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

BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (80 sequences as of 2022-03-20) #1523

Closed
c19850727 opened this issue Jan 6, 2023 · 5 comments
Closed

BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (80 sequences as of 2022-03-20) #1523

c19850727 opened this issue Jan 6, 2023 · 5 comments
Assignees
@InfrPopGen
Labels
BQ.1 designated Saltation Appears on long branch length with no intermediates
Milestone
FF.1

Comments

@c19850727
Copy link

c19850727 commented Jan 6, 2023 •
edited by corneliusroemer

Description

Sublineage of: BQ.1.8.2
Earliest sequence: 2022/11/10 (Ireland)
Most recent sequence: 2022/12/22 (UK-Scotland)
Countries circulating: Ireland (2/38), UK (36/38)
Mutations on top of BQ.1.8.2: G25052A (S:V1164I), then C22329T (S:S256L), G23401T (S:Q613H), A1451G (ORF1a:I396V), C17999T (ORF1b:T1511I)
GISAID and Cov-spectrum query: A1451G, C17999T, G23401T

In total, this proposed sublineage has a total of 5 amino changes at Spike relative to BQ.1 basal:

  • S:Y144del (defining change of BQ.1.8),
  • S:A688V (defining change of BQ.1.8.2),
  • S:S256L, S:Q613H and S:V1164I

Evidence

Usher tree:
image
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16514_777410.json?c=gt-nuc_1451&label=id:node_6359183

Genomes:

EPI_ISL_15812059, EPI_ISL_16074239, EPI_ISL_16074295, EPI_ISL_16075133, EPI_ISL_16094643, EPI_ISL_16097965, EPI_ISL_16108464, EPI_ISL_16108466, EPI_ISL_16108468, EPI_ISL_16108530-16108531, EPI_ISL_16108565, EPI_ISL_16108574, EPI_ISL_16108627, EPI_ISL_16108645, EPI_ISL_16108654, EPI_ISL_16108724, EPI_ISL_16108731, EPI_ISL_16108738, EPI_ISL_16148676, EPI_ISL_16179755, EPI_ISL_16198746, EPI_ISL_16198769, EPI_ISL_16198974, EPI_ISL_16212929, EPI_ISL_16256315, EPI_ISL_16256371, EPI_ISL_16256380, EPI_ISL_16256545, EPI_ISL_16261075, EPI_ISL_16274110, EPI_ISL_16274317, EPI_ISL_16281111, EPI_ISL_16390784
(only 34 of 38 sequences are on GISAID now)
@corneliusroemer
Copy link
Contributor

The 2 extra S AA muts are interesting, but it seems to have disappeared recently, only 1 upload since December 26 - so I'd wait a bit more.

@corneliusroemer corneliusroemer added the monitor currently too small, watch for future developments label Jan 9, 2023
@thomasppeacock thomasppeacock added the Saltation Appears on long branch length with no intermediates label Jan 10, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (38 sequences as of 2022-01-05) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (41 sequences as of 2022-01-10) Jan 11, 2023
@c19850727
Copy link
Author

41 sequences as of 2022-01-10.

@c19850727
Copy link
Author

47 sequences as of 2022-01-14, newly found in Croatia.

@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (41 sequences as of 2022-01-10) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (51 sequences as of 2022-01-20) Jan 22, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (51 sequences as of 2022-01-20) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (56 sequences as of 2022-01-25) Jan 25, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (56 sequences as of 2022-01-25) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (59 sequences as of 2022-01-27) Jan 28, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (59 sequences as of 2022-01-27) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (61 sequences as of 2022-02-03) Feb 5, 2023
@corneliusroemer corneliusroemer changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164L, ORF1a:I396V, ORF1b:T1511I (61 sequences as of 2022-02-03) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (61 sequences as of 2022-02-03) Feb 11, 2023
@corneliusroemer
Copy link
Contributor

64 now. It's 1164I by the way, capital i :)

@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (61 sequences as of 2022-02-03) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (67 sequences as of 2022-02-11) Feb 12, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (67 sequences as of 2022-02-11) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (73 sequences as of 2022-02-23) Feb 24, 2023
@Mydtlwn Mydtlwn mentioned this issue Mar 3, 2023
Closed
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (73 sequences as of 2022-02-23) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (74 sequences as of 2022-03-04) Mar 5, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (74 sequences as of 2022-03-04) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (75 sequences as of 2022-03-15) Mar 16, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (75 sequences as of 2022-03-15) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (80 sequences as of 2022-03-15) Mar 21, 2023
@c19850727 c19850727 changed the title BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (80 sequences as of 2022-03-15) BQ.1.8.2 sublineage with S:S256L, S:Q613H, S:V1164I, ORF1a:I396V, ORF1b:T1511I (80 sequences as of 2022-03-20) Mar 21, 2023
@InfrPopGen InfrPopGen self-assigned this Mar 22, 2023
InfrPopGen added a commit that referenced this issue Mar 22, 2023
@InfrPopGen
Merge pull request #1788 from InfrPopGen/master
c0aa9f5 
Added new lineage FF.1 from #1523 with 65 new sequence designations, and 0 updated
@InfrPopGen InfrPopGen added designated and removed monitor currently too small, watch for future developments labels Mar 22, 2023
@InfrPopGen InfrPopGen added this to the FF.1 milestone Mar 22, 2023
@InfrPopGen
Copy link
Contributor

Thanks for submitting. We've added lineage FF.1 with 65 newly designated sequences, and 0 updated. Defining mutation C22329T (S:S256L) (following A1451G (ORF1a:I396V), C17999T (ORF1b:T1511I), G23401T (S:Q613H)).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@InfrPopGen InfrPopGen

Labels
BQ.1 designated Saltation Appears on long branch length with no intermediates
Projects
None yet
Milestone
FF.1
Development

No branches or pull requests
4 participants
@corneliusroemer @InfrPopGen @thomasppeacock @c19850727