PP_0081WYX.1

Kenya/KEN_NPHL_NGMSL_BDBV_002/2026-10-09
Aricha Steve, Okonji Jully & Kihuga Moses

National Public Health Laboratories

Sample details

Collection date
2026-10-09
Sampling location
Kenya
Isolate name
KEN_NPHL_NGMSL_BDBV_002

Outbreak

Amino acid substitutions from outbreak clade founder
  • GP:P344S
  • L:A138V
  • L:I1562L
  • NP:S528T
Outbreak
Bdbv-2026

Data use terms

Data use terms
RESTRICTED
Data use terms URL

Sampling

Purpose of sampling
Contact with A positive case
Anatomical material
Whole blood
Collection method
Phlebotomy

Host

Host
Host age
32
Host gender
Female
Host origin country
Kenya
Host health state
Under Observation
Host health outcome
Alive
Travel history
NO
Exposure event
Contact
Host role
Patient
Host vaccination status
Unknown

Sequencing

Sequencing date
2026-10-16
Sequencing instrument
Illumina MiSeq
Sequencing protocol
VSP
Sequencing library source
VIRAL RNA
Sequencing assay type
WGS
Sequenced by - organization
NPHL_NGMSL_Kenya
Sequenced by - contact name
Steve, Aricha; Jully, Okonji; Moses, Kihuga
Sequenced by - contact email
arichasteve@gmail.com
Reference genome accession
DRAGEN Microbial Enrichment Plus
Consensus sequence software name
Dragen Microbial Enrichment Plus
Consensus sequence software version
1.1.1

Diagnostics

Diagnostic measurement - method
RT-PCR

Submission details

Submission ID
KEN_NPHL_NGMSL_BDBV_002
Submitting group
Date submitted
2026-10-20 07:26:23 UTC
Date released
2026-10-20 07:27:49 UTC
Earliest release date
2026-10-20

Files

Annotations

Alignment and QC

Length
18907 (99.6%)
# of SNPs
236
# of inserted bases
3
# of deleted bases
10
# of unknown bases
46

Nucleotide mutations

Mutations called relative to the NC_014373.1 reference

Substitutions
  • A17T
  • G19C
  • T26C
  • G29C
  • A31T
  • C135T
  • G373T
  • C530T
  • A532G
  • T586C
  • G832A
  • C1018T
  • A1066G
  • T1375C
  • T1405C
  • C1675A
  • C1702T
  • T1774G
Deletions
22, 23, 37, 38, 18906-18911
Insertions
ins_11:T, ins_26:C, ins_18712:T

Amino acid substitutions

Substitutions called relative to the NC_014373.1 reference

Substitutions

GP

  • GP:Y151F
  • GP:E188K
  • GP:P344S
  • GP:P365S
  • GP:P367L
  • GP:Y387H
  • GP:P389L
  • GP:R394G
  • GP:T458I
  • GP:P481L
  • GP:T486I
  • GP:A489V
  • GP:R506S

GP_003

  • GP_003:Y151F
  • GP_003:E188K
  • GP_003:T320I
  • GP_003:P328L
  • GP_003:Q367*

L

  • L:A138V
  • L:V402I
  • L:L1011F
  • L:S1323A
  • L:N1342H
  • L:I1562L
  • L:K1570R
  • L:L1595Q
  • L:I1664R
  • L:K1738N
  • L:Q1770R
  • L:N1771D
  • L:I1784V
  • L:R1954G
  • L:E1969D
  • L:A2191V

NP

  • NP:N496D
  • NP:Q517R
  • NP:G524S
  • NP:S528T
  • NP:V531A
  • NP:R537K
  • NP:V544I
  • NP:D546N
  • NP:A569V

VP24

  • VP24:S24N

VP30

  • VP30:H5Y

VP35

  • VP35:N79S
  • VP35:G187E
  • VP35:M192I

VP40

  • VP40:I14M
  • VP40:A31S
Deletions
N/A
Insertions
N/A

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