Practical Introduction to Next-Generation Sequencing using Oxford Nanopore's MinION Platform for Microbiologists and Public Health Professionals
Mpox virus (formerly known as Monkeypox virus) is a double-stranded DNA virus belonging to the Poxviridae family and the genus Orthopoxvirus. The first human case of mpox was later described in a child in the Democratic Republic of Congo (DRC) in 1970. Since then, there have been sporadic mpox outbreaks with increasing frequency, particularly due to cross-border travel within mpox endemic regions. In 2022, a multi-country global outbreak of Mpox (Clade IIB) was declared by the WHO. The outbreak was predominantly described in Men Having Sex with Men (MSM) communities, although infections were also reported in individuals engaged in sexual contact with infected individuals. In addition, since the beginning of 2023 there has been reports of a sharp increase of suspected mpox cases in the Democratic Republic of Congo (DRC) with the highest annual number of cases ever reported, new cases in geographic areas that had previously not reported mpox and an estimated case fatality rate of 4.6% (https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON493). Despite the seeming severity of the situation only very basic genomic information is currently available, suggesting the DRC outbreak is caused by Clade I viruses (Kibungu et al, 2024). However, in view of the ongoing outbreak and suggestions of changing epidemiology, obtaining sequence information of the outbreak strain(s) is crucial. Therefore, mpox whole genome Nanopore sequencing training was given in Rwanda to train local scientists from Rwanda and DRC to perform both wet-lab and the dry-lab sequence analysis. Here, we present sequences from recently diagnosed cases in South Kivu, DRC. (https://virological.org/t/novel-clade-i-genome-sequences-from-the-ongoing-mpox-virus-outbreak-of-kamituga-in-south-kivu-province-democratic-republic-of-congo/956)