Frontiers in Microbiology (Jul 2014)

Metagenomic analysis of a sample from a patient with respiratory tract infection reveals the presence of a γ-papillomavirus

  • Marta eCanuti,
  • Martin eDeijs,
  • Seyed Mohammad Jazaeri Farsani,
  • Melle eHolwerda,
  • Maarten F Jebbink,
  • Michel ede Vries,
  • Saskia evan Vugt,
  • Curt eBrugman,
  • Theo eVerheij,
  • Christine eLammens,
  • Herman eGoossens,
  • Katherine eLoens,
  • Margaretha eIeven,
  • Lia eVan Der Hoek

DOI
https://doi.org/10.3389/fmicb.2014.00347
Journal volume & issue
Vol. 5

Abstract

Read online

Previously unknown or unexpected pathogens may be responsible for that proportion of respiratory diseases in which a causative agent cannot be identified. The application of broad-spectrum, sequence independent virus discovery techniques may be useful to reduce this proportion and widen our knowledge about respiratory pathogens. Thanks to the availability of high throughput sequencing (HTS) technology, it became today possible to detect viruses which are present at a very low load, but the clinical relevance of those viruses must be investigated. In this study we used VIDISCA-454, a restriction enzyme based virus discovery method that utilizes Roche 454 HTS system, on a nasal swab collected from a subject with respiratory complaints. A γ-papillomavirus was detected (complete genome: 7142 bp) and its role in disease was investigated. Respiratory samples collected both during the acute phase of the illness and two weeks after full recovery contained the virus. The patient presented antibodies directed against the virus but there was no difference between IgG levels in blood samples collected during the acute phase and two weeks after full recovery. We therefore concluded that the detected γ-papillomavirus is unlikely to be the causative agent of the respiratory complaints and its presence in the nose of the patient is not related to the disease. Although HTS based virus discovery techniques proved their great potential as a tool to clarify the aetiology of some infectious diseases, the obtained information must be subjected to cautious interpretations. This study underlines the crucial importance of performing careful investigations on viruses identified when applying sensitive virus discovery techniques, since the mere identification of a virus and its presence in a clinical sample are not satisfactory proofs to establish a causative link with a disease.

Keywords