Kenya/KEN_NPHL_NGMSL-BDBV_003/2026-10-14
Stephen Aricha, Jully Okonji, Moses Kihuga, Abdi Roba, Millicent Ndia, Judy Nasengo, Marygorett Mbeneka, Pul Lang'at, Prof. Thumbi, Frank Onyambu, Brian Ogoti, Kepher Otieno, Edwin Ochieng, Juma Bonventure, Naomi Licchi, Daniel Langat, Emmanuel Okunga, Esther Sigilai, Stephen Muleshe, Kamene Kimenye & Patrick Amoth

National Genomic and Molecular Surveillance Laboratory (NGMSL), Kenya National Public Health Institute (KNPHI), Ministry of Health, Nairobi, Kenya; National Virology Reference Laboratory (NVRL), Kenya National Public Health Institute (KNPHI), Nairobi, Kenya; Association of Public Health Laboratories, Global Health Program, Silver Spring, MD, USA; Meru University, Meru, Kenya; Centre for Epidemiological Modelling and Analysis, University of Nairobi, Nairobi, Kenya; Division of Global Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, Kenya; Directorate of Public Health Intelligence and Population Health, Kenya National Public Health Institute (KNPHI), Nairobi, Kenya; Directorate of Public Health, Emergency Preparedness and Response, Kenya National Public Health Institute (KNPHI), Nairobi, Kenya; Directorate of National Laboratory Science and Biosecurity, Kenya National Public Health Institute (KNPHI), Nairobi, Kenya; Directorate of Public Health, Ministry of Health, Nairobi, Kenya; Kenya National Public Health Institute (KNPHI), Nairobi, Kenya; Ministry of Health, Kenya

Sample details

Collection date
2026-10-14
Sample received date
2026-10-14
Sampling location
Kenya (NGMSL)
Isolate name
KEN_NPHL_NGMSL-BDBV_003

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

Sampling

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

Host

Host age
65
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_003
Date submitted
2026-10-24 15:48:56 UTC
Date released
2026-10-24 15:49:14 UTC
Earliest release date
2026-10-20

Files


Alignment and QC

Length
18907 (97.8%)
# of SNPs
233
# of inserted bases
3
# of deleted bases
10
# of unknown bases
400
# of frame shifts
1
Frame shifts
L:2065-2211(nt:17758-18199)

Nucleotide mutations

Mutations called relative to the NC_014373.1 reference

Substitutions
  • A17T
  • G19C
  • T26C
  • G29C
  • A31T
  • G118C
  • C135T
  • C261T
  • A266G
  • C530T
  • A532G
  • T586C
  • G832A
  • C1018T
  • A1066G
  • T1375C
  • T1405C
  • C1675A
Deletions
22, 23, 37, 38, 17756, 17757, 18906-18909
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

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

L

L:2064
Insertions
N/A

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