EG.5.1.3/XCH.1 recombinant that may be removed by usher(8 seqs, 4 countries)

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EG.5.1.3/XCH.1 recombinant that may be removed by usher(8 seqs, 4 countries) #846

Closed aviczhl2 closed 7 months ago

aviczhl2 commented 11 months ago

@AngieHinrichs, there's an Australian EG.5.1.3/XCH.1 recomb that may be removed by usher by reversions, please put it on list.

EPI_ISL_18285932

XBB.1.5+C1889T,G2144A,C2334T, G5720A,T6649C,C9693T,T10254C,C12789T, A16878T, A18492G，G18703T,C22624T,G22927T,T22928C,C23280T, C23673T,G25947C, C26907T,C27741T,T28297C, C28657T

Orf1a:R542C,V627I,A690V,G1819S,A3143V,L3330S,T4175I Orf1b:D1746Y S:L455F,F456L,T573I,S704L Orf3a:Q185H Orf8:P38S Orf9b:I5T

C1889T, C2334T, G5720A,C9693T, C12789T, A16878T, A18492G from EG.5.1.3 G2144A,T6649C,T10254C,G18703T from where? seems private. Is it related with XBB.1.16?

C22624T,G22927T,T22928C,C23280T, C23673T,G25947C, C26907T,C27741T,T28297C, C28657T from XCH.1

Try to make a query for this: G2144A,G18703T,C28657T

usher

AngieHinrichs commented 11 months ago

Added to list. It should appear in 2023-09-21 tree. Thanks!

aviczhl2 commented 11 months ago

@AngieHinrichs @FedeGueli There's one more of this. EPI_ISL_18324408

aviczhl2 commented 11 months ago

There is a 3rd one EPI_ISL_18324447 @FedeGueli @AngieHinrichs @corneliusroemer

usher

FedeGueli commented 11 months ago

Sorry i was thinking it was just an usher issue. So this is Flip and has 3 lineages as parental, right?

aviczhl2 commented 11 months ago

Sorry i was thinking it was just an usher issue. So this is Flip and has 3 lineages as parental, right?

Yeah, Flip+573+704+Orf9b:I5T, following XCH.1 but has the Orf1ab part replaced to something new. (EG.5.1.3+some private?)

Initially there's only 1 seq so you're right only usher issue. But now it has 3.

AngieHinrichs commented 10 months ago

Added, thanks, should be in 2023-10-03.

aviczhl2 commented 10 months ago

There is a 4th one @AngieHinrichs EPI_ISL_18352383

AngieHinrichs commented 10 months ago

Added, thanks. (BTW 2023-10-06 run has not started yet because 2023-10-05 run is hanging! I think it's the first time that usher-sampled has gone off into deadlock or infinite loop land like this. @yceh I sent you a message in Slack; if you have time to look into it, that would be super helpful.]

FedeGueli commented 10 months ago

no recent sample . closing it , ping for @corneliusroemer

aviczhl2 commented 8 months ago

+1 USA +1 Switzerland

FedeGueli commented 8 months ago

Still not very recent please reopen it if some sample come from late Nov.December.

aviczhl2 commented 7 months ago

+1 Austria

FedeGueli commented 7 months ago

this disappears and then reappers . reopened for a while

aviczhl2 commented 7 months ago

+1 Australia

FedeGueli commented 7 months ago

Likely dying off.

aviczhl2 commented 7 months ago

No new seqs.

FedeGueli commented 7 months ago

thx