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Genetic diversity characterization of porcine reproductive and respiratory syndrome virus isolates in Romania, based on phylogenetic analysis.

Zaulet M, Gurau MR, Petrovan V, Buburuzan L - Int J Mol Sci (2012)

Bottom Line: One Romanian isolate (Rom3) was found in three of the four different investigated farms.The phylogenetic analysis revealed that the Romanian PRRSV nucleotide sequences clustered in three groups within the subtype 1 of the virus.The analysis of amino acid sequences evidenced for GP5 and N-nucleocapsid proteins confirmed that the Romanian virus belonged to type 1.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Bucharest, 91-95 Splaiul Independentei, 5th district Bucharest, Romania; E-Mails: zaulet_mihaela@yahoo.com (M.Z.); petrovan.vlad@gmail.com (V.P.).

ABSTRACT
Porcine reproductive and respiratory syndrome (PRRS) is a disease produced by the (PRRS) virus, characterized by endemic evolution in the majority of countries, which remains in actuality being a permanent threat to health and economic free farms, as well as for those infected. The aim of this study was to evaluate the genetic diversity of Romanian PRRSV isolates from the four most important pig farms in Romania by comparing the nucleotide sequences obtained for ORF5 and ORF7 with a wide range of sequences from GenBank belonging to the main types of PRRSV; the type 1. Eighteen different sequences were obtained for ORF5 gene and 10 for ORF7 gene. One Romanian isolate (Rom3) was found in three of the four different investigated farms. The phylogenetic analysis revealed that the Romanian PRRSV nucleotide sequences clustered in three groups within the subtype 1 of the virus. The analysis of amino acid sequences evidenced for GP5 and N-nucleocapsid proteins confirmed that the Romanian virus belonged to type 1.

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Related in: MedlinePlus

Maximum Likelihood tree based on ORF5 for the Romanian sequences, together with similar sequences from GenBank Database. The evolutionary distances were computed using the Tamura-Nei + G + I method. The bootstrap values adjacent to the main nodes represent the probabilities based on 1000 replicates.
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f2-ijms-13-12046: Maximum Likelihood tree based on ORF5 for the Romanian sequences, together with similar sequences from GenBank Database. The evolutionary distances were computed using the Tamura-Nei + G + I method. The bootstrap values adjacent to the main nodes represent the probabilities based on 1000 replicates.

Mentions: In 2008, Stadejek et al. proposed the division of the type 1 PRRSV genotype into three subtypes, based on ORF7 analysis [10]. Two phylogenetic trees were constructed, based on the complete sequences obtained for ORF5 gene and ORF7 gene of PRRSV Romanian isolates, together with a wide range of sequences selected from GenBank (Table 3). The evolutionary history was inferred using the Maximum Likelihood method [11]. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed [12]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura-Nei method [13] and are in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1) with Invariant. The differences in the composition bias among sequences were considered in evolutionary comparisons [14]. The analysis involved 72 nucleotide sequences for ORF5 and 99 nulcleotide sequences for ORF7. Codon positions included were 1st + 2nd + 3rd + Noncoding. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted in MEGA4 [15] (Figures 1 and 2). The type 1 PRRSV clade is clearly divided into three clusters corresponding to subtypes 1, 2 and 3 [10].


Genetic diversity characterization of porcine reproductive and respiratory syndrome virus isolates in Romania, based on phylogenetic analysis.

Zaulet M, Gurau MR, Petrovan V, Buburuzan L - Int J Mol Sci (2012)

Maximum Likelihood tree based on ORF5 for the Romanian sequences, together with similar sequences from GenBank Database. The evolutionary distances were computed using the Tamura-Nei + G + I method. The bootstrap values adjacent to the main nodes represent the probabilities based on 1000 replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3472791&req=5

f2-ijms-13-12046: Maximum Likelihood tree based on ORF5 for the Romanian sequences, together with similar sequences from GenBank Database. The evolutionary distances were computed using the Tamura-Nei + G + I method. The bootstrap values adjacent to the main nodes represent the probabilities based on 1000 replicates.
Mentions: In 2008, Stadejek et al. proposed the division of the type 1 PRRSV genotype into three subtypes, based on ORF7 analysis [10]. Two phylogenetic trees were constructed, based on the complete sequences obtained for ORF5 gene and ORF7 gene of PRRSV Romanian isolates, together with a wide range of sequences selected from GenBank (Table 3). The evolutionary history was inferred using the Maximum Likelihood method [11]. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed [12]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura-Nei method [13] and are in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1) with Invariant. The differences in the composition bias among sequences were considered in evolutionary comparisons [14]. The analysis involved 72 nucleotide sequences for ORF5 and 99 nulcleotide sequences for ORF7. Codon positions included were 1st + 2nd + 3rd + Noncoding. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted in MEGA4 [15] (Figures 1 and 2). The type 1 PRRSV clade is clearly divided into three clusters corresponding to subtypes 1, 2 and 3 [10].

Bottom Line: One Romanian isolate (Rom3) was found in three of the four different investigated farms.The phylogenetic analysis revealed that the Romanian PRRSV nucleotide sequences clustered in three groups within the subtype 1 of the virus.The analysis of amino acid sequences evidenced for GP5 and N-nucleocapsid proteins confirmed that the Romanian virus belonged to type 1.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Bucharest, 91-95 Splaiul Independentei, 5th district Bucharest, Romania; E-Mails: zaulet_mihaela@yahoo.com (M.Z.); petrovan.vlad@gmail.com (V.P.).

ABSTRACT
Porcine reproductive and respiratory syndrome (PRRS) is a disease produced by the (PRRS) virus, characterized by endemic evolution in the majority of countries, which remains in actuality being a permanent threat to health and economic free farms, as well as for those infected. The aim of this study was to evaluate the genetic diversity of Romanian PRRSV isolates from the four most important pig farms in Romania by comparing the nucleotide sequences obtained for ORF5 and ORF7 with a wide range of sequences from GenBank belonging to the main types of PRRSV; the type 1. Eighteen different sequences were obtained for ORF5 gene and 10 for ORF7 gene. One Romanian isolate (Rom3) was found in three of the four different investigated farms. The phylogenetic analysis revealed that the Romanian PRRSV nucleotide sequences clustered in three groups within the subtype 1 of the virus. The analysis of amino acid sequences evidenced for GP5 and N-nucleocapsid proteins confirmed that the Romanian virus belonged to type 1.

Show MeSH
Related in: MedlinePlus