Clinical and biological insights from viral genome sequencing

Abstract

Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.

Figure 1. Methods for sequencing viral genomes from clinical specimens.

All specimens originally comprise a mix of host (in blue) and pathogen (in red) DNA sequences. For pathogens that have RNA genomes, RNA in the sample is converted into complementary DNA (cDNA) before PCR and library preparation. Direct metagenomic sequencing provides an accurate representation of the sequences in the sample, although at high sequencing and data analysis and storage costs. PCR amplicon sequencing uses many discrete PCR reactions to enrich the viral genome, which increases the workload for large genomes substantially but decreases the costs. Target enrichment sequencing uses virus-specific nucleotide probes that are bound to a solid phase, such as beads, to enrich the viral genome in a single reaction, which reduces workload but increases the cost of library preparation compared with PCR. PowerPoint slide