Correction - Recombinants with duplicate references on alias_key.json

[3dgiordano]

You'll be able to see the duplicate value fir each designation here.

XAC - BA.2* duplicated https://github.com/cov-lineages/pango-designation/blob/master/pango_designation/alias_key.json#L131

XAZ - BA.2.5 duplicated https://github.com/cov-lineages/pango-designation/blob/master/pango_designation/alias_key.json#L151

XBC - "BA.2","B.1.617.2" duplicated https://github.com/cov-lineages/pango-designation/blob/master/pango_designation/alias_key.json#L154

XBL - XBB.1 duplicated https://github.com/cov-lineages/pango-designation/blob/master/pango_designation/alias_key.json#L162

[silcn]

These refer to recombinants with multiple breakpoints, showing the order in which sections derived from each donor occur.

[3dgiordano]

Hi @silcn

I'm trying to understand what you're telling me, but I don't know if I'm the one who didn't understand or maybe you didn't get what I meant. I understand the use of the asterisk, what I mention is not in reference to that usage.

I will try to explain one of the indicated examples

From lineage_note.txt

XBC Recombinant lineage of BA.2 and B.1.617.2*, predominantly in Philippines, from pango-designation issue #1100

The text on lineage_note.txt for XBC is clear the reference to two possible lineages references.

in alias_keys.json the two lineages appear as duplicates.

"XBC": ["BA.2","B.1.617.2","BA.2","B.1.617.2"],

If the idea is to mention the breakpoints, it is not clear to me that these duplicates are for that reason.

[AnonymousUserUse]

I think it would be better to describe _in a similar way as in aliaskey.json in lineage_note.txt, e.g. XBC Recombinant lineage of BA.2, B.1.627.2, BA.2, and B.1.627.2, predominantly in Philippines, from pango-designation issue https://github.com/cov-lineages/pango-designation/issues/1100

[silcn]

in alias_keys.json the two lineages appear as duplicates.

"XBC": ["BA.2","B.1.617.2","BA.2","B.1.617.2"],

If the idea is to mention the breakpoints, it is not clear to me that these duplicates are for that reason.

@3dgiordano the duplicates clearly are for that reason: XBC is a recombinant of two lineages with three breakpoints in precisely the pattern indicated by that line. Perhaps a further explanation of the convention used in that file should be added somewhere.

[3dgiordano]

Thanks @silcn for the clarification.

Such a pattern is not easy to guess or visualize. An explanation in some document might help.

If it's okay to you, I don't see a problem in closing this issue, since this issue is due to a misinterpretation of the format for recombinants.

[Mydtlwn]

XBC is a pedigree with three breakpoints, while XBL is a pedigree with two breakpoints, and * is a pedigree representing the family formed by this branch. It means a branch of this family.

[corneliusroemer]

It's exactly as @silcn explained