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. 2016 Nov 17;12(1):256.
doi: 10.1186/s12917-016-0885-3.

Molecular evolution of type 2 porcine reproductive and respiratory syndrome viruses circulating in Vietnam from 2007 to 2015

Hai Quynh Do  1 , Dinh Thau Trinh  1 , Thi Lan Nguyen  1 , Thi Thu Hang Vu  2 , Duc Duong Than  2 , Thi Van Lo  2 , Minjoo Yeom  3 , Daesub Song  3 , SeEun Choe  4 , Dong-Jun An  4 , Van Phan Le  5
Affiliations

Molecular evolution of type 2 porcine reproductive and respiratory syndrome viruses circulating in Vietnam from 2007 to 2015

Hai Quynh Do et al. BMC Vet Res. .

Abstract

Background: Porcine respiratory and reproductive syndrome (PRRS) virus is one of the most economically significant pathogens in the Vietnamese swine industry. ORF5, which participates in many functional processes, including virion assembly, entry of the virus into the host cell, and viral adaptation to the host immune response, has been widely used in molecular evolution and phylogeny studies. Knowing of molecular evolution of PRRSV fields strains might contribute to PRRS control in Vietnam.

Results: The results showed that phylogenetic analysis indicated that all strains belonged to sub-lineages 8.7 and 5.1. The nucleotide and amino acid identities between strains were 84.5-100% and 82-100%, respectively. Furthermore, the results revealed differences in nucleotide and amino acid identities between the 2 sub-lineage groups. N-glycosylation prediction identified 7 potential N-glycosylation sites and 11 glycotypes. Analyses of the GP5 sequences, revealed 7 sites under positive selective pressure and 25 under negative selective pressure.

Conclusions: Phylogenetic analysis based on ORF5 sequence indicated the diversity of PRRSV in Vietnam. Furthermore, the variance of N-glycosylation sites and position under selective pressure were demonstrated. This study expands existing knowledge on the genetic diversity and evolution of PRRSV in Vietnam and assists the effective strategies for PRRS vaccine development in Vietnam.

Keywords: ORF5; PRRSV; Phylogeny; Vietnam.

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Figures

Fig. 1
Fig. 1
Phylogenetic tree based on nucleotide sequence of the ORF5 gene of 144 PRRSV strains isolated in Vietnam during 2007–2015. The phylogenetic tree, generated via the MCMC method using BEAST v1.8.2 software, identified three different groups. The inserted histogram illustrates pairwise sequence comparisons of Vietnamese PRRSV type 2 strains. Three distinct nucleotide identity distribution peaks are shown. The time-scale (in years) represented in the tree is indicated by the scale bar
Fig. 2
Fig. 2
Amino acids under selective pressure. Upper rectangles indicate the ecto-domain 1, ecto-domain 2, and endo-domain, whereas lower rectangles indicate the signal peptide, trans-membrane 1, and trans-membrane 2 regions. The red lines and blue lines indicate sites under significant positive and negative selection, respectively. dN-dS represents the normalized dN–dS value according to the FEL method
See this image and copyright information in PMC

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