A one-tube RAA-PfAgo system for rapid and sensitive detection of Monkeypox virus

Monkeypox virus (MPXV), a key pathogen within the genus Orthopoxvirus, requires rapid and sensitive diagnostic strategies to support effective outbreak prevention and control. In this study, we established a one-tube, rapid, highly specific, and ultrasensitive MPXV detection assay by integrating Recombinase-Aided Amplification (RAA) with Pyrococcus furiosus Argonaute (PfAgo). Using paraffin wax serves as a physical barrier to spatially and temporally separate RAA amplification and PfAgo cleavage in a single tube. We systematically optimized key parameters including RAA amplification conditions, guide DNA (gDNA) screening, as well as the concentrations of PfAgo and gDNA. Targeting the MPXV-specific F3L gene, the one-tube RAA-PfAgo assay specifically distinguished MPXV from other orthopoxviruses and achieved single-copy-level detection. In addition, its applicability was validated using clinical and environmental samples. Owing to its one-tube, paraffin-separated format, simple operation, short reaction time (completed within 60 min), and independence from large laboratory equipment, the one-tube RAA-PfAgo assay offers a robust and field-deployable diagnostic tool to support frontline surveillance and control.