Closed FedeGueli closed 1 year ago
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.
6 now, NY-PRL-230728_81D05/2023|OR398243.1|2023-07-23
, NY and EPI_ISL_18104574
, FL
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.
two more sequences from Sweden
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.
LAST FROM UK.
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.
Thank you i am proposing it. it will the first FLip +478 to reaching "designation standards"
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