Background Porcine respiratory and reproductive symptoms (PRRS) virus is one of

Background Porcine respiratory and reproductive symptoms (PRRS) virus is one of the most economically significant pathogens in the Vietnamese swine market. effective strategies for PRRS vaccine development in Vietnam. Electronic supplementary material The online version AZ-960 of this article (doi:10.1186/s12917-016-0885-3) contains supplementary material, which is available to authorized users. family [5]. Its genome of approximately15 kb in size is structured into 10 open reading frames (ORFs) [24, 38]. Two large ORF1a and ORF1b genes encode non-structural proteins that play important tasks in viral replication and virulence [13, 18]. The additional ORFs encode for structural proteins that are necessary for production of infectious virions [44]. ORF5, which participates in many functional processes, including virion assembly [44], entry of the virus into the sponsor cell [7], and viral adaptation to the sponsor immune response [41], has been widely used in molecular development and phylogeny studies [30, 34, 35]. Evolutionary studies indicate that PRRSV diverged long before the first detected outbreaks of the disease. Evolutional analyses based on ORF5, as well as serological evidence, indicated that PRRSV type 2 first appeared around the 1980s [3, 35, 48]. In contrast, type 1 PRRSV originated approximately 100?years ago [30]. Further analysis of the whole PRRSV genome shows that the two types of PRRSV diverged from a common ancestor about 800?years ago [46]. Furthermore, genetic analyses indicate that the evolutionary trends, antigenic characteristics, and genetic diversity of PRRSV in different regions have distinct patterns [6, 11, 17, 32, 36, 40]. Thus far, type 2 PRRSV has been divided into 10 sub-lineages, including 9 old sub-lineages [34] occurring worldwide, and a new sub-lineage, which recently appeared in Thailand [40]. In Vietnam, several studies show that the circulating PRRSV strains belong to a highly pathogenic (HP) variant that recently emerged in China and South East Asian countries [12, 28]. However, few studies have focused on the evolutionary trends and characterization of PRRSV presenting in Vietnam. Thus, the aim of this study was to investigate the genetic diversity, selective pressure, and glycosylation patterns in GP5 of PRRSV strains that appeared in Vietnam during 2007C2015. Methods Sample collection For this study, we used 40 PRRS-positive sera or tissue samples, as confirmed by RT-PCR; the samples were collected from pigs in provinces in North Vietnam during 2011C2015. Total PRRSV RNA was extracted using TRIzol Reagent (Invitrogen, USA) according to the manufacturers instruction. Reverse transcription was performed using SuperScript? III First-Strand Synthesis SuperMix (Thermo Fisher, USA). ORF5 sequences were amplified by RT-PCR using previously AZ-960 described primers [12]. PCR products were directly sequenced (Macrogen, Seoul, Korea). The raw sequences were assembled and aligned using BioEditv7.2.5 [14] against the corresponding ORF5 sequences from GenBank to construct the complete ORF5 sequence. Additional 104 Vietnamese ORF5 reference sequences from field isolates collected from GenBank were also used in this study (Additional file 1: Table S1). Phylogenetic analysis and AZ-960 classification In order to identify the lineage classifications for all the PRRSV strains PPARgamma circulating in Vietnam, an ORF5-based phylogeny was reconstructed using a restricted parameter substitution model [35] with IQ-TREE software [27]. AZ-960 The total data set in this study contained 144 Vietnamese ORF5 gene sequences and 612 worldwide ORF5 research sequences for lineages 1 AZ-960 to 9 [35]. Bootstrap ideals were acquired using the ultrafast bootstrap approximation technique with 1000 replicates [25] (both applications can be found at Bayesian phylogenetic inference of ORF5 from Vietnamese strains The coalescent-based Bayesian Markov String Monte Carlo (MCMC) technique was used to research.