title: Quasispecies variation of porcine reproductive and respiratory syndrome virus during natural infection.
abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) displays notorious genetic, antigenic, and clinical variability. Little is known, however, about the nature and extent of viral variation present within naturally infected animals. By amplifying and cloning the open reading frame 5 gene from tonsils of naturally infected swine, and by sequencing individual clones, we characterized viral diversity in nine animals from two farms. All animals harbored multiple PRRSV variants at both the nucleic and the amino acid levels. Structural variation and rates of synonymous and nonsynonymous nucleotide substitution were no different within known epitopes than elsewhere. Analysis of molecular variance indicated that differences between farms, among animals within farms, and within individual animals accounted for 92.94, 3.84, and 3.22% of the total viral genetic variability observed, respectively. PRRSV exists during natural infection as a quasispecies distribution of related genotypes. Positive natural selection for immune evasiveness does not appear to maintain this diversity.
authors.affiliation: Department of Veterinary Pathobiology, University of Illinois, 2001 South Lincoln Avenue, Urbana, IL 61802, USA. tlgoldbe@uiuc.edu
authors.forename: Tony L
authors.initials: TL
authors.lastname: Goldberg
authors.forename: James F
authors.initials: JF
authors.lastname: Lowe
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Milburn
authors.forename: Lawrence D
authors.initials: LD
authors.lastname: Firkins
mesh_terms: D000818:Animals; D001769:Blood / Q000821:virology; D003001:Cloning, Molecular; D005260:Female; D014644:Genetic Variation; D008969:Molecular Sequence Data; D014066:Palatine Tonsil / Q000821:virology; D010802:Phylogeny; D019318:Porcine Reproductive and Respiratory Syndrome / Q000503:physiopathology / Q000821:virology*; D019316:Porcine respiratory and reproductive syndrome virus / Q000145:classification* / Q000235:genetics*; D012367:RNA, Viral / Q000032:analysis / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013552:Swine; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014759:Viral Envelope Proteins; C114789:glycoprotein 5, PRRSV