The Simpson Lab has been a regular contributor to the analysis of COVID-19 as part of CanCOGeN.
Our work on ncov-tools, an analysis pipeline used in determining quality metrics for SARS-CoV-2 genomes, has provided labs with the tools needed to assess their samples. Among this work, a collaboration with Ramzi Fattouh’s lab at Unity Health Toronto has uncovered mutations in the nucleocapsid (N) gene resulting in issues with PCR detection of SARS-CoV-2 across Canada. The details of this study can be found in a recent publication which outlines the methods used and the implications of potential genomic “blind spots”.