title: Numerical taxonomy of the genus Pestivirus: new software for genotyping based on the palindromic nucleotide substitutions method.
abstract: The genus Pestivirus from the family Flaviviridae is represented by four established species; Bovine viral diarrhea virus 1 (BVDV-1); Bovine viral diarrhea virus 2 (BVDV-2); Border disease virus (BDV); and Classical swine fever virus (CSFV); as well a tentative species from a Giraffe. The palindromic nucleotide substitutions (PNS) in the 5' untranslated region (UTR) of Pestivirus RNA has been described as a new, simple and practical method for genotyping. New software is described, also named PNS, that was prepared specifically for this PNS genotyping procedure. Pestivirus identification using PNS was evaluated on five hundred and forty-three sequences at genus, species and genotype level using this software. The software is freely available at www.pns-software.com.
authors.affiliation: Department of Veterinary Microbiology, School of Veterinary Medicine, Faculty of Agriculture, Iwate University, 18-8 Ueda 3, Chome, Morioka, 020-8550 Iwate, Japan. giangasp@gmail.com
authors.forename: Massimo
authors.initials: M
authors.lastname: Giangaspero
authors.forename: Claudio
authors.initials: C
authors.lastname: Apicella
authors.forename: Ryô
authors.initials: R
authors.lastname: Harasawa
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D005838:Genotype; D055029:Inverted Repeat Sequences; D009711:Nucleotides / Q000235:genetics*; D010576:Pestivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018182:Pestivirus Infections / Q000175:diagnosis / Q000662:veterinary; D012367:RNA, Viral / Q000235:genetics*; D012984:Software; D014773:Virology / Q000379:methods
chemical_list: D020121:5' Untranslated Regions; D009711:Nucleotides; D012367:RNA, Viral