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

LF.8.1.1+Orf1a:L4391F+S:K478T(rev) (24 seqs) #1982

Closed
xz-keg opened this issue Sep 4, 2024 · 6 comments
Closed

LF.8.1.1+Orf1a:L4391F+S:K478T(rev) (24 seqs) #1982

xz-keg opened this issue Sep 4, 2024 · 6 comments
Labels
designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest FLiRT FLiRT is an Acronym for S:R346T + S:F456L Reversions S:22 S:31 S:153 S:478
Milestone
ND.1.1

Comments

@xz-keg
Copy link
Contributor

xz-keg commented Sep 4, 2024 •
edited
Loading

LF.8.1.1+C13436T+A22995C(rev)

GISAID query: C13436T,-22995,C9169T,C21654T,C21627A

No. of seqs: 3(USA , 2 from Qatar)

EPI_ISL_19362364, 2024-8-19, USA-VA
EPI_ISL_19375171,19375176, 2024-8-23, USA from Qatar

usher
image
@xz-keg xz-keg added S:478 S:153 S:31 S:22 FLiRT FLiRT is an Acronym for S:R346T + S:F456L Reversions Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest labels Sep 4, 2024
@FedeGueli
Copy link

Interestingly this is the second branch with 478T beside the one with also 222V in comments in the original issue.

@xz-keg
Copy link
Contributor Author

xz-keg commented Sep 24, 2024

No new seqs

@xz-keg xz-keg closed this as not planned Won't fix, can't repro, duplicate, stale Sep 24, 2024
@xz-keg xz-keg mentioned this issue Oct 5, 2024
Closed
@FedeGueli FedeGueli reopened this Oct 5, 2024
@FedeGueli FedeGueli changed the title LF.8.1.1+Orf1a:L4391F+Orf6:I33M, S:K478T(rev) (3 seqs, 2 countries) LF.8.1.1+Orf1a:L4391F+Orf6:I33M, S:K478T(rev) (5 seqs, 3 Places) Oct 5, 2024
@xz-keg
Copy link
Contributor Author

xz-keg commented Oct 16, 2024

+1 USA-OH
+2 China, from Hubei and Gansu

@xz-keg xz-keg changed the title LF.8.1.1+Orf1a:L4391F+Orf6:I33M, S:K478T(rev) (5 seqs, 3 Places) LF.8.1.1+Orf1a:L4391F+Orf6:I33M, S:K478T(rev) (8 seqs, 6 Places) Oct 16, 2024
@FedeGueli FedeGueli added this to the ND.1 milestone Oct 20, 2024
@FedeGueli
Copy link

FedeGueli commented Oct 20, 2024 •
edited
Loading

Designated ND.1.1 via cov-lineages/pango-designation@bb7b4ed

FedeGueli referenced this issue in cov-lineages/pango-designation Oct 20, 2024
@corneliusroemer
Designate LF.8.1.1 sublineages (ND)
bb7b4ed
@FedeGueli FedeGueli modified the milestones: ND.1, ND.1.1 Oct 20, 2024
@xz-keg xz-keg changed the title LF.8.1.1+Orf1a:L4391F+Orf6:I33M, S:K478T(rev) (8 seqs, 6 Places) LF.8.1.1+Orf1a:L4391F+S:K478T(rev) (8 seqs, 6 Places) Oct 21, 2024
@xz-keg xz-keg changed the title LF.8.1.1+Orf1a:L4391F+S:K478T(rev) (8 seqs, 6 Places) LF.8.1.1+Orf1a:L4391F+S:K478T(rev) (24 seqs) Oct 21, 2024
@xz-keg
Copy link
Contributor Author

xz-keg commented Oct 21, 2024

It seems that there are also a lot of non-Orf6:I33M seqs now. Edit proposal accordingly to match ND.1.1

@FedeGueli
Copy link

C13436T,-22995,C9169T,C21654T,C21627A

yeah i think the tree now collectes all the singlets with 478T too, we spotted them at the start but they werent together in the same branch

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest FLiRT FLiRT is an Acronym for S:R346T + S:F456L Reversions S:22 S:31 S:153 S:478
Projects
None yet
Milestone
ND.1.1
Development

No branches or pull requests
2 participants
@xz-keg @FedeGueli