Characterization of emerging European-like porcine reproductive and respiratory syndrome virus isolates in the United States

Genetic variation in NSP4 of type 1 porcine reproductive and respiratory syndrome virus in China

BACKGROUND

Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by a high mutation rate. Although research has largely focused on PRRSV-2, the detection rate of PRRSV-1 in China is increasing. To investigate the prevalence and genetic variation of NSP4, a key gene in the regulation of host immunity, in PRRSV-1 in China, publicly available whole-genome sequence data and NSP4 sequences were obtained for analyses of nucleotide and amino acid homology, substitutions, and phylogenetic relationships.

RESULTS

The nucleotide homology of NSP4 between 32 PRRSV-1 and 8 PRRSV-2 strains ranged from 57.3 to 62.4%, and the amino acid homology ranged from 58.6 to 64.5%. Among the 32 PRRSV-1 strains, the nucleotide homology of NSP4 ranged from 75.4 to 100.0% and the amino acid homology ranged from 81.3 to 100.0%. Comparisons of NSP4 amino acid sequences of 32 PRRSV-1 and 8 PRRSV-2 strains revealed a deletion at the 83rd amino acid residue in PRRSV-1 and mutations at various amino acid residues. A phylogenetic analysis showed that the PRRSV-1 strains isolated in China clustered into four subgroups of Subtype I Global: Amervac-like, BJEU06-1-like, HKEU16-like, and NMEU09-1-like strains.

CONCLUSION

PRRSV-1 NSP4 exhibits similarities to Subtype I Global strains and clusters into four subgroups. Although it differs from PRRSV-2 NSP4 with a deletion in the 83rd amino acid residue, the amino acid residues of the catalytic triad are conserved. These findings have important implications for the development of secure and reliable detection methods as well as new drugs and vaccines and are expected to guide further research on PRRSV-1.

A single recall vaccination lapse in sows triggers PRRSV resurgence and boosts viral genetic diversity

BACKGROUND

Porcine reproductive and respiratory syndrome virus (PRRSV) persists on certain farms despite vaccination and control efforts, with genetic diversity suspected as a contributing factor. This study examined the evolution and persistence dynamics of PRRSV-1 on a farrow-to-fattening farm with 1,700 sows vaccinated quarterly, focusing on a summer vaccination lapse.

RESULTS

Over eight months, three farrowing batches were monitored from birth to nine weeks of age using virological (RT-qPCR, whole-genome, and ORF5 sequencing) and serological (ELISA and neutralizing antibody) analyses. An incident related to elevated temperatures during the summer involving unproper vaccine handling occurred during the last blanket vaccination, before sampling the third batch. Viral circulation was primarily confined to the nurseries, with a notable surge of incidence and mortality in this last batch, linked to lower maternal antibody levels likely due to vaccination failure. Phylogenetic analyses showed the persistence of the same viral strain throughout the study, with increased genetic diversity in Batch 3 driven by selection and recombination. Ultimately, reestablishing the vaccination program led to a PRRSV-positive-stable with vaccination status.

CONCLUSIONS

Overall, a single vaccination lapse caused increased PRRSV-1 incidence and genetic diversity in weaners, linked to declining maternal antibody levels, underscoring the importance of strict vaccination adherence.

Refining genetic classification of global porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) and investigating their geographic and temporal distributions

Porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) primarily circulates in Europe but is also detected in North America and Asia. Based on ORF5 sequences, previous studies classified PRRSV-1 into four subtypes. Subtype 1 was further classified into 12 clades (A-L) or into three lineages with lineage 1 including clades 1A-1G and lineage 3 including clades 3A-3G, but the systems are inconsistent and have not been adopted. In this study, we proposed a statistically supported PRRSV-1 genetic classification system based on 10,446 global PRRSV-1 ORF5 sequences spanning 1991-2023. We replaced the colloquial "subtype" designation with "lineage" to reflect evolutionary history and, subsequently, PRRSV-1 was classified into four lineages (L1-L4) with L1 including 18 sublineages (L1.1 to L1.18). The proposed classification system is flexible and may be amended if additional lineages, sublineages, or more granular classifications are needed to reflect contemporary PRRSV-1 detections and evolution. Geographic distributions of PRRSV-1 at lineage and sublineage levels were distinct, with L1 globally distributed and L2, L3 and L4 more restricted. Temporal dynamic changes in some countries were quantified. Classification and ORF5 nucleotide identity of six commercial PRRSV-1 vaccines to each lineage and sublineage and detection frequency of vaccine-like viruses were determined. The phylogenies based on whole-genome and ORF5 sequences demonstrated slightly different tree topologies. Recombination of PRRSV-1 was observed at within-sublineage and between-sublineage levels. A set of ORF5 reference sequences representing the refined classification is available for future diagnostic and epidemiological applications. This study provides a benchmark delineating the current genetic diversity of PRRSV-1 and introduces a refined classification system to support the global standardization and application of ORF5-based genetic classification for PRRSV-1.

Concurrent but consecutive vaccination of modified live PRRSV-1 and PRRSV-2 provides better protection in nursery pigs

Porcine reproductive and respiratory syndrome (PRRS) virus is a severe threat to the global swine industry. Modified live virus vaccines (MLVs) for two PRRSV species (PRRSV-1 and PRRSV-2) are the most widely used approach to control PRRSV-caused diseases. For swine herds influenced by PRRSV-1 and PRRSV-2, how to rationalize MLV immunization strategies for robust and cross-protective immune responses has been a long-lasting need. In this study, we found that the replication of PRRSV-1 is strongly suppressed by co-infection with PRRSV-2 in vitro, especially under concurrent co-infection conditions. We compared the adaptive immune responses between consecutive and concurrent vaccination methods in nursery pigs, vaccinated either 3 days apart (PRRSV-1 MLV followed by PRRSV-2 MLV, consecutive) or together on the same day (concurrent). PRRSV-1 RNAs were mainly detectable in the sera of consecutively vaccinated pigs. In contrast, PRRSV-2 RNAs in sera were not changed in both vaccination strategies. After the homologous PRRSV-1 or PRRSV-2 challenge, we found that consecutive vaccination slightly improved PRRSV-1 viremia clearance and did not attenuate the PRRSV-2 viremia clearance. Both vaccination strategies induced comparable T-helper cell responses against PRRSV-1 and PRRSV-2 in peripheral blood before and after the challenge. Interestingly, consecutive vaccination induced significantly higher PRRSV-1-specific post-challenge T-helper and cytotoxic T cells responses in the tracheobronchial lymph nodes than concurrent vaccination. Furthermore, consecutive vaccination significantly improved neutralizing antibody responses against PRRSV-1 and PRRSV-2 in comparison with concurrent vaccination. In conclusion, consecutive vaccination appears to be better for viral clearance and induction of adaptive immune response, and our study provides a preliminary rationale to optimize PRRS MLV immunization strategy for better dual protection.

