REAL-TIME TRACKING OF QUEBEC SARS-COV-2 EVOLUTION
CoVSeQ is a partnership between the Institut National de Santé Publique du Québec (INSPQ) and the McGill Genome Center to sequence the viral genome of Quebec patients with COVID-19 disease. The viral samples are taken from a Quebec viral biobank, termed the CoVBanQ, which is hosted in the Laboratoire de Santé; Publique du Québec (LSPQ). The website is based on Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data. It provides powerful analytic and visualization tools to aid epidemiological understanding and improve outbreak response.
In the course of an infection and over an epidemic, pathogens naturally accumulate random mutations to their genomes. This is an inevitable consequence of error-prone genome replication. Since different genomes typically pick up different mutations, mutations can be used as a marker of transmission in which closely related genomes indicate closely related infections. By reconstructing a phylogeny we can learn about important epidemiological phenomena such as spatial spread, introduction timings and epidemic growth rate (reference: Nextstrain.org).
However, if pathogen genome sequences are going to inform public health interventions, then analyses have to be rapidly conducted and results widely disseminated. Current scientific publishing practices hinder the rapid dissemination of epidemiologically relevant results. We thought an open online system that implements robust bioinformatic pipelines to synthesize data from across research groups has the best capacity to make epidemiologically actionable inferences.
Read more at: CoVSeQ
Institut national de santé publique du Québec
Canadian Centre for Computational Genomics
Laboratoire de santé publique du Québec
Université de Montréal
Sarah Reiling, PhD
Shu-Huang "Sherry" Chen
Lena Li Chun Fong
Haig Hugo Vrej Djambazain