PP_0011CQ4.2

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

Submission details

Submission ID
CL292200
Submitting group
EVD 2025 outbreak
Date submitted
2025-02-03 16:35:55 UTC
Date released
2025-02-04 08:41:03 UTC
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

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-02-03 15:02skanyereziOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Sequencing

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

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

Bioproject accession
PRJEB85569
Biosample accession
SAMEA117658922
INSDC accession
OZ222062.1

Alignment and QC metrics

Completeness
96.56%
Length
18875
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
171
Total stop codons
0
Total unknown nucs
650

Sample details

Earliest release date
2025-02-03
Collection city
Kampala
Collection country
Uganda
Collection date
2025-01-19
Collection date (lower bound)
2025-01-19
Collection date (upper bound)
2025-01-19
Sample received date
2025-01-19

Host

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

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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