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

Potential BN.1.2/BQ.1.25 recombinant, similar to XBP but with Spike: R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V (50 sequences in Canada, USA, England...) #1667

Closed
ilevade opened this issue Feb 17, 2023 · 3 comments
Closed

Potential BN.1.2/BQ.1.25 recombinant, similar to XBP but with Spike: R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V (50 sequences in Canada, USA, England...) #1667

ilevade opened this issue Feb 17, 2023 · 3 comments
Labels
recombinant recombinant proposal

Comments

@ilevade
Copy link

ilevade commented Feb 17, 2023 •
edited
Loading

New recombinant Omicron/BA.2.75/22D,Omicron/BA.5/22B (BN.1.2*,BQ.1*) identified BA.5.2.1 by Pangolin and BQ.1.25 by Nextclade.

Spike: T19I, K147E, W152R, F157L, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K

Earliest date: 2022-11-20

Countries: Austria, Canada, Czech Republic, England, Israel, USA

Potential breakpoint: 22034:22189 in RBD

Mutation profile:
image

nuc unique C241T, T670G, C2790T, C3037T, C3796T, C3927T, G4184A, C4321T, C4586T, C5183T, C9344T, A9424G, C9534T, C9866T, C10029T, C10198T, G10447A, C10449A, G12160A, A12444G, C12880T, C14408T, G15451A, C15714T, C17410T, A18163G, C19955T, A20055G, C21618T, A22001G, T22016C, C22033A, T22200G, G22578A, G22599C, C22674T, T22679C, C22686T, A22688G, G22775A, A22786C, G22813T, T22882G, A22893C, T22917G, T22942A, G22992A, C22995A, A23013C, T23018G, A23055G, A23063T, T23075C, A23403G, C23525T, T23599G, C23604A, C23854A, G23948T, A24424T, T24469A, C25000T, C25584T, C26060T, C26270T, G26529A, C26577G, G26709A, C27807T, C27889T, A28271T, C28311T, C28312T, G28681T, G28881A, G28882A, G28883C, A29510C
ORF1ab unique S135R, T842I, S1221L, G1307S, P1640S, L3027F, T3090I, L3201F, T3255I, P3395H, N4060S, P4715L, G5063S, R5716C, I5967V, T6564I
S unique T19I, K147E, W152R, F157L, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
ORF3a unique T223I
E unique T9I
M unique D3N, Q19E, A63T
N unique P13L, E136D, R203K, G204R, S413R

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_10daf_fd6db0.json?c=country&label=id:node_7057413
image

Genomes:

Slovenia/23-003655-MB/2023|EPI_ISL_16848357|2023-01-24
England/LSPA-3269939B/2023|OX418381.1|2023-01-11
England/QEUH-32645F21/2022|OX403031.1|2022-12-20
Austria/LB-R00116-S266/2022|EPI_ISL_16192386|2022-12-14
England/PHEC-YY84OGE/2023|2023-01-07
England/PHEC-YY8HM56/2023|2023-01-11
England/PHEC-YY8HIUR/2023|2023-01-11
England/LSPA-3269A2AC/2023|OX416957.1|2023-01-10
England/LSPA-326959CA/2023|2023-01-10
England/LSPA-32699EA9/2023|OX417082.1|2023-01-10
England/LSPA-32699FC4/2023|OX418423.1|2023-01-10
England/LSPA-32699CCD/2023|OX417062.1|2023-01-10
England/BRBR-326B5E4D/2023|2023-01-30
England/QEUH-326A7EC6/2023|OX420769.1|2023-01-17
USA/CA-HLX-STM-D88AKQBNP/2022|EPI_ISL_16602765|2022-12-19
USA/CA-HLX-STM-WS389Z448/2023|EPI_ISL_16888466|2023-01-12
Israel/ICH-741192391/2022|EPI_ISL_15927302|2022-11-20
USA/CA-CDPH-FS47307798/2023|EPI_ISL_16735084|2023-01-03
USA/CA-CDC-QDX44940066/2022|OQ205135.1|2022-12-24
England/LSPA-3267F54A/2022|OX412460.1|2022-12-20
USA/CA-CDC-STM-FXV5UD8TC/2023|OQ284979.1|2023-01-06
USA/CA-CDC-LC0971431/2022|OQ165752.1|2022-12-16
USA/CA-CDC-LC0985776/2023|OQ258527.1|2023-01-04
Israel/CVL-8013810/2023|EPI_ISL_16738930|2023-01-10
England/QEUH-326B5FD1/2023|2023-01-29
England/PHEC-YY8ATRX/2023|2023-01-04
USA/CA-LACPHL-AF18831/2023|EPI_ISL_16921096|2023-01-22
USA/CA-HLX-STM-HUQ8BB3RA/2022|EPI_ISL_16818068|2022-12-21
USA/CA-CDC-LC0981944/2022|OQ263495.1|2022-12-29
USA/CA-CDC-QDX45038137/2022|OQ264851.1|2022-12-23
USA/CA-CDC-STM-SF2FXJVT2/2022|OQ219932.1|2022-12-23
USA/CA-HLX-STM-BV73SAGDD/2022|EPI_ISL_16703822|2022-12-24
CzechRepublic/77SVUPHA_6857730198/2022|EPI_ISL_16180548|2022-11-23
USA/CA-CDC-LC0981935/2022|OQ263496.1|2022-12-29
England/PHEC-YY8WB1K/2022|2022-12-21
England/QEUH-326A0267/2023|OX417995.1|2023-01-11
England/QEUH-326557F9/2022|OX404125.1|2022-12-16
England/PHEC-YY8H143/2023|2023-01-05
England/PHEC-YY8HUIN/2023|2023-01-05
England/DHSC-CY8QMQK/2023|2023-01-20
England/PHEC-YY8HAF6/2023|2023-01-12
USA/CA-HLX-STM-A8JYWVS4D/2022|EPI_ISL_16602385|2022-12-21
USA/CA-HLX-STM-73MEW6WSU/2022|EPI_ISL_16602238|2022-12-21
Canada/Qc-L00568616001/2022
Canada/QC-L00568616001/2022|EPI_ISL_16460518|2022-12-19
Canada/QC-L00577144001/2023|EPI_ISL_16690171|2023-01-15
Canada/QC-L00574704001/2023|EPI_ISL_16619552|2023-01-10
Canada/QC-L00575410001/2023|EPI_ISL_16619263|2023-01-10
Canada/QC-L00574703001/2023|EPI_ISL_16619390|2023-01-09
Canada/QC-L00571972001/2023|EPI_ISL_16509912|2023-01-02
@Mydtlwn
Copy link
Contributor

Mydtlwn commented Feb 17, 2023

The strain seems interesting.

@c19850727
Copy link

It looks like a duplicate to #1567 and #1637 ?

image

@thomasppeacock thomasppeacock added the recombinant recombinant proposal label Feb 18, 2023
@corneliusroemer
Copy link
Contributor

Yep, duplicate

@corneliusroemer corneliusroemer closed this as not planned Won't fix, can't repro, duplicate, stale Feb 19, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
recombinant recombinant proposal
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@corneliusroemer @ilevade @Mydtlwn @thomasppeacock @c19850727