Developing standards and workflows for high-throughput and surveillance diagnostics applications

Abstract

With globalisation there comes an increased risk of the emergence and spread of infectious diseases with pandemic potential. Many nations are not currently equipped with the tools necessary to perform biosurveillance and rapidly respond to biological risks through the development and implementation of suitable diagnostics. This thesis describes the develop- ment of suitable Working Standards for RNA and DNA viral pathogens that can be utilised for diagnostic development. A SARS-CoV-2 RNA Working Standard was developed in response to the SARS-CoV-2 pandemic and used to validate a high-throughput extraction and RT-qPCR diagnostic workflow, along with other alternative molecular assays. The workflow was then further optimised by validating an adaptive group testing approach in an accredited diagnostic laboratory and exploring the potential of non-adaptive group testing. Finally, all materials for producing the Standards were made available under the openMTA and protocols for diagnos- tic development published to allow for companies, health agencies and academics to develop their own diagnostic workflows to respond to current and future biological threats.