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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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HN.1 (FL.1.5.1 + S:A67S) with 4 further NTD mutations: I68V, E156Q, M177V, N185G (6 seqs) #477

Closed BorisUitham closed 7 months ago

BorisUitham commented 1 year ago

Only 2 sequences so far, but interesting in the amount of mutations in the NTD region, as well as inheriting 456l+478r from its ancestor. One seq is from dominican republic (5/7), where hn.1 and fl.1.5.1 are already establishing dominance, but recently another sample has been uploaded from florida (12/7). This is indicated as baseline surveillance rather than airport screening. Of course both are in the carribean region so the spread might not be too interesting, but for such mutated lineage it might be worth monitoring.

Note that all these NTD mutations are relatively rare: 67s (9k), 177v (5k), 68v (1.5k), 156q (1.1k), 185g (4, of which these 2 are half)

Gisaid query: a21764g, g22028c, a22091g, a22115g, a22116g

hn 1 1 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2b6ca_3d520.json?c=gt-S_156

FedeGueli commented 1 year ago

@BorisUitham could you add a nucleotides query for this one?

BorisUitham commented 1 year ago

Sure: for the ntd muts its a21764g, g22028c, a22091g, a22115g, a22116g. Ill add it in main post, there are probably more succint queries but thisll manage

FedeGueli commented 1 year ago

it doesnt seem super fast hopefully,

FedeGueli commented 1 year ago

no new seq closing it for now.

BorisUitham commented 9 months ago

I think this can stay closed because i highly highly doubt this is relevant but I'm quite surprised to see a fifth sequence submitted yesterday, 4 months after the previously found sequence in new jersey: EPI_ISL_18779138 Collected just before christmas, 12-20! Both NJ sequences aren't very related to eachother and branch off of S:N1023S which it shares with a dominican republic sequence, but not the NY sequence. This latest one also adds S:T573I.

Boggles my mind how this one was still alive. Perhaps its a long term infection that passed on to someone else because I can't imagine this having a lot of community transmission.

FedeGueli commented 9 months ago

i have put it under monitoring. thank you!

FedeGueli commented 8 months ago

I see 6 samples now the last collected in 2024

BorisUitham commented 8 months ago

Very mysterious this sudden reappearance in NJ of a seemingly unfit sublineage in the JN.1-dominant era! This one adds N:S193N and N:P365L. Also i had a typo in my previous comment, its S:T573I instead of S:T572I

FedeGueli commented 7 months ago

re closing this