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

Franzo G, Cortey M, Olvera A, Novosel D, Castro AM, Biagini P, Segalés J, Drigo M - Virol. J. (2015)

Bottom Line: The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro, PD, 35020, Italy. giovanni.franzo@unipd.it.

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.

No MeSH data available.


Related in: MedlinePlus

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)
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Fig1: 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)

Mentions: Phylogenetic trees reconstructed from PCV2 ORF2 using NJ (Fig. 1a) and ML (Fig. 1b) methods displayed very similar topologies and four main clades were identified. These four clades substantially corresponded to the previously defined PCV2a, PCV2b, PCV2c and PCV2d genotypes. Very few strains (n = 7) showed contradictory clustering between PCV2a and PCV2d clades in the ORF2 trees (Additional file 1). The same clustering in four major groups was obtained rooting the tree using PCV1 sequences as outgroup (data not shown). Similarly, phylogenetic trees reconstructed using complete genome showed a similar topology even if with a closer relationship between remaining PCV2d and PCV2a strains (named according to ORF2 classification).Fig. 1


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

Franzo G, Cortey M, Olvera A, Novosel D, Castro AM, Biagini P, Segalés J, Drigo M - Virol. J. (2015)

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)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4551364&req=5

Fig1: 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)
Mentions: Phylogenetic trees reconstructed from PCV2 ORF2 using NJ (Fig. 1a) and ML (Fig. 1b) methods displayed very similar topologies and four main clades were identified. These four clades substantially corresponded to the previously defined PCV2a, PCV2b, PCV2c and PCV2d genotypes. Very few strains (n = 7) showed contradictory clustering between PCV2a and PCV2d clades in the ORF2 trees (Additional file 1). The same clustering in four major groups was obtained rooting the tree using PCV1 sequences as outgroup (data not shown). Similarly, phylogenetic trees reconstructed using complete genome showed a similar topology even if with a closer relationship between remaining PCV2d and PCV2a strains (named according to ORF2 classification).Fig. 1

Bottom Line: The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro, PD, 35020, Italy. giovanni.franzo@unipd.it.

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.

No MeSH data available.


Related in: MedlinePlus