Field deployable viral genomic surveillance using panviral integrated indexed primers

Abstract Rapid viral identification near the point of emergence could support outbreak investigation where sequencing infrastructure is limited. The Panviral integrated indexed Primer (PiiP) assay combines broadly reactive viral primers with integrated Oxford Nanopore indices and offline analysis. The workflow was evaluated using human, animal, and environmental samples from Cambodia and deployed with a portable laboratory at a live bird market under tropical conditions. Laboratory evaluation demonstrated detection across diverse sample matrices, although sensitivity varied by viral target and influenza subtype assignment was limited. During field deployment, environmental samples, including air samples, were processed on site, with initial viral read characterization available within 6.5 hours of sample receipt. The workflow reduces library preparation steps and enables same day viral screening outside centralized laboratories. These findings support further evaluation of PiiP for decentralized genomic surveillance, with confirmatory analysis required for uncertain taxonomic assignments.