A novel recombinant porcine reproductive and respiratory syndrome virus with significant variation in cell adaption and pathogenicity

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.

Ursonic acid from medicinal herbs inhibits PRRSV replication through activation of the innate immune response by targeting the phosphatase PTPN1

Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), has caused substantial economic losses to the global swine industry due to the lack of effective commercial vaccines and drugs. There is an urgent need to develop alternative strategies for PRRS prevention and control, such as antiviral drugs. In this study, we identified ursonic acid (UNA), a natural pentacyclic triterpenoid from medicinal herbs, as a novel drug with anti-PRRSV activity in vitro. Mechanistically, a time-of-addition assay revealed that UNA inhibited PRRSV replication when it was added before, at the same time as, and after PRRSV infection was induced. Compound target prediction and molecular docking analysis suggested that UNA interacts with the active pocket of PTPN1, which was further confirmed by a target protein interference assay and phosphatase activity assay. Furthermore, UNA inhibited PRRSV replication by targeting PTPN1, which inhibited IFN-β production. In addition, UNA displayed antiviral activity against porcine epidemic diarrhoea virus (PEDV) and Seneca virus A (SVA) replication in vitro. These findings will be helpful for developing novel prophylactic and therapeutic agents against PRRS and other swine virus infections.

Diltiazem HCl suppresses porcine reproductive and respiratory syndrome virus infection in susceptible cells and in swine

Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen for swine, resulting in substantial economic losses to the swine industry. However, there has been little success in developing effective vaccines or drugs for PRRSV control. In the present study, we discovered that Diltiazem HCl, an inhibitor of L-type Ca2+ channel, effectively suppresses PRRSV replication in MARC-145, PK-15CD163 and PAM cells in dose-dependent manner. Furthermore, it demonstrates a broad-spectrum activity against both PRRSV-1 and PRRSV-2 strains. Additionally, we explored the underlying mechanisms and found that Diltiazem HCl -induced inhibition of PRRSV associated with regulation of calcium ion homeostasis in susceptible cells. Moreover, we evaluated the antiviral effects of Diltiazem HCl in PRRSV-challenged piglets, assessing rectal temperature, viremia, and gross and microscopic lung lesions. Our results indicate that Diltiazem HCl treatment alleviates PRRSV-induced rectal temperature spikes, pulmonary pathological changes, and serum viral load. In conclusion, our data suggest that Diltiazem HCl could serve as a novel therapeutic drug against PRRSV infection.

Whole-genome analysis of the recombination and evolution of newly identified NADC30-like porcine reproductive and respiratory syndrome virus strains circulated in Gansu province of China in 2023

Porcine reproductive and respiratory syndrome virus (PRRSV) remains one of the major threats to swine industry, resulting in huge economic losses worldwide. Currently, PRRSV has diversified into multiple lineages with characteristics of extensive recombination in China. In this research, three virus strains were isolated and four virus whole genome sequences were generated and analyzed from clinical samples collected in Gansu province of China in 2023. The four virus strains were designated GSTS4-2023, GSLX2-2023, GSFEI2-2023 and GSBY4-2023. Phylogenetic analysis based on ORF5 sequences showed that GSTS4-2023, GSLX2-2023, GSFEI2-2023 and GSBY4-2023 shared 91.7, 91.2, 93.2 and 92.9% homology with NADC30 strain respectively, and belonged to lineage 1 of PRRSV-2. In addition, one amino acid deletion was observed at position 33 in ORF5 of GSTS4-2023, GSLX2-2023 and GSFEI2-2023. Moreover, amino acid alignment of the four strains showed a typical discontinuous 131-amino acid (aa) deletion in NSP2 for NADC30-like virus strains. Recombination analysis revealed that all four strains originated from NADC30 (lineage 1), with their minor parents coming from JXA1-like strains (lineage 8), VR-2332-like strains (lineage5) and QYYZ-like strains (lineage3). Finally, the three isolated virus strains, GSTS4-2023, GSLX2-2023 and GSFEI2-2023 showed relatively low levels of replication in cell culture. Our findings provide important implications for the field epidemiology of PRRSV.

Vidofludimus inhibits porcine reproductive and respiratory syndrome virus infection by targeting dihydroorotate dehydrogenase

Porcine reproductive and respiratory syndrome virus (PRRSV) infection has caused huge economic losses in global swine industry over the last 37 years. PRRSV commercial vaccines are not effective against all epidemic PRRSV strains. In this study we performed a high-throughput screening (HTS) of an FDA-approved drug library, which contained 2339 compounds, and found vidofludimus (Vi) could significantly inhibits PRRSV replication in Marc-145 cells and primary porcine alveolar macrophages (PAMs). Compounds target prediction, molecular docking analysis, and target protein interference assay showed that Vi interacts with dihydroorotate dehydrogenase (DHODH), a rate-limiting enzyme in the de novo pyrimidine synthesis pathway. Furthermore, PRRSV infection was restored in the presence of excess uridine and cytidine which promote pyrimidine salvage, or excess orotate which is the product of DHODH in the de novo pyrimidine biosynthesis pathway, thus confirming that the antiviral effect of Vi against PRRSV relies on the inhibition of DHODH. In addition, Vi also has antiviral activity against Seneca virus A (SVA), encephalomyocarditis virus (EMCV), porcine epidemic diarrhea virus (PEDV), and pseudorabies virus (PRV) in vitro. These findings should be helpful for developing a novel prophylactic and therapeutic strategy against PRRSV and other swine viral infections.

Epidemiological investigation and pathogenicity of porcine reproductive and respiratory syndrome virus in Sichuan, China

Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) lineage 8 was first detected in mainland China in 2006 and has since rapidly spread to become the primary epidemic strain in the country. In this study, samples such as lung tissue, hilar lymph nodes, abortