Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case

In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore Whole Genome Sequencing of a local monkeypox sample on a PromethION 24. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. Nanopore sequencing is a highly versatile method to characterize a virus in real-time without pre-sequencing target enrichment.