Diagnostic phylogenetics reveals a new Porcine circovirus 2 cluster

•Novel, highly divergent, PCV2 viruses were identified in a veterinary diagnostic sequencing database.•A novel 238 amino acid PCV2 capsid protein was identified.•The novel PCV2 isolates were widely distributed in the USA and Mexico.•The novel PCV2 may be ancestral to other PCV2 genotypes. Porcine ci...

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Bibliographic Details
Published in:Virus research 2016-06, Vol.217, p.32-37
Main Authors: Davies, Brendan, Wang, Xiong, Dvorak, Cheryl M.T., Marthaler, Douglas, Murtaugh, Michael P.
Format: Article
Language:English
Subjects:
amino acids
Animals
Biodiversity
capsid
Circovirus - classification
Circovirus - genetics
Diagnostics
DNA, Viral
genetic analysis
Genetic Variation
genotype
mutants
Open Reading Frames
PCV2
Phylogenetics
Phylogeny
Porcine circovirus 2
Sequence Analysis, DNA
structural proteins
Swine
Virology
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Summary:•Novel, highly divergent, PCV2 viruses were identified in a veterinary diagnostic sequencing database.•A novel 238 amino acid PCV2 capsid protein was identified.•The novel PCV2 isolates were widely distributed in the USA and Mexico.•The novel PCV2 may be ancestral to other PCV2 genotypes. 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.
ISSN:0168-1702
1872-7492
DOI:10.1016/j.virusres.2016.02.010