High Throughput Sequencing, Biosecurity and Policy in Plant Virus Diagnostics

Abstract

The goal of the High Throughput Sequencing Working Group (HTSWG), a working group for the Subcommittee on Plant Health Diagnostics (SPHDs) is to facilitate the implementation of high throughput sequencing (HTS) standards and guidelines for plant health diagnostics in Australian jurisdictions and inclusion in National Diagnostic Protocols (NDPs). The uses of HTS in plant health diagnostics are many and varied. These cover anything from amplicon sequencing protocols to whole genome sequencing and even metagenomics. This means there is no one size fits all approach to assessing risk, meeting obligations under biosecurity at both state and federal levels and in developing new policy to ensure the results of HTS applications are reproducible, meaningful and relevant to our stakeholders. There is an increased risk of unintended consequences when complete sets of plant virus HTS data are uploaded to public databases owing to the fact they are often actually a plant metagenome, containing a wealth of other information which was never the original aim or target of the experiment. In this presentation, members of the working group hope to highlight the challenges with navigating the use of new methods in the plant virus diagnostics space where the policy and guidelines don’t always keep pace with new developments in technology. We discuss, and challenge everyone to consider these potential unintended or incidental findings that could be lurking in your data.