]

pango	designation	ncov-recombinant
XE	cov-lineages/pango-designation#454	ktmeaton/ncov-recombinant#145
XH	cov-lineages/pango-designation#448	ktmeaton/ncov-recombinant#141

These two Pango X lineages cause a major recombinant node as shown in the recombinant backbone here #297. Related discussion started here #286.

As per sc2ts, the left and right Pango parents are BA.1.17.2 and BA.2.
And the breakpoint interval is 10448-11537.

For both these Pango X lineages, the ground truth left and right Pango parents are BA.1* and BA.2*.
And the breakpoint interval is 10447-11288.

They are quite concordant.

[jeromekelleher]

Looking at the designation issues, my best guess as to what happened here is that people didn't spot the similarity between XH and XE is because the sequences weren't going into the Usher tree at the time (cov-lineages/pango-designation#454 (comment)). Otherwise, the only real difference between the reports is that one is mainly based in the UK and the other Denmark.