Lateral flow devices can fast-track rabies virus genomic surveillance

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Abstract
Viral genomic data can resolve rabies transmission and guide outbreak response, but surveillance is often limited less by sequencing capacity than by getting suitable specimens from remote collection sites to a laboratory, a process that can take months. Here, we show that lateral flow devices (LFDs) used for rabies diagnosis can also serve as genomic specimens, integrating diagnosis and genomic sampling into a single workflow without additional specimen collection. We evaluated LFDs and FTA cards for rabies virus genome recovery under laboratory and field conditions. During surveillance across the island provinces of MIMAROPA, Philippines, the Bionote LFD had 99.1% sensitivity and 100% specificity against the gold-standard direct fluorescent antibody test (n = 319), with results available a median of 1 day after sampling versus 5 days for DFAT confirmation. Under laboratory conditions simulating field storage (ambient temperature or 37°C for up to 21 days), both residual LFD material and FTA cards supported near-complete genome sequencing, although genome recovery declined with storage duration, particularly at elevated temperatures. Consistent with this, field-collected LFDs yielded near-complete genomes up to 23 days of ambient storage but only partial genomes after 29-77 days, indicating a practical window of around three weeks for use. Repurposing LFDs already embedded in diagnostic workflows offers a practical route to decentralised genomic surveillance without additional sample collection or a cold chain. FTA cards provide a complementary preservation option, while further optimisation of specimen preparation, extraction and storage could improve genome recovery and extend the sequencing window.

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