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

New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 71 seqs 14 countries #2069

Closed
FedeGueli opened this issue Jun 27, 2023 · 8 comments
Closed

New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 71 seqs 14 countries #2069

FedeGueli opened this issue Jun 27, 2023 · 8 comments

Comments

@FedeGueli
Copy link
Contributor

FedeGueli commented Jun 27, 2023 •
edited
Loading

Transferred from sars-cov-2-variants/lineage-proposals#224
Defining mutations:
XBB.1.5 > C24130T > Orf1b:L1681F ( C18508T = NSP14_L157F ) , S:F456L (T22928C)

Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1bc72_b239e0.json?f_userOrOld=uploaded%20sample&label=id:node_6800911
Schermata 2023-06-27 alle 20 01 53

Schermata 2023-06-27 alle 20 01 25

Gisaid query: C24130T ,C18508T,T22928C,T23019C,C24130T ,C18508T,T22928C,T23018C

Samples:
EPI_ISL_17501116, EPI_ISL_17501127, EPI_ISL_17516924,
EPI_ISL_17654258, EPI_ISL_17658202, EPI_ISL_17660153,
EPI_ISL_17662414, EPI_ISL_17671275, EPI_ISL_17737756,
EPI_ISL_17776739, EPI_ISL_17785440, EPI_ISL_17786197,
EPI_ISL_17799142, EPI_ISL_17809979, EPI_ISL_17837344-17837345,
EPI_ISL_17852519, EPI_ISL_17853832, EPI_ISL_17853966,
@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 19 seqs from Preprop #224 New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 24 seqs from Preprop #224 Jul 5, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 24 seqs from Preprop #224 New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 27 seqs Jul 10, 2023
@FedeGueli
Copy link
Contributor Author

FedeGueli commented Jul 10, 2023 •
edited
Loading

To be noted that, out of 6 sequences from June, 2 are from Argentina (25 uploaded from there)

@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 27 seqs New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 27 seqs 8 countries (Argentina, Brazil Chine, Canada , Italy, Portugal, France , Italy) Jul 10, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 27 seqs 8 countries (Argentina, Brazil Chine, Canada , Italy, Portugal, France , Italy) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 28 seqs 8 countries (Argentina, Brazil Chine, Canada , Italy, Portugal, France , Italy) Jul 13, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 28 seqs 8 countries (Argentina, Brazil Chine, Canada , Italy, Portugal, France , Italy) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 29 seqs 9 countries (Argentina, Brazil Chine, Canada , Italy, Portugal, France , Panama) Jul 16, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 29 seqs 9 countries (Argentina, Brazil Chine, Canada , Italy, Portugal, France , Panama) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 29 seqs 9 countries (Argentina, Brazil China, Canada , Italy, Portugal, France , Panama) Jul 16, 2023
@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 29 seqs 9 countries (Argentina, Brazil China, Canada , Italy, Portugal, France , Panama) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 38 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) Jul 26, 2023
@FedeGueli
Copy link
Contributor Author

FedeGueli commented Jul 26, 2023 •
edited
Loading

Multiple samples Uploaded from Uruguay and one from Bolivia

it represents 3 out of 7 of recent sequences from uruguay

cc @corneliusroemer

@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 38 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 41 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) Aug 1, 2023
@FedeGueli
Copy link
Contributor Author

last samples coming from California, Texas Puertorico

@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 41 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 43 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) Aug 8, 2023
@FedeGueli
Copy link
Contributor Author

+2 Utah

@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 43 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 47 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) Aug 9, 2023
@FedeGueli
Copy link
Contributor Author

+3 US +1 Brazil

@FedeGueli FedeGueli changed the title New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 47 seqs 11 countries (Argentina, Bolivia, Brazil China, Canada , Italy, Portugal, France , Panama, Uruguay) New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 71 seqs 14 countries Aug 18, 2023
@FedeGueli
Copy link
Contributor Author

This is widespreaad and keeps on growing.

@FedeGueli
Copy link
Contributor Author

But it cant compete: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C24130T%2CC18508T%2CT22928C%2CT23019C%2CC24130T%2CC18508T%2CT22928C%2CT23018C&analysisMode=CompareToBaseline&

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Aug 18, 2023
FedeGueli referenced this issue Oct 15, 2023
@corneliusroemer
Designate XBB.1.5.107 (C24130T, Argentina/Uruguay/Bolivia), JZ.1 (XBB…
856edb1 
….1.5.107.1, S:F456L)
@FedeGueli
Copy link
Contributor Author

Designated JZ.1 via 856edb1

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@FedeGueli