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

Abstract

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 2 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 2 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 etiology 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.

Viral metagenomics and blood safety

“…The cDNA-AFLP method was developed by Bachem et al [58] and adapted for virus discovery (VIDISCA method) by van der Hoek et al [59] for successful identification of a novel human coronavirus, HCoV-NL63, in a child suffering from bronchiolitis and conjunctivitis. Later, VIDISCA was used to discover novel parvoviruses [60,61] and papillomavirus [62] in veterinary and clinical human samples, respectively.…”

Molecular methods for identification and characterization of novel papillomaviruses

“…NGS has frequently been used to analyse amplicons of various PVspecific broad-range PCRs to avoid the laborious and timeconsuming cloning procedure and selection of bacterial transformants harbouring novel HPV sequences [30,41,42]. NGS has similarly been commonly used to analyse amplicons containing PV sequences generated by different WGA methods, including the original RCA method [38,[42][43][44][45][46][47][48]. Partial sequences of several putatively novel HPV types have been identified using NGS, including in specimens previously negative for these types using broad-range PCR assays [42,44].…”

Reduced maternal levels of common viruses during pregnancy predict offspring psychosis: Potential role of enhanced maternal immune activity?

“…VIDISCA-454 (Virus Discovery cDNA-AFLP) is a virus discovery technique that, combined with Roche 454 next generation sequencing, is able to detect virtually all DNA or RNA viruses from various clinical samples (Canuti et al, , 2014aJazaeri Farsani et al, 2013Oude Munnink et al, 2013Tan et al, 2013;Pariani et al, 2014;Shaukat et al, 2014). Since this method is specifically designed to detect extracellular genetic material which is not susceptible to nucleases (viral genomes protected by a protein capsid), this system cannot be used to detect other human pathogens, such as bacteria and parasites.…”

“…Sequence independent virus identification techniques allow the simultaneous molecular detection of multiple viruses from a clinical sample without requiring any prior knowledge of its virological composition, and the possibility of combining them with next generation sequencing confers to these methods high efficiency and sensitivity (Delwart, 2007). One of these methods is VIDISCA-454, a restriction enzyme based virus discovery technique which is able to detect virtually any DNA or RNA virus from clinical samples and which was successfully used for virus discovery and metagenomic studies (Canuti et al, , 2014aJazaeri Farsani et al, 2013Oude Munnink et al, 2014. For this work VIDISCA-454 was applied on sera collected from pregnant mothers of offspring with or without schizophrenia or BD with psychotic features to evaluate the hypotheses of a viral etiology of psychoses.…”