title: Characterization of a genetically heterogeneous porcine rotavirus C, and other viruses present in the fecal virome of a non-diarrheic Belgian piglet.
abstract: Next-generation sequencing (NGS) technologies are becoming increasingly accessible, leading to an expanded interest in the composition of the porcine enteric virome. In the present study, the fecal virome of a non-diarrheic Belgian piglet was determined. Although the virome of only a single piglet was analyzed, some interesting data were obtained, including the second complete genome of a pig group C rotavirus (RVC). This Belgian strain was only distantly related to the only other completely characterized pig RVC strain, Cowden. Its relatedness to RVC strains from other host species was also analyzed and the porcine strain found in our study was only distantly related to RVCs detected in humans and cows. The gene encoding the outer capsid protein VP7 belonged to the rare porcine G3 genotype, which might be serologically distinct from most other pig RVC strains. A putative novel RVC VP6 genotype was identified as well. A group A rotavirus strain also present in this fecal sample contained the rare pig genotype combination G11P[27], but was only partially characterized. Typical pig RVA genotypes I5, A8, and T7 were found for the viral proteins VP6, NSP1, and NSP3, respectively. Interestingly, the fecal virome of the piglet also contained an astrovirus and an enterovirus, of which the complete genomes were characterized. Results of the current study indicate that many viruses may be present simultaneously in fecal samples of non-diarrheic piglets. In this study, these viruses could not be directly associated with any disease, but still they might have had a potential subclinical impact on pig growth performance. The fast evolution of NGS will be a powerful tool for future diagnostics in veterinary practice. Its application will certainly lead to better insights into the relevance of many (sub)clinical enteric viral infections, that may have remained unnoticed using traditional diagnostic techniques. This will stimulate the development of new and durable prophylactic measures to improve pig health and production.
authors.affiliation: Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium. Electronic address: sebastiaan.theuns@ugent.be.
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: Theuns
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical Virology, B-3000, Leuven, Belgium.
authors.forename: Nádia
authors.initials: N
authors.lastname: Conceição-Neto
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium.
authors.forename: Mark
authors.initials: M
authors.lastname: Zeller
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Heylen
authors.affiliation: Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium.
authors.forename: Inge D M
authors.initials: ID
authors.lastname: Roukaerts
authors.affiliation: Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium.
authors.forename: Lowiese M B
authors.initials: LM
authors.lastname: Desmarets
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical Virology, B-3000, Leuven, Belgium.
authors.forename: Marc
authors.initials: M
authors.lastname: Van Ranst
authors.affiliation: Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Nauwynck
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium.
authors.forename: Jelle
authors.initials: J
authors.lastname: Matthijnssens
mesh_terms: D000818:Animals; D019200:Astroviridae / Q000302:isolation & purification; D001530:Belgium; D004770:Enterovirus / Q000302:isolation & purification; D005243:Feces / Q000821:virology*; D018740:Genetic Heterogeneity; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010802:Phylogeny; D012401:Rotavirus / Q000145:classification* / Q000235:genetics; D012400:Rotavirus Infections / Q000662:veterinary*; D017423:Sequence Analysis, RNA; D013552:Swine; D013553:Swine Diseases / Q000821:virology*; D014758:Viral Core Proteins / Q000235:genetics*
chemical_list: D014758:Viral Core Proteins
keywords: Astrovirus; Enterovirus; Group C rotavirus; Group a rotavirus; Pig; Viral metagenomics