![]() Single incursions of the disease can therefore spread rapidly within and between poultry farms 3, resulting in any detections of the virus leading to strict quarantine measures, mass depopulation and decontamination of the area in order to stop the spread 4. The disease manifests in the respiratory tract of avian species 1 which, in severe cases can cause widescale death, particularly in poultry farms where birds are in confined spaces, allowing easy transmission of the virus 2. The avian influenza virus (AIV) is highly contagious and can cause a globally significant disease of both farmed poultry and wild bird populations with the capacity for human transmission and subsequent pandemic potential. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. ![]() Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry.
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