Whole Genome Characterization and Pathogenicity of a SC2020-1-Like PRRSV-1 Strain Emerging in Southwest China

Porcine reproductive and respiratory syndrome virus (PRRSV), encompassing PRRSV-1 and PRRSV-2, significantly impacts the global pig industry by causing reproductive disorders and respiratory difficulties. In this paper, we isolated a novel PRRSV-1 strain, named SCPJ2023, from weaned piglets in Sichuan. Utilizing primary macrophages, we isolated SCPJ2023 and performed complete genome sequencing through metagenomic analysis. Phylogenetic analysis classified SCPJ2023 as pan-European subtype 1. SCPJ2023 showed a 95.3% similarity to SC2020-1. Amino acid analysis identified differences in Nsp2, GP3, and GP4 between SCPJ2023 and other representative strains. In vivo challenge experiments demonstrated that SCPJ2023 induced clinical symptoms in piglets, including coughing, fever, reduced appetite, and depression. Pathological examinations revealed hemorrhage and congestion, increased inflammatory cells, thickening of the alveolar wall, and collapse of the alveolar cavity in SCPJ2023-infected piglets. Altogether, our study identified a novel pathogenic isolate of PRRSV-1, expanding the newly named SC2020-1-like subgroup by identifying additional strains beyond the initial SC2020-1 isolate.

Isolation and identification, genome-wide analysis and pathogenicity study of a novel PRRSV-1 in southern China

Porcine reproductive and respiratory syndrome virus (PRRSV) has caused severe economic losses to the global swine industry. In recent years, the incidence of PRRSV-1 has been gradually increasing in China, but there are still few studies on it. In this study, clinical samples for PRRS virus isolation were collected from a pig farm in South China in 2022. We effectively isolated a strain of PRRSV utilizing PAM cells and demonstrated its consistent transmission capability on Marc-145 cells. The isolated strain was confirmed as PRRSV-1 by RT-qPCR, IFA, electron microscopy, etiolated spot purification and whole genome sequencing, the strain was named GD2022. The length of GD2022 genome is 15058nt; Based on the genome-wide genetic evolutionary analysis of GD2022, the strain was classified as PRRSV-1. Further genetic evolutionary analysis of its ORF5 gene showed that GD2022 belonged to PRRSV-1 subtype 1 and formed an independent branch in the evolutionary tree. Compared with the sequence of the classical PRRSV-1 strain (LV strain), GD2022 has several amino acid site mutations in the antigenic region from GP3 to GP5, these mutations are different from those of other PRRSV-1 strains in China. Recombination analysis showed no recombination events with GD2022. In addition, piglets infected with GD2022 displayed clinical respiratory symptoms and typical pathological changes. In this study, a strain of the PRRSV-1 virus was isolated using both PAM cells and Marc-145 and proved to be pathogenic to piglets, providing an important reference for the identification, prevention, and control of PRRSV-1.

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.

Recombination of Porcine Reproductive and Respiratory Syndrome Virus: Features, Possible Mechanisms, and Future Directions

Recombination is a pervasive phenomenon in RNA viruses and an important strategy for accelerating the evolution of RNA virus populations. Recombination in the porcine reproductive and respiratory syndrome virus (PRRSV) was first reported in 1999, and many case reports have been published in recent years. In this review, all the existing reports on PRRSV recombination events were collected, and the genotypes, parental strains, and locations of the recombination breakpoints have been summarized and analyzed. The results showed that the recombination pattern constantly changes; whether inter- or intra-lineage recombination, the recombination hotspots vary in different recombination patterns. The virulence of recombinant PRRSVs was higher than that of the parental strains, and the emergence of virulence reversion was caused by recombination after using MLV vaccines. This could be attributed to the enhanced adaptability of recombinant PRRSV for entry and replication, facilitating their rapid propagation. The aim of this paper was to identify common features of recombinant PRRSV strains, reduce the recombination risk, and provide a foundation for future research into the mechanism of PRRSV recombination.

Characterization and Pathogenicity of the Novel Porcine Reproductive and Respiratory Syndrome Virus 1 Strain SL-01 in China

Currently, PRRSV-1 causes a large number of clinical infections in Chinese swine herds, and the prevalence of new strains has presented great challenges. In this study, the novel PRRSV-1 strain SL-01 was isolated, with a genome length of 14,978 bp, and genetic evolution analysis revealed that it belonged to a new subtype branch. Sequence homology analysis showed that the strain was only 82.2%-86.7% identical to the current classical PRRSV-1 strains. In particular, the novel strain exhibited a unique deletion pattern in Nsp2. In addition, GP3 and GP4 of the SL-01 strain showed four consecutive amino acid deletions in the highly variable regions at amino acids 243-248 and 63-68, respectively. Further challenges in piglet and pregnant sow demonstrated that the SL-01 strain could cause the piglet fever and death but less pathogenic to pregnant sow. Overall, the characterization and pathogenicity of a novel PRRSV-1 strain were first explored and provide a prevention for pig farms.

A nanobody inhibiting porcine reproductive and respiratory syndrome virus replication via blocking self-interaction of viral nucleocapsid protein

Porcine reproductive and respiratory syndrome (PRRS) is a serious global pig industry disease. Understanding the mechanism of viral replication and developing efficient antiviral strategies are necessary for combating with PRRS virus (PRRSV) infection. Recently, nanobody is considered to be a promising antiviral drug, especially for respiratory viruses. The present study evaluated two nanobodies against PRRSV nucleocapsid (N) protein (PRRSV-N-Nb1 and -Nb2) for their anti-PRRSV activity in vitro and in vivo. The results showed that intracellularly expressed PRRSV-N-Nb1 significantly inhibited PRRSV-2 replication in MARC-145 cells (approximately 100%). Then, the PRRSV-N-Nb1 fused with porcine IgG Fc (Nb1-pFc) as a delivering tag was produced and used to determine its effect on PRRSV-2 replication in porcine alveolar macrophages (PAMs) and pigs. The inhibition rate of Nb1-pFc against PRRSV-2 in PAMs could reach >90%, and it can also inhibit viral replication in vivo. Epitope mapping showed that the motif Serine 105 (S105) in PRRSV-2 N protein was the key amino acid binding to PRRSV-N-Nb1, which is also pivotal for the self-interaction of N protein via binding to Arginine 97. Moreover, viral particles were not successfully rescued when the S105 motif was mutated to Alanine (S105A). Attachment, entry, genome replication, release, docking model analysis, and blocking enzyme-linked immunosorbent assay (ELISA) indicated that the binding of PRRSV-N-Nb1 to N protein could block its self-binding, which prevents the viral replication of PRRSV. PRRSV-N-Nb1 may be a promising drug to counter PRRSV-2 infection. We also provided some new insights into the molecular basis of PRRSV N protein self-binding and assembly of viral particles.IMPORTANCEPorcine reproductive and respiratory syndrome virus (PRRSV) causes serious economic losses to the swine industry worldwide, and there are no highly effective strategies for prevention. Nanobodies are considered a promising novel approach for treating diseases because of their ease of production and low costing. Here, we showed that PRRSV-N-Nb1 against PRRSV-N protein significantly inhibited PRRSV-2 replication in vitro and in vivo. Furthermore, we demonstrated that the motif Serine 105 (S105) in PRRSV-N protein was the key amino acid to interact with PRRSV-N-Nb1 and bond to its motif R97, which is important for the self-binding of N protein. The PRRSV-N-Nb1 could block the self-interaction of N protein following viral assembly. These findings not only provide insights into the molecular basis of PRRSV N protein self-binding as a key factor for viral replication for the first time but also highlight a novel target for the development of anti-PRRSV replication drugs.

