Enhanced genomic tracking of COVID-19 importations and transmissions in NSW

Project summary How can sensitive, enhanced WGS techniques enable high-resolution SARS-CoV-2 genome sequencing from low viral load samples? We intent to improve SARS-CoV-2 genome surveillance and enhance its consequent public health utility and impact in NSW. What is the issue for NSW? This research addresses a major and immediate challenge for genomic surveillance of SARS-CoV-2 in NSW and nationally - a low viral load in many diagnostic samples. It is extremely difficult to generate a full genome sequence from low viral load COVID-19 samples, which are increasingly collected from cases with minimal disease and asymptomatic infection. This in turn limits tracking of transmission events and linking cases. What does the research aim to do and how? This proposal will improve sensitivity of SARS-CoV-2 genome sequencing from clinical samples with low viral loads by implementing novel, highly sensitive methods of target genome enrichment that have proven successful with other viruses. Specific aims are to: (i) investigate sensitivity and precision of probe-based capture and spiked primer enrichment-based genome sequencing, and (ii) evaluate the impact of this enhanced whole genome sequencing (enhanced WGS) approach on public health genomic surveillance in NSW. We will focus particularly on samples and genomic sequences from one of Australia's most exposed risk groups, namely, healthcare workers (HCW).