High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Abstract

Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler’s encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

Keywords:

• cardiovirus
• metagenomics
• picornavirus
• Rattus norvegicus
• sequencing
• viral discovery

Villum Fonden and Innovation Fund Denmark (The Genome Denmark platform, grant NO 019-2011-2) funded this study. This study was funded in part by the US National Science Foundation III:AF:1513629 to Tandy Warnow (Departments of Bioengineering and Computer Science, The University of Illinois at Urbana—Champaign, Urbana, Illinois, 61801-2302, USA). We acknowledge Salvatore Cosentino (Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark) and Anne Ahlmann Nielsen (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark) for valuable input on data analysis and experimental setup, respectively. We acknowledge Claus Schultz, Andy Brigham from Rentokil and Claus Christensen from Hovedstadsområdets Forsyningsselskab (HOFOR) for arranging and assisting with sample collection and the Copenhagen University Hospital (Rigshospitalet) and Section of Heart and Circulatory Research, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark for contributing samples. Also we thank The National High-throughput DNA Sequencing Centre for excellent execution of sequencing.

Supplementary Information for this article can be found on the Emerging Microbes & Infections website (http://www.nature.com/emi)