PP_002XJ0K.1

Display Name: Switzerland/PP_002XJ0K.1/2023-12
Rainer Gosert, Karoline Leuzinger, Alexander Kuznetsov & Richard Neher

Sample details

Collection date
2023-12
Latitude
47.56065954497
Longitude
7.58504484478
Country
Switzerland
Admin level 1
Basel-Stadt
City
Basel

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-05-26 11:47akuznetsovOPEN
Data use terms URL

Lineage

Lineage
B.D.E.1

Authors

Author affiliations
Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland, Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland; Biozentrum, University of Basel, Basel, Switzerland; Biozentrum, University of Basel, Basel, Switzerland

INSDC

INSDC accession
BioProject accession
BioSample accession
GCA accession

Host

Host taxon ID
Host name - scientific
Homo sapiens
Host name - common
Human
Host role
Patient [OMRSE:00000030]
Host vaccination status
Not Vaccinated [GENEPIO:0100102]
Is lab host
False

Sequencing

Amplicon PCR primer scheme
500 bp primers were designed using PRIMAL tool. Additionally, 2000bp-NAT primers and 1000bp-RSV-A and RSV-B subgroup-specific NAT primers were used from Wang et al. (doi: 10.1016/j.jviromet.2021.114335), and used in 2 separate primer pools.
Amplicon size
500bp, 1000bp, 2000bp
Sequencing instrument
Illumina MiniSeq [OBI:0003114]
Sequencing protocol
Genomes were generated through amplicon sequencing of 500, 1000, and 2000 bp amplicons in separate primer pools. Libraries were created using KAPA HyperPrep Kit, and sequence data was produced using Illumina MiniSeq
Sequencing assay type
whole genome sequencing assay [OBI:0002117]
Reference genome accession
PP109421.1
Depth of coverage
3407
Breadth of coverage
99

Alignment and QC metrics

Length
15204
Completeness
99.86%
# of SNPs
133
# of inserted bases
0
# of deleted bases
2
# of ambiguous bases
0
# of unknown bases
6
# of frame shifts
0
# of stop codons
0

Submission details

Submission ID
YG87H679YR
Submitting group
Date submitted
2025-05-26 11:47:26 UTC
Date released
2025-05-26 11:49:33 UTC
Earliest release date
2025-05-26

Nucleotide mutations

Mutations called relative to the OP975389.1 reference

Substitutions

  • G1A
  • C3G
  • G60A
  • A276G
  • G513T
  • G579A
  • T907C
  • G1029A
  • G1385A
  • G1732A
  • G1768A
  • T1846C
  • C2074T
  • C2198T
  • C2260T
  • T2328C
  • C2534T
  • C2554T
    • Deletions
    973, 4586
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the OP975389.1 reference

    Substitutions

    F

  • F:S190N
  • F:S211N
  • F:S389P

    • G

  • G:A74V
  • G:S100G
  • G:T131A
  • G:I137T
  • G:P214S
  • G:P221L
  • G:I227T
  • G:I252T
  • G:S265P
  • G:I268T
  • G:S275P
  • G:Y285H

    • L

  • L:D147N
  • L:S169P
  • L:K570R
  • L:R1759K
  • L:V1775M
  • L:A1927T
  • L:T1987I

    • M

  • M:I144V

    • M2-1

  • M2-1:E118D

    • M2-2

  • M2-2:I2T
  • M2-2:M27T
  • M2-2:D35N
  • M2-2:C49F

    • N

  • N:V97I

    • NS1

  • NS1:G2R
  • NS1:K74E

    • P

  • P:A77V
    • Deletions
    None
    Insertions
    None

    Report an issue with this sequence or metadata

    Create GitHub issue