Phylogeny-Based Evolutionary, Demographical, and Geographical Dissection of North American Type 2 Porcine Reproductive and Respiratory Syndrome Viruses

Abstract

Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 in the United States and now occurs in most commercial swine industries throughout the world. In this study, we investigated the epidemiological and evolutionary behaviors of type 2 PRRSV. Based on phylogenetic analyses of 8,624 ORF5 sequences, we described a comprehensive picture of the diversity of type 2 PRRSVs and systematically classified all available sequences into lineages and sublineages, including a number of previously undescribed lineages. With the rapid growth of sequence deposition into the databases, it would be technically difficult for veterinary researchers to genotype their sequences by reanalyzing all sequences in the databases. To this end, a set of reference sequences was established based on our classification system, which represents the principal diversity of all available sequences and can readily be used for further genotyping studies. In addition, we further investigated the demographic histories of these lineages and sublineages by using Bayesian coalescence analyses, providing evolutionary insights into several important epidemiological events of type 2 PRRSV. Moreover, by using a phylogeographic approach, we were able to estimate the transmission frequencies between the pig-producing states in the United States and identified several states as the major sources of viral spread, i.e., "transmission centers." In summary, this study represents the most extensive phylogenetic analyses of type 2 PRRSV to date, providing a basis for future genotyping studies and dissecting the epidemiology of type 2 PRRSV from phylogenetic perspectives.Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important virus which infects swine and causes reproductive failure in sows and respiratory problems in growing pigs. As a member of the Arteriviridae family (15,47,59,66), PRRSV has a positive-sense RNA genome of approximately 15 kb that carries eight overlapping open reading frames (ORFs), designated ORFs 1a, 1b, and 2 to 7 (15, 47). Among these ORFs, ORF5, encoding the major envelope glycoprotein, is an ideal candidate for phylogenetic tree construction, because it exhibits marked genetic variation within its relatively short length.PRRSV can be classified into two genotypes: type 1 (EUlike), comprising mainly European strains and represented by the prototype strain Lelystad (75); and type 2 (NA-like), comprising mainly North American strains and represented by the prototype strain VR-2332 (14). Although clinical diseases are similar following infections with these viruses, they differ significantly in terms of antigenic properties (18, 74) and genetic content (42,48,51). This has sparked hot debates on the evolutionary history and divergence time of these two genotypes (24,25,29,58), but no substantial consensus has been reached.Classification and epidemiology of type 2 PRRSV. Clinical disease due to type 2 PRRSV was first recorded in 1987 in the United Stat...

Attenuation of Porcine Reproductive and Respiratory Syndrome Virus by Molecular Breeding of Virus Envelope Genes from Genetically Divergent Strains

“…BHK-21 and MARC-145 cells were grown at 37°C in Dulbecco's minimum essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics. The North American type 2 PRRSV was systematically classified into 9 genetically distinct lineages based on the ORF5 gene sequences of 8,624 PRRSV strains (16). To produce a chimeric virus by molecular breeding, a total of 7 genetically different strains of PRRSV, each representing a distinct genetic lineage or sublineage in the phylogenetic tree (16), i.e., MN184B (lineage 1), VR2385 (lineage 5.1), VR2430 (lineage 5.2), S132 (lineage 6), Chinese highly pathogenic strain JXA1 (lineage 8.7), FL-12 (lineage 8.9), and NADC20 (lineage 9), were selected for DNA shuffling in the study.…”

“…Phylogenetic tree based on the GP5 genes of selected PRRSV strains from different genetic lineages of type 2 PRRSV, as reported by Shi et al (16). The phylogenetic tree was constructed by using the neighbor-joining method with bootstraps in 1,000 replicates.…”

“…Within type 2, there are at least 9 distinct genetic lineages (16). The PRRSV genome consists of at least 9 overlapping open reading frames (ORFs) (17,18).…”

Immunological and biochemical characterisation of 7ap, a short protein translated from an alternative frame of ORF7 of PRRSV

“…The nucleotide identity between the two serotypes is only 55-70%. Type I PRRSV, also known as the European genotype, is prevalent in Europe (although it may also cause infections in Asia and North America), while type II, also known as the North American genotype, causes infections mainly in China and North America (Stadejek et al, 2006;Shi et al, 2010). The high genetic diversity of PRRSV hinders the development of protective measures against the virus (Mateu and Diaz, 2008).…”

Epidemiology and Evolutionary Characteristics of the Porcine Reproductive and Respiratory Syndrome Virus in China between 2006 and 2010

“…Furthermore, strains within each genotype vary considerably, particularly in the Nsp2 and ORF5 genes, with sequence differences of as high as 20% (15,24,27). Thus, ORF5 and Nsp2 have become the regions of choice for monitoring the evolution of PRRSV and for molecular epidemiology research on PRRSV (7,25,33).…”