Complete nucleotide and amino acid sequences and genetic organization of porcine kobuvirus, a member of a new species in the genus Kobuvirus, family Picornaviridae

Arch Virol. 2009;154(1):101-8. doi: 10.1007/s00705-008-0288-2. Epub 2008 Dec 19.

Abstract

Kobuvirus is a new genus in the family Picornaviridae. Two species are currently known: Aichi virus (human kobuvirus) and Bovine kobuvirus (U-1). In this study, the complete nucleotide and amino acid sequences and genetic organization of porcine kobuvirus (Kobuvirus/swine/S-1-HUN/2007/Hungary, EU787450) were determined. The structure of the S-1-HUN genome, VPg-5'UTR-leader protein-structural proteins (VP0, VP3, VP1)-non-structural proteins (2A-2C, 3A-3D)-3'UTR-poly(A) tail, was found to be typical of picornavirus. The 8210-nucleotide (nt)-long RNA genome contains a large open reading frame (7467 nt) encoding a potential polyprotein precursor of 2488 amino acids (aa) that has 57/56% and 63/64% nt/aa identity with Aichi virus and U-1, respectively. The 5'UTR contains a hepacivirus/pestivirus-like internal ribosomal entry site (IRES type IV group-B-like) with conserved pseudoknot, II and IIIa-f domains. A tandem repeat (a 30-amino-acid-long motif) was detected in 2B. Thirty-nine (65%) of the 60 fecal samples from pigs under the age of 6 months at the tested farm were positive (the incidence was 90% under the age of 3 weeks). Porcine kobuvirus belongs to a potential new species-the third-in the genus Kobuvirus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • 5' Untranslated Regions / genetics
  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • DNA Primers
  • Feces / virology
  • Gene Order*
  • Genome, Viral / genetics
  • Kobuvirus / classification*
  • Kobuvirus / genetics*
  • Molecular Sequence Data
  • Open Reading Frames
  • Picornaviridae / classification*
  • Picornaviridae / genetics*
  • Picornaviridae Infections / veterinary
  • RNA, Viral / chemistry
  • Swine
  • Swine Diseases / virology
  • Viral Proteins / chemistry
  • Viral Proteins / genetics

Substances

  • 3' Untranslated Regions
  • 5' Untranslated Regions
  • DNA Primers
  • RNA, Viral
  • Viral Proteins

Associated data

  • GENBANK/EU787450