XBB.1.16.6 (S:F456L) with S:L455F emerging in Florida (14 seqs)

[FedeGueli]

I was monitoring a sublineage of XBB.1.16.6 since it was one sequences that gained convergently S:L455F, as today it reached 4 sequences so it is better to track it here:

Defining mutations: XBB.1.16.6 >> C8947T > A10861G > T23986C > S:L455F (G22927T)

Gisaid query:G22927T, A10861G,T12730A,-C27937T

Samples: 4 (Florida 2, New Jersey 1 with travel history, Washington 1 )

EPI_ISL_17971832, EPI_ISL_18037649, EPI_ISL_18060741

Tree: (Note that already S:L455F has popped up in XBB.1.16.6 ) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ad1e_b9e410.json?c=gt-S_455&label=id:node_6715319

[ryhisner]

I noticed that two of the three sequences from Florida have A13912T + A13913C. I figured adjacent A->T and A->C mutations had to be TRS-related, and they are. It's a bit strange because most of the matching nucs here are in the 5' extended homology region rather than the core TRS.

Normal view on top, annotated version on bottom.

I looked to see if any other sequences with A13912T + A13913C had additional nucleotide mutations that would make an ever better match for the TRS-L, and it turns out there have been 19 sequences with T13906C, A13907T, & T13908G. Those form ORF1b:Y147L (NSP12_Y156L)

Again, unannotated view on top, annotated version on bottom.

[NkRMnZr]

6 now, NY-PRL-230728_81D05/2023|OR398243.1|2023-07-23, NY and EPI_ISL_18104574, FL

[FedeGueli]

G22927T, A10861G,T12730A,-C27937T

Many thx for some reason this got deleted from my list or mistakenly renamed or misplaced so i ve lost track of it. many thx for the ping.

[FedeGueli]

two more sequences from Sweden

[NkRMnZr]

There's another branch follows XBB.1.16.6 > A10861G > G22927T(S:L455F) Query: A10861G, A12397G, G22927T, C29386T, -T23986C finds 3 as of Aug 17, 2 from Sweden and another is from EWR (NJ) airpot screening with known travel history.

[FedeGueli]

LAST FROM UK.

[FedeGueli]

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_38fc8_f79060.json?label=id:node_6855109

[NkRMnZr]

14 now, new seqs from France and USA (plus one with travel history to Mexico), I think it's time to transfer to main repo.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_352ee_590760.json?c=gt-S_455&label=id:node_6862783

[FedeGueli]

Thank you i am proposing it. it will the first FLip +478 to reaching "designation standards"

[FedeGueli]

Designated JF.1 via https://github.com/cov-lineages/pango-designation/commit/7e6a6613234930ff49365e7984615e9ad93e1b63