Restricted-Use sequence

This sequence is only available under the Restricted Use Terms. This prohibits publications that use this sequence as focal data during the restricted-use period, except with the consent of the sequence submitters.
Canada/PP_006XDHK.6/2026-05-15
Jonathan Audet, Mable Chan, Dave Safronetz, John Tyson, Tracy Lee, Branco Cheung, Natalie Prystajecky, Eric Eckbo, Muhammad Morshed, Agatha Jassem & Linda Hoang

Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada; BC Center for Disease Control Public Health Laboratory

Sample details

Collection date
2026-05-15
Sampling location
Canada

Data use terms

Data use terms
RESTRICTED

Sampling

Anatomical material
Blood

Sequencing

Sequencing date
2026-05-17
Sequencing instrument
This sequence is specific to Illumina generated sequence data, but Oxford Nanopore sequence data was also generated and showed only 2 additional mixed base positions across all segments.
Sequencing protocol
The RNA was extracted using the QIAamp Viral RNA Mini Kit (Qiagen). The reverse transcription was performed using SuperScript IV (ThermoFisher) following manufacturers recommendations, using 8 µL of RNA extract. A two pool 400bp tiled amplicon scheme was designed using PrimalScheme with PP_006WBLH.2 as the reference genome ( https://labs.primalscheme.com/detail/bccdc-andv-2026/400/v1....

Submission details

Submission ID
MC202601-001-WB
Submitting group
Date submitted
2026-05-29 20:43:37 UTC
Date released
2026-05-29 20:43:44 UTC
Earliest release date
2026-05-17

Alignment and QC

Length L
6505 (99.1%)
# of SNPs L
389
Length M
3568 (97.2%)
# of SNPs M
207
Length S
1766 (94.2%)
# of SNPs S
127
# of inserted bases S
6
# of deleted bases S
2

Nucleotide mutations

Mutations called relative to the NC_003468.2, NC_003467.2 & NC_003466.1 references

Substitutions

L

  • T47C
  • G62A
  • T68G
  • C74T
  • C131T
  • C146T
  • C147T
  • G149A
  • C155T
  • C173T
  • T182C
  • T215C
  • A218G
  • A233C
  • T278C
  • A296G
  • T297C
  • A302G

M

  • T74C
  • T90C
  • G114A
  • C147T
  • C174T
  • C190T
  • A192G
  • C231T
  • C243T
  • A264G
  • T312C
  • C315T
  • G339C
  • T345C
  • A360G
  • T363C
  • A381G
  • T387C

S

  • G63A
  • G66A
  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T244C
  • T306C
  • G315A
  • A318G
  • C328T
  • C417T
  • C444A
  • G450A
  • T454C
  • C459T
  • G465A
Deletions

S

1443, 1573
Insertions

S

ins_1486:T, ins_1555:A, ins_1631:TTT, ins_1668:T

Amino acid substitutions

Substitutions called relative to the NC_003468.2, NC_003467.2 & NC_003466.1 references

Substitutions

GPC

  • GPC:V8A
  • GPC:I114V
  • GPC:H294Y
  • GPC:V346I
  • GPC:T353V
  • GPC:T516I
  • GPC:I537V
  • GPC:T1023A
  • GPC:S1055T
  • GPC:V1127I

NSs

  • NSs:Q5R
  • NSs:E33G
  • NSs:L35S
  • NSs:I62T

RdRp

  • RdRp:T141I
  • RdRp:L277S
  • RdRp:S338A
  • RdRp:R346K
  • RdRp:I402V
  • RdRp:A541V
  • RdRp:D780N
  • RdRp:N1033D
  • RdRp:D1303E
  • RdRp:V1665I
  • RdRp:K1750R
  • RdRp:T2113A
Deletions
N/A
Insertions
N/A

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