New EG.5.1.1-Flip lineage(83 seqs, 9 countries, 1,5% Finland, 2% Lithuania) and its sub-branch of S:G184S (19 seqs, 5 countries) displaying an insertion TTT resulting in Orf8:107F

[xz-keg]

There is a new EG.5.1.1-Flip lineage not in #537, and seems fast growing now.

EG.5.1.1->T14988C, A23014T->C1471T->C12823T->G25459T,G22927T(Orf3a:A23S,S:L455F), ins28214TTT?(or T or TT )

GISAID query: C12823,G25459, C1471,C29625T
No. of seqs: 58(Denmark 2 Finland 28 France 4 Lithuania 13 Netherlands 3 Sweden 8)

16/657 of Finland 12-15 batch, 11/326 of Lithuania 12-4 batch

Sub-lineage of S:G184S: >T16456C,G22112A(Orf1b:S997P,S:G184S)

GISAID query: C12823T,G22112,G25459,16456
No. of seqs: 13(Lituania 4 France 2 Netherlands 3 Sweden 4)

usher

[FedeGueli]

Many sequences of this sublineage from different countries display a weird insertion of TTT or TT in Orf8:107 ,
the ones with TT have a frameshift while the ones with TTT have Orf8:ins107F

[FedeGueli]

CovSpectrum sees the insertion in 20 out of 35 sequences with the following differences:
ins_28214:TT (10 seqs)• ins_28214:TTT (6 seqs)• ins_28214:TTTT (2 seqs)• ins_28214:T (1 seqs)• ins_28214:TTTTTN (1 seqs)

[FedeGueli]

cc @thomasppeacock @ryhisner @corneliusroemer could you take a look please?

[FedeGueli]

If i put the sequences with the insertion on the tree they are scattered over many branches so very likely it is present in every sequence of this sublineage: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_392b3_dc40.json?c=userOrOld&label=id:node_3442857

[xz-keg]

Many sequences of this sublineage from different countries display a weird insertion of TTT or TT in Orf8:107

As Orf8 is truncated it can be TT or T or other forms too.

[xz-keg]

Main branch: 75, USA, Poland, 14/435 in Lithuania 12-21 batch, still 3.5%

G184S branch is 19 seqs and in USA.

[FedeGueli]

Please propose once reaches 100. it has had very fast bumps still prefer to see a cleare pattern but it is not slow.

[xz-keg]

78, UK for main branch

[ryhisner]

Comes right where there's already a stretch of five Ts in a row, which is usually how these things happen. I'm noticing more of these lately.

There have been a few TTC insertions at S:254-255, where there are already three TTCs in a row. Here's an example uploaded today.

Another example is a GAA insertion in the NSP3 region that's absolutely loaded with D and E residues and features two close triple-GAA motifs. The one below from today is in the second GAAGAAGAA stretch, but I bet if you search, there are similar insertions in the first stretch as well. [EDIT: Yup. GISAID search for ins3073GAA returns 1095 sequences and ins3055GAA 661 sequences.]

[ryhisner]

Ah, dang, I just realized this is the explanation for XBC's ORF1b:814D insertion (ins_25909:GAT). There are two GATs in a row there already, so this another one of those RdRp-stutter insertions.

[FedeGueli]

Ah, dang, I just realized this is the explanation for XBC's ORF1b:814D insertion (ins_25909:GAT). There are two GATs in a row there already, so this another one of those RdRp-stutter insertions.

Thanks Ryan please add this to the original XBC issue on Pango!

[FedeGueli]

@aviczhl2 propose it is clearly still growing better letting Cornelius know about it.

[FedeGueli]

Updated prevalence after Nov 20

[FedeGueli]

please propose it.