Overcoming the challenges of pen‐side molecular diagnosis of African swine fever to support outbreak investigations under field conditions

Abstract

African swine fever (ASF) is a devastating disease of pigs. Without a vaccine, early detection and rapid diagnosis of ASF is a crucial step towards effective disease control. In many countries where ASF is endemic, laboratory infrastructure including sampling and sample shipment is inadequate, and a rapid laboratory confirmation would require that the diagnosis is performed at regional laboratories close to the pig farms of concern, or even at the farm-side. This study intended to evaluate measures including sample preparation methods, a dried-down assay, and a portable, battery-powered real-time PCR instrument, to improve molecular diagnosis under field conditions. A simple dilution of blood samples, either in Phosphate-buffered saline or a commercial buffer, worked similarly to beads-based nucleic acid extraction using a magnet as the core equipment; the latter method did work as well for those samples with low viral load or high Ct values. The real-time PCR assay using a Universal ProbeLibrary (UPL) probe tolerated suspected inhibitory substances present in the prepared samples better, whereas the dried-down assay had a higher diagnostic sensitivity. Additionally, an inhibition control assay proved to be helpful in avoiding false negative results when interpreting negative results of samples that might be of low quality or with inadequate reduction in inhibitory substances. When tested with synthetic DNA standards, the portable instrument performed at a level approaching stationary thermocyclers. In summary, the developments of suitable sample preparation methods, robust and thermal-stable real-time PCR assays with inhibition control, and battery-powered portable thermocyclers with middle-throughput offer one way forward to provide rapid, reliable molecular diagnosis under challenging field conditions.