I checked the major branches of it and seems that all the major branches are all gained after the recomb event. No seqs with mutations on major branch has C29625T.
Major branches include
G25459A (Query: C5031T,G13627A,G25459A)
A27321G,T23584C (Query: C5031T,G13627A,A27321G)
A9488G,C24715T(Query:C5031T,G13627A,A9488G)
G6850A (Query:C5031T,G13627A,G6850A)
……
All above has 0 seqs with C29625T.
Some of the major branches have both seqs with or without S:L455F. This suggests that S:L455F may be independently gained after the recomb.
May also be 29625 rev. But 29625 is just gained in EG.5, reverting it immediately seems weird. (Not impossible though, like FR.1.4)
What is more likely? Recomb or reversion?
HK.27+T29625C(rev)
Orf10:F23S(rev)
HK.27--anything(non EG.5, XBB.2.3)
Breakpoint between 25573 and 29624 (depend on donor)
GISAID query: G13627A,T28297C, C5031T,-29625
No. of seqs: 415(Australia 4 China 28 (Beijing 1 Gansu 1 Henan 2 Hong Kong 1 Hubei 6 Jiangsu 1 Qinghai 1 Shanghai 5(1 from South Korea) Sichuan 3 Taiwan 2 (1 from Thailand) Xinjiang 1 Yunnan 4 ) Canada 68 Denmark 3 Finland 1 France 7 Germany 2 Greece 1 Italy 1 Japan 4 Netherlands 1 New Zealand 1 Norway 1 Poland 2 Russia 1 Singapore 36(1 from China) Slovenia 2 South Korea 203(1 from China) Sweden 2 Switzerland 11 USA 35(1 from Belgium)
GISAID query for S:L455F(maybe independently gained on different branches) : G13627A,T28297C, C5031T,G22927T, -29625 (391 seqs)
aviczhl2
commented
5 months ago
From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1316 I used to think it is some sort of artefact, but it seems to be a real XDB-like recomb here.
I checked the major branches of it and seems that all the major branches are all gained after the recomb event. No seqs with mutations on major branch has C29625T.
Major branches include G25459A (Query: C5031T,G13627A,G25459A)
A27321G,T23584C (Query: C5031T,G13627A,A27321G)
A9488G,C24715T(Query:C5031T,G13627A,A9488G)
G6850A (Query:C5031T,G13627A,G6850A)
……
All above has 0 seqs with C29625T.
Some of the major branches have both seqs with or without S:L455F. This suggests that S:L455F may be independently gained after the recomb.
May also be 29625 rev. But 29625 is just gained in EG.5, reverting it immediately seems weird. (Not impossible though, like FR.1.4)
What is more likely? Recomb or reversion?
HK.27+T29625C(rev)
Orf10:F23S(rev)
HK.27--anything(non EG.5, XBB.2.3) Breakpoint between 25573 and 29624 (depend on donor)
GISAID query: G13627A,T28297C, C5031T,-29625 No. of seqs: 415(Australia 4 China 28 (Beijing 1 Gansu 1 Henan 2 Hong Kong 1 Hubei 6 Jiangsu 1 Qinghai 1 Shanghai 5(1 from South Korea) Sichuan 3 Taiwan 2 (1 from Thailand) Xinjiang 1 Yunnan 4 ) Canada 68 Denmark 3 Finland 1 France 7 Germany 2 Greece 1 Italy 1 Japan 4 Netherlands 1 New Zealand 1 Norway 1 Poland 2 Russia 1 Singapore 36(1 from China) Slovenia 2 South Korea 203(1 from China) Sweden 2 Switzerland 11 USA 35(1 from Belgium)
GISAID query for S:L455F(maybe independently gained on different branches) : G13627A,T28297C, C5031T,G22927T, -29625 (391 seqs)
First:EPI_ISL_18049529, China-Beijing, 2023-5-30 Latest:EPI_ISL_18749511, Canada, 2024-1-1
usher
Most seqs are placed under HK.27.1. Top branch with 5031 rev are HK.3 recombs not this recomb.