title: Diagnostic phylogenetics reveals a new Porcine circovirus 2 cluster.
abstract: Porcine circovirus 2 (PCV2) was prevalent in swine in the United States before PCV2-associated disease (PCVAD) appeared in 2006. Limited nucleotide sequencing of open reading frame 2 (ORF2) encoding capsid, the only structural protein, revealed the presence of two genotypes, PCV2a and PCV2b. Later, PCV2c and mutant PCV2b, or PCV2d, were also described. However, extensive PCV2 ORF2 sequence databases in veterinary diagnostic laboratories have not been analyzed systematically to determine the genetic diversity of field isolates. Here, we interrogated >1100 PCV2 ORF2 nucleotide sequences to assess population diversity and genetic variation. We detected a novel PCV2 genotype that is substantially different, primarily in ORF2, from all known PCV2. Notably, ORF2 contains a unique carboxyl terminal amino acid insertion resulting in a 238 amino acid ORF2. All other PCV2 ORF2 proteins are 233 or 234 aa in length. Phylogenetic analysis indicates that it is more ancient than other PCV2 genotypes. The findings demonstrate the value of analyzing routine diagnostic laboratory sequence databases in population genetic analyses of animal pathogens.
authors.affiliation: Departments of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, United States.
authors.forename: Brendan
authors.initials: B
authors.lastname: Davies
authors.affiliation: Departments of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, United States.
authors.forename: Xiong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Departments of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, United States.
authors.forename: Cheryl M T
authors.initials: CM
authors.lastname: Dvorak
authors.affiliation: Departments of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, United States.
authors.forename: Douglas
authors.initials: D
authors.lastname: Marthaler
authors.affiliation: Departments of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, United States. Electronic address: murta001@umn.edu.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Murtaugh
mesh_terms: D000818:Animals; D044822:Biodiversity; D017925:Circovirus / Q000145:classification* / Q000235:genetics; D004279:DNA, Viral; D014644:Genetic Variation; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral
keywords: Diagnostics; PCV2; Phylogenetics; Swine; Virology