Novel poly-uridine insertion in the 3′UTR and E2 amino acid substitutions in a low virulent classical swine fever virus

Liani Coronado, Matthias Liniger, Sara Muñoz-González, Alexander Postel, Lester Josue Pérez, Marta Pérez-Simó, Carmen Laura Perera, Maria Teresa Frías- Lepoureau, Rosa Rosell, Adam Grundhoff, Daniela Indenbirken, Malik Alawi, Nicole Fischer, Paul Becher, Nicolas Ruggli, Llilianne Ganges

Research output: Contribution to journalArticlepeer-review


In this study, we compared the virulence in weaner pigs of the Pinar del Rio isolate and the virulent Margarita strain. The latter caused the Cuban classical swine fever (CSF) outbreak of 1993. Our results showed that the Pinar del Rio virus isolated during an endemic phase is clearly of low virulence. We analysed the complete nucleotide sequence of the Pinar del Rio virus isolated after persistence in newborn piglets, as well as the genome sequence of the inoculum. The consensus genome sequence of the Pinar del Rio virus remained completely unchanged after 28 days of persistent infection in swine. More importantly, a unique poly-uridine tract was discovered in the 3′UTR of the Pinar del Rio virus, which was not found in the Margarita virus or any other known CSFV sequences. Based on RNA secondary structure prediction, the poly-uridine tract results in a long single-stranded intervening sequence (SS) between the stem-loops I and II of the 3′UTR, without major changes in the stem- loop structures when compared to the Margarita virus. The possible implications of this novel insertion on persistence and attenuation remain to be investigated. In addition, comparison of the amino acid sequence of the viral proteins Erns, E1, E2 and p7 of the Margarita and Pinar del Rio viruses showed that all non-conservative amino acid substitutions acquired by the Pinar del Rio isolate clustered in E2, with two of them being located within the B/C domain. Immunisation and cross-neutralisation experiments in pigs and rabbits suggest differences between these two viruses, which may be attributable to the amino acid differences observed in E2. Altogether, these data provide fresh insights into viral molecular features which might be associated with the attenuation and adaptation of CSFV for persistence in the field.

Original languageEnglish (US)
Pages (from-to)103-112
Number of pages10
JournalVeterinary Microbiology
StatePublished - Mar 1 2017
Externally publishedYes


  • Amino acid differences
  • Antigenic differences
  • B/C domain
  • CSFV
  • E2 glycoprotein
  • Immunogenicity
  • Pigs
  • Poly-U insertion
  • Rabbits
  • Secondary structure

ASJC Scopus subject areas

  • Microbiology
  • veterinary(all)


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