Research Progress on Porcine Reproductive and Respiratory Syndrome Virus NSP7 Protein

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious and severe infectious disease caused by the PRRS virus (PRRSV). PRRS is characterized by reproductive disorders in sows and respiratory dysfunction in pigs. Non-structural protein 7 (NSP7) is one of the most conserved functional proteins in PRRSV, and it plays an important role in viral replication and humoral immune responses in infected hosts. This review discusses the biological characteristics of NSP7 to provide theoretical support for its application in PRRS diagnosis, novel vaccine design, and therapeutic drug development.

Recent Progress in Studies of Porcine Reproductive and Respiratory Syndrome Virus 1 in China

Due to the high incidence of PRRSV mutation and recombination, PRRSV infection is difficult to prevent and control in China and worldwide. Two species of PRRSV, Betaarterivirus suid 1 (PRRSV-1) and Betaarterivirus suid 2 (PRRSV-2), exist in China, and PRRSV-1 has always received less attention in China. However, the number of PRRSV-1 strains detected in China has increased recently. To date, PRRSV-1 has spread to more than 23 regions in China. Based on the phylogenetic analysis of ORF5 and the whole genome of PRRSV-1, Chinese PRRSV-1 can be divided into at least seven independent subgroups. Among them, BJEU06-1-like has become the mainstream subgroup in some regions of China. This subgroup of strains has a 5-aa (4 + 1) characteristic discontinuous deletion pattern at aa 357~aa 360 and aa 411 in Nsp2. Previous studies have indicated that the pathogenicity of PRRSV-1 in China is mild, but recent studies found that the pathogenicity of PRRSV-1 was enhanced in China. Therefore, the emergence of PRRSV-1 deserves attention, and the prevention and control of PRRSV-1 infection in China should be strengthened. PRRSV infection is usually prevented and controlled by a combination of virus monitoring, biosafety restrictions, herd management measures and vaccination. However, the use of PRRSV-1 vaccines is currently banned in China. Thus, we should strengthen the monitoring of PRRSV-1 and the biosafety management of pig herds in China. In this review, we summarize the prevalence of PRRSV-1 in China and clarify the genomic characteristics, pathogenicity, vaccine status, and prevention and control management system of PRRSV-1 in China. Consequently, the purpose of this review is to provide a basis for further development of prevention and control measures for PRRSV-1.

Metagenomic and Pathogenic Assessments Identify a Pathogenic Porcine Reproductive and Respiratory Syndrome Virus 1 with New Deletions from Adult Slaughter Pig in 2022

Since we first reported porcine reproductive and respiratory syndrome virus 1 (PRRSV1) wild type strains in mainland China in 2011, PRRSV1 infection has been detected in more than 20 provinces in China. During the routine investigation of PRRSV1 epidemiology in 2022, we isolated a novel PRRSV1 strain (SD1291) from an adult slaughter pig in Linyi, Shandong Province. The SD1291 could only be isolated with primary alveolar macrophages (PAMs), not with Marc-145 cells. In addition, the 2022 SD1291 isolate has higher in vitro replication efficacy than the 2014 PRRSV1 HLJB1 isolate in PAMs. Due to high genetic variation, the complete genome of SD1291 was determined by metagenomic sequencing, which showed that SD1291 shares the highest genome similarity (88.12%) with the PRRSV1 HeB47 isolate. Sequence alignment results identified a four-amino-acid deletion in nsp2 and a five-amino-acid deletion in the GP3 and GP4 overlap region of SD1291. A complete-genome-based phylogenetic tree showed that SD1291 is grouped with BJEU06-1-like PRRSV1 isolates. A piglets' challenge study showed that SD1291 can cause high fever (the highest is 41°C), reduced weight gain, mild lung consolidation, and interstitial pneumonia indicating that SD1291 is a pathogenic PRRSV1 isolate. Overall, this study first identified a novel pathogenic PRRSV1 isolate from an adult slaughter pig in China. Our findings also suggested that new PRRSV1 variants could escape the current PRRSV vaccination system and circulate in adult swine herds, which deserve more attention.

Genomic Characterization and Pathogenicity of BJEU06-1-Like PRRSV-1 ZD-1 Isolated in China

Porcine reproductive and respiratory syndrome virus (PRRSV)-1 and PRRSV-2 have long been cocirculating in China. To date, all PRRSV-1 strains in China have been classified as subtype 1. We investigated the prevalence of PRRSV-1 in several areas of China from 2016 to 2022 and found that BJEU06-1-like strains comprised the main epidemic branch of PRRSV-1. Pathogenicity data for this subgroup are currently lacking. In this study, the Chinese BJEU06-1-like PRRSV-1 strain ZD-1 was isolated from primary alveolar macrophages (PAMs). ZD-1 has undergone no recombination and has a 5-aa discontinuous deletion in the Nsp2 protein, similar to other BJEU06-1-like strains; additionally, ZD-1 has a 26 aa C-terminal truncation in the GP3 gene. Pathogenicity studies revealed that ZD-1 causes obvious clinical symptoms: prolonged fever; reduced body weight; alveolar epithelial proliferation and moderate alveolar diaphragm widening in the lungs; diffuse lymphocytic hyperplasia in the lymph nodes; high levels of viremia in the serum; and elevated viral loads in the lungs, lymph nodes, and tonsils. These results suggested that the BJEU06-1-like PRRSV-1 strain ZD-1 is moderately pathogenic to piglets. This is the first study to evaluate the pathogenicity of the BJEU06-1-like branch in China, enriching the understanding of PRRSV-1 in China.

Genomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus 1 Revealed Extensive Recombination and Potential Introduction Events in China

Simple Summary

Porcine reproductive and respiratory syndrome, caused by the porcine reproductive and respiratory syndrome virus, is considered one of the most devastating swine diseases worldwide. Porcine reproductive and respiratory syndrome virus 1 was first isolated in China in 2006, and there have been few reports concerning its genetic characteristics in China. We hope to find out the regularity of genetic diversity, recombination, and evolution of the virus by analyzing all available genomic sequences during 1991–2018. We found that high-frequency recombination regions were concentrated in non-structural protein 2 and structural proteins 2 to 4 and extensive deletions in non-structural protein 2; phylogenetic analysis revealed four independent introductions in China. Our results suggest that attention should be paid to the prevention and control of porcine reproductive and respiratory syndrome virus 1 and the rational use of vaccine strains. These results will help us to understand the recombination of porcine reproductive and respiratory syndrome virus and strengthen viral inspection before mixing herds of swine to reduce the probability of novel recombinant variants. Moreover, our study might form the basis of monitoring and control measures to prevent the spread of this economically important virus.

Abstract

Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is considered one of the most devastating swine diseases worldwide. PRRSV-1 was first isolated in China in 2006. However, there were few reports concerning the genetic characteristics of PRRSV-1 in China. In this study, three PRRSV-1 strains (HL85, HeB3, and HeB47) were detected by a general RT-qPCR method from clinical samples in 2018. HeB47 was identified as a recombinant between the BJEU06-1 and CReSA228-like strains. To further analyze the recombination and deletion features of PRRSV-1, all the available 88 complete genome sequences (isolated in 19 countries) from 1991 to 2018 in GenBank were analyzed. The high-frequency recombination regions were concentrated in NSP2 and GP2 to GP4. More importantly, phylogenetic analysis of PRRSV-1 revealed four independent introductions in China. Therefore, it is necessary to strengthen the important monitoring of breeding pigs and pork products and epidemiological surveys on pig farms to prevent the further spread of PRRSV-1.

