Mpox Virus Genomic Surveillance Using Illumina VSP2 in East Africa

This project investigates the operational limits of sample pooling for hybrid-capture sequencing of Mpox virus (MPXV) using the Illumina Viral Surveillance Panel v2 (VSP2) on the iSeq100 platform. Multiple isolates from the 2024 outbreak in Burundi were sequenced to evaluate how pooling depth affects genome recovery, variant calling, and epidemiological utility. The study demonstrates that pooling up to six samples per reaction maintains high-quality genomic data, while cautious pooling of up to nine samples supports reliable presence/absence detection. These findings provide practical guidance for resource-limited public health laboratories, enabling more efficient use of sequencing reagents and infrastructure during outbreak response. Data generated here contribute to genomic surveillance capacity building and inform strategies for sustainable pathogen monitoring in Africa.