title: Novel poly-uridine insertion in the 3'UTR and E2 amino acid substitutions in a low virulent classical swine fever virus.
abstract: 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 28days 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.
authors.affiliation: Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
authors.forename: Liani
authors.initials: L
authors.lastname: Coronado
authors.affiliation: Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland.
authors.forename: Matthias
authors.initials: M
authors.lastname: Liniger
authors.affiliation: IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Muñoz-González
authors.affiliation: EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, Hannover, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Postel
authors.affiliation: Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba.
authors.forename: Lester Josue
authors.initials: LJ
authors.lastname: Pérez
authors.affiliation: IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Pérez-Simó
authors.affiliation: Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba.
authors.forename: Carmen Laura
authors.initials: CL
authors.lastname: Perera
authors.affiliation: Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Frías-Lepoureau
authors.affiliation: IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Departamentd'Agricultura, Ramaderia, Pesca, Alimentació i Medi Natural, (DAAM), Generalitat de Catalunya, Spain.
authors.forename: Rosa
authors.initials: R
authors.lastname: Rosell
authors.affiliation: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany.
authors.forename: Adam
authors.initials: A
authors.lastname: Grundhoff
authors.affiliation: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany.
authors.forename: Daniela
authors.initials: D
authors.lastname: Indenbirken
authors.affiliation: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany; Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
authors.forename: Malik
authors.initials: M
authors.lastname: Alawi
authors.affiliation: Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Fischer
authors.affiliation: EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, Hannover, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Becher
authors.affiliation: Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Ruggli
authors.affiliation: IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. Electronic address: llilianne.ganges@irta.cat.
authors.forename: Llilianne
authors.initials: L
authors.lastname: Ganges
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D001483:Base Sequence; D006691:Classical Swine Fever / Q000821:virology*; D006692:Classical Swine Fever Virus / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification / Q000472:pathogenicity; D000939:Epitopes; D016254:Mutagenesis, Insertional; D011817:Rabbits; D016415:Sequence Alignment / Q000662:veterinary; D017422:Sequence Analysis, DNA / Q000662:veterinary; D013552:Swine; D014529:Uridine / Q000235:genetics; D014759:Viral Envelope Proteins / Q000235:genetics*; D014774:Virulence / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D000939:Epitopes; D014759:Viral Envelope Proteins; C087086:glycoprotein E2, classical swine fever virus; D014529:Uridine
keywords: Amino acid differences; Antigenic differences; B/C domain; CSFV; E2 glycoprotein; Immunogenicity; Pigs; Poly-U insertion; Rabbits; Secondary structure