A microreactor system for point-of-care viral genome sequencing

Viral genome sequencing is critical for understanding viral biology, identifying strain mutations, and managing public health during pandemics. Although sequencing technologies have progressed over the years in terms of throughput and cost, a portable platform that integrates sample processing, library preparation, and sequencing remains critical for point-of-care viral sequencing that combats viral outbreaks in the field. In here, we demonstrate a semi-automated, field-deployable microreactor system to produce nanopore sequencing libraries from viral samples. The system integrates isothermal amplification, purification, and enzymatic processing within a closed-channel format, minimizing contamination risk and operational complexity. Using Senecavirus A (SVA) as a surrogate for high-consequence pathogens, we demonstrate the system's ability to prepare sequencing libraries targeting three dispersed genomic regions comprising ~16% of the viral genome and identify single nucleotide variations with high confidence. Together with a portable nanopore sequencer, this microreactor offers a robust solution for decentralized genomic surveillance and rapid diagnostics in resource-limited or outbreak-prone environments. Overall design: RT-LAMP sequencing of vesicular lession fluid extracted from SVA-positive pigs using an Oxford Nanopore Minion device with Flongle attachment. SVA positive pigs (as determined by RT-PCR) had total RNA extracted from collected vesicular lession samples. RNA samples underwent reverse transcription loop mediated isothermal amplification (RT-LAMP), performed on a custom designed microfluidic device. This device was then used to purify the generated RT-LAMP amplicons, before performing library preparation for nanopore sequencing. Sequenced samples were analysed to evaluate diagnostic and variant monitoring capabilities of the designed platform.