This is a summary, written by members of the CITF Secretariat, of:

Coope RJN, Matic N, Pandoh PK, Corbett RD, Smailus DE, Pleasance S, Lowe CF, Ritchie G, Chorlton SD, Young M, Ally AA, Asano JK, Carlsen RE, Chahal SS, Zhao Y, Holmes DT, Romney MG, Jones SJM, Marra MA. Automated Library Construction and Analysis for High-throughput Nanopore Sequencing of SARS-CoV-2. Journal of Applied Laboratory Medicine, 2022;, jfac054,

The results and/or conclusions contained in the research do not necessarily reflect the views of all CITF members.

A recent CITF-funded study published in the Journal of Applied Laboratory Medicine by Drs. Marco Marra, Steven Jones and Marc Romney (University of British Columbia) demonstrates an optimized workflow for high-throughput whole-genome sequencing of SARS-CoV-2 samples. This would enable clinical laboratories and public health teams to promptly investigate potential outbreaks of COVID-19, cases of SARS-CoV-2 re-infection or post-vaccination breakthroughs, and to monitor for new or emerging variants of concern.

Key findings

  • Genetic sequencing of the SARS-CoV-2 virus required 12 hours for sample preparation, up to 24 hours for sequencing, and one hour for analysis; sequencing analysis required 20-60 minutes, depending on the number of samples in the pool. 50% of the samples sequenced could be successfully analyzed after five hours of sequencing.
  • It could conceivably be operated to provide a sub-24 hour sequencing analysis turnaround, based on previously extracted samples, particularly for samples with abundant RNA.
  • This method demonstrated the robust reliability of its analysis.
  • Consistency rate of single nucleotide polymorphism PCR testing used to detect the mutations and whole genome sequencing using this pipeline for variants of concern detection was 99.8% accurate.

Overall, this work might benefit public health and Infection control officials. Viral sequencing is being increasingly used to investigate outbreaks of SARS-CoV-2 by establishing linkages between disease clusters and helping to illuminate mechanisms of transmission. This pipeline is also effective at characterizing variants of concern.

A total of 2179 SARS-CoV-2 samples were sequenced in 25 runs, with each plate of up to 92 samples and controls. The sample set contained a median of 24 mutations per sample and a total of 1281 unique mutations. A total of 10 separate strains were observed in the sample set, including three variants of concerns prevalent in British Columbia in the spring of 2021.