Evolutionary Dynamics of a Highly Pathogenic Type 2 Porcine Reproductive and Respiratory Syndrome Virus: Analyses of Envelope Protein-Coding Genes

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) has long been an economically devastating swine viral disease. The recent emergence of a highly pathogenic type 2 PRRSV with high mobility and mortality in China, spreading in Vietnam, Laos, and Thailand has placed neighbouring countries at risk. This study applied a codon-based extension of the Bayesian relaxed clock model and the fixed effects maximum-likelihood method to investigate and compare the evolutionary dynamics of type 2 PRRSV for all of known structural envelope protein-coding genes. By comparing the highly pathogenic type 2 PRRSV clade against the typical type 2 PRRSV clade, this study demonstrated that the highly pathogenic clade evolved at high rates in all of the known structural genes but did not display rapid evolutionary dynamics compared with typical type 2 PRRSV. In contrast, the ORF3, ORF5 and ORF6 genes of the highly pathogenic clade evolved in a qualitatively different manner from the genes of the typical clade. At the population level, several codons of the sequence elements that were involved in viral neutralization, as well as codons that were associated with in vitro attenuation/over-attenuation, were predicted to be selected differentially between the typical clade and the highly pathogenic clade. The results of this study suggest that the multigenic factors of the envelope protein-coding genes contribute to diversifying the biological properties (virulence, antigenicity, etc.) of the highly pathogenic clade compared with the typical clade of type 2 PRRSV.

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

“…This result might be due to the high substitution rate detected in the ORF5 gene. In addition, the substitution rate in the ORF5 gene of the Vietnamese strains, which was 4459 × 10 −3 , was slightly faster than the substitution rates observed in common type II PRRSV strains [31] This supports our hypothesis. According to our analysis, the T MRCA of sub-lineage 5.1 strains was approximately 17 years ago, which is supported by serological evidence for anti-PRRSV antibodies in Vietnam during this time.…”

“…Nguyen et al [31] can not conclude the role of selected position in typical PRRSV and HP-PRRSV. In this study, our analysis of sites under selective pressure indicated that most of the sites undergoing positive selection (amino acids 33, 34, 35, 58, and 59) are located in ecto-domain 1, which contains the linear epitope, and an additional positive selection site is also predicted in ecto-domain 2 (amino acid 104).…”

“…The SRD06 codon-based model was used as a nucleotide substitution model [29, 31] and combined with (i) 5 molecular clock models (Strict clock, uncorrelated lognormal relaxed clock, uncorrelated exponential relaxed clock, random clock, and fixed local clock) and (ii) 7 demographic coalescent tree models (constant size, exponential growth, logistic growth, expansion growth, Bayesian skyline, extended Bayesian skyline plot, and Bayesian skygrid). In each analysis, the MCMC chain (50 million generations, sampling every 5000 stages) was performed using BEAST v1.8.2 software [9].…”

Establishment of MDCK Stable Cell Lines Expressing TMPRSS2 and MSPL and Their Applications in Propagating Influenza Vaccine Viruses in Absence of Exogenous Trypsin

“…Low-passage Madin-Darby canine kidney (MDCK) cells were maintained in DMEM containing 10% fetal bovine serum (FBS). Influenza viruses Re-5 [ 22 ], Re-6 [ 23 ], and Re-9 were provided by the National Animal Influenza Reference Laboratory. Viruses were generated with a “6 + 2” strategy: all three viruses contained 6 internal genes from A/Puerto Rico/8/1934 (H1N1).…”

NADC30-Like Porcine Reproductive and Respiratory Syndrome in China

“…The infection of pigs of all ages featured by high fever (41-42°C), high morbidity (50%-100%) and mortality (20%-100%) was initially addressed as “swine high fever disease (SHFD)” [ 24 , 25 ]. In the next couple of months, the disease spread to most provinces of China and some other Asian countries such as Mongolia, Vietnam, Thailand, India, and Laos [ 26 - 30 ]. The outbreak of HP-PRRSV resulted in a dramatic decline of pig stock and high prices of pork meat in China [ 31 ].…”