Rapid WGS of SARS-CoV-2 and respiratory viruses for disease surveillance using nanopore sequencing

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The current COVID-19 pandemic requires advanced diagnostics assays which can be rapidly deployed across many laboratories, globally and to allow for both diagnostic COVID-19 testing but additionally a for surveillance and monitoring of the disease within and between populations by public health institutions.To date ourselves and others have developed and deployed multiple rapid antigen testing kits for diagnostic COVID-19 testing using both quantitiative real time PCR or indeed next generation sequencing (NGS).Nonacus plan to test and validate a novel and highly rapid Whole Genome Sequencing library preparation approach for sequencing Viral genomes with nanopore sequencing.With the continuous development of the pandemic, accurate real-time monitoring of virus mutations in close proximity (decentralised) to samples and obtaining effective information in a short period of time is critical. It is particularly important to understand the development and spread of the epidemic, guide prevention and control work, and vaccine research.This method will provide the first commercially available method and a more rapid, lower cost and higher throughput advancement to current nanopore methods being used for whole genome sequencing (WGS) of SARS-CoV-2\.Additionally as part of the technology validation we will validate the technology more broadly than just for SARS-CoV-2 and will develop the technology out as a Pan- Respiratory-Viral WGS screening technology, such that for any future viral outbreaks the technology could be used and also so that we can in the surveillance setting better understand using a single method what respiratory virus' are spreading in the population.This grant will enable us to undertake final validation and optimisation work for the SARS-CoV-2 WGS library prep product within the Nonacus lab before validating this protocol within 2 clinical laboratories already undertaking SARS-CoV2 work.Further to validating the method with SARS-CoV-2 we would then start the work up and early validation of a Pan-Respiratory-Viral product.This project and the product which will be commercialised from its work is innovative as there is no existing commercially available rapid and low cost, highly multiplexed COVID-19 / respiratory virus WGS workflow or product ahead on nanopore sequencing. Further the existing open source protocols such as ARTIC while performing satisfactorily suffer with being longer, more complex and much more expensive than we have planned and also lack capacity for higher multiplexing.We expect the outcome to be the first commercially available rapid and low cost whole genome sequencing methodology by nanopore sequencing for SAR-CoV-2\.