ORF5-based evolutionary and epidemiological dynamics of the type 1 porcine reproductive and respiratory syndrome virus circulating in Korea

Dissecting Genetic Diversity and Evolutionary Trends of Chinese PRRSV-1 Based on Whole-Genome Analysis

Porcine reproductive and respiratory syndrome (PRRS) poses a serious threat to the Chinese swine industry. The etiological agent PRRSV can be classified as either PRRSV-1 or PRRSV-2. Recent studies have revealed an increase in the rates of PRRSV-1 detection and a wider PRRSV-1 distribution. However, the PRRSV-1 genome in China has yet to be fully characterized. In this study, 24 whole PRRSV-1 genomes from different swine farms were assembled and subjected to whole-genome analysis. A phylogenetic analysis based on the complete genome and ORF5 sequences revealed that the PRRSV-1 strains from China belonged to Western European Subtype I and could be classified into seven subgroups. Statistical analysis revealed that BJEU06-1-Like PRRSV is currently the predominant PRRSV-1 strain. Moreover, a similarity analysis showed low pairwise similarity between most PRRSV-1 genomes from different pig farms. Amino acid alignments of the Nsp2 gene revealed that the BJEU06-1-Like subgroup had five discontinued aa deletions (4 + 1). The new subgroup 1 had 11 continued aa deletions and an aa insertion, the new subgroup 2 had two discontinued aa deletions (1 + 1), and, except for in the case of HKEU16, the HKEU16-Like subgroup had five discontinuous aa deletions (1 + 4). Recombination analysis revealed that the BJEU06-1-Like and NMEU09-1-Like strains participated extensively in recent recombination events. The analysis of positive selection suggested that there were 15 positively selected codons in site model, and there were five sites under positive selection in the BJEU06-1-Like subgroup in the branch-site model. The mean rate and tMRCA for PRRSV-1 strains from China were 4.11 × 10-3 substitutions/site/year and 1,969.63, respectively. Thus, it is crucial to strengthen epidemiological surveys of PRRSV-1 in China, especially those monitoring BJEU06-1-Like PRRSV.

Genetic diversity of porcine reproductive and respiratory syndrome virus 1 in the United States of America from 2010 to 2018

Porcine reproductive and respiratory syndrome virus 1 (PRRSV-1) was first detected in the United States of America (USA) in 1999, several strains were also recognized soon later, and these isolates are typically called North American (NA) PRRSV-1. However, few reports have characterized PRRSV-1 viruses in the USA. We explored the genetic characteristics and diversity of PRRSV-1 viruses circulating in the USA. PRRSV-1 PCR-positive samples collected from seven states in 2010-2018 (n = 27) were subjected to next-generation sequencing. The 27 PRRSV-1 viruses had 88.4-91.3% nucleotide identity to the PRRSV-1 Lelystad-virus strain (the type 1 prototype strain) and 87.4-89.8% to the previously reported NA PRRSV-1 viruses. Individual proteins had several unique genetic characteristics and only one of the 27 tested samples had the characteristic 17-amino acid (aa) deletion in Nsp2, a genetic marker of NA PRRSV-1 viruses described previously. Fourteen isolates displayed a 3-aa C-terminal truncation in the highly conserved Nsp12 gene; 16 samples had a 21- or 18-aa C-terminal truncation in GP3 gene; and one was observed with a 1-aa deletion at the overlapping region of GP3 and GP4. In addition, the GP5 protein in most isolates, excluding one exception, demonstrated similar genetic variation as other reported NA PRRSV-1 isolates. All tested isolates clustered within subtype 1 together with other available NA PRRSV-1 viruses. Collectively, our results provide up-to-date information on PRRSV-1 viruses circulating in the USA in the past 9 years although the number of PRRSV-1 isolates included in this study is limited. These PRRSV-1 viruses have undergone gradual genetic variation and exhibited some previously undescribed genetic characteristics and diversity, which complicates the diagnosis and control of NA PRRSV-1.

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

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0885-3) contains supplementary material, which is available to authorized users.

Unusual severe cases of type 1 porcine reproductive and respiratory syndrome virus (PRRSV) infection in conventionally reared pigs in South Korea

BACKGROUND

Porcine reproductive and respiratory syndrome virus (PRRSV) causes a loss of approximately US$ 70 million every year to the South Korean pork industry. There are two distinct genotypes: European (type 1) and North American (type 2). In South Korea, type 1 and type 2 PRRSV are widely distributed and have evolved continuously since the infection was first described. Here, we present two field cases of type 1 PRRSV infection with unusually severe pathogenicity.

CASE PRESENTATION

The first case farm was a two-site production system comprising farrow-to-grower and grower-to-finish units and was historically free from PRRSV infections. The PRRSV vaccine had not been used in both units. In October 2014, pigs in the grower-to-finish unit experienced severe respiratory distress with the mortality rate reaching to 22%. Despite antibiotic treatment, clinical signs were still noticed in most pigs. The second case farm was also a two-site production system, but had two separate farrow-to-grower units (unit A and unit B). Historically, type 1 PRRSV was continuously present in unit A, but unit B was free from PRRSV. Thus, all grower pigs of unit B were vaccinated before being moved to the grower-to-finish unit. In November 2014, severe respiratory distress was seen in pigs of the grower-to-finish unit. Significant respiratory distress was observed in only the grower herd moved from unit B, and the mortality of those pigs was ~50%. However, no disease was shown in the grower pigs from unit A.

CONCLUSIONS

To our knowledge, the present study is the first observation of the cases of infection by highly pathogenic type 1 PRRSV in South Korea. The Korean type 1 PRRSV strains have undergone unique evolutionary dynamics for the last decade in this country. Although there are known to be three clusters of Korean type 1 PRRSV, their pathogenicity could not be categorized owing to their high level of genetic diversity. Therefore, further studies are needed to demonstrate the novel classification of Korean type 1 PRRSV strains according to their virulence factors.