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. 2015 Aug 28:12:131.
doi: 10.1186/s12985-015-0361-x.

Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge

Giovanni Franzo  1 , Martí Cortey  2 , Alex Olvera  3 , Dinko Novosel  4 , Alessandra Marnie Martins Gomes De Castro  5 , Philippe Biagini  6 , Joaquim Segalés  7   8 , Michele Drigo  9
Affiliations

Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge

Giovanni Franzo et al. Virol J. .

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.

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Figures

Fig. 1
Fig. 1
Phylogenetic trees reconstructed using Neighbor Joining (a) and Maximum likelihood (b) methods based on the ORF2 database after removing the recombinant strains detected by RDP. Bootstrap support has been reported using gray scale ranging from white (i.e. bootstrap support = 0) to black (i.e. bootstrap support = 1)
Fig. 2
Fig. 2
PASC analysis of complete PCV2 genome database (a) and of ORF2 sequences (b). The percentage of pairwise p-distances comprised within a 0.01 p-distance interval is reported
Fig. 3
Fig. 3
Substitution rates and 95 % CI for the PCV2 genotypes obtained using BEAST
See this image and copyright information in PMC

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