title: Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing.
abstract: BACKGROUND
  Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV.
  
  
  RESULTS
  We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5.
  
  
  CONCLUSIONS
  Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events.
authors.forename: Zen H
authors.initials: ZH
authors.lastname: Lu
authors.forename: Alexander
authors.initials: A
authors.lastname: Brown
authors.forename: Alison D
authors.initials: AD
authors.lastname: Wilson
authors.forename: Jay G
authors.initials: JG
authors.lastname: Calvert
authors.forename: Monica
authors.initials: M
authors.lastname: Balasch
authors.forename: Pablo
authors.initials: P
authors.lastname: Fuentes-Utrilla
authors.forename: Julia
authors.initials: J
authors.lastname: Loecherbach
authors.forename: Frances
authors.initials: F
authors.lastname: Turner
authors.forename: Richard
authors.initials: R
authors.lastname: Talbot
authors.forename: Alan L
authors.initials: AL
authors.lastname: Archibald
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK. tahar.aitali@roslin.ed.ac.uk.
authors.forename: Tahar
authors.initials: T
authors.lastname: Ait-Ali
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D008264:Macrophages / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D019316:Porcine respiratory and reproductive syndrome virus / Q000145:classification* / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013552:Swine; D014776:Virus Cultivation
chemical_list: D012367:RNA, Viral