Abstract
Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely used sequencing protocols by the ARTIC network and Freed et al. Three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada. We provide laboratory validation of protocol modifications that restored sequencing performance. The study findings indicate that genomic sequencing protocols require immediate updating to address emerging mutations. This work also suggests that routine monitoring and protocol updates will be necessary as SARS-CoV-2 continues to evolve. The bioinformatic and laboratory approaches used here provide guidance for this kind of assay maintenance.
Keywords: Amplicon sequencing; COVID-19; Genomic surveillance; SARS-CoV-2; Variant of concern; Viral genomics.
【저자키워드】 COVID-19, SARS-CoV-2, Genomic surveillance, variant of concern, viral genomics., Amplicon sequencing, 【초록키워드】 public health, coronavirus, Mutation, protocol, Sequencing, Genomic surveillance, mutations, variant, severe acute respiratory syndrome Coronavirus, Laboratory, Surveillance, outbreak, P.1, Lineage, Canada, Guidance, genomic sequencing, Amplicon sequencing, Amplicon, acute respiratory syndrome, routine monitoring, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, viral genome sequence, specimen, ARTIC Network, Modification, viral genome sequences, sequencing protocols, Affect, widespread, approach, generate, interfere, restored, sequencing protocol, 【제목키워드】 Lineage, genomic sequencing, specimen, disrupt,