Secondary structure analysis of swine pasivirus (family Picornaviridae) RNA reveals a type-IV IRES and a parechovirus-like 3' UTR organization

Arch Virol. 2015 May;160(5):1363-6. doi: 10.1007/s00705-015-2371-9. Epub 2015 Feb 27.

Abstract

The potential RNA structures of the 5' and 3' untranslated regions (UTRs) and cis-acting replication elements (CREs) of a novel pasivirus (PaV) genotype (family Picornaviridae) were analysed. PaV-A3 (KM259923) was identified in a faecal sample from a domestic pig in Hungary with posterior paraplegia of unknown etiology. Based on likely structural features of the 5' UTR, the pasiviruses were inferred to possess Hepacivirus/Pestivirus-like type-IV IRES. The pasivirus CRE was mapped to the 2B genome region, similar to Ljungan virus. The secondary RNA structure of the pasivirus 3' UTR was structurally similar to that of human parechoviruses. The genome, CRE, and 3' UTR of pasiviruses provide further evidence of the common origin of the members of the genera Parechovirus and Pasivirus, although their different 5' UTR IRES types suggest that a recombination event occurred during the divergence these viruses.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions*
  • 5' Untranslated Regions
  • Animals
  • Binding Sites
  • Evolution, Molecular
  • Feces / virology
  • Hungary
  • Models, Molecular
  • Molecular Sequence Data
  • Paraplegia / veterinary
  • Paraplegia / virology
  • Picornaviridae / chemistry*
  • Picornaviridae / genetics*
  • Picornaviridae / isolation & purification
  • RNA Folding*
  • RNA, Viral / chemistry*
  • Ribosomes / metabolism*
  • Sequence Analysis, DNA
  • Sus scrofa
  • Swine
  • Swine Diseases / virology

Substances

  • 3' Untranslated Regions
  • 5' Untranslated Regions
  • RNA, Viral

Associated data

  • GENBANK/KM259923