Alternate primers for whole-genome SARS-CoV-2 sequencing

As the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43 per cent of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.

Automated summary

Efforts are being made globally to control the spread and evolution of SARS-CoV-2 by sequencing its genome, but a significant percentage of generated genomes each month have gaps, reducing their information content. This study identifies the frequencies and positions of these genome gaps and provides a new primer set and sequencing scheme to enhance the quality and coverage of the genomes.