Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens

• DOI: 10.1016/j.ijid.2021.10.050
• Publication Date: 2021-10-29T15:44:23Z
• Authors: Kevin S. Kuchinski; Jason Nguyen; Tracy D. Lee; Rebecca Hickman; Agatha N. Jassem; Linda M.N. Hoang; Natalie A. Prysta...; John R. Tyson
• Keywords: 0301 basic medicine; British Columbia; SARS-CoV-2; Short Communication; COVID-19; Infectious and parasitic diseases; RC109-216; Genome, Viral; Genomics; 3. Good health; Variant of concern; 03 medical and health sciences; Genomic surveillance; Mutation; Humans; Viral genomics; Amplicon sequencing

AbstractMutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to generate high-quality genome sequences for COVID-19 surveillance. Here, we identify 46 mutations in current variant of concern lineages affecting the widely used laboratory protocols for SARS-CoV-2 genomic sequencing by Freed et al. and the ARTIC network. We provide laboratory data showing how three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada, and we also demonstrate how we modified the Freed et al. protocol to restore performance.