Genetic Diversity and Epidemic Types of Porcine Reproductive and Respiratory Syndrome (PRRS) Virus in Japan from 2018 to 2020

To clarify the genetic diversity of the porcine reproductive and respiratory syndrome virus (PRRSV) in Japan in recent years, we determined the nucleotide sequence of open reading frame 5 of 2482 PRRSV sequences obtained from samples collected from pigs between January 2018 and December 2020. As a result of molecular phylogenetic analysis, Cluster II represented the largest proportion (44.9−50.6%) throughout the study period, followed by Cluster IV (34.0−40.8%), Cluster III (7.8−12.1%), Cluster I (3.1−6.7%), and Cluster V (0.1−0.2%). The relative distributions between Clusters varied between geographic regions and between years: in 2018, Cluster II was the most prevalent in all regions. In 2019, Cluster II was dominant in the Hokkaido and Tohoku regions, while in other regions Cluster IV was dominant. In 2020, Cluster IV was dominant in the Kanto/Tosan and Kyushu/Okinawa regions, whilst in other regions Cluster II was predominant. Compared with a previous study, the proportions of genome sequences classified in Clusters II and IV significantly increased (p = 0.042 and 0.018, respectively) and those classified in Cluster III significantly decreased (p < 0.01). The widespread use of live attenuated vaccines using strains that belong to Cluster II might have accounted for these changes in the relative distribution between Clusters.

Lineage 1 Porcine Reproductive and Respiratory Syndrome Virus Attenuated Live Vaccine Provides Broad Cross-Protection against Homologous and Heterologous NADC30-Like Virus Challenge in Piglets

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that endangers the swine industry worldwide. Recently, lineage 1 PRRSVs, especially NADC30-like PRRSVs, have become the major endemic strains in many pig-breeding countries. Since 2016, NADC30-like PRRSV has become the predominant strain in China. Unfortunately, current commercial vaccines cannot provide sufficient protection against this strain. Here, an attenuated lineage 1 PRRSV strain, named SD-R, was obtained by passaging an NADC30-like PRRSV strain SD in Marc-145 cells for 125 passages. Four-week-old PRRSV-free piglets were vaccinated intramuscularly with 105.0TCID50 SD-R and then challenged intramuscularly (2 mL) and intranasally (2 mL) with homologous NADC30-like PRRSV SD (1 × 105.0TCID50/mL) and heterologous NADC30-like PRRSV HLJWK108-1711 (1 × 105.0TCID50/mL). The results showed that antibodies against specific PRRSVs in 5 of 5 immunized piglets were positive after a 14-day post-vaccination and did not develop fever or clinical diseases after NADC30-like PRRSV challenges. Additionally, compared with challenge control piglets, vaccinated piglets gained significantly more weight and showed much milder pathological lesions. Furthermore, the viral replication levels of the immunized group were significantly lower than those of the challenge control group. These results demonstrate that lineage 1 PRRSV SD-R is a good candidate for an efficacious vaccine, providing complete clinical protection for piglets against NADC30-like PRRSVs.

Development of a Nanobody-Based Competitive Enzyme-Linked Immunosorbent Assay for Efficiently and Specifically Detecting Antibodies against Genotype 2 Porcine Reproductive and Respiratory Syndrome Viruses

Porcine reproductive and respiratory syndrome virus (PRRSV) infection causes considerable economic loss to the global pig industry. Efficient detection assay is very important for the prevention of the virus infection. Nanobodies are the advantages of small molecular weight, simple genetic engineering, and low production cost for promising diagnostic application. In this study, to develop a nanobody-based competitive ELISA (cELISA) for specifically detecting antibodies against PRRSV, three nanobodies against PRRSV-N protein were screened by camel immunization, library construction, and phage display. Subsequently, a recombinant HEK293S cell line stably secreting nanobody-horseradish peroxidase (HRP) fusion protein against PRRSV-N protein was successfully constructed using the lentivirus transduction assay. Using the cell lines, the fusion protein was easily produced. Then, a novel cELISA was developed using the nanobody-HRP fusion protein for detecting antibodies against PRRSV in pig sera, exhibiting a cut-off value of 23.19% and good sensitivity, specificity, and reproducibility. Importantly, the cELISA specifically detect anti-genotype 2 PRRSV antibodies. The cELISA showed more sensitive than the commercial IDEXX ELISA kit by detecting the sequential sera from the challenged pigs. The compliance rate of cELISA with the commercial IDEXX ELISA kit was 96.4%. In addition, the commercial IDEXX ELISA kit can be combined with the developed cELISA for the differential detection of antibodies against genotype 1 and 2 PRRSV in pig sera. Collectively, the developed nanobody-based cELISA showed advantages of simple operation and low production cost and can be as an assay for epidemiological investigation of genotype 2 PRRSV infection in pigs and evaluation after vaccination.

Molecular detection and characterization of highly pathogenic porcine reproductive and respiratory syndrome virus from a natural outbreak in wild pigs, Mizoram, India

This study reports for the first time a natural outbreak of highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) caused by HP-PRRS virus (HP-PRRSV) in wild pigs characterized by sudden onset of depression, anorexia, respiratory distress, and high fever. The disease has caused severe haemorrhagic pneumonia, haemorrhagic lymphadenitis, enlarged spleen with areas of infarction, and petechial haemorrhages on the myocardium and on the surface of kidneys. HP-PRRSV was detected in representative tissue samples by reverse transcription-PCR, and the field strain was isolated in the MA104 cell line. The phylogenetic analyses based on the whole genome sequences and nucleotide sequences of open reading frame 5 (ORF5) gene showed close grouping with the subtype IV of lineage 8/8.7 of PRRSV II, which represents the HP-PRRSV strains that predominate in the pig population of China since 2010. The amino acid sequence analysis of the ORF5 gene revealed the replacement of leucine (L) at position 39 to isoleucine (I) in the primary neutralizing epitope. Among the four potential N glycosylation sites, the N34 was mutated and found to be restricted to only three N glycosylation sites. The present findings have indicated that HP-PRRSV can cause fatal outbreaks and may emerge as a major threat to the wild pig population.

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.

A swine arterivirus deubiquitinase stabilizes two major envelope proteins and promotes production of viral progeny

Arteriviruses are enveloped positive-strand RNA viruses that assemble and egress using the host cell’s exocytic pathway. In previous studies, we demonstrated that most arteriviruses use a unique -2 ribosomal frameshifting mechanism to produce a C-terminally modified variant of their nonstructural protein 2 (nsp2). Like full-length nsp2, the N-terminal domain of this frameshift product, nsp2TF, contains a papain-like protease (PLP2) that has deubiquitinating (DUB) activity, in addition to its role in proteolytic processing of replicase polyproteins. In cells infected with porcine reproductive and respiratory syndrome virus (PRRSV), nsp2TF localizes to compartments of the exocytic pathway, specifically endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and Golgi complex. Here, we show that nsp2TF interacts with the two major viral envelope proteins, the GP5 glycoprotein and membrane (M) protein, which drive the key process of arterivirus assembly and budding. The PRRSV GP5 and M proteins were found to be poly-ubiquitinated, both in an expression system and in cells infected with an nsp2TF-deficient mutant virus. In contrast, ubiquitinated GP5 and M proteins did not accumulate in cells infected with the wild-type, nsp2TF-expressing virus. Further analysis implicated the DUB activity of the nsp2TF PLP2 domain in deconjugation of ubiquitin from GP5/M proteins, thus antagonizing proteasomal degradation of these key viral structural proteins. Our findings suggest that nsp2TF is targeted to the exocytic pathway to reduce proteasome-driven turnover of GP5/M proteins, thus promoting the formation of GP5-M dimers that are critical for arterivirus assembly.

Arteriviruses are a rapidly expanding family of positive-stranded RNA viruses, which includes economically important veterinary pathogens like equine arteritis virus (EAV) and two species of porcine reproductive and respiratory syndrome virus (PRRSV-1 and PRRSV-2). In our previous studies, we uncovered an unprecedented arterivirus gene expression mechanism: a highly efficient -2 programmed ribosomal frameshift (PRF) that is controlled by an interaction of viral protein nsp1ß with specific RNA sequences and host poly(C) binding proteins. It is used by PRRSVs, and most other arteriviruses, to efficiently produce a previously unknown nonstructural protein variant, nsp2TF. In this study, we demonstrate that PRRSV nsp2TF interacts with the two major arteriviral envelope proteins, GP5 and M, whose heterodimerization in the secretory pathway is a key step in envelope protein trafficking and virus assembly. Our findings suggest that nsp2TF promotes arterivirus assembly by antagonizing the ubiquitination-dependent proteasomal degradation of GP5 and M proteins. This mechanism is based on the DUB activity of the PLP2 protease domain located within the N-terminal region of nsp2TF. To our knowledge, this is the first study to demonstrate that viruses can express a DUB that functions specifically to counteract the ubiquitination and degradation of key viral structural proteins.

A nidovirus perspective on SARS-CoV-2

Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.

An Outbreak of a Respiratory Disorder at a Russian Swine Farm Associated with the Co-Circulation of PRRSV1 and PRRSV2

We conducted a cross-sectional study to identify the major respiratory pathogen responsible for an outbreak of respiratory disease at a swine farm in West Siberia in 2019. We discovered that the peak of morbidity and mortality coincided with a high level of porcine reproductive and respiratory syndrome virus (PRRSV) 1 and 2-related viremia. Based on longer PRRSV2 viremia, the dominant role of PRRSV2 over PRRSV1 in the outbreak was assumed. Phylogenetic analysis revealed that the PRRSV1 strain belonged to sub-genotype 2—one of the predominant groups of genotype 1 PRRSVs in Russia. A partial open reading frame 7 sequence of the PRRSV2 isolate demonstrated a high identity with modified live vaccine-related strains from Denmark (93%) and wild-type VR2332 (92%). We identified the first instance of PRRSV1/PRRSV2 mixed infection in Russia. This finding indicates that further field investigations are needed to access PRRSV2 epidemiology in eastern Europe.

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 characterization of type 1 porcine reproductive and respiratory syndrome viruses (PRRSV) isolated in the Netherlands from 2014 to 2016

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of a devastating pig disease present all over the world. The remarkable genetic variation of PRRSV, makes epidemiological and molecular analysis of circulating viruses highly important to review current diagnostic tools and vaccine efficacy. Monitoring PRRS viruses supports modern herd management by explaining the source of found viruses, either internally or externally from the herd. No epidemiological or molecular study has been published on circulating PRRS-viruses in the Netherlands, since the early nineties. Therefore, the objective of this study is to investigate circulating PRRS-viruses in the Netherlands in 2014, 2015 and 2016 on a molecular level by sequencing ORF2, ORF3, ORF4, ORF5, ORF6 and ORF7. The results demonstrate that the 74 PRRSV strains belong to PRRSV-1, but the diversity among strains is high, based on nucleotide identity, individual ORF length and phylogenetic trees of individual ORFs. Furthermore, the data presented here show that the phylogenetic topology of some viruses is ORF dependent and suggests recombination. The identity of the strain of interest might be misinterpreted and wrong conclusions may be drawn in a diagnostic and epidemiological perspective, when only ORF5 is analyzed, as performed in many routine sequencing procedures.

Development of an immunochromatographic strip for detection of antibodies against porcine reproductive and respiratory syndrome virus

A simple and rapid immunochromatographic test strip incorporating a colloidal gold-labeled recombinant Nsp7 antigen probe was successfully developed for the detection of anti-porcine reproductive and respiratory syndrome virus (PRRSV) antibodies in swine. Recombinant Nsp7 protein of PRRSV labeled with colloidal gold was dispensed on a conjugate pad for use as the detector. Staphylococcal protein A and purified porcine anti-Nsp7 antibodies were blotted on a nitrocellulose membrane to form test and control lines, respectively. A comparison of the strip with standard diagnostic tests, enzyme-linked immunosorbent assays and immunoperoxidase monolayer assay, was also performed. The immunochromatographic test strip was shown to be of high specificity and sensitivity. Furthermore, the strip assay is rapid and easy to perform with no requirement for professional-level skills or equipment. It is suggested that the immunochromatographic test strip can be used to quickly and accurately detect PRRSV antibody and to be suitable for diagnostic purposes in the field.

MicroRNA-like viral small RNA from porcine reproductive and respiratory syndrome virus negatively regulates viral replication by targeting the viral nonstructural protein 2

Many viruses encode microRNAs (miRNAs) that are small non-coding single-stranded RNAs which play critical roles in virus-host interactions. Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically impactful viruses in the swine industry. The present study sought to determine whether PRRSV encodes miRNAs that could regulate PRRSV replication. Four viral small RNAs (vsRNAs) were mapped to the stem-loop structures in the ORF1a, ORF1b and GP2a regions of the PRRSV genome by bioinformatics prediction and experimental verification. Of these, the structures with the lowest minimum free energy (MFE) values predicted for PRRSV-vsRNA1 corresponded to typical stem-loop, hairpin structures. Inhibition of PRRSV-vsRNA1 function led to significant increases in viral replication. Transfection with PRRSV-vsRNA1 mimics significantly inhibited PRRSV replication in primary porcine alveolar macrophages (PAMs). The time-dependent increase in the abundance of PRRSV-vsRNA1 mirrored the gradual upregulation of PRRSV RNA expression. Knockdown of proteins associated with cellular miRNA biogenesis demonstrated that Drosha and Argonaute (Ago2) are involved in PRRSV-vsRNA1 biogenesis. Moreover, PRRSV-vsRNA1 bound specifically to the nonstructural protein 2 (NSP2)-coding sequence of PRRSV genome RNA. Collectively, the results reveal that PRRSV encodes a functional PRRSV-vsRNA1 which auto-regulates PRRSV replication by directly targeting and suppressing viral NSP2 gene expression. These findings not only provide new insights into the mechanism of the pathogenesis of PRRSV, but also explore a potential avenue for controlling PRRSV infection using viral small RNAs.

Reproductive effects of arteriviruses: equine arteritis virus and porcine reproductive and respiratory syndrome virus infections

Equine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV) are the most economically important members of the family Arteriviridae. EAV and PRRSV cause reproductive and respiratory disease in equids and swine, respectively and constitute a significant economic burden to equine and swine industries around the world. Furthermore, they both cause abortion in pregnant animals and establish persistent infection in their natural hosts, which fosters viral shedding in semen leading to sexual transmission. The primary focus of this article is to provide an update on the effects of these two viruses on the reproductive tract of their natural hosts and provide a comparative analysis of clinical signs, virus-host interactions, mechanisms of viral pathogenesis and viral persistence.

Surveillance of porcine reproductive and respiratory syndrome virus in the United States using risk mapping and species distribution modeling

Porcine reproductive and respiratory syndrome virus (PRRSv) outbreaks cause significant financial losses to the U.S. swine industry, where the pathogen is endemic. Seasonal increases in the number of outbreaks are typically observed using PRRSv epidemic curves. However, the nature and extent to which demographic and environmental factors influence the risk for PRRSv outbreaks in the country remains unclear. The objective of this study was to develop risk maps for PRRSv outbreaks across the United States (U.S.) and compare ecological dynamics of the disease in five of the most important swine production regions of the country. This study integrates spatial information regarding PRRSv surveillance with relevant demographic and environmental factors collected between 2009 and 2016. We used presence-only Maximum Entropy (Maxent), a species distribution modeling approach, to model the spatial risk of PRRSv in swine populations. Data fitted the selected model relatively well when the modeling approach was conducted by region (training and testing AUCs<0.75). All of the Maxent models selected identified high-risk areas, with probabilities greater than 0.5. The relative contribution of pig density to PRRSv risk was highest in pig-densely populated areas (Minnesota, Iowa and North Carolina), whereas climate and land cover were important in areas with relatively low pig densities (Illinois, Indiana, South Dakota, Nebraska, Kansas, Oklahoma, Colorado, and Texas). Although many previous studies associated the risk of PRRSv with high pig density and climatic factors, the study here quantifies, for the first time in the peer-reviewed literature, the spatial variation and relative contribution of these factors across different swine production regions in the U.S. The results will help in the design and implement of early detection, prevention, and control strategies for one of the most devastating diseases affecting the swine industry in the U.S.

Genetic diversity in envelope genes of contemporary U.S. porcine reproductive and respiratory syndrome virus strains influences viral antigenicity

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases in swine caused by porcine reproductive and respiratory syndrome virus (PRRSV). Genome sequences of sixty-six PRRSV strains were obtained using metagenomic sequencing of serum samples collected in the U.S. in 2014 to explore contemporary genetic diversity. Phylogenetic analysis of the genes encoding the envelope proteins identified four to eight distinct lineages with >87% intraclade identity. To explore the effect of the observed genetic diversity on antigenicity, the genome regions encoding either GP2a-GP3-GP4 or GP5-M in strain SD95-21 were replaced with alleles from each of eight distinct PRRSV strains using reverse genetics. The GP2a-GP3-GP4 region from only four of the eight strains yielded viable recombinant virus. When viable, both GP2a-GP3-GP4 and GP5-M variably affected antigenicity. A strain-dependent significant loss in cross reactivity was variably observed by indirect immunofluorescence assays using antisera from pigs vaccinated with commercial modified-live vaccines following replacement of GP2a-GP3-GP4 or GP5-M. Significantly reduced neutralization titers were similarly measured using antisera from naturally PRRSV-exposed pigs. These results illustrate the need to consider genomic regions besides GP5 for PRRSV epidemiology and vaccination.

Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States

The US swine industry has been impaired over the last 25 years by the far-reaching financial losses caused by the porcine reproductive and respiratory syndrome (PRRS). Here, we explored the relations between the spatial risk of PRRS outbreaks and its phylodynamic history in the U.S during 1998–2016 using ORF5 sequences collected from swine farms in the Midwest region. We used maximum entropy and Bayesian phylodynamic models to generate risk maps for PRRS outbreaks and reconstructed the evolutionary history of three selected phylogenetic clades (A, B and C). High-risk areas for PRRS were best-predicted by pig density and climate seasonality and included Minnesota, Iowa and South Dakota. Phylodynamic models demonstrated that the geographical spread of the three clades followed a heterogeneous spatial diffusion process. Furthermore, PRRS viruses were characterized by typical seasonality in their population size. However, endemic strains were characterized by a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal rates when compared to emerging strains. We demonstrated the prospects of combining inferences derived from two unique analytical methods to inform decisions related to risk-based interventions of an important pathogen affecting one of the largest food animal industries in the world.

Molecular epidemiology of porcine reproductive and respiratory syndrome virus in Central China since 2014: The prevalence of NADC30-like PRRSVs

Porcine reproductive and respiratory syndrome (PRRS), characterized by respiratory disorders in piglets and reproductive failure in sows, is still the great threat of swine industry. Recently, Emergence of the novel NADC30-like PRRS viruses (PRRSVs) has caused widespread outbreaks of PRRS. To investigate the epidemic characteristics of PRRSVs in Central China since 2014, 6372 clinical serum samples were tested by ELISA, 250 tissue samples were tested by RT-PCR, and among these, 30 ORF5 and 17 Nsp2 genes sequences were analyzed. Phylogenetic tree based on ORF5 revealed that, 17 isolates were clustered into subgroup 1, represented by the NADC30. And for the Nsp2, The strains which had a discontinuous 131-amino-acid deletion in Nsp2, called NADC30-like strains, were clustered into subgroup 2. Our data suggested that the NADC30-like PRRSV strains spread quickly and are now circulating and prevalent in Central China as well as the classical HP-PRRSV strains. In addition, amino acid variation analysis of GP5 revealed that the amino acid sequences of NADC30-like PRRSV strains underwent rapid evolution and contained extensive amino acid substitutions in important motifs, such as potential neutralization epitope and the N-glycosylation sites. In summary, our data would provide a large amount of detailed information on molecular variation and genetic diversity of PRRSV in central China.

Genomic sequence and virulence evaluation of MN184A-like porcine reproductive and respiratory syndrome virus in Japan

In this study, a porcine reproductive and respiratory syndrome virus (PRRSV) that was isolated from a 9-week-old diseased pig on a farm in Japan with a high mortality rate during 2007-2008 was characterized. This unique isolate, designated as Jpn5-37, did not have a high nucleotide identity in open reading frame 5 against any Japanese isolates. Among all available type 2 PRRSV complete genome sequences, Jpn5-37 shared the highest nucleotide identity (93.6%) with virulent strain MN184A. The genomic characteristics of Jpn5-37 were highly conserved with respect to the virulent MN184A, including a continuous eight amino acid deletion in the nonstructural protein 2 region. Moreover, virus distribution, viremia and the gross and microscopic characteristics of lesions were investigated in pigs 10 days post-inoculation to elucidate the pathogenicity of the isolate. Intranasal inoculation was found to rapidly result in viremia and dissemination of the Jpn5-37 isolate to several tissues in a similar manner to EDRD1; however, the amounts of Jpn5-37 RNA in serum were significantly greater. Similarly, the quantities of Jpn5-37 viral RNA in all organs tested tended to be higher than with EDRD1 infection. Mean rectal temperatures were significantly higher in the Jpn5-37-inoculated than in the control group at 4 and 6 days post infection (dpi) and in the EDRD1-inoculated group at 6 and 8 dpi. These results suggest that the Jpn5-37 strain replicates and is more efficiently distributed to the organs than is EDRD1 under the same conditions.

