XBB.1.5.92 with ORF1a:L3829F (nsp6_L260F) (98 seqs, mainly in Costa Rica and Ecuador, 12 countries)

[NkRMnZr]

Defining Mutations: XBB.1.5.92 (C3768T= ORF1a:T1168I) > C11750T(ORF1a:L3829F)
Query: C3768T, C11750T, T17124C
Earliest seq: 2023-03-06 (EPI_ISL_17240745, Ecuador)
Latest seq: 2023-06-23 (EPI_ISL_17961597, Ecuador)
Sampled Countries: Costa Rica (24), Ecuador (24), USA (12, California/5, New Jersey/2, New York/2, North Carolina/1, Pennsylvania/1, Texas/1), Guatemala (8), Germany (2), Belgium (1), Spain (1, Canary Islands), Colombia (1), Mexico (1), Panama (1), UK (1, Wales)

Genomes:

EPI_ISL_17240745, EPI_ISL_17429082, EPI_ISL_17519027,
EPI_ISL_17519102, EPI_ISL_17525650, EPI_ISL_17527944,
EPI_ISL_17527949, EPI_ISL_17582793-17582796, EPI_ISL_17582798,
EPI_ISL_17582806, EPI_ISL_17612038, EPI_ISL_17612061,
EPI_ISL_17621288, EPI_ISL_17654589, EPI_ISL_17654598,
EPI_ISL_17654687, EPI_ISL_17654750, EPI_ISL_17654777,
EPI_ISL_17654789, EPI_ISL_17674267, EPI_ISL_17683020,
EPI_ISL_17683043-17683044, EPI_ISL_17684571, EPI_ISL_17684577,
EPI_ISL_17695468, EPI_ISL_17695472, EPI_ISL_17712005,
EPI_ISL_17712018, EPI_ISL_17713984, EPI_ISL_17722436,
EPI_ISL_17730094, EPI_ISL_17763506, EPI_ISL_17766883,
EPI_ISL_17774107, EPI_ISL_17774126, EPI_ISL_17774131,
EPI_ISL_17774145, EPI_ISL_17774195-17774196, EPI_ISL_17774198,
EPI_ISL_17774203-17774207, EPI_ISL_17788960, EPI_ISL_17798393,
EPI_ISL_17800566, EPI_ISL_17801644, EPI_ISL_17833803,
EPI_ISL_17833855, EPI_ISL_17833862, EPI_ISL_17834337,
EPI_ISL_17834418, EPI_ISL_17838695, EPI_ISL_17854201,
EPI_ISL_17854470, EPI_ISL_17856036, EPI_ISL_17879866,
EPI_ISL_17950535, EPI_ISL_17954111, EPI_ISL_17954147,
EPI_ISL_17954610, EPI_ISL_17961499, EPI_ISL_17961554,
EPI_ISL_17961593, EPI_ISL_17961597, EPI_ISL_17961609,
EPI_ISL_17961637, EPI_ISL_17970749, EPI_ISL_17972754,
EPI_ISL_17972779

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3eab3_97aef0.json?f_userOrOld=uploaded%20sample

view from XBB.1.5's T17124C polytomy

details

Trivia:

• Probably high local prevalence in certain South America countries, too little samples to confirm this.
  

• ORF1a:L3829F is the notorious chronic infection hallmark, this may be worth monitoring for a while.

[NkRMnZr]

Tracking updates:

07-11: 3 seqs from Panama, UK and USA

1 from Wales, UK: EPI_ISL_17975019
1 from Maryland, USA: EPI_ISL_17976828
1 from Panama: EPI_ISL_17977448

07-23: 3 seqs from Guatemala, Mexico and USA

1 from Guatemala: EPI_ISL_17982593
1 from Indiana, USA: EPI_ISL_17998564
1 from Mexico: EPI_ISL_18011964

07-28: 9 seqs from China, UK, USA

08-08, 2 seqs from Ecuador and USA

08-18, 5 seqs from USA

[Over-There-Is]

@AngieHinrichs As a sublineage of new-designated XBB.1.5.92, this lineage is placed under a Orf1a:Y1467C> Orf1a:T1168I> Orf1a:C1467Yrev flip-flop branch. And the sequences with C823T, C3768T, C10615T (parental branch of #170) are placed under C823T branch, but I think they are also a subbranch of XBB.1.5.92.
But C3768T(Orf1a:T1168I) is too homoplastic, some of the sequences with T1168I is actually unrelated to XBB.1.5.92.

[FedeGueli]

There are at least three ecuadorean sublineage of XBB.1.5 with Orf1a:T1168I :
1
The parental lineage of the one proposed here with Orf1a:L3829F That is legit XBB.1.5.92 (according to Usher and Nextclade)
I think @AngieHinrichs fixed the flip flop thing that was highlighted above by @Over-There-Is

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_1007a_27cc00.json?c=gt-nuc_823&label=id:node_7037790
2
Another XBB.1.5 with C823T and then Orf1a:T1168I that acquired S:E554K ( proposed in #170 ) that ctually could be one of the fastest lineages at least in South America

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1007a_27cbf0.json?label=id:node_6889930
3
a small unproposed lineage in a flip flop branch with S:W258C>W that further acquired three key NTD mutations(S:K182T,S:E183D,S:A222S):


https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_1007a_27cc00.json?c=userOrOld&label=id:node_6936104

[FedeGueli]

ping @corneliusroemer see discussion above, please.

[AngieHinrichs]

@Over-There-Is I see that C3768T (ORF1a:T1168I) happens several times in XBB.1.5, but in each case there are more sequences with XBB.1.5 > [some mutation] than XBB.1.5 > [some mutation] > C3768T. So to me, the evidence for each of those other mutations occurring first looks pretty strong, and I think it's plausible that either C3768T happened multiple times after those other mutations (and perhaps is sometimes an artefact, especially from Ecuador and Sweden?).

Why do you think the C823T, C3768T, C10615T sequences in particular belong in XBB.1.5.92? I see 134 sequences on the branch with all three of those mutations, but even more (207) that have C823T (but not C3768T and C10615T). Also some of the sequences with C823T have older dates like USA/MA-CDCBI-CRSP_YEAJAWGEG53EKBFX/2022|OP987449.1|2022-11-21. So I think it's plausible (though not certain) that C823T came first.

[NkRMnZr]

07-28: 9 seqs from China, UK, USA
6 seqs from USA: EPI_ISL_18012775, EPI_ISL_18012803, EPI_ISL_18037770, EPI_ISL_18039665-18039666, EPI_ISL_18045781
1 from Guangdong, China: EPI_ISL_18034452
2 from Wales, UK: EPI_ISL_18015720, EPI_ISL_18044446

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e0ca_380ef0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Last one from Texas.
Likely cannot compete with EG.5/FL.1.5 wave: https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?nextcladePangoLineage=EG.5.1*&nucMutations1=C3768T%2CC11750T%2CT17124C&analysisMode=CompareToBaseline&

[NkRMnZr]

08-08, 2 seqs from Ecuador and USA: EPI_ISL_18057501, EPI_ISL_18075680

[NkRMnZr]

08-18, 5 from USA (NY, CA):
EPI_ISL_18080198, EPI_ISL_18103756, EPI_ISL_18104230, EPI_ISL_18114056, EPI_ISL_18114201

[NkRMnZr]

gone stale