Michaella Jaba, Univeristy Of Manitoba

Michaella Jaba1, Jia B. Kangbai2, Jason Kindrachuk1,3,4,5 1Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada 2Department of Biological Sciences, Njala University, Bo, Sierra Leone 3Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada 4Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada 5National Microbiology Laboratory Branch, Public Health Agency of Canada, Canada

Damaging & Spreading

Introduction: The Mpox virus (MPXV) is a re-emerging zoonotic disease with two clades: Clade 1, comprising subclades 1a and 1b, which has been the second public health concern in Central Africa, and Clade 2, with subclades 2a and 2b in West Africa. The 2025 MPXV outbreak in Sierra Leone represents a critical opportunity to integrate rapid qPCR diagnostics and genomic sequencing for real-time characterization of viral dynamics and identifying gaps in public health responses. Methods: qPCR and genomic sequencing for rapid detection and clade-specific characterization of MPXV during Sierra Leone's 2025 outbreak were used. To achieve this, I performed qPCR-based MPXV diagnosis on 200 lesion swap samples collected from positive MPXV patients, extracted the DNA using the QiaAmp DNA mini kit, and used a real-time PCR assay to target MPXV-specific genes. I further selected samples with low CT values <20 for genomic analysis. Results: The phylogenetic analysis was done by assembling the genomes using reference-based mapping to construct maximum-likelihood phylogenies with global clade sequences. Bioinformatic analyses showed that all generated sequences belong to clade 2b and are classified within the G1 Lineage. To better position these Sierra Leone sequences in the global context and confirm their phylogenetic placement, we compared them to a set of sequences also belonging to clade 2b, downloaded from the Pathoplexus database, based on country of origin (Sierra Leone and other countries), based on sequence type (our generated sequences and downloaded ones), and one based on lineage (G for our sequences, and H and A for comparison).