XAY

[szhan]

XAY seems to be a pretty messy case.

There are 11 XAY* samples in Viridian v04.

Sc2ts inferred six breakpoints, with the following seven segments inherited from the parents:

sample	segment1	segment2	segment3	segment4	segment5	segment6	segment7
SRR22375991	0:6428	6428:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904
SRR22243770	0:7124	7124:10198	10198:15026	15026:22017	22017:24912	24912:27575	27575:29904
SRR22743619	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904
SRR22972722	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27393	27393:29904
ERR10707172	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27638	27638:29904
SRR23200104	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904
ERR10770411	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27638	27638:29904
SRR23489537	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904
SRR23489545	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904
SRR23497420	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904
SRR22243763	0:7124	7124:10198	10198:15451	15451:22118	22118:24912	24912:27575	27575:29904

At some point in the pango-designation issue (cov-lineages/pango-designation#844), they were looking at this "Constellation 1" pattern which has six breakpoints and seven segments (https://github.com/cov-lineages/pango-designation/files/9115923/pango844.xlsx).

parental VOC	segment (inclusive)
Omicron	210-6402
Delta	7124-9534
Omicron	10029-13812
Delta	15451-22034
Omicron	22200-24469
Delta	25000-26767
Omicron	27638-29742

What sc2ts inferred seems pretty concordant with Constellation 1 to me.

What isn't clear to me from the pango-designation issue is how it ended with four breakpoints in the alias key file.

The inheritance structure from the 11 Viridian samples can be summarised as:
BA.2* + AY* + BA.2* + AY.4* + BA.5* + AY.4* + BA.2*

Below is the inheritance structure from the alias key file:
BA.2* + AY.45 + BA.2* + AY.45 + BA.2*

From the pango-designation issue, there seems to be some doubt that BA.5 was involved (probably related to artifactual reversions caused by assembly errors). So my guess is that the 22200-24469 segment (contribution from BA.5 supported by likely reversions) was dropped before designation.