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

Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 23 seqs, 16 countries) #109

Closed
aviczhl2 opened this issue May 29, 2023 · 8 comments
Closed
Labels
designated New mutations Lineage with an unusual/new/interesting mutation
Milestone

Comments

@aviczhl2
Copy link
Contributor

aviczhl2 commented May 29, 2023

Baseline variant: cov-lineages/pango-designation#2005

(XBB.2.3.3 >> > C19884T > Orf8:E106Q (G28209C) >Orf1a:I4205V (A12878G NSP9_I65V)

Additional mutations:
C1549T,C2902T, A3394T, G6008A, A6948G, G29229A, C1150T, C22227T

ORF1ab | V1915I, N2228S
S | A222V
N | R319H

GISAID query: C2902T, A3394T, G6008A, A6948G, G29229A, C1150T, C22227T
No. of seqs: 11 (India 2 China 1 USA 2(1 from Spain), Switzerland 1 South Korea 1 Austria 1 �Australia 3)

First seq: EPI_ISL_17720450, India ,4-15
Latest: EPI_ISL_17719397, Switzerland, 5-7

Propose this because I found the S:A222V branch is quite widespread.

usher

Screenshot 2023-05-29 at 09 56 39
@FedeGueli FedeGueli changed the title Widespread 8-nuc/4-aa branch of XBB.2.3.3 (S:A222V, 11 seqs, 8 countries) Sublineage of #2005 : Widespread 8-nuc/4-aa branch of XBB.2.3.3 (S:A222V, 11 seqs, 8 countries) May 29, 2023
@FedeGueli FedeGueli added the New mutations Lineage with an unusual/new/interesting mutation label May 29, 2023
@FedeGueli FedeGueli changed the title Sublineage of #2005 : Widespread 8-nuc/4-aa branch of XBB.2.3.3 (S:A222V, 11 seqs, 8 countries) Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 11 seqs, 8 countries) Jun 2, 2023
@FedeGueli
Copy link

FedeGueli commented Jun 2, 2023

parental lineage has now been designated GJ.1

@FedeGueli
Copy link

FedeGueli commented Jun 2, 2023

Spotted a very recent sequence of this sublineage from NZL with S:R357T

Schermata 2023-06-02 alle 15 15 40

There is an older one from NSW : EPI_ISL_17561122. A Sublineage to track , even if we never saw 357 position i n top lineages was quite good mutated to K in BA.2.12.2 and i think it was in some few other lineages we tracked without designation ( @c19850727 i remember something from you but maybe i m wrong)

@FedeGueli FedeGueli changed the title Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 11 seqs, 8 countries) Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 18 seqs, 10 countries) Jun 2, 2023
@aviczhl2
Copy link
Contributor Author

aviczhl2 commented Jun 3, 2023

new countries are New Zealand, Italy, Singapore and Canada, so 12 countries.

@aviczhl2 aviczhl2 changed the title Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 18 seqs, 10 countries) Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 18 seqs, 12 countries) Jun 3, 2023
@aviczhl2
Copy link
Contributor Author

aviczhl2 commented Jun 9, 2023

23 seqs, Trinidad& Tobago, UK, Slovenia, Norway.

@aviczhl2 aviczhl2 changed the title Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 18 seqs, 12 countries) Widespread 8-nuc/4-aa branch of GJ.1 (S:A222V, 23 seqs, 16 countries) Jun 9, 2023
@FedeGueli
Copy link

Before adding the label I want to wait some more time to see if while the philippines wave goes down then it slows exportations too. But i think this is one of the things to be proposed.

@FedeGueli
Copy link

It got designated GJ.1.1 !! via cov-lineages/pango-designation@1e361de

@aviczhl2
Copy link
Contributor Author

@FedeGueli Please add a milestone for this.

@FedeGueli FedeGueli added this to the GJ.1 milestone Jul 21, 2023
@aviczhl2
Copy link
Contributor Author

@FedeGueli It shall be GJ.1.1

@FedeGueli FedeGueli modified the milestones: GJ.1, GJ.1.1 Jul 21, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
designated New mutations Lineage with an unusual/new/interesting mutation
Projects
None yet
Development

No branches or pull requests

2 participants