EC Microbiology

Objectives: To detect and genetically characterize Mpox virus (MPXV) cases in South Sudan using both real-time PCR and GeneXpert assays.

Methods: Active Mpox surveillance was conducted at border sites, sentinel hospitals and in community in early 2025. Clinical samples collected from suspected cases were tested using real-time PCR and GeneXpert assays, followed by whole-genome sequencing (WGS) using Illumina MiSeq and analysis via the DRAGEN pipeline.

Results: Eight suspected cases were reported. Three (37.5%) tested positive via PCR and GeneXpert. All three cases were from Juba, with one individual reporting travel to Uganda. Sequencing confirmed all three belonged to Clade 1b, with high genome coverage (94.6% to 99.4%). Phylogenetic analysis indicated close relatedness to strains from Uganda and the DRC.

Conclusion: This study confirms the presence of Clade 1b MPXV in South Sudan, suggesting local transmission. Strengthened genomic surveillance and regional coordination are vital to contain the spread and inform public health responses.

 Keywords: Monkeypox Virus; Clade 1b; Genomic Surveillance; South Sudan; PCR; GeneXpert; Illumina

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