Quantitative Real-Time PCR Detection of Inactivated H5 Avian Influenza Virus in Raw Milk Samples by Miniaturized Instruments Designed for On-Site Testing

Highly pathogenic avian influenza virus (HPAIV) of H5 and H7 subtypes has emerged as one of the most important zoonotic pathogens in the 21st century with significant economic consequences. The recent outbreak of H5N1 avian influenza (AI) in dairy cattle highlighted the importance of early detection in managing and mitigating HPAIV outbreaks. A successful high-speed diagnostic response requires rapid site and specimen access, minimal time for test protocols, and prompt communication of the diagnostic results to government officials. A new diagnostic paradigm that consists of miniaturized extractor and qPCR instruments (EZextractor and EZcycler MiniQ), designed for mobile, on-site testing has been compared with a platform of benchtop instruments (QIAGEN RNeasy and QuantStudio 5) for detecting inactivated H5 avian influenza virus (AIV) spiked in raw milk samples. Two sets of experiments were performed: 1) 15 raw milk samples, obtained from 15 different farms, diluted with phosphate-buffered saline and spiked with the virus to reach approximately 10 copies/L virus concentration, and 2) raw milk samples from two farms, each spiked with the inactivated AIV H5 followed by 5 series of dilution to reach AIV concentrations of 1000, 100, 10, 1 and 0.1 copies/L. Results show that despite the inhibitors in raw milk, AIV in all samples can be detected by both platforms. The MT platform showed higher sensitivity than the benchtop platform: the Ct values from the MT were [~]2 units lower than the benchtop Ct values. Our findings demonstrate the robustness of the MT platform for diagnosing AIV H5 in raw milk samples and support its use as an on-site diagnostic for rapid surveillance and response.