Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains

Diagn Microbiol Infect Dis. 2015 Oct;83(2):133-8. doi: 10.1016/j.diagmicrobio.2015.06.017. Epub 2015 Jun 29.

Abstract

Multiplex PCR assays for respiratory viruses are widely used in routine diagnostics, as they are highly sensitive, rapid, and cost effective. However, depending on the assay system, cross-reactivity between viruses that share a high sequence homology as well as detection of rare virus isolates with sequence variations can be problematic. Virus sequence-independent metagenomic high-throughput sequencing allows for accurate detection of all virus species in a given sample, as we demonstrate here for human Enterovirus and Rhinovirus in a lung transplant patient. While early in infection a commercial PCR assay recorded Rhinovirus, high-throughput sequencing correctly identified human Enterovirus C104 as the source of infection, highlighting the potential of the technology and the benefit of applying open assay formats in complex diagnostic situations.

Keywords: Enterovirus; Metagenomic; Next generation sequencing; PCR; Rhinovirus; Virus diagnostic.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Enterovirus / classification*
  • Enterovirus / genetics
  • Enterovirus / isolation & purification*
  • Enterovirus Infections / diagnosis*
  • Enterovirus Infections / virology
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Lung Transplantation / adverse effects
  • Male
  • Metagenomics / methods*
  • Middle Aged
  • Respiratory Tract Infections / diagnosis*
  • Respiratory Tract Infections / virology