Massive High Throughput COVID-19 Testing Using Next Generation Sequencing (NGS): Addressing the Urgent Need for Widescale Testing Capacity Within Communities [Funder: Genome Atlantic, Research NS]

PUBLIC HEALTH ISSUE: In Canada, the current COVID-19 testing approaches are operating near full capacity and key reagent supply chains are stressed. Current Public Health testing priority is for symptomatic individuals and close contacts. This is a highly valued and validated standard of care approach but does not readily identify pre- or asymptomatic virus spreaders. Due to the highly transmissible nature of the SARS-Cov-2 virus, operational challenges make COVID-19 detection and containment very difficult within the Canadian population. The Chief Medical Officer of Canada has identified an urgent need to ramp up testing capacity for COVID-19 and epidemiologists are strongly recommending expanded testing capacity to inform collective infection control efforts. The overall goal through many mitigations, is to reduce the reproductive rate (R value) of COVID-19 to less than 1. Widescale testing, isolation, and contract tracing are central to reducing the impact of future waves of COVID-19 disease, at least until an effective vaccine is available. We propose to pilot an innovative protocol that benefits from fewer sample extraction steps and massive scaling potential due to the use of DNA molecular barcodes. SPECIFIC AREA TO BE ADDRESSED: The goal is to broadly expand testing for COVID-19 into communities and workplaces to measure virus burden thus providing essential molecular survey evidence. This evidence can then be used to make decisions about enacting (or reducing) stringent isolation measures.These decisions may include: • When to impose self-isolation, quarantine measures, and altered workplace schedules • When to re-open schools, community facilities, businesses, and to reduce control measures Next Generation Sequencing (NGS) diagnostic screening (ref. 1) has the advantage of massive COVID-19 test scaling and cost effectiveness (about 1$/test). It can be readily modified for future pandemic preparedness due to its adaptable NGS pipeline. In our proposed approach, we will be using DNA barcoding and detecting two viral SARS-CoV-2 PCR amplicons. We will not be using antigen tests.