Targeted metagenomic detection and characterization of SARSCoV- 2 and co-infecting viruses [Funder: Genome Prairie, SK Research Foundation,NSERC]

Laboratory testing supports the diagnosis and treatment of infectious diseases, but you can't detect what you don't test for. During the current COVID-19 pandemic, laboratory efforts are focused on testing for the novel coronavirus, SARS-CoV-2. Health Canada approved assays detect SARS-CoV-2 but not co-infections by other respiratory viruses. Without such data, we cannot know the prevalence of co-infections or the impact of co-infections on the severity of COVID-19 disease. In the proposed research initiative, the established partnership of virologists and microbial geneticists at the Roy Romanow Provincial Laboratory (SK), Cadham Provincial Laboratory (MB), Centre for Disease Control (BC), and the University of Regina will optimize and deploy genome capture. This technique will enable the detection of coronavirus plus other co-infecting viruses in patient specimens. Co-infection by respiratory viruses is common and bad for patients, yet we know very little about co-infection in the context of the COVID-19 pandemic. Integrating the genomic detection of respiratory viruses to better understand the severity of COVID-19 infection will directly and immediately improve public health interventions and clinical treatment plans. Additionally, the genome capture approach restores diagnostics for co-infections at a time when testing capabilities are compromised by the pressures of the COVID-19 pandemic. Our project will enhance public health lab membership in the Genome Canada-supported Canadian COVID-19 Genomics Network (CanCOGeN) by expanding SARS-CoV-2 genome sequencing on the prairies and providing genomics protocols for each public health lab, which is not part of CanCOGeN. Capacity building for genomic understanding of COVID-19 and diagnosis of co-infection is timely and highly feasible as it leverages existing resources in MB and SK along with proven national partnerships for knowledge translation.