On-Demand Point-of-Care SARS-CoV-2 Genomic Sequencing to Support Nosocomial Outbreak Investigations: A Prospective Molecular Epidemiology Study in Montreal

This study will include infected healthcare workers (HCW) and patients for whom a nosocomial infection in CHUM is suspected. The CHUM laboratory is responsible for COVID-19 diagnostic testing in all eligible HCW and patients. After initial diagnosis on standard PCR testing, samples are maintained at -80. Viral RNA is extracted and next-generation sequencing of the viral genome is performed using Nanopore long read sequencing platform. Preliminary data suggest that SARS-CoV-2 has a "molecular clock" of 2 single nucleotide polymorphism (SNP) per month. The analysis and between-isolate comparaison of those SNP among epidemiologically related cases will allow to support or refute the hypothesis of person to person nosocomial transmission. All infected patients will be matched 1:1 with contemporary community cases to provide a viral genome back catalog and better contextualize molecular epidemiology analyses. Molecular clusters will be reported to infection prevention and control teams and resulting interventions will be monitored.