PP_004JXMM.1

Display Name: South_Africa/PP_004JXMM.1/2025-10-03
J. Maritz, D. Goedhals, J. Pekeur, T. Maponga, M. Claassen, T. Stander, G. van Zyl, W. Preiser, L. M. Hofstra, L. Chabuka, K. W. Liedeman, S. De Villiers, V. Wentzel, L. Singh, T. Ramakutoane, H. Tegally, E. Wilkinson & T. de Oliveira

Sample details

Collection date
2025-10-03
Sample received date
2025-10-05
Country
South Africa
Admin level 1
Northern Cape
Admin level 2
Kimberley
City
Kimberley
Site
Kimberley

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-02-13 06:27stepfandvOPEN
Data use terms URL

Lineage

Lineage
B1

Authors

Author affiliations
Centre for Epidemic Response and Innovation (CERI), BMRI building, Tygerberg, Stellenbosch University, Francie Van Zjil Drive, Cape Town, South Africa; PathCare Molecular Lab, PathCare Reference Laboratory, Neels Bothma Street, 7460, Cape Town, South Africa

INSDC

INSDC accession
BioProject accession
BioSample accession
GCA accession

Sampling

Sample type
Swab

Host

Host name - scientific
Homo sapiens
Host name - common
Human
Host age bin
0 - 1
Host gender
M
Host origin country
South Africa

Sequencing

Purpose of sequencing
Surveillance
Sequencing instrument
Illumina NextSeq
Sequencing assay type
WGS
Sequenced by - organization
Centre for Epidemic Response and Innovation (CERI), BMRI building, Tygerberg, Stellenbosch University, Francie Van Zjil Drive, Cape Town, South Africa
Sequenced by - contact name
Stepfan de Villiers
Sequenced by - contact email
stepfan@sun.ac.za
Reference genome accession
NC_039199.1
Consensus sequence software name
Genome Detective
Consensus sequence software version
Pan-viral (2.21.4)
Depth of coverage
6366
Breadth of coverage
98

Alignment and QC metrics

Length
13115
Completeness
98.61%
# of SNPs
2423
# of inserted bases
37
# of deleted bases
86
# of ambiguous bases
0
# of unknown bases
0
# of frame shifts
2
# of stop codons
3
Frame shifts
G:143-160(nt:6671-6725),G:216-237(nt:6890-6957)
Stop Codons
SH:177,SH:179,SH:180

Submission details

Submission ID
hMPV/B/SouthAfrica/PATH-CERI-C071137/2025
Submitting group
Date submitted
2026-02-13 06:27:18 UTC
Date released
2026-02-13 06:27:29 UTC
Earliest release date
2026-02-13

Nucleotide mutations

Mutations called relative to the NC_039199.1 reference

Substitutions

  • G11A
  • A12G
  • G34A
  • G36A
  • G63A
  • T70C
  • A72G
  • G81A
  • G105A
  • G126A
  • T129C
  • C150T
  • G177T
  • G195T
  • T198C
  • G199A
  • T207C
  • G208A
    • Deletions
    24, 3009, 4684-4722, 6053, 6110-6113, 6196, 6210-6215, 6667-6670, 6889, 6981-6983, 7012, 7030-7033, 7045-7060, 7144-7147
    Insertions
    ins_5470:TAAAAATAA, ins_5813:AGA, ins_6693:CATAGA, ins_6725:GGGGAAGAGGAAAAGA, ins_6945:AT, ins_6965:C

    Amino acid mutations

    Mutations called relative to the NC_039199.1 reference

    Substitutions

    F

  • F:V6M
  • F:F9I
  • F:A61T
  • F:R82K
  • F:V122I
  • F:T135N
  • F:N139G
  • F:K143Q
  • F:D167E
  • F:R175S
  • F:K179R
  • F:N233Y
  • F:F258I
  • F:V286I
  • F:G294E
  • F:K296N
  • F:Q312K
  • F:K348R

    • G

  • G:K4R
  • G:T10A
  • G:L14F
  • G:R17K
  • G:V18I
  • G:V22I
  • G:A23R
  • G:R24S
  • G:K26R
  • G:F28Y
  • G:K29R
  • G:N30Y
  • G:S32T
  • G:V34I
  • G:I38L
  • G:I43M
  • G:Y48F
  • G:I50V

    • L

  • L:L4F
  • L:N5C
  • L:I50V
  • L:I55V
  • L:K61R
  • L:N65M
  • L:S66T
  • L:I75V
  • L:V89M
  • L:T109S
  • L:I115M
  • L:D127N
  • L:S132N
  • L:S141V
  • L:K162R
  • L:V182I
  • L:I189V
  • L:S228N

    • M

  • M:I23V
  • M:E103D
  • M:E111D
  • M:T156I
  • M:K237R
  • M:T241S

    • M2-1

  • M2-1:A5T
  • M2-1:E20D
  • M2-1:I37L
  • M2-1:R52K
  • M2-1:S88G
  • M2-1:V108T
  • M2-1:V130I
  • M2-1:R149K
  • M2-1:K160R
  • M2-1:A169T
  • M2-1:E170D
  • M2-1:S173P

    • M2-2

  • M2-2:E18K
  • M2-2:V22K
  • M2-2:V28S
  • M2-2:D37E
  • M2-2:A41T
  • M2-2:N55S
  • M2-2:A68T

    • N

  • N:A54T
  • N:A57T
  • N:I67M
  • N:S71C
  • N:R96K
  • N:I103G
  • N:N106S
  • N:D110E
  • N:A136V
  • N:M201V
  • N:D212E
  • N:H220Y
  • N:M258L
  • N:A280S
  • N:K356R
  • N:V385M
  • N:D387G
  • N:S389N
  • N:N391D

    • P

  • P:L19I
  • P:R28K
  • P:P30S
  • P:S35T
  • P:I39V
  • P:V46I
  • P:R57K
  • P:K60R
  • P:P61S
  • P:T62S
  • P:I63T
  • P:P64L
  • P:S65L
  • P:T72A
  • P:K74N
  • P:G75S
  • P:A77T
  • P:T80I

    • SH

  • SH:I2K
  • SH:K14E
  • SH:T17N
  • SH:H18Q
  • SH:I22T
  • SH:D25K
  • SH:L44F
  • SH:I50V
  • SH:I61A
  • SH:T66N
  • SH:D72V
  • SH:S73T
  • SH:S74K
  • SH:S75L
  • SH:V80T
  • SH:T82I
  • SH:K83R
  • SH:T84P
    • Deletions
    G:141, G:142, G:215
    Insertions
    ins_G:137:KSTX, ins_G:189:TT, ins_SH:107:D

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