Closed corneliusroemer closed 11 months ago
Yes, that's one of the many forms of extended homology for the ORF9b/N TRS. It adds five additional nucleotides of perfect extended homology with the TRS-L. One of the constants in SARS-CoV-2 evolution seems to be mutations to increase ORF9b/N expression.
I think usher shall mask 28245-28254 site. @AngieHinrichs
1:Although they're real, they are very convergent but only have minor effects. 2:They usually contain insertions that usher cannot handle. For example, ins28250CT is one of the most common form, and usher always misread it and forms something messy and incorrect. 3:Usher always put a lot of mutations in these region, this makes neighboring lineages with such kind of late-Orf8 form shift don't be in the correct place, only follows the largest nearby group with the same late-orf8 form.
Sorry about the slow reply. I agree, and it looks like masking 28245, 28251 and 28254 will take care of most of the problems. I will mask those in the BA.2 branch (includes BA.4, BA.5 & XBB) starting in today's build 2023-11-09.
14 sequences now but a bit slow/small for designation
Quite a saltation though
I was tracking it from @ryhisner proposal : https://github.com/sars-cov-2-variants/lineage-proposals/issues/986 that came after this one.
Not quite sure why I closed this as not planned, it keeps popping up and it's really a big saltation, I just rediscovered it 🤦 and had entirely forgotten I had made this issue a month ago. Thanks @ryhisner for tracking it in https://github.com/sars-cov-2-variants/lineage-proposals/issues/986
Not quite sure why I closed this as not planned, it keeps popping up and it's really a big saltation, I just rediscovered it 🤦 and had entirely forgotten I had made this issue a month ago. Thanks @ryhisner for tracking it in sars-cov-2-variants/lineage-proposals#986
I also usually have a case of forgetting, and my solution is to create a JSON file called a catalog so I can always look it up and see the title of the issues as well as the content, time, and author information.
Came across what looks like an interesting saltation that popped up fairly suddenly in US and Austria.
@ryhisner do you know whether this pattern of T28251G,C28253T,A28254C could have something to do with TRSs? Doesn't look like for me, do you know of other reasons such a pattern could occur frequently?
Usher placement:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5cae6_bd3fe0.json
Usher seems to mask the 28253 mutation?
This is the new pattern: