ABSTRACT
We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library. Furthermore, this method enabled us to determine nearly full-length genome sequence of porcine parainfluenza virus 1 and greatly increased Breadth, a value indicating the ratio of the mapping consensus length in the reference genome, in pig samples. Our data showed usefulness of SureSelect target enrichment system for comprehensive analysis of genomic information of various viruses in field samples.
Subject(s)
Chromosome Mapping/veterinary , Cytopathogenic Effect, Viral/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing/veterinary , Livestock/virology , Viruses/genetics , Viruses/isolation & purification , Animals , Cattle , Chromosome Mapping/methods , High-Throughput Nucleotide Sequencing/methods , Swine , Viruses/pathogenicityABSTRACT
Small ruminant lentiviruses (SRLVs), which comprise caprine arthritis-encephalitis virus (CAEV) and maedi-visna virus (MVV), are prevalent in goats and sheep worldwide, including in Japan. However, little is known about the molecular characteristics of goat lentiviruses in Japan. In this study, a molecular and phylogenetic analysis of the long gag region was performed. The phylogenic tree demonstrated that all samples belonged to SRLV subtype B1. Two clusters were identified, with one cluster distinct from previously reported strains of subtype B1. In addition, several alterations in the amino acid sequence were detected in immunodominant epitopes of the gag region. To gain a deeper understanding of the genetic diversity of SRLVs in Japan, it will be necessary to increase the sample size and conduct a broader survey. The present report is important for establishing baseline information on the prevalence of SRLV in Japan and providing data to develop a new, more sensitive diagnostic test for effective control of SRLV.
Subject(s)
Arthritis-Encephalitis Virus, Caprine/isolation & purification , Goat Diseases/virology , Goats , Lentivirus Infections/veterinary , Visna-maedi virus/isolation & purification , Visna/virology , Animals , Female , Goat Diseases/epidemiology , Japan , Lentivirus Infections/epidemiology , Lentivirus Infections/virology , Male , Sheep , Visna/epidemiologyABSTRACT
Goat diarrheal feces were subjected to metagenome analysis by the next-generation sequencing. Nucleotide sequences with homology to enteroviruses were obtained. Primers for RT-PCR were designed based on the nucleotide sequence of these sequences at the 5'-untranslated region, and we determined 563 bp nucleotide sequences that showed homology to bovine-like and ovine enteroviruses (77-87 %). We named the virus detected in this study goat enterovirus G1 (GEV-G1). In the phylogenetic analysis, GEV-G1 belonged to a cluster containing ovine enteroviruses. To our knowledge, this is the first report on nucleotide sequences of an enterovirus infecting Japanese goats.
