PP_002Y2UA.1

Display Name: Sierra_Leone/PP_002Y2UA.1/2025-05-07
Campbell, Allan K.O.; Parker, Edyth; Miller, Choe; Campbell, Julian; Folorunso, Vidalyn; Daniel-Sesay, Naomi; Williams, Anu J.; Mani, Sia; Lansana, Roberta; Kargbo, Amanda; Koninga, Komba; Adi, Harry; Ruhweza, Simon; James, Abu; Greene, Jonathan; Forster, Monique; Klena, John; Gigante, Crystal; Park, Danny; Kebede, Abebaw; Tanui, Collins; Tessema, Sofonias; Kebede, Yenew; Koroma, Aminata; ...; Sahr, Foday

Submission details

Submission ID
CPHRL_MPX_845
Submitting group
Date submitted
2025-05-31 22:45:35 UTC
Date released
2025-05-31 22:45:43 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-05-31 22:45oakcampbell25@gmail.comOPEN
Data use terms URL

Authors

Author affiliations
Central Public Health Reference Laboratory, National Public Health Agency (NPHA) Sierra Leone, Africa Centers for Disease Control and Prevention, U.S. Centers for Disease Control and Prevention, World Health Organization, The Broad Institute of MIT and Harvard Cambridge MA USA, Institute of Genomics and Global Health Redeemer’s University Ede Osun State Nigeria, College of Medicine and Allied Health Sciences

INSDC

BioProject accession
BioSample accession
INSDC accession

Clade & Lineage

Clade
IIb
Lineage
A.2.2
Outbreak
hMPXV-1

Sampling

Collection device
Lesion Swabs
Collection method
Vesicle or pustule lesion swab
Sample type
Lesion swab

Alignment and QC metrics

Completeness
99.99%
Frame shifts
OPG174:290-347(nt:148355-148528)
Length
197193
Total ambiguous nucs
0
Total deleted nucs
17
Total frame shifts
1
Total inserted nucs
1
Total SNPs
79
Total stop codons
0
Total unknown nucs
11

Sample details

Earliest release date
2025-05-31
Collection subdivision level 1
Western Area Urban
Collection subdivision level 2
Freetown
Collection city
Freetown
Collection country
Sierra Leone
Collection date
2025-05-07
Collection date (lower bound)
2025-05-07
Collection date (upper bound)
2025-05-07
Sample received date
2025-05-08

Host

Host disease
Mpox
Host gender
Female
Host health state
Select Region
Host name - common
Human
Host name - scientific
Homo Sapien
Host origin country
Sierra Leone
Host taxon ID

Sequencing

Purpose of sequencing
Genomic Surveillance
Sequenced by - contact email
oakcampbell25@gmail.com
Sequenced by - contact name
Allan Kevin Olayemi Campbell
Sequenced by - organization
Central Public Health Reference Laboratory
Sequencing assay type
Capture-based sequencing
Sequencing date
2025-05-23
Sequencing instrument
Miniseq
Sequencing protocol
VSP 2.0

Nucleotide mutations

Mutations called relative to the NC_063383.1 reference

Substitutions

  • C4611T
  • G4969A
  • C6105T
  • C6555T
  • G8560A
  • C10173T
  • C11880T
  • G11948A
  • C13298T
  • C14790T
  • A18769G
  • C18792T
  • G19676A
  • G20913A
  • C21359T
  • G21991A
  • G23118A
  • G28139A
    • Deletions
    607-609, 148529-148535, 163211-163214, 196615-196617
    Insertions
    ins_170904:T

    Amino acid mutations

    Mutations called relative to the NC_063383.1 reference

    Substitutions

    OPG015

  • OPG015:D18N

    • OPG021

  • OPG021:S196L

    • OPG023

  • OPG023:S318F
  • OPG023:D341N

    • OPG025

  • OPG025:D160N

    • OPG031

  • OPG031:D13N

    • OPG036

  • OPG036:S51F

    • OPG037

  • OPG037:S148L
  • OPG037:V359I

    • OPG044

  • OPG044:D17N

    • OPG047

  • OPG047:D187N

    • OPG049

  • OPG049:S95L

    • OPG053

  • OPG053:G38E

    • OPG060

  • OPG060:S107L

    • OPG083

  • OPG083:R341K

    • OPG098

  • OPG098:E162K

    • OPG106

  • OPG106:R29K

    • OPG112

  • OPG112:E85K

    • OPG113

  • OPG113:V528I
  • OPG113:E553K

    • OPG118

  • OPG118:K606E

    • OPG122

  • OPG122:H198Y

    • OPG132

  • OPG132:M357I

    • OPG133

  • OPG133:S616F

    • OPG136

  • OPG136:A327T

    • OPG145

  • OPG145:D29N

    • OPG150

  • OPG150:S43L

    • OPG172

  • OPG172:E56K

    • OPG174

  • OPG174:G11R
  • OPG174:S44L

    • OPG176

  • OPG176:Q22*

    • OPG180

  • OPG180:D442N

    • OPG185

  • OPG185:D68N

    • OPG188

  • OPG188:H120Y

    • OPG190

  • OPG190:P221S

    • OPG198

  • OPG198:E57K

    • OPG204

  • OPG204:E314K

    • OPG205

  • OPG205:R689C

    • OPG210

  • OPG210:D159N
  • OPG210:E1657K
  • OPG210:D1877N
    • Deletions
    OPG174:288, OPG174:289
    Insertions
    None

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