PP_004JQQN.1

Canada/PP_004JQQN.1/2025
Benedicte Mpia Moni, Placide Mbala-Kingebeni, Arinjay Banerjee, Mable Chan & Jonathan Audet

Vaccine and Infectious Disease Organization, Canada; Institut National de Recherche Biomédicale, Democratic Republic of the Congo; National Microbiology Laboratory, Canada

Sample details

Collection date
2025
Sample received date
2025-03-01
Sampling location
Canada

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-02-10 19:03jaudetOPEN
Data use terms URL

Clade & Lineage

Clade
IIb
Outbreak
sh2017
Lineage
B.1.4

INSDC

INSDC accession
BioProject accession
BioSample accession
GCA accession

Host

Cell line
Vero E6

Sequencing

Sequencing date
2025-03-22
Sequencing instrument
MinION
Sequencing protocol
Genomes were generated through amplicon sequencing of 5 kb amplicons with Isabel schema primers. Libraries were created using the Oxford Nanopore SQK-NBD114.24 Native Barcoding Kit and sequenced on a MinION Mk1B and R10.4.1 flowcell. Missing amplicons were amplified individually and sequenced with the same protocol. Reads were aligned to NC_003310.1 using nf-ViralMutations.

Submission details

Submission ID
VIDO_IIb_S1
Submitting group
Date submitted
2026-02-10 19:03:18 UTC
Date released
2026-02-10 19:06:38 UTC
Earliest release date
2026-02-10

Alignment and QC

Length
197202 (99.8%)
# of SNPs
73
# of inserted bases
324
# of deleted bases
27
# of unknown bases
89

Nucleotide mutations

Mutations called relative to the NC_063383.1 reference

Substitutions

  • G1262A
  • G2591A
  • G3111A
  • G3522A
  • C3818T
  • C7771T
  • C10672T
  • G14000T
  • G15428A
  • A18769G
  • G21723A
  • C23564T
  • G25661A
  • T28175C
  • G30367A
  • G31053A
  • G34308A
  • G34459A
Deletions

133177-133186, 150586-150602
Insertions

ins_179243:CATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATACATTATATA

Amino acid substitutions

Substitutions called relative to the NC_063383.1 reference

Substitutions

OPG001

  • OPG001:S105L

OPG002

  • OPG002:S54F

OPG003

  • OPG003:D264N

OPG022

  • OPG022:E63K

OPG025

  • OPG025:A423D

OPG047

  • OPG047:R48C

OPG053

  • OPG053:P78S
  • OPG053:S128L

OPG056

  • OPG056:E125K

OPG057

  • OPG057:E353K

OPG071

  • OPG071:L108F

OPG072

  • OPG072:D56N

OPG092

  • OPG092:D196N

OPG093

  • OPG093:S30L
  • OPG093:D88N

OPG094

  • OPG094:M142I

OPG098

  • OPG098:E162K

OPG105

  • OPG105:S734L

OPG109

  • OPG109:H740Y

OPG118

  • OPG118:K606E

OPG136

  • OPG136:D98N

OPG139

  • OPG139:A17T

OPG145

  • OPG145:E62K
  • OPG145:R243Q
  • OPG145:E435K

OPG150

  • OPG150:S307L

OPG176

  • OPG176:H221Y

OPG193

  • OPG193:L263F

OPG210

  • OPG210:D209N
  • OPG210:P722S
  • OPG210:M1741I
Deletions
N/A
Insertions
N/A

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