Skip to content

EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (21 seqs, 8 countries) #745

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
Closed
xz-keg opened this issue Sep 3, 2023 · 13 comments
Closed

EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (21 seqs, 8 countries) #745

xz-keg opened this issue Sep 3, 2023 · 13 comments
Labels
Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest S:52 s:157 S:456

Comments

@xz-keg
Copy link
Contributor

xz-keg commented Sep 3, 2023 •
edited
Loading

EG.5.1.1+
A1982G,C10408T,C22033A,C27507A(rev),C28000T, A28182G, A28447G,C29386T,T29625C(rev)

EG.5.1.1--XBB.1.16
breakpoint between 25573 and 27506

Private mutations: C10408T,C28000T(Orf8:P36L)

GISAID query: C28000T,C25572T,-27507,G13627A(edited)
No. of seqs: 3(China 1 Japan 1 USA 1)

First: EPI_ISL_18105530, China, 2023-8-1
Latest: EPI_ISL_18144757, USA, 2023-8-16

usher

image

Rapid picture of this recombinant (edited)
Schermata 2023-09-03 alle 23 52 14
@FedeGueli
Copy link

Good catch and apparently good recombinant.

@xz-keg
Copy link
Contributor Author

xz-keg commented Sep 20, 2023

+1 Canada

@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (3 seqs, 3 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (4 seqs, 4 countries) Sep 20, 2023
@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (4 seqs, 4 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (5 seqs, 4 countries) Sep 21, 2023
@xz-keg
Copy link
Contributor Author

xz-keg commented Sep 22, 2023

+2 New Zealand

@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (5 seqs, 4 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (7 seqs, 5 countries) Sep 22, 2023
@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 labels Sep 29, 2023
@FedeGueli
Copy link

It seems slow

@xz-keg
Copy link
Contributor Author

xz-keg commented Sep 29, 2023

It seems slow

This one seems to be circulating at some undersampled regions, and exporting to different countries from time to time

@FedeGueli FedeGueli added the Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest label Sep 29, 2023
@FedeGueli
Copy link

It seems slow

This one seems to be circulating at some undersampled regions, and exporting to different countries from time to time

Yes likely added the label.

@xz-keg
Copy link
Contributor Author

xz-keg commented Oct 4, 2023

9, Israel

@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (7 seqs, 5 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (9 seqs, 6 countries) Oct 4, 2023
@FedeGueli
Copy link

It doensnt seem fit enough to circulate. closing for now . Ping to @corneliusroemer for recombinant search

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Oct 20, 2023
@Walde1nsamkeit Walde1nsamkeit mentioned this issue Oct 20, 2023
Closed
@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (9 seqs, 6 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (11 seqs, 6 countries) Oct 25, 2023
@xz-keg
Copy link
Contributor Author

xz-keg commented Nov 1, 2023

+1 USA from Sweden

@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (11 seqs, 6 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (12 seqs, 7 countries) Nov 1, 2023
@FedeGueli FedeGueli reopened this Nov 1, 2023
@FedeGueli
Copy link

Having added a new recent sample from a new country i ve reopened it to keep it tracked.

@xz-keg
Copy link
Contributor Author

xz-keg commented Nov 11, 2023

+1 Australia

@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (12 seqs, 7 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (13 seqs, 8 countries) Nov 11, 2023
@FedeGueli
Copy link

Thank you for the new query still it struggles to grow significantly closing it for now

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Nov 13, 2023
@xz-keg
Copy link
Contributor Author

xz-keg commented Nov 24, 2023

+4 Sweden

@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (13 seqs, 8 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (17 seqs, 8 countries) Nov 24, 2023
@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (17 seqs, 8 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (18 seqs, 8 countries) Dec 2, 2023
@xz-keg xz-keg changed the title EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (18 seqs, 8 countries) EG.5.1.1/XBB.1.16 recombinant with additional 5-nuc,4-aa including S:F157L (21 seqs, 8 countries) Dec 8, 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. Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest S:52 s:157 S:456
Projects
None yet
Milestone
No milestone
Development

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