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.

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

New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 19 sequences Uk, Canada #2565

Closed
FedeGueli opened this issue Apr 23, 2024 · 6 comments

Comments

@FedeGueli
Copy link
Contributor

FedeGueli commented Apr 23, 2024

Formerly tracked as Branch 94 of sars-cov-2-variants/lineage-proposals#1089
JN.1 > S:H1101Y > S:F456L > S:R346T > S:S71F
Query: C24863T, G22599C, T3565C,C21774T
Samples: 9 Uk, US, Canada
EPI_ISL_19010354, EPI_ISL_19059574, EPI_ISL_19062909-19062913,
EPI_ISL_19062915, EPI_ISL_19064899

It further gained S:L1203F:
JN.1 > S:H1101Y > S:F456L > S:R346T > S:S71F > Orf1a:P1912S (C6026T) > A7285G > S:L1203F (C25169T)
Query: C25169T,A7285G
Samples: 2 (Scotland)

Tree: updated at 05/07:
Screenshot 2024-05-07 alle 09 56 08
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice8_genome_2696e_95ba50.json?label=id:node_6958379

To be noted that there is another lineage that has JN.1 > S:S71F > S:R346T > S:F456L without S:H1101Y
tracked as branch 99 in sars-cov-2-variants/lineage-proposals#1089
View it here :

Same lineage??? Query:C21774T ,G22599C ,T22928C,T3565C,-C7113T,-C24863T [tree](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_464f0_7af8b0.json?label=id:node_6936214) Screenshot 2024-04-23 alle 14 56 12
cc @AngieHinrichs @corneliusroemer
@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y) Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 11 sequences Uk, Canada Apr 29, 2024
@FedeGueli
Copy link
Contributor Author

+2

@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 11 sequences Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 12 sequences Uk, Canada May 7, 2024
@FedeGueli
Copy link
Contributor Author

FedeGueli commented May 7, 2024

12 on Gisaid , 14 on Usher. Typical stepwise evolution tree (updated with new samples in the main proposal) with last sample carrying a further S2 mutation : S:L1203F

@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 12 sequences Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 13 sequences Uk, Canada May 7, 2024
@FedeGueli
Copy link
Contributor Author

13

@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 13 sequences Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 14 sequences Uk, Canada May 13, 2024
@FedeGueli
Copy link
Contributor Author

14

@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 14 sequences Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 14 sequences Uk, Canada with a further branch with S:L1203F (2, Scotland)) May 13, 2024
@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 14 sequences Uk, Canada with a further branch with S:L1203F (2, Scotland)) New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 14 sequences Uk, Canada with a further branch with S:L1203F (2, Scotland) May 13, 2024
@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 14 sequences Uk, Canada with a further branch with S:L1203F (2, Scotland) New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 15 sequences Uk, Canada with a further branch with S:L1203F (2, Scotland) May 19, 2024
@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 15 sequences Uk, Canada with a further branch with S:L1203F (2, Scotland) New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 16 sequences Uk, Canada May 22, 2024
@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 16 sequences Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 18 sequences Uk, Canada Jun 10, 2024
@FedeGueli
Copy link
Contributor Author

18 seqs but not relevant for designation

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Jun 10, 2024
@DailyCovidCases
Copy link

Tracked in tracker49

@FedeGueli FedeGueli changed the title New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 18 sequences Uk, Canada New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 19 sequences Uk, Canada Jul 14, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants