Comparative genomic analysis of five pairs of virulent parental/attenuated vaccine strains of PRRSV

Construction and characterization of a gE/gI/TK-gene-deleted recombinant pseudorabies virus variant expressing the GP5 of the highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) and NADC30-like PRRSV

Porcine reproductive and respiratory syndrome (PRRS) and pseudorabies (PR) are still the major problems of the worldwide pork industry. Previous studies showed that PR virus (PRV) and PRRS virus (PRRSV) commercial vaccines available in China could not provide complete protection against PRV variants and currently prevalent PRRSV strains. In the present study, a recombinant pseudorabies virus rPRV-GP5/HP-GP5/NA expressing the GP5 of the highly pathogenic PRRSV (HP-PRRSV) and NADC30-like PRRSV was constructed by transfecting the transfer plasmid pG-GP5/HP-GP5/NA-EGFP into ST cells inoculated with gE/gI/TK-gene-deleted rPRV NY-gE-/gI-/TK- using homologous recombination and CRISPR/Cas9 gene editing technique. The recombinant virus rPRV-GP5/HP was also constructed. The expression of the GP5 protein was confirmed by Western blot and indirect immunofluorescence assay. These two viruses were similar to the parental virus rPRV-gE-/gI-/TK- in terms of growth curve, morphogenesis and virus plaque sizes, and proliferated in different cell types. The animal test results showed that ELISA antibodies against PRRSV could be detected in piglets immunized with these two recombinant viruses, and the antibody levels were slightly lower than those of commercial vaccines, but these two recombinant viruses elicited high levels of PRV ELISA antibody and neutralizing antibody, as is the case with commercial vaccine. These two recombinant viruses could provide some protection against virulent PRRSV and PRV, and could effectively inhibit virus proliferation in tissues. These findings provide insights that these two viruses need to be optimally engineered as promising bivalent vaccine candidates against PRV and PRRSV for the control and eradication of the variant PRV and currently prevalent PRRSV. IMPORTANT: Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine pseudorabies virus (PRV) can infect pigs of all ages with high mortality. Due to the appearance of the PRRSV variant (HP-PRRSV and NADC30-Like-PRRSV) and the outbreak of PRV variant in China, the current commercial vaccines available cannot provide complete protection against PRV variants and prevalent PRRSV strains, which causes a major economic loss in pig industry worldwide. Therefore, safe and effective new vaccines are urgently developed to simultaneously control and even eradicate the two viruses. This study intends to use the modified attenuated PRV strain as the carrier and the main antigen gene ORF5 of PRRSV as the exogenous gene to construct the recombinant virus strain, and further validate the protective effect of recombinant strains in vitro and in vivo against the challenge of PRRSV and PRV, which is expected to become a candidate vaccine strain.

Enhanced Porcine Reproductive and Respiratory Syndrome Virus Replication in Nsp4- or Nsp2-Overexpressed Marc-145 Cell Lines

Porcine reproductive and respiratory syndrome (PRRS) causes significant economic losses to the swine industry. The killed PRRSV vaccine has been reported to be safe and could elicit humoral responses. The killed PRRSV vaccine with a high viral antigen load combined with robust adjuvants could provide good protection against the infection. However, the high virus titer of PRRSV on the successive production cell lines is the prerequisite for this strategy. In this study, we explored PRRSV production in two recombinant Marc-145 cell lines expressing Nsp2 or Nsp4 through a lentivirus system. The results demonstrated that either Nsp2 or Nsp4 expressing Marc-145 cells did not affect cell morphology and growth kinetics but significantly enhanced PRRSV replication. Overall, our exploration may enable the production of high-yield PRRSV and offer a potential tool for developing safer and more effective PRRSV vaccines.

Characterization and Pathogenicity of a Porcine Reproductive and Respiratory Syndrome Virus Strain with Strong Homology to a HP-PRRSV Vaccine Strain in the Field

A PRRSV strain, PRRSV2/CN/FJLX06/2021, with strong homology to an MLV-like strain HeN1201 that evolved from the highly pathogenic PRRSV vaccine virus HuN4-F112, was isolated from a dying piglet in China. BLAST and phylogenetic analyses showed that PRRSV2/CN/FJLX06-2021 was most closely related to HeN1201 and HuN4 (the parental strain of MLV HuN4-F112) and clustered with Chinese HP-PRRSV strains in PRRSV-2 lineage 8.7. Importantly, 29 of the 39 characteristic amino acid mutations in the HuN4-F112 genome were found at the corresponding sites of PRRSV2/CN/FJLX06-2021. Animal studies showed that piglets infected with PRRSV2/CN/FJLX06-2021 had a persistent high fever, higher viremia, presence of interstitial pneumonia, and a higher mortality rate (40%) within 2 weeks than those vaccine-inoculated with HuN4-F112. Taken together, these data suggest that PRRSV2/CN/FJLX06-2021 is an MLV-like strain that has evolved from MLV HuN4-F112 and is highly pathogenic to piglets.

Attenuated Porcine Reproductive and Respiratory Syndrome Virus Regains Its Fatal Virulence by Serial Passaging in Pigs or Porcine Alveolar Macrophages To Increase Its Adaptation to Target Cells

Porcine reproductive and respiratory syndrome (PRRS) is a globally important disease threatening the pork industry, and modified live-virus (MLV) vaccines are widely used for its prevention. However, PRRS MLV shows high potential for reversion to virulence, leading to a major concern about its safety. Yet the revertant mechanism is still poorly understood. Here, attenuated virus JXwn06-P80, derived from the highly pathogenic PRRS virus (PRRSV) strain JXwn06 by serial passaging in MARC-145 cells, was reversely passaged in pigs through intranasal inoculation to mimic natural infection for 13 rounds, and the pathogenicity of viruses at the 3rd, 5th, 9th, 10th, and 11th passages was evaluated in pigs. From the 9th passage, the viruses caused mortality, which was related to their increased adaptability and replication efficiency (100 times higher than those of JXwn06-P80) in porcine alveolar macrophage (PAM) target cells. Similarly, JXwn06-P80 could also regain fatal virulence through reverse passage in PAMs for 25 or more passages, indicating that the increased adaptability in PAMs directly contributes to its regained fatal virulence. Next, the full-genome sequences were analyzed to explore the genetic evolutionary processes during adaptation both in vivo and in vitro. Finally, by a reverse genetic operation, four reverse mutation sites, NSP12-W121R, ORF2b (open reading frame 2b)-H9D, ORF5-H15L, and ORF5-V189L, were finally identified to partially contribute to the ability of the virus to adapt to PAMs, which may be related to virulence reversion during reverse passage. These findings provided direct scientific evidence for the virulence reversion of PRRS MLV and provided valuable clues for exploring its molecular mechanism. IMPORTANCE Reversion to virulence of a live attenuated vaccine is a public concern; however, direct scientific evidence is limited, and the mechanism is still poorly understood. Here, we present direct evidence for the reversion to virulence of PRRS MLV after serial passaging in pigs or target cells and found a correlation between virulence reversion and increased replication fitness in primary PAMs. The genetic evolutionary process during adaptation will provide valuable clues for exploring the molecular mechanism of PRRS MLV virulence reversion and offer important implications for understanding the reversion mechanisms of other vaccines.

Research Progress in Porcine Reproductive and Respiratory Syndrome Virus–Host Protein Interactions

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease caused by porcine reproductive and respiratory syndrome virus (PRRSV), which has been regarded as a persistent challenge for the pig industry in many countries. PRRSV is internalized into host cells by the interaction between PRRSV proteins and cellular receptors. When the virus invades the cells, the host antiviral immune system is quickly activated to suppress the replication of the viruses. To retain fitness and host adaptation, various viruses have evolved multiple elegant strategies to manipulate the host machine and circumvent against the host antiviral responses. Therefore, identification of virus–host interactions is critical for understanding the host defense against viral infections and the pathogenesis of the viral infectious diseases. Most viruses, including PRRSV, interact with host proteins during infection. On the one hand, such interaction promotes the virus from escaping the host immune system to complete its replication. On the other hand, the interactions regulate the host cell immune response to inhibit viral infections. As common antiviral drugs become increasingly inefficient under the pressure of viral selectivity, therapeutic agents targeting the intrinsic immune factors of the host protein are more promising because the host protein has a lower probability of mutation under drug-mediated selective pressure. This review elaborates on the virus–host interactions during PRRSV infection to summarize the pathogenic mechanisms of PRRSV, and we hope this can provide insights for designing effective vaccines or drugs to prevent and control the spread of PRRS.

A Novel Motif in the 3′-UTR of PRRSV-2 Is Critical for Viral Multiplication and Contributes to Enhanced Replication Ability of Highly Pathogenic or L1 PRRSV

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) with enhanced replication capability emerged in China and has become dominant epidemic strain since 2006. Up to now, the replication-regulated genes of PRRSV have not been fully clarified. Here, by swapping the genes or elements between HP-PRRSV and classical PRRSV based on infectious clones, NSP1, NSP2, NSP7, NSP9 and 3′-UTR are found to contribute to the high replication efficiency of HP-PRRSV. Further study revealed that mutations at positions 117th or 119th in the 3′-UTR are significantly related to replication efficiency, and the nucleotide at position 120th is critical for viral rescue. The motif composed by 117–120th nucleotides was quite conservative within each lineage of PRRSV; mutations in the motif of HP-PRRSV and currently epidemic lineage 1 (L1) PRRSV showed higher synthesis ability of viral negative genomic RNA, suggesting that those mutations were beneficial for viral replication. RNA structure analysis revealed that this motif maybe involved into a pseudoknot in the 3′-UTR. The results discovered a novel motif, 117–120th nucleotide in the 3′-UTR, that is critical for replication of PRRSV-2, and mutations in the motif contribute to the enhanced replicative ability of HP-PRRSV or L1 PRRSV. Our findings will help to understand the molecular basis of PRRSV replication and find the potential factors resulting in an epidemic strain of PRRSV.

Generation of a cold-adapted PRRSV with a nucleotide substitution in the ORF5 and numerous mutations in the hypervariable region of NSP2

A cold-adapted porcine reproductive and respiratory syndrome virus (CA-VR2332) was generated from the modified live virus strain VR2332. CA-VR2332 showed impaired growth when cultured at 37°C with numerous mutations (^S731^F, ^E819^D, ^G975^E, and ^D1014^N) in the hypervariable region of the NSP2, in which the mutation ^S731^F might play a vital role in viral replication at 30°C. Conserved amino acid sequences of the GP5 protein suggests that CA-VR2332 is a promising candidate for producing an effective vaccine against PRRSV infection. Further studies on replication and immunogenicity in vivo are required to evaluate the properties of CA-VR2332.

Porcine Reproductive and Respiratory Syndrome Virus: Immune Escape and Application of Reverse Genetics in Attenuated Live Vaccine Development

Porcine reproductive and respiratory syndrome virus (PRRSV), an RNA virus widely prevalent in pigs, results in significant economic losses worldwide. PRRSV can escape from the host immune response in several processes. Vaccines, including modified live vaccines and inactivated vaccines, are the best available countermeasures against PRRSV infection. However, challenges still exist as the vaccines are not able to induce broad protection. The reason lies in several facts, mainly the variability of PRRSV and the complexity of the interaction between PRRSV and host immune responses, and overcoming these obstacles will require more exploration. Many novel strategies have been proposed to construct more effective vaccines against this evolving and smart virus. In this review, we will describe the mechanisms of how PRRSV induces weak and delayed immune responses, the current vaccines of PRRSV, and the strategies to develop modified live vaccines using reverse genetics systems.

Phenotypic and Genetic Evolutions of a Porcine Reproductive and Respiratory Syndrome Modified Live Vaccine after Limited Passages in Pigs

Modified live vaccines (MLVs) against the porcine reproductive and respiratory syndrome virus (PRRSV) have been regularly associated with safety issues, such as reversion to virulence. In order to characterize the phenotypic and genetic evolution of the PRRSV-1 DV strain from the Porcilis^® PRRS MLV after limited passages in pigs, three in vivo experiments were performed. Trial#1 aimed (i) at studying transmission of the vaccine strain from vaccinated to unvaccinated contact pigs. Trial#2 and Trial#3 were designed (ii) to assess the reproducibility of Trial#1, using another vaccine batch, and (iii) to compare the virulence levels of two DV strains isolated from vaccinated (passage one) and diseased contact pigs (passage two) from Trial#1. DV strain isolates from vaccinated and contact pigs from Trial#1 and Trial#2 were submitted to Next-Generation Sequencing (NGS) full-genome sequencing. All contact animals from Trial#1 were infected and showed significantly increased viremia compared to vaccinated pigs, whereas no such change was observed during Trial#2. In Trial#3, viremia and transmission were higher for inoculated pigs with passage two of the DV strain, compared with passage one. In this study, we showed that the re-adaptation of the DV strain to pigs is associated with faster replication and increased transmission of the vaccine strain. Punctually, a decrease of attenuation of the DV vaccine strain associated with clinical signs and increased viremia may occur after limited passages in pigs. Furthermore, we identified three mutations linked to pig re-adaptation and five other mutations as potential virulence determinants.

The Function of the PRRSV-Host Interactions and Their Effects on Viral Replication and Propagation in Antiviral Strategies

Porcine reproductive and respiratory syndrome virus (PRRSV) affects the global swine industry and causes disastrous economic losses each year. The genome of PRRSV is an enveloped single-stranded positive-sense RNA of approximately 15 kb. The PRRSV replicates primarily in alveolar macrophages of pig lungs and lymphatic organs and causes reproductive problems in sows and respiratory symptoms in piglets. To date, studies on how PRRSV survives in the host, the host immune response against viral infections, and pathogenesis, have been reported. PRRSV vaccines have been developed, including inactive virus, modified live virus, attenuated live vaccine, DNA vaccine, and immune adjuvant vaccines. However, there are certain problems with the durability and effectiveness of the licensed vaccines. Moreover, the high variability and fast-evolving populations of this RNA virus challenge the design of PRRSV vaccines, and thus effective vaccines against PRRSV have not been developed successfully. As is well known, viruses interact with the host to escape the host’s immune response and then replicate and propagate in the host, which is the key to virus survival. Here, we review the complex network and the mechanism of PRRSV–host interactions in the processes of virus infection. It is critical to develop novel antiviral strategies against PRRSV by studying these host–virus interactions and structures to better understand the molecular mechanisms of PRRSV immune escape.

Porcine Reproductive and Respiratory Syndrome Modified Live Virus Vaccine: A "Leaky" Vaccine with Debatable Efficacy and Safety

Porcine reproductive and respiratory syndrome (PRRS) caused by the PRRS virus (PRRSV) is one of the most economically important diseases, that has significantly impacted the global pork industry for over three decades, since it was first recognized in the United States in the late 1980s. Attributed to the PRRSV extensive genetic and antigenic variation and rapid mutability and evolution, nearly worldwide epidemics have been sustained by a set of emerging and re-emerging virus strains. Since the first modified live virus (MLV) vaccine was commercially available, it has been widely used for more than 20 years, for preventing and controlling PRRS. On the one hand, MLV can induce a protective immune response against homologous viruses by lightening the clinical signs of pigs and reducing the virus transmission in the affected herd, as well as helping to cost-effectively increase the production performance on pig farms affected by heterologous viruses. On the other hand, MLV can still replicate in the host, inducing viremia and virus shedding, and it fails to confer sterilizing immunity against PRRSV infection, that may accelerate viral mutation or recombination to adapt the host and to escape from the immune response, raising the risk of reversion to virulence. The unsatisfied heterologous cross-protection and safety issue of MLV are two debatable characterizations, which raise the concerns that whether it is necessary or valuable to use this leaky vaccine to protect the field viruses with a high probability of being heterologous. To provide better insights into the immune protection and safety related to MLV, recent advances and opinions on PRRSV attenuation, protection efficacy, immunosuppression, recombination, and reversion to virulence are reviewed here, hoping to give a more comprehensive recognition on MLV and to motivate scientific inspiration on novel strategies and approaches of developing the next generation of PRRS vaccine.

A Triple Amino Acid Substitution at Position 88/94/95 in Glycoprotein GP2a of Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV1) Is Responsible for Adaptation to MARC-145 Cells

The Meat Animal Research Center-145 (MARC-145) cell line has been proven to be valuable for viral attenuation regarding vaccine development and production. Cell-adaptation is necessary for the efficient replication of porcine reproductive and respiratory syndrome virus (PRRSV) in these cells. Multiple sequence analysis revealed consistent amino acid substitutions in GP2a (V88F, M94I, F95L) of MARC-145 cell-adapted strains. To investigate the putative effect of these substitutions, mutations at either position 88, 94, 95, and their combinations were introduced into two PRRSV1 (13V091 and IVI-1173) infectious clones followed by the recovery of viable recombinants. When comparing the replication kinetics in MARC-145 cells, a strongly positive effect on the growth characteristics of the 13V091 strain (+2.1 log10) and the IVI-1173 strain (+1.7 log10) compared to wild-type (WT) virus was only observed upon triple amino acid substitution at positions 88 (V88F), 94 (M94I), and 95 (F95L) of GP2a, suggesting that the triple mutation is a determining factor in PRRSV1 adaptation to MARC-145 cells.

High reversion potential of a cell-adapted vaccine candidate against highly pathogenic porcine reproductive and respiratory syndrome

Modified live vaccine (MLV) based on highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) is prone to quick reversion of virulence upon circulating in host animals. The objective of this study was to evaluate the virulence reversion potential of HP-PRRSV MLV and to identify elements within the HP-PRRSV genome contributing to this phenomenon. A blind passage, cell-adaptation strategy was attempted to attenuate a HP-PRRSV strain JX143, which was isolated during the atypical PRRS outbreak in 2006. Two attenuated candidates passage 87 (JXM87) and passage 105 (JXM105) used as MLVs showed the best balance of safety and efficacy in 4 week-old piglets (unpublished data). Two studies were performed during which the candidates were assessed for reversion to virulence through five back passages in susceptible piglets (21 ± 3 days of age). Both study results showed increase in clinical signs, pyrexia and lung lesions as well as decreased average daily weight gain as of passage 3 in susceptible pigs clearly, and it indicated that both candidates regained virulence, irrespective of the passage level. Increase in respective parameters was accompanied by increase in viremia in piglets: JXM87 virus titer increased from Passage 1 (P1) 4.40 Lg TCID₅₀/mL to P4 5.75 Lg TCID₅₀/mL, and JXM105 virus titer increased from P1 3.78 Lg TCID₅₀/mL to P4 6.42 Lg TCID₅₀/mL. Next generation sequencing (NGS) was performed on clinical samples (serum, lung tissue) from P4 animals. Sequence analysis comparing P4 materials with their parental strains revealed 10 amino acid mutations in 4 proteins for JXM87 and 14 amino acid mutations in 9 proteins for JXM105, respectively. Interestingly, five amino acid mutations were identical for the two candidates, which were located in nsp1β, GP5a and nsp10 coding regions, suggesting nsp1β, GP5a and nsp10 could contribute to virulence in HP-PRRSV.

Efficacy of a modified-live virus vaccine in pigs experimentally infected with a highly pathogenic porcine reproductive and respiratory syndrome virus type 1 (HP-PRRSV-1)

PRRS is one of the main viral diseases in pig production, causing huge economic losses to the swine industry worldwide. The virus shows an intrinsic genomic instability and is able to change continuously, with the emergence of new strains, with different pathogenicity patterns. Commercially available vaccines only partially prevent or counteract the disease and the correlated losses. Moreover, the emergence of highly virulent and pathogenetic isolates represents a particular concern for PRRS control and diagnosis. The purpose of this study was to evaluate the efficacy of a modified-live virus (MLV) PRRSV-1 commercial vaccine in reducing the severity of the disease and minimizing losses upon challenge with a highly pathogenic PRRSV-1.1 Italian isolate (PRRSV-1_PR40/2014). Four different groups were compared: C (unvaccinated-uninfected), VAC-C (vaccinated-uninfected), PR40 (unvaccinated-infected) and VAC-PR40 (vaccinated-infected). The tested vaccine provided partial, but statistically significant clinical, virological and pathological protection after challenge under experimental conditions. In particular, vaccinated animals showed reduced viremia in terms of duration and magnitude, reduced respiratory signs and pathological lesions. Vaccination was able to trigger adaptive immunity able to respond efficiently also against the HP PR40 isolate. Vaccinated animals showed higher average daily weight gain, even during the viremic period, compared to non-vaccinated challenged pigs.

Evolutionary analysis of six isolates of porcine reproductive and respiratory syndrome virus from a single pig farm: MLV-evolved and recombinant viruses

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens with economic significance for swine industry globally. The virus is characterized by its genetically extraordinary variability and diversified strains due to high mutation frequency and recombination rates. In the current study, we analyzed the genomes of six PRRSV strains isolated in different years from a single pig farm practicing HP-PRRSV-derived modified-live virus (MLV) vaccination in China, and in detail dissected their evolutionary relationship to MLV vaccines. The results show that all the six isolates belong to type 2 PRRSV, and are clustered into two lineages (lineage 1 and 8) based on their ORF5 genes. Further comparative analyses of genomes and the characteristic amino acid sites show that both HeN1201 and HeN1502 are MLV-like strains evolved from the MLV HuN4-F112. Recombination analyses reveal that HeN1301 is a recombinant virus emerged from the recombination event between two MLV-like strains evolved from the MLV TJM-F92 and HuN4-F112, and HeN1501 is a recombinant virus between two MLV-like strains evolved from HuN4-F112, while HeN1401 and HeN1601 are recombinant viruses derived from the recombination between NADC30-like and a MLV-like strain evolved from TJM-F92. Our findings provide more evidence for the fact that MLV-derived from the Chinese HP-PRRSV can be evolved and reversed in the field and enrich the data about the recombination between the viruses evolved from MLV and newly infected strain of PRRSV. This study stresses the necessity for pig producers to restrain the use of HP-PRRSV MLV vaccines in the field.

Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus in southern China from 2007 to 2014

Porcine reproductive and respiratory syndrome virus (PRRSV) has a high degree of genetic variation. In this study, we characterized the genetic variation and evolutionary relationships among circulating PRRSV strains in southern China. We analyzed 29 NSP2 strains and 150 ORF5 strains from clinical samples collected in southern China during 2007–2014. The alignment results showed that the nucleotide identity similarities of the two genes among these strains were 80.5%–99.7% and 80.9%–100%, respectively. Phylogenetic analysis based on the NSP2 gene showed that highly pathogenic (HP)-PRRSV was still the dominant virus in southern China from 2013 to 2014. Compared with reference strains CH-1a and VR-2332, the field strain 131101-GD-SHC, which shared high homology with JXA1-P170, had a novel 12 amino acid deletion at position 499–510. Phylogenetic analysis based on the ORF5 gene showed that HP-PRRSV, VR2332-like strains, and QYYZ-like strains were simultaneously circulating in southern China from 2007 to 2014, suggesting that, in recent years, the type 2 PRRSV was more diverse in southern China. In conclusion, mutations in the decoy epitope and primary neutralizing epitope could be markers of viral evolution and used to study evolutionary relationships among PRRSV strains in China.

Development of a broadly protective modified-live virus vaccine candidate against porcine reproductive and respiratory syndrome virus

Modified-live virus (MLV) vaccines are widely used to protect pigs against porcine reproductive and respiratory syndrome virus (PRRSV). However, current MLV vaccines do not confer adequate levels of heterologous protection, presumably due to the substantial genetic diversity of PRRSV isolates circulating in the field. To overcome this genetic variation challenge, we recently generated a synthetic PRRSV strain containing a consensus genomic sequence of PRRSV-2. We demonstrated that our synthetic PRRSV strain confers unprecedented levels of heterologous protection. However, the synthetic PRRSV strain at passage 1 (hereafter designated CON-P1) is highly virulent and therefore, is not suitable to be used as a vaccine in pigs. In the present study, we attenuated CON-P1 by continuously passaging the virus in MARC-145 cells, a non-natural host cell line. Using a young pig model, we demonstrated that the synthetic virus at passages 90 and 122 (designated as CON-P90 and CON-P122, respectively) were fully attenuated, as evidenced by the significantly reduced viral loads in serum and tissues and the absence of lung lesion in the infected pigs. Most importantly, CON-P90 confers similar levels of heterologous protection as its parental strain CON-P1. Taken together, the results indicate that CON-P90 is an excellent candidate for the formulation of next generation of PRRSV MLV vaccines with improved levels of heterologous protection.

Porcine reproductive and respiratory disease virus: Evolution and recombination yields distinct ORF5 RFLP 1-7-4 viruses with individual pathogenicity

Recent cases of porcine reproductive and respiratory syndrome virus (PRRSV) infection in United States swine-herds have been associated with high mortality in piglets and severe morbidity in sows. Analysis of the ORF5 gene from such clinical cases revealed a unique restriction fragment polymorphism (RFLP) of 1-7-4. The genome diversity of seventeen of these viruses (81.4% to 99.8% identical; collected 2013-2015) and the pathogenicity of 4 representative viruses were compared to that of SDSU73, a known moderately virulent strain. Recombination analyses revealed genomic breakpoints in structural and nonstructural regions of the genomes with evidence for recombination events between lineages. Pathogenicity varied between the isolates and the patterns were not consistent. IA/2014/NADC34, IA/2013/ISU-1 and IN/2014/ISU-5 caused more severe disease, and IA/2014/ISU-2 did not cause pyrexia and had little effect on pig growth. ORF5 RFLP genotyping was ineffectual in providing insight into isolate pathogenicity and that other parameters of virulence remain to be identified.

Pathogenesis and control of the Chinese highly pathogenic porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) has remained a major threat to the worldwide swine industry ever since its first discovery in the early 1990s. Under the selective pressures in the field, this positive-stranded RNA virus undergoes rapid genetic evolution that eventually leads to emergence in 2006 of the devastating Chinese highly pathogenic PRRSV (HP-PRRSV). The atypical nature of HP-PRRSV has caused colossal economic losses to the swine producers in China and the surrounding countries. In this review, we summarize the recent advances in our understanding of the pathogenesis, evolution and ongoing field practices on the control of this troubling virus in China.

A single amino acid substitution alter antigenicity of Glycosylated protein 4 of HP-PRRSV

Background

Porcine reproductive and respiratory syndrome (PRRS) is an important pig endemic disease in pork-producing countries worldwide. The etiology, porcine reproductive and respiratory syndrome virus (PRRSV), is characterized by fast antigen variability. Glycosylated protein 4 (GP4) is a minor protein in PRRSV virion, but contributes to induce protective immune responses. However, the antigenic characterization of PRRSV GP4 and the role of the mutations in this protein in PRRSV evolution are not clear.

Methods

Peptides chip scanning and peptide based ELISA was used to analyze the antigenic characterization of HP-PRRSV GP4. A total of 142 peptides printed on a chip were used to reveal the antigen reaction characteristics of the HP-PRRSV. The reactions of these peptides with HP-PRRSV-specific pig serum were scanned and quantified using the software PepSlide® Analyzer by fluorescence intensity. The active reaction regions (AR) were identified based on the scanning results and then the amino acids (aa) sequences of AR(s) is aligned among PRRSV strains for further identify the key aa site(s) impact the antigenicity of the protein. Peptide based ELISA is then reacted with PRRSV positive sera derived from pig inoculated with different PRRSV strains for further analysis the role of specific amino acid in AR.

Results

The intensity plot was used to show the reactions of the peptides with PRRSV serum and it showed that enormously different response happened to various parts of GP4. The highest reaction intensity value reached 6401.5 against one peptide with the sequence DIKTNTTAASDFVVL. An AR from S29 to G56 was identified. Sequence alignment revealed various mutations in site 43 and possibly played an important role in this AR. Peptides ELISA reaction with sera from pigs inoculated with different PRRSV strain revealed that the change of aa in site 43 reduced the reaction of the peptide with PRRSV positive sera derived from pigs inoculated with the peptide related PRRSV strains.

Conclusion

In this study, one AR covering S29 to G56 was identified in GP4. The aa in site 43 play an important role in determining the antigenic character of GP4. The continual mutations (S → G → D → N) occurred in this site alter the antigenicity of PRRSV GP4.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0586-3) contains supplementary material, which is available to authorized users.

Pathogenicity and genetic characteristics associated with cell adaptation of a virulent porcine reproductive and respiratory syndrome virus nsp2 DEL strain CA-2

Porcine reproductive and respiratory syndrome virus (PRRSV) is the most common and world-widespread viral pathogen of swine. We previously reported genomic sequences and pathogenicity of type 2 Korean PRRSV strains belonging to the virulent lineage 1 family, which contain remarkable amino acid deletions in nonstructural protein 2 (nsp2 DEL) compared to VR-2332. Here, a virulent type 2 Korean PRRSV nsp2 DEL strain, CA-2, was serially propagated in MARC-145 cells for up to 100 passages (CA-2-P100). As the passage number increased, the phenotypic characteristics of cell-adapted CA-2 strains were altered, in terms of higher viral titers and larger plaque sizes compared to the parental virus. Pro-inflammatory cytokine genes, including TNF-α, IL-8, MCP-1, and MCP-2, were found to be significantly down-regulated in PAM cells with the CA-2-P100 strain compared to its parental nsp2 DEL virus. Animal inoculation studies demonstrated that the virulence of CA-2-P100 was reduced significantly, with showing normal weight gain, body temperatures, and lung lesions comparable to the control group. Furthermore, high-passage CA-2-P100 showed declined and transient viremia kinetics, as well as delayed and low PRRSV-specific antibody responses in infected pigs. In addition, we determined whole genome sequences of low to high-passage derivatives of CA-2. The nsp2 DEL pattern was conserved for 100 passages, whereas no other deletions or insertions arose during the cell adaptation process. However, CA-2-P100 possessed 54 random nucleotide substitutions that resulted in 27 amino acid changes distributed throughout the genome, suggesting that these genetic drifts provide a possible molecular basis correlated with the cell-adapted features in vitro and the attenuated phenotype in vivo. Taken together, our data indicate that the cell-attenuated CA-2-P100 strain is a promising candidate for developing a safe and effective live PRRSV vaccine.

Challenges in Veterinary Vaccine Development and Immunization

In approaching the development of a veterinary vaccine, researchers must choose from a bewildering array of options that can be combined to enhance benefit. The choice and combination of options is not just driven by efficacy, but also consideration of the cost, practicality, and challenges faced in licensing the product. In this review we set out the different choices faced by veterinary vaccine developers, highlight some issues, and propose some pressing needs to be addressed.

Comparative Genomic Analysis of Classical and Variant Virulent Parental/Attenuated Strains of Porcine Epidemic Diarrhea Virus

Since 2010, the variant porcine epidemic diarrhea virus (PEDV) has been the etiological agent responsible for the outbreak of porcine epidemic diarrhea (PED) worldwide. In this study, a variant PEDV strain YN1 was isolated, serially propagated on the Vero cells and was characterized for 200 passages. To better elucidate the molecular basis of Vero cell adaptation of variant PEDV strains, we sequenced, compared, and analyzed the full-genome sequences of parental YN1 and passages 15, 30, 60, 90, 144, and 200. The results showed that the variations increased with the viral passage. The nucleotides sequences of non-structural protein (NSP)2, NSP4-7, NSP10, NSP12 and NSP13 genes did not change during the Vero cell adaptation process. After comparison of the variation characteristic of classical, variant virulent/attenuated strains, it was found that attenuation of PEDV virus was associated with 9−26 amino acid (aa) changes in open reading frames (ORF) 1a/b and S protein, early termination in ORF3, 1–3 aa changes in E, M and N protein and some nucleotide sequences’ synonymous mutations. The aa deletion at about 144 aa of S protein could be the attenuation marker for the PEDV. The pig study showed that the early termination in ORF3 was more important for virus cell adaptation than virus attenuation.

Nsp9 and Nsp10 contribute to the fatal virulence of highly pathogenic porcine reproductive and respiratory syndrome virus emerging in China

Atypical porcine reproductive and respiratory syndrome (PRRS), which is caused by the Chinese highly pathogenic PRRS virus (HP-PRRSV), has resulted in large economic loss to the swine industry since its outbreak in 2006. However, to date, the region(s) within the viral genome that are related to the fatal virulence of HP-PRRSV remain unknown. In the present study, we generated a series of full-length infectious cDNA clones with swapped coding regions between the highly pathogenic RvJXwn and low pathogenic RvHB-1/3.9. Next, the in vitro and in vivo replication and pathogenicity for piglets of the rescued chimeric viruses were systematically analyzed and compared with their backbone viruses. First, we swapped the regions including the 5′UTR+ORF1a, ORF1b, and structural proteins (SPs)-coding region between the two viruses and demonstrated that the nonstructural protein-coding region, ORF1b, is directly related to the fatal virulence and increased replication efficiency of HP-PRRSV both in vitro and in vivo. Furthermore, we substituted the nonstructural protein (Nsp) 9-, Nsp10-, Nsp11- and Nsp12-coding regions separately; or Nsp9- and Nsp10-coding regions together; or Nsp9-, Nsp10- and Nsp11-coding regions simultaneously between the two viruses. Our results indicated that the HP-PRRSV Nsp9- and Nsp10-coding regions together are closely related to the replication efficiency in vitro and in vivo and are related to the increased pathogenicity and fatal virulence for piglets. Our findings suggest that Nsp9 and Nsp10 together contribute to the fatal virulence of HP-PRRSV emerging in China, helping to elucidate the pathogenesis of this virus.

PRRS is a considerable threat to the pig industry worldwide. A large-scale atypical PRRS caused by highly pathogenic PRRSV (HP-PRRSV) that emerged in 2006 has resulted in considerable economic loss to Chinese pig production. The disease is characterized by a high body temperature (41°C–42°C), morbidity and by mortality of the affected pigs. Although the genomic marker, the 30-amino-acid deletion in its Nsp2-coding region has been previously verified to have no relation to its increased pathogenicity, the genomic region(s) associated with the fatal virulence of HP-PRRSV remain unclear. A series of chimeric viruses with swapped coding regions between HP- and LP-PRRSV were constructed, and their growth abilities and pathogenicities in piglets were analyzed. Our results demonstrated that Nsp9 and Nsp10 together contribute to the replication efficiency and the fatal virulence of HP-PRRSV for piglets. Our finding is not only the first unambiguous illumination concerning the key virulence determinant of Chinese HP-PRRSV but it also provides a novel insight for understanding the molecular pathogenesis of this virus and for designing new drugs and vaccines against PRRSV infection in the future.

Attenuation and immunogenicity of a live high pathogenic PRRSV vaccine candidate with a 32-amino acid deletion in the nsp2 protein

A porcine reproductive and respiratory syndrome virus (PRRSV) QY1 was serially passed on Marc-145 cells. Virulence of different intermediate derivatives of QY1 (P5, P60, P80, and P100) were determined. The study found that QY1 had been gradually attenuated during the in vitro process. Pathogenicity study showed that pigs inoculated with QY1 P100 and P80 did not develop any significant PRRS clinic symptoms. However, mild-to-moderate clinical signs and acute HP-PRRSV symptoms of infection were observed in pigs inoculated with QY1 P60 and P5, respectively. Furthermore, we determined the whole genome sequences of these four intermediate viruses. The results showed that after 100 passages, compared to QY1 P5, a total of 32 amino acid mutations were found. Moreover, there were one nucleotide deletion and a unique 34-amino acid deletion found at 5′UTR and in nsp2 gene during the attenuation process, respectively. Such deletions were genetically stable in vivo. Following PRRSV experimental challenge, pigs inoculated with a single dose of QY1 P100 developed no significant clinic symptoms and well tolerated lethal challenge, while QY1 P80 group still developed mild fever in the clinic trial after challenge. Thus, we concluded that QY1 P100 was a promising and highly attenuated PRRSV vaccine candidate.

A new porcine reproductive and respiratory syndrome virus strain with highly conserved molecular characteristics in its parental and attenuated strains

Porcine reproductive and respiratory syndrome virus (PRRSV) causes substantial economic losses to many swine-producing regions. In this study, PRRSV strain NT0801-F80 was derived from its parental isolate NT0801 by 80 passages in Marc-145 cells. Experimental infection of piglets clearly demonstrated that strain NT0801-F80 is less virulent than NT0801. However, whole genome sequencing showed that the genomes of the parental and attenuated strains are highly conserved compared with those of four other pairs of virulent parental/attenuated vaccine strains (VR2332 and RespPRRS MLV, JA142 and Ingelvac(®) ATP MLV, CH-1a and CH-1R, and JXA1 and JXAR). The attenuated strain NT0801-F80 has only 21 nucleotide changes, producing only 14 amino acid changes in NSP2, GP2, GP3, and GP5, compared with those aa sequences of the virulent parental strain. These mutated aa in the attenuated virus may be involved in virulence. These data provide valuable information on the attenuation mechanism of PRRSV that should be useful in future research.

The vOTU domain of highly-pathogenic porcine reproductive and respiratory syndrome virus displays a differential substrate preference

Arterivirus genus member Porcine reproductive and respiratory syndrome virus (PRRSV) causes an economically devastating disease, recently exacerbated by the emergence of highly pathogenic strains (HP-PRRSV). Within the nonstructural protein 2 of PRRSV is a deubiquitinating enzyme domain belonging to the viral ovarian tumor (vOTU) protease superfamily. vOTUs, which can greatly vary in their preference for their host ubiquitin (Ub) and Ub-like substrates such as interferon stimulated gene 15 (ISG15), have been implicated as a potential virulence factor. Since various strains of PRRSV have large variations in virulence, the specificity of vOTUs from two PRRSV strains of varying virulence were determined. While both vOTUs showed de-ubiquitinating activity and markedly low deISGylating activity, HP-PRRSV demonstrated a strong preference for lysine 63-linked poly-Ubiquitin, tied to innate immune response regulation. This represents the first report of biochemical activity unique to HP-PRRSV that has implications for a potential increase in immunosuppression and virulence.

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

This study applied a number of advanced genetic analysis tools to investigate the evolutionary trajectories and epidemiological dynamics of Korean type 1 PRRSV based on variations in the ORF5 gene over a long-term period from 2005 to 2013. Maximum likelihood phylogenetic analysis performed on large, worldwide ORF5 sequences (n=1127) strongly suggested no further introduction of genetically novel type 1 PRRSV into Korean pig farms, with the identification of only two clusters (I and II) in circulation to date. Using a codon-based extension of the Bayesian relaxed clock model, this study was able to distinguish between synonymous and non-synonymous substitutions and demonstrated that, while the absolute rates of synonymous substitution (E[S]) were similar between clusters I and II, the absolute rate of non-synonymous substitution (E[N]) was significantly different between the clusters. Cluster I was found to have an elevated E[N]/E[S] ratio relative to cluster II on the internal branches, compared to the external branches. Additionally, many fewer sites were predicted under diversifying selection in cluster II than in cluster I. Utilizing the Bayesian skyride method and the novel Bayesian birth-death skyline plot method, this study provided insights into the epidemiological dynamics of type 1 PRRSV in Korea by revealing that each cluster experienced a unique epidemic growth and by uncovering correlations between the effective population size and effective reproductive number.

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

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.

Two natural recombinant highly pathogenic porcine reproductive and respiratory syndrome viruses with different pathogenicities

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) is a variant of type 2 PRRSV with high virulence. Genetic and pathogenic characteristics of HP-PRRSV vary rapidly during the evolution. In this study, we determined the complete genome of a HP-PRRSV isolate designated 10FUJ-2, which shared 98.34 % nucleotide identity with HP-PRRSV reference strain JXA1. Genomic analyses by phylogenetic tree and recombination detection program confirmed 10FUJ-2 to be a recombinant with 09JS and JXA1 as potential parental viruses. Furthermore, we identified that 10FUJ-2 has high virulence as similar as the parental viruses by animal challenge study. In addition, we found that SY0909 was also a recombination virus probably from JXA1 and NT0801, which has been reported to be low pathogenic. Recombination analysis also revealed that Glycoproteins GP2 to GP5 of HP-PRRSV might contain major virulence determinants. Identification of two natural recombinants with different virulence supports the notion that recombination is a driving force affecting HP-PRRSV pathogenicity and a common mechanism contributing to HP-PRRSV evolution.

Genomic sequencing reveals mutations potentially related to the overattenuation of a highly pathogenic porcine reproductive and respiratory syndrome virus

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to evolve when serially passaged in Marc-145 cells. In this study, we analyzed the genomic and antigenic variants of HP-PRRSV strain JXA1 during in vitro passage. Protective efficacies of JXA1 from passages 100, 110, 120, 140, and 170 against the high-virulence parental virus were evaluated by inoculating pigs with each of these viruses and then challenging with JXA1 from passage 5 at 28 days postimmunization. We found that the antigenicities of JXA1 from passages after 110 were significantly reduced. Inoculation with JXA1 from passages after 110 provided only insufficient protection against the parental strain challenge, indicating that the immunogenicity of JXA1 is significantly decreased when it is in vitro passaged for 110 times and more. To identify the genomic variants that emerged during the overattenuation, eight complete genomes of highly passaged JXA1 were sequenced. One guanine deletion in the 5' untranslated region (UTR), two nucleotide substitutions in the 3' UTR, and 65 amino acid mutations in nonstructural and structural proteins that accompanied with the attenuation and overattenuation were determined. Genomic sequencing of in vitro serially passaged HP-PRRSV first identified the mutations potentially correlated with the overattenuation of a HP-PRRSV strain. These results facilitate the research aimed at elucidating the mechanisms for PRRSV genomic and antigenic changes and may also contribute to developing a safe and effective PRRSV vaccine.

Genomic sequence and virulence comparison of four Type 2 porcine reproductive and respiratory syndrome virus strains

Porcine reproductive and respiratory syndrome virus (PRRSV) is a ubiquitous and costly virus that exhibits substantial sequence and virulence disparity among diverse isolates. In this study, we compared the whole genomic sequence and virulence of 4 Type 2 PRRSV isolates. Among the 4 isolates, SDSU73, MN184, and NADC30 were all clearly more virulent than NADC31, and among the 3 more virulent isolates, there were subtle differences based on viral replication, lung lesions, lymphadenopathy, febrile response, decreased weight gains, and cytokine responses in the lung. Lesions consistent with bacterial bronchopneumonia were present to varying degrees in pigs infected with PRRSV, and bacteria typically associated with the porcine respiratory disease complex were isolated from the lung of these pigs. Genomic sequence evaluation indicates that SDSU73 is most similar to the nucleotide sequence of JA142, the parental strain of Ingelvac(®) PRRS ATP, while the nucleotide sequences of NADC30 and NADC31 are more similar to strain MN184. Both the NADC30 and NADC31 isolates of PRRSV, isolated in 2008, maintain the nonstructural protein 2 (nsp2) deletion seen in MN184 that was isolated in 2001, but NADC31 has two additional 15 and 36 nucleotide deletions, and these strains are 8-14% different on a nucleotide basis from the MN184 strain. These results indicate that newer U.S. Type 2 strains still exhibit variability in sequence and pathogenicity and although PRRSV strains appear to be reducing the size of the nsp2 over time, this does not necessarily mean that the strain is more virulent.

Effect of porcine circovirus type 2a or 2b on infection kinetics and pathogenicity of two genetically divergent strains of porcine reproductive and respiratory syndrome virus in the conventional pig model

To determine differences in infection kinetics of two temporally and genetically different type 2 porcine reproductive and respiratory syndrome virus (PRRSV) isolates in vivo with and without concurrent porcine circovirus (PCV) type 2a or 2b infection, 62 pigs were randomly assigned to one of seven groups: negative controls (n=8); pigs coinfected with a 1992 PRRSV strain (VR-2385) and PCV2a (CoI-92-2a; n=9), pigs coinfected with VR-2385 and PCV2b (CoI-92-2b; n=9), pigs coinfected with a 2006 PRRSV strain (NC16845b) and PCV2a (CoI-06-2a; n=9), pigs coinfected with NC16845b and PCV2b (CoI-06-2b; n=9), pigs infected with VR-2385 (n=9), and pigs infected with NC16845b (n=9). Blood samples were collected before inoculation and at day post-inoculation (dpi) 3, 6, 9 and 12 and tested for the presence of PRRSV antibody and RNA, PCV2 antibody and DNA, complete blood counts, and interferon gamma (IFN-γ) levels. Regardless of concurrent PCV2 infection, VR-2385 initially replicated at higher levels and reached peak replication levels at dpi 6. Pigs infected with VR-2385 had significantly higher amounts of viral RNA in serum on both dpi 3 and dpi 6, compared to pigs infected with NC16845b. The peak of NC16845b virus replication occurred between dpi 9 and dpi 12 and was associated with a delayed anti-PRRSV antibody response in these pigs. PCV2 coinfection resulted in significantly more severe macroscopic and microscopic lung lesions and a stronger anti-PRRSV IgG response compared to pigs infected with PRRSV alone. This work further emphasizes in vivo replication differences among PRRSV strains and the importance of coinfecting pathogens.

Mutations in the genome of the highly pathogenic porcine reproductive and respiratory syndrome virus potentially related to attenuation

A live-attenuated highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) virus (HP-PRRSV) TJM vaccine strain was derived from the HP-PRRSV TJ strain by passage 92 times in the African green monkey kidney epithelial cell line Marc-145. We found that the virulence of the TJ strain to piglets was decreased greatly from passage 19. To identify mutations associated with attenuation of the TJM vaccine strain, we determined the nucleotide changes that arose during Marc-145 passage of the HP-PRRSV TJ virus. The TJM strain contains a 360 nucleotide (120 amino acids) deletion and a 118 nucleotide mutation that resulted in 48 amino acid changes. Analysis of the complete nucleotide sequences of intermediate passage-level viruses F19, F46 and F78 showed that 31 (64.6%) of the 48 amino acid mutations occurred in F19, 7 (14.6%) occurred in F46, 7 (14.6%) occurred in F78 and 3 (6.3%) occurred in F92. The 120 amino acid deletion occurred from F19 to TJM. Therefore, we hypothesized that the 31 amino acid mutations distributed in nsp1β, nsp2-nsp5, nsp7, nsp9, nsp10, GP4 and GP5 and the continuous 120 amino acid deletion in the nsp2 region from F19 provide a strong potential molecular basis for the observed attenuated phenotype.