PP_0011CQ4.2

Display Name: Uganda/PP_0011CQ4.2/2025-01-19
Susan Nabadda, Isaac Sewanyana, Henry Kyobe Bosa, Misaki Wayengera, Sofonias Kifle Tessema, Deo Ssemwanga, Peter van Heusden, Alan Christoffels, Gerald Mboowa, Daniel J. Park, Harris Onywera, Collins Kipngetich Tanui, Sarah Wambui Mwangi, Stephen Balinandi, Tebba Andrew, Julius Sseruyange, Hellen Rosette Oundo, Wilson Tenywa, Godwin Tusabe Wenka, Moses Murungi, Jupiter Marina Kabahita, Valeria Nakintu, Caroline Makoha, Aloysious Ssemaganda, Stephen Kanyerezi & Alisen Ayitewala

Sample details

Collection date
2025-01-19
Sample received date
2025-01-19
Country
Uganda
City
Kampala

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-02-03 15:02skanyereziOPEN
Data use terms URL

Authors

Author affiliations
Africa CDC,Broad Institute of MIT and Harvard,Central Emergency Response Laboratory,Central Public Health Laboratories,Ministry of Health,National Health Laboratory & Diagnostic Services,South African National Bioinformatics Institute,Uganda Virus Research Institute

INSDC

INSDC accession
BioProject accession
BioSample accession
GCA accession

Host

Host name - scientific
Homo Sapiens
Host age
32
Host gender
Male
Host origin country
Uganda
Host disease
Ebola
Host health outcome
Deceased
Travel history
three healthcare facilities, one in Kampala one in Wakiso and another in Mbale district
Host role
Nurse

Sequencing

Purpose of sequencing
Investigate source of outbreak
Sequencing date
2025-01-19
Amplicon PCR primer scheme
Artic-pan-ebola
Amplicon size
1000
Sequencing instrument
GridION and Miseq
Sequenced by - organization
The Central Public Health Laboratories
Sequenced by - contact name
genomics@cphl.go.ug
Raw sequence data processing method
Inhouse custom pipeline
Dehosting method
Alignment
Consensus sequence software name
Inhouse custom pipeline
Consensus sequence software version
Inhouse custom pipeline
Depth of coverage
30
Breadth of coverage
97

Alignment and QC metrics

Length
18225
Completeness
96.56%
# of SNPs
171
# of inserted bases
0
# of deleted bases
0
# of ambiguous bases
0
# of unknown bases
0
# of frame shifts
0
# of stop codons
0

Submission details

Submission ID
CL292200
Version comment
Nearly complete genome of index case for the 2025 SUDV outbreak in Uganda. https://virological.org/t/near-real-time-genomic-characterization-of-the-2025-sudan-ebolavirus-outbreak-in-uganda-s-index-case-insights-into-evolutionary-origins/990
Submitting group
Date submitted
2025-02-03 16:35:55 UTC
Date released
2025-02-04 08:41:03 UTC
Earliest release date
2025-02-03

Nucleotide mutations

Mutations called relative to the NC_006432.1 reference

Substitutions

  • A134C
  • A135G
  • A337G
  • C354T
  • T895C
  • A1126C
  • C1321T
  • G1450T
  • C1646T
  • T1885C
  • C1893T
  • A1978G
  • C2247T
  • T2356C
  • G2390A
  • C2452T
  • C2618T
  • T2662A
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_006432.1 reference

    Substitutions

    GP

  • GP:S17N
  • GP:P411L
  • GP:T417M
  • GP:P419L
  • GP:T442A
  • GP:P451S

    • L

  • L:K43R
  • L:N120S
  • L:I954V
  • L:D1383E
  • L:S1585P
  • L:T1704P
  • L:A1748V
  • L:V1760I
  • L:P1877S
  • L:V1889I

    • NP

  • NP:T479I
  • NP:S597L
  • NP:G645R
  • NP:L721F

    • VP30

  • VP30:V71I

    • VP35

  • VP35:V185I
  • VP35:I190T

    • VP40

  • VP40:M276I

    • sGP

  • sGP:S17N

    • ssGP

  • ssGP:S17N
    • Deletions
    None
    Insertions
    None

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