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_006XDJH.4/2026-05-15
Jonathan Audet, Mable Chan & Dave Safronetz

Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada

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
MinION Mk1D
Sequencing protocol
The RNA was extracted using the Qiagen viral RNA kit. The reverse transcription was performed using SuperScript IV (ThermoFisher) following the manufacturer’s recommendation, using 8 µL of RNA. The PCR step was carried out using Phusion U Multiplex Master Mix (ThermoFisher) with 2 µL of template in 25 µL reactions. The cycling conditions were 98°C for 2 minutes,...

Submission details

Submission ID
NML_ANDV_0001-NP
Submitting group
Date submitted
2026-05-20 18:37:37 UTC
Date released
2026-05-20 18:38:21 UTC
Earliest release date
2026-05-17

Alignment and QC

Length L
6391 (87.3%)
# of SNPs L
348
# of unknown bases L
662
Length M
3584 (75.9%)
# of SNPs M
151
# of unknown bases M
799
Length S
1739 (89%)
# of SNPs S
118
# of inserted bases S
6
# of deleted bases S
2
# of unknown bases S
70

Nucleotide mutations

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

Substitutions

L

  • C131T
  • C146T
  • C147T
  • G149A
  • C155T
  • C173T
  • T182C
  • T215C
  • A218G
  • A233C
  • T278C
  • A296G
  • T297C
  • A302G
  • T326C
  • T329C
  • T332C
  • T344C

M

  • T74C
  • G114A
  • C147T
  • C174T
  • C190T
  • A192G
  • C231T
  • C243T
  • A264G
  • T312C
  • C315T
  • G339A
  • T345C
  • A360G
  • T363C
  • A381G
  • T387C
  • A391G

S

  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T244C
  • T306C
  • G315A
  • A318G
  • C328T
  • C417T
  • C444A
  • G450A
  • T454C
  • C459T
  • G465A
  • A483G
  • G504A
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:V346I
  • GPC:T353V
  • 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:T2113A
Deletions
N/A
Insertions
N/A

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