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Improved surveillance of diseases using nano-pore sequencing

Neil Boonham: Fera Science Ltd

<div>Next generation sequencing (NGS) has revolutionised plant pathogen diagnostics, as prices continue to fall and applications continue to expand. At the forefront of this revolution are the detection, diagnosis and characterisation of plant viruses. In 2011 a new disease emerged in maize production in Kenya. Whilst early attempts to provide a diagnosis using conventional methods failed, NGS was used to rapidly identify suspect viruses (<em>Maize chlorotic mottle virus </em>and<em> Sugarcane mosaic virus</em>) which were later confirmed using PCR testing, whilst mechanical inoculation satisfied Koch’s postulate. The rapid identification of the causal agents of an emerging disease (maize lethal necrosis) enabled rapid development and deployment of qPCR tests in local labs enabling diagnosis of suspected outbreaks and seed testing. The genomes analysed from Kenya, South Sudan, Rwanda and Ethiopia shows that the isolates of MCMV recovered are highly conserved, whilst the sequence of ScMV is divergent and in some cases other potyviruses are present. This suggests that the spread of MCMV is driving the disease epidemic, whilst potyviruses are a frequent local infection. Follow-on testing suggests that in some locations the disease symptoms in the field are being confused with those caused by other viruses. The most commonly detected of these was the recently characterised ‘maize yellow mosaic virus’ at a number of locations. These data show the value of incorporating NGS into routine diagnostics, especially in outbreak situations. The use of nanopore sequencing (Oxford Nanopore) was explored which may be more suited to resource poor settings. The results show that despite the increased error rate, the technology can be used to provide valuable genome sequence data and cloud based analysis supports use by non-specialists and negates the need for elaborate IT infrastructure.</div>