title: Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge.
abstract: BACKGROUND
  PCV2 has emerged as one of the most devastating viral infections of swine farming, causing a relevant economic impact due to direct losses and control strategies expenses. Epidemiological and experimental studies have evidenced that genetic diversity is potentially affecting the virulence of PVC2. The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification.
  
  
  METHODS
  Nine hundred seventy five PCV2 complete genomes and 1,270 ORF2 sequences available from GenBank were subjected to recombination, PASC and phylogenetic analyses and results were used for comparison with previous classification scheme.
  
  
  RESULTS
  The outcome of these analyses favors the recognition of four genotypes on the basis of ORF2 sequences, namely PCV2a, PCV2b, PCV2c and PCV2d-mPCV2b. To deal with the difficulty of founding an unambiguous classification and accounting the impossibility to define a p-distance cut-off, a set of reference sequences that could be used in further phylogenetic studies for PCV2 genotyping was established. Being aware that extensive phylogenetic analyses are time-consuming and often impracticable during routine diagnostic activity, ORF2 nucleotide positions adequately conserved in the reference sequences were identified and reported to allow a quick genotype differentiation.
  
  
  CONCLUSIONS
  Globally, the present work provides an updated scenario of PCV2 genotypes distribution and, based on the limits of the previous classification criteria, proposes new rapid and effective schemes for differentiating the four defined PCV2 genotypes.
authors: Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro, PD, 35020, Italy. giovanni.franzo@unipd.it.
authors: Giovanni
authors: G
authors: Franzo
authors: The Pirbright Institute, Pirbright, Woking, UK. marti.cortey@irta.cat.
authors: Martí
authors: M
authors: Cortey
authors: IrsiCaixa - HIVACAT, Badalona, Spain. alex.olvera@cresa.uab.cat.
authors: Alex
authors: A
authors: Olvera
authors: Department of Pathology, Croatian Veterinary Institute, Zagreb, Croatia. dinko.novosel@gmail.com.
authors: Dinko
authors: D
authors: Novosel
authors: Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of Sao Paulo, Brazil/College of Veterinary Medicine, United Metropolitan College complex (FMU), Sao Paulo, Brazil. alessandramarnie@gmail.com.
authors: Alessandra Marnie Martins Gomes De
authors: AM
authors: Castro
authors: Unité de Virologie Moléculaire, Emergence et Co-évolution Virale UMR CNRS, Marseille, 7268, France. philippe.biagini@efs.sante.fr.
authors: Philippe
authors: P
authors: Biagini
authors: UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Bellaterra, 08193, Spain. joaquim.Segales@irta.cat.|Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, Bellaterra, 08193, Spain. joaquim.Segales@irta.cat.
authors: Joaquim
authors: J
authors: Segalés
authors: Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro, PD, 35020, Italy. michele.drigo@unipd.it.
authors: Michele
authors: M
authors: Drigo
mesh_terms: D000818:Animals; D017925:Circovirus / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology; D004279:DNA, Viral / Q000235:genetics*; D016679:Genome, Viral; D005838:Genotype; D010802:Phylogeny; D013552:Swine
chemical_list: D004279:DNA, Viral