Canada/MC202601-001-NP/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 part
Nasopharynx
Collection device
Swab
Collection method
Swab

Sequencing

Sequencing date
2026-05-17
Sequencing instrument
ILLUMINA
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-NP
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

Files


Alignment and QC

Length L
6105 (93%)
# of SNPs L
361
Length M
3172 (86.4%)
# of SNPs M
183
Length S
1766 (85.1%)
# of SNPs S
114
# of inserted bases S
6
# of deleted bases S
2
# of ambiguous bases S
1
# of unknown bases S
169

Nucleotide mutations

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

Substitutions

L

  • G452T
  • C457T
  • T458C
  • A461G
  • T476C
  • G542A
  • G548A
  • C554T
  • T557C
  • A608T
  • A618C
  • A650G
  • T653A
  • G659A
  • T668C
  • G677A
  • C680T
  • A686G

M

  • T462C
  • A468G
  • C489T
  • T508C
  • A525T
  • T570C
  • T643C
  • A645G
  • T663C
  • T681G
  • C699T
  • G714A
  • A720G
  • A747G
  • G756A
  • G771A
  • G786A
  • G837A

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

Gc

  • Gc:T372A
  • Gc:S404T
  • Gc:V476I

Gn

  • Gn:H294Y
  • Gn:V346I
  • Gn:T353V
  • Gn:T516I
  • Gn:I537V

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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