Estimation of Time-Dependent Reproduction Numbers for Porcine Reproductive and Respiratory Syndrome across Different Regions and Production Systems of the US

Porcine reproductive and respiratory syndrome (PRRS) is, arguably, the most impactful disease for the North American swine industry, due to its known considerable economic losses. The Swine Health Monitoring Project (SHMP) monitors and reports weekly new PRRS cases in 766 sow herds across the US. The time-dependent reproduction number (TD-R) is a measure of a pathogen's transmissibility. It may serve to capture and report PRRS virus (PRRSV) spread at the regional and system levels. The primary objective of the study here was to estimate the TD-R values for PRRSV using regional and system-level PRRS data, and to contrast it with commonly used metrics of disease, such as incidence estimates and space-time clusters. The second objective was to test whether the estimated TD-Rs were homogenous across four US regions. Retrospective monthly incidence data (2009-2016) were available from the SHMP. The dataset was divided into four regions based on location of participants, and demographic and environmental features, namely, South East (North Carolina), Upper Midwest East (UME, Minnesota/Iowa), Upper Midwest West (Nebraska/South Dakota), and South (Oklahoma panhandle). Generation time distributions were fit to incidence data for each region, and used to calculate the TD-Rs. The Kruskal-Wallis test was used to determine whether the median TD-Rs differed across the four areas. Furthermore, we used a space-time permutation model to assess spatial-temporal patterns for the four regions. Results showed TD-Rs were right skewed with median values close to "1" across all regions, confirming that PRRS has an overall endemic nature. Variation in the TD-R patterns was noted across regions and production systems. Statistically significant periods of PRRSV spread (TD-R > 1) were identified for all regions except UME. A minimum of three space-time clusters were detected for all regions considering the time period examined herein; and their overlap with "spreader events" identified by the TD-R method varied according to region. TD-Rs may help to measure PRRS spread to understand, in quantitative terms, disease spread, and, ultimately, support the design, implementation, and monitoring of interventions aimed at mitigating the impact of PRRSV spread in the US.

Domain Organization and Evolution of the Highly Divergent 5' Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus

In five experimentally characterized arterivirus species, the 5'-end genome coding region encodes the most divergent nonstructural proteins (nsp's), nsp1 and nsp2, which include papain-like proteases (PLPs) and other poorly characterized domains. These are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here we present results of a bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related virus, wobbly possum disease virus (WPDV), determined by a modified 5' rapid amplification of cDNA ends (RACE) protocol. By combining profile-profile comparisons and phylogeny reconstruction, we identified an association of the four distinct domain layouts of nsp1-nsp2 with major phylogenetic lineages, implicating domain gain, including duplication, and loss in the early nsp1 evolution. Specifically, WPDV encodes highly divergent homologs of PLP1a, PLP1b, PLP1c, and PLP2, with PLP1a lacking the catalytic Cys residue, but does not encode nsp1 Zn finger (ZnF) and "nuclease" domains, which are conserved in other arteriviruses. Unexpectedly, our analysis revealed that the only catalytically active nsp1 PLP of equine arteritis virus (EAV), known as PLP1b, is most similar to PLP1c and thus is likely to be a PLP1b paralog. In all non-WPDV arteriviruses, PLP1b/c and PLP1a show contrasting patterns of conservation, with the N- and C-terminal subdomains, respectively, being enriched with conserved residues, which is indicative of different functional specializations. The least conserved domain of nsp2, the hypervariable region (HVR), has its size varied 5-fold and includes up to four copies of a novel PxPxPR motif that is potentially recognized by SH3 domain-containing proteins. Apparently, only EAV lacks the signal that directs -2 ribosomal frameshifting in the nsp2 coding region.IMPORTANCE Arteriviruses comprise a family of mammalian enveloped positive-strand RNA viruses that include some of the most economically important pathogens of swine. Most of our knowledge about this family has been obtained through characterization of viruses from five species: Equine arteritis virus, Simian hemorrhagic fever virus, Lactate dehydrogenase-elevating virus, Porcine respiratory and reproductive syndrome virus 1, and Porcine respiratory and reproductive syndrome virus 2 Here we present the results of comparative genomics analyses of viruses from all known 14 arterivirus species, including the most distantly related virus, WPDV, whose genome sequence was completed in this study. Our analysis focused on the multifunctional 5'-end genome coding region that encodes multidomain nonstructural proteins 1 and 2. Using diverse bioinformatics techniques, we identified many patterns of evolutionary conservation that are specific to members of distinct arterivirus species, both characterized and novel, or their groups. They are likely associated with structural and functional determinants important for virus replication and virus-host interaction.

Phylogenetic characterization of genes encoding for viral envelope glycoprotein (ORF5) and nucleocapsid protein (ORF7) of porcine reproductive & respiratory syndrome virus found in Malaysia in 2013 and 2014

Background

Porcine reproductive and respiratory syndrome (PRRS) is one of the most expensive diseases of modern swine production & results in annual economic losses and cost the industry over 600 million USD in U.S. alone and billions of dollars worldwide. Two atypical PRRS cases were observed in 2013 and 2014 characterized by late-term abortion, fever and sudden increase in sow mortality which persisted for a prolonged period of time.

Methods

Lungs, lymph nodes and other samples were collected for disease investigation. Sequencing of the viral envelope glycoprotein (ORF5) and nucleocapsid protein (ORF7) of PRRSV was done using the BigDye Terminator v3.1 cycle sequencing kit chemistry. The phylogenetic tree was constructed by using the Maximum Likelihood method, generated by Mega 6.06®.

Results

Analysis of the ORF5 and ORF7 showed high degree of sequence homology to PRRSV parent vaccine strain VR-2332, RespPRRSV and other mutant/chimeric virus strains.

Conclusions

Our study suggests that recombination events between vaccine strains and field isolates may contribute to PRRSV virulence in the field.

Complete genomic characterization of two European-genotype porcine reproductive and respiratory syndrome virus isolates in Fujian province of China

Porcine reproductive and respiratory syndrome (PRRS) is considered one of the most devastating swine diseases worldwide, resulting in immense economic losses. PRRS virus (PRRSV) is divided into two major genotypes, European (type 1) and the North American (type 2). Type 1 PRRSV have recently emerged in Fujian province (South China), and this might have a significant impact on the Chinese pig industry. From 2013 to 2014, two type 1 PRRSV strains, named FJEU13 and FJQEU14, were isolated from piglets and sows with respiratory problems and reproductive disorders in Fujian province. The full genome length of the two isolates was 14,869-15,062 nucleotides (nt), excluding the poly(A) tail. These isolates shared 86.0-89.9% sequence identity with the prototypic strains Lelystad virus (LV) and 82.8-92% with Chinese type 1 PRRSV strains, but only 59.9-60.1% with the North American reference strain VR-2332. However, they were 82.9% identical to each other. Nonstructural protein 2 (Nsp2) and ORF3-ORF5 were the most variable regions when compared to other type 1 PRRSV strains. Nsp2 and ORF3 contained multiple discontinuous deletions and a 204-bp deletion in NSP2 in isolate FJQEU14, which has never been described in other Chinese type 1 PRRSV strains. All of these results might be useful for understanding the epidemic status of type 1 PRRSV in China.

Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Modulates Interferon-β Expression Mainly Through Attenuating Interferon-Regulatory Factor 3 Phosphorylation

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) that emerged from classic PRRSV causes more severe damage to the swine industry. The earlier reports indicating inhibition of interferon-β (IFN-β) expression by PRRSV through total blockage of IFN-regulatory factor 3 (IRF3) nuclear translocation made us investigate the mechanism of IFN-β expression in HP-PRRSV infection. For this purpose, the IRF3 nuclear translocation in the control group [Poly (I:C)] and test group [Poly (I:C)+HP-PRRSV] was detected by immunofluorescence, and the results showed that IRF3 nuclear translocation in cells with PRRSV was weaker than cells without PRRSV, which was different from the previous study. In addition, the IFN-β mRNA and protein expression was observed to be inhibited by HP-PRRSV along with decreased IRF3 mRNA and total protein, and IRF3 nuclear translocation of test group was suppressed in MARC-145 and porcine alveolar macrophage cells in comparison with the control group. The quantity of phosphorylated IRF3 protein was also reduced after HP-PRRSV infection. However, CREB-binding protein (CBP) expression did not change between the control and test group. These results indicate that the inhibition of IFN-β expression is mainly due to the quantitative change in the amount of phosphorylated IRF3 in the cytoplasm, but not dependent on the complete blockage of IRF3 nuclear translocation or the restraining of CBP expression in the nucleus by HP-PRRSV.

Porcine Reproductive and Respiratory Syndrome Virus Utilizes Nanotubes for Intercellular Spread

Intercellular nanotube connections have been identified as an alternative pathway for cellular spreading of certain viruses. In cells infected with porcine reproductive and respiratory syndrome virus (PRRSV), nanotubes were observed connecting two distant cells with contiguous membranes, with the core infectious viral machinery (viral RNA, certain replicases, and certain structural proteins) present in/on the intercellular nanotubes. Live-cell movies tracked the intercellular transport of a recombinant PRRSV that expressed green fluorescent protein (GFP)-tagged nsp2. In MARC-145 cells expressing PRRSV receptors, GFP-nsp2 moved from one cell to another through nanotubes in the presence of virus-neutralizing antibodies. Intercellular transport of viral proteins did not require the PRRSV receptor as it was observed in receptor-negative HEK-293T cells after transfection with an infectious clone of GFP-PRRSV. In addition, GFP-nsp2 was detected in HEK-293T cells cocultured with recombinant PRRSV-infected MARC-145 cells. The intercellular nanotubes contained filamentous actin (F-actin) with myosin-associated motor proteins. The F-actin and myosin IIA were identified as coprecipitates with PRRSV nsp1β, nsp2, nsp2TF, nsp4, nsp7-nsp8, GP5, and N proteins. Drugs inhibiting actin polymerization or myosin IIA activation prevented nanotube formation and viral clusters in virus-infected cells. These data lead us to propose that PRRSV utilizes the host cell cytoskeletal machinery inside nanotubes for efficient cell-to-cell spread. This form of virus transport represents an alternative pathway for virus spread, which is resistant to the host humoral immune response.

IMPORTANCE

Extracellular virus particles transmit infection between organisms, but within infected hosts intercellular infection can be spread by additional mechanisms. In this study, we describe an alternative pathway for intercellular transmission of PRRSV in which the virus uses nanotube connections to transport infectious viral RNA, certain replicases, and certain structural proteins to neighboring cells. This process involves interaction of viral proteins with cytoskeletal proteins that form the nanotube connections. Intercellular viral spread through nanotubes allows the virus to escape the neutralizing antibody response and may contribute to the pathogenesis of viral infections. The development of strategies that interfere with this process could be critical in preventing the spread of viral infection.

MYH9 is an Essential Factor for Porcine Reproductive and Respiratory Syndrome Virus Infection

Porcine reproductive and respiratory syndrome (PRRS) caused by the PRRS virus (PRRSV) is an important swine disease worldwide. PRRSV has a limited tropism for certain cells, which may at least in part be attributed to the expression of the necessary cellular molecules serving as the virus receptors or factors on host cells for virus binding or entry. However, these molecules conferring PRRSV infection have not been fully characterized. Here we show the identification of non-muscle myosin heavy chain 9 (MYH9) as an essential factor for PRRSV infection using the anti-idiotypic antibody specific to the PRRSV glycoprotein GP5. MYH9 physically interacts with the PRRSV GP5 protein via its C-terminal domain and confers susceptibility of cells to PRRSV infection. These findings indicate that MYH9 is an essential factor for PRRSV infection and provide new insights into PRRSV-host interactions and viral entry, potentially facilitating development of control strategies for this important swine disease.

Efficacy of commercial genotype 1 porcine reproductive and respiratory syndrome virus (PRRSV) vaccine against field isolate of genotype 2 PRRSV

Although several recent studies have found that type 1 porcine reproductive and respiratory syndrome virus (PRRSV) modified live virus (MLV) vaccine showed appreciable levels of cross-protection against type 2 PRRSV infection, the possibility of cross-protection between two genotype of PRRSV is still controversial. To determine potential protective efficacy against hetero-genotype field strain of PRRSV and to improve understandings of the mechanisms underlying performance improvement after infection in vaccinated animals, piglets were vaccinated with type 1 PRRSV MLV vaccine and challenged with type 2 field strain of PRRSV. As a result, vaccinated animals gained on average 8.45 kg in comparison to 4.77 kg measured in non-vaccinated animals during a 3-week period after viral challenge, which shows using a certain PRRSV vaccine could be clinically effective against heterologous genotypic virus challenge. In vaccinated animals, viremia was reduced and cleared rapidly, whilst viral load was much higher and reduced more slowly, indicating rebound viremia in non-vaccinated animals. The titers of neutralizing antibody against the type 2 PRRSV did not exceed the protective level in any animal from both vaccinated and control groups. Instead, antibody avidity of vaccinated animals was much higher than in the control group clearly. Furthermore, a strong negative correlation between antibody avidity and viremia was noted in 80% of vaccinated animals. Through those results from tests evaluating degree of antibody maturation and its relevance with clearing viremia, it could be suggested that non-neutralizing antibodies induced by vaccination prior to challenge might play a key role in protection against PRRSV infection, especially in early time course.

Effect of Nonstructural Protein 2 Hypervariable Regions in the Replication of Porcine Reproductive and Respiratory Syndrome Virus in Marc-145 Cells

BACKGROUND

Highly pathogenic (HP) porcine reproductive and respiratory syndrome virus (PRRSV) causes prolonged high fever, red discoloration of the body, blue ears and a high mortality. Previously, we found that the PRRSV vaccine strain TJM contained a deletion of 120 amino acids (aa 628-747) in nonstructural protein 2 (Nsp2). We aimed to explore the replication features of PRRSV after adding the transiently expressed product of these 120 aa in vitro.

METHODS

We constructed seven eukaryotic expression plasmids containing different parts of the 120-aa sequence, transfected them into Marc-145 cells and then inoculated the cells with 103 TCID50 TJM per well. We detected virus replication at mRNA and protein level by real-time RT-PCR and Western blotting, respectively, and determined the virus titer.

RESULTS

The transiently expressed 120 aa and one of its truncated polypeptides inhibited PRRSV TJM propagation on Marc-145 cells. The complete 120-aa sequence induced a remarkable decrease in PRRSV replication, causing a reduction in structural protein levels between 36 and 48 h after infection. Additionally, aa 628-727 partly reduced the replication of PRRSV on Marc-145 cells.

CONCLUSIONS

The 120 aa from Nsp2, especially aa 628-727, play a negative role in PRRSV TJM proliferation.