Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

FY.3.1 (XBB.1.22.1.3.1) sublineage with S:Q613H and S:D950N (10 seqs in Japan) #522

Closed
HynnSpylor opened this issue Aug 2, 2023 · 5 comments
Closed

FY.3.1 (XBB.1.22.1.3.1) sublineage with S:Q613H and S:D950N (10 seqs in Japan) #522

HynnSpylor opened this issue Aug 2, 2023 · 5 comments
Labels
Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. S:613

Comments

@HynnSpylor
Copy link

Defining mutations:
FY.3.1>G4109T (ORF1a:D1282Y)>C25669T (ORF3a:H93Y)>T17688C, G23401C (S:Q613H)

GISAID query: A22161G, G4109T, G23401C
Earliest seq: 2023-07-05 (Japan, EPI_ISL_18051378)
Most recent seq: 2023-07-12 (Japan, EPI_ISL_18051430)
Countries detected: Japan (7)

Usher Tree:
QQ截图20230802001445

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8bcf_92bee0.json?c=gt-S_613

S:Q613H is popular in FK.1 and EG.1 nowadays. All seqs are from Fukuoka, Japan and the IDs are consecutive, hence they may be two infection chains.

Genomes:
EPI_ISL_18051378-18051379, EPI_ISL_18051381, EPI_ISL_18051426-18051427, EPI_ISL_18051429-18051430
@NkRMnZr NkRMnZr mentioned this issue Aug 1, 2023
Open
12 tasks
@HynnSpylor
Copy link
Author

2 more seqs from Japan
and I omitted that they also get S:D950N (which emerged in Delta lineages)

@HynnSpylor HynnSpylor changed the title FY.3.1 (XBB.1.22.1.3.1) sublineage with S:Q613H (7 seqs in Japan) FY.3.1 (XBB.1.22.1.3.1) sublineage with S:Q613H and S:D950N (9 seqs in Japan) Aug 7, 2023
@FedeGueli FedeGueli added the To be proposed Green light for proposal label Aug 7, 2023
@FedeGueli
Copy link

Please propose it.

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Rapid review needed To be proposed Green light for proposal labels Aug 20, 2023
@FedeGueli
Copy link

It seems to have slowed down . lets track it till the end of this month.

@HynnSpylor
Copy link
Author

1 more seq but still in Fukuoka, Japan. It really slowed down.

@HynnSpylor HynnSpylor changed the title FY.3.1 (XBB.1.22.1.3.1) sublineage with S:Q613H and S:D950N (9 seqs in Japan) FY.3.1 (XBB.1.22.1.3.1) sublineage with S:Q613H and S:D950N (10 seqs in Japan) Aug 28, 2023
@FedeGueli
Copy link

Closing for now. ping me if it starts again to pop up.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Aug 28, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. S:613
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@FedeGueli @HynnSpylor