Quasispecies in the 5' untranslated genomic region of bovine viral diarrhoea virus from a single individual

• Published in: Journal of general virology 2002-09, Vol.83 (9), p.2161-2168
• Main Authors: Jones, Leandro Roberto, Zandomeni, Ruben, Weber, E. Laura
• Format: Article
• Language: English
• Subjects: 5' Untranslated Regions - genetics; Animals; Base Sequence; Cattle; Cloning, Molecular; Diarrhea Viruses, Bovine Viral - classification; Diarrhea Viruses, Bovine Viral - genetics; Diarrhea Viruses, Bovine Viral - isolation & purification; Hemorrhagic Syndrome, Bovine - virology; Kidney - virology; Lung - virology; Molecular Sequence Data; Phylogeny; Polymorphism, Genetic; Sequence Alignment; Sequence Analysis; Species Specificity; Spleen - virology
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/0022-1317-83-9-2161

Instituto de Virología, CICVyA, INTA-Castelar, CC77 (1708) Morón, Buenos Aires, Argentina 1 Instituto de Microbiología y Zoología Agrícola, CICVyA, INTA-Castelar, CC77 (1708) Morón, Buenos Aires, Argentina 2 Consejo Nacional de Investigaciones Científicas, Argentina 3 Author for correspondence: Leandro Jones. Fax [phone]. e-mail ljones{at}cicv.inta.gov.ar The variability of the 5' untranslated genomic region (5'UTR) of bovine viral diarrhoea virus (BVDV) RNA obtained from a single individual was analysed. Lung, kidney and spleen tissues from a naturally infected foetus were used as the source of viral RNA. A fragment of 288 bases of the internal ribosome entry site from the BVDV 5'UTR was amplified by RT–PCR using a proofreading DNA polymerase. PCR products were cloned into pGem and, subsequently, transformed into Escherichia coli . The single-strand conformational polymorphisms of 158 lung-derived clones were analysed; a total of 11 banding patterns was observed. DNAs corresponding to all patterns were sequenced. Of the randomly selected clones, 11 and 10 clones derived from the kidney and spleen, respectively, were also sequenced. All sequences presented differences ranging from 1 to 6 nt substitutions. Analysis of the secondary structure of the variant sequences and comparisons to variant nucleotide sites from the 5'UTR of several BVDV isolates showed that the observed changes were almost free of randomness. Clustering and phylogenetic analyses suggested the existence of low-kinetic variants. BVDV quasispecies may be involved in establishing persistent infections by means of eluding maternal antibodies. The methods described here may be adapted easily both to analyse large numbers of samples from other genomic regions and for the study of BVDV quasispecies evolution in other systems.