Nested recombinants: XQ/XAM/XR/XAA/XAG/XU

[szhan]

pango	designation	ncov-recombinant
XQ	cov-lineages/pango-designation#468	ktmeaton/ncov-recombinant#135
XR	cov-lineages/pango-designation#469	ktmeaton/ncov-recombinant#134
XAM	cov-lineages/pango-designation#759	ktmeaton/ncov-recombinant#110
XAA	cov-lineages/pango-designation#664	ktmeaton/ncov-recombinant#126
XAG	cov-lineages/pango-designation#709	ktmeaton/ncov-recombinant#121
XU	cov-lineages/pango-designation#522	ktmeaton/ncov-recombinant#131

Discussion started here #286

[szhan]

Quoting Yan here #286 (comment):
"Our ARG suggests that some pango-X recombinants are simply derived versions of previous recombinants (and do not represent a separate recombination event). A clear example of this is XR which pretty clearly descends from XQ (both are UK from the same date, I think(. In other words, we think that XR should really be labelled XQ.2 (or something like that). I think it is probably quite a nice argument to make that sc2ts can find simple descendant lineages like this, and simplify the terminology."

Copying image from Yan in #286 around the nested recombinant origin of XQ and XR. We want to see the others: XAM, XAA, XAG, and XU.

[szhan]

As per sc2ts, the left and right Pango parents are BA.1.1.15 and BA.2.9.
And the breakpoint interval is 4322-5386.

Ground truth from the pango-designation issues collated by RecombinHunt authors.

pango	left_parent	right_parent	left_breakpoint	right_breakpoint
XQ	BA.1.1*	BA.2*	4321	5386
XR	BA.1.1*	BA.2*	4321	4892
XAM	BA.1.1	BA.2.9	8087	9192
XAA	BA.1*	BA.2*	8938	9344
XAG	BA.1*	BA.2*	6515	8393
XU	BA.1*	BA.2*	6517	9344

XQ caused the recombinant as shown in the subgraph above, and then XR descended from it. Not sure where the rest are.