PP_0011CQ4.1

Display Name: Uganda/PP_0011CQ4.1/2025-01-19
Susan, Nabadda; Isaac, Sewanyana; Henry, Kyobe Bosa; Misaki, Wayengera; Sofonias, Kifle Tessema; Deo, Ssemwanga; Peter, van Heusden; Alan, Christoffels; Gerald, Mboowa; Daniel, Park J.; 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

Submission details

Submission ID
CL292200
Submitting group
EVD 2025 outbreak
Date submitted
2025-02-03 15:02:12 UTC
Date released
2025-02-03 15:02:28 UTC
Version comment
Nearly complete genome of index case for the 2025 SUDV outbreak in Uganda

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
Quality control details
NA
Quality control determination
NA
Quality control issues
NA
Quality control method name
NA
Quality control method version
NA
Raw sequence data processing method
Inhouse custom pipeline
Sequenced by - contact email
NA
Sequenced by - contact name
genomics@cphl.go.ug
Sequenced by
The Central Public Health Laboratories
Sequencing assay type
NA
Sequencing date
2025-01-19
Sequencing instrument
GridION and Miseq
Sequencing protocol
NA

Sampling

Anatomical part
NA
Body product
NA
Collection device
NA
Collection method
NA
Environmental material
NA
Environmental site
NA
Food product
NA
Food product properties
NA
Presampling activity
NA
Purpose of sampling
NA
Sample type
NA

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

Host

Cell line
NA
Exposure details
NA
Exposure event
NA
Exposure setting
Na
Host age
32
Host age bin
NA
Host disease
Ebola
Host gender
Male
Host health outcome
Deceased
Host health state
NA
Host name common
NA
Host name scientific
Homo Sapiens
Host origin country
Uganda
Host role
Nurse
Host vaccination status
NA
Is lab host
NA
Passage method
NA
Previous infection (disease)
NA
Previous infection (organism)
NA
Signs and symptoms
NA
Travel history
three healthcare facilities, one in Kampala one in Wakiso and another in Mbale district

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

Culture ID
NA
Earliest release date
2025-02-03
Collection subdivision level 1
NA
Collection subdivision level 2
NA
Collection city
Kampala
Collection country
Uganda
Collection site
NA
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
Isolate name
NA

Diagnostics

Diagnostic measurement method
NA
Diagnostic measurement unit
Na
Diagnostic measurement value
Na
Gene name
NA
Diagnostic target presence
NA

Specimen processing

Experimental specimen role type
NA
Specimen processing
NA
Specimen processing details
NA

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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