Infectious Disease Tracking Study Compares Genome Sequencing Approaches

For a paper in BMC Genomics, researchers from the Erasmus Medical Center's viroscience department consider sequencing methods for detecting and tracking viruses in genomic epidemiology applications. Using samples containing Flaviviridae family Zika, West Nile, Yellow Fever, or Usutu viruses at a range of concentrations, the team compared metagenomic sequencing, amplicon-based genome sequencing, and capture-based sequencing on Illumina short read or Oxford Nanopore platforms. While capture-based Illumina sequencing was a sensitive strategy for characterizing viral genomes, for example, the authors saw benefits for rapid Nanopore amplicon sequencing when it came to profiling samples in certain viral load ranges. "Choosing a sequencing platform and approach is important for labs adopting genome sequencing, but depends on the stage of an outbreak and the to-be-answered questions in public health decision making," they write, noting that their data "offers a deep insight in the characteristics of each approach and help making this choice."