Metagenomic sequencing of mpox virus clade Ib lesions

Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Little is known about the interplay of microbial organisms in mpox lesions, which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a unified metagenomic Nanopore sequencing approach involving slow-speed centrifugation and differential lysis on 19 mpox lesion swabs of hospitalised patients in South Kivu province (eastern DRC) to characterize bacteria, antimicrobial resistance genes, mpox virus (MPXV) and viral co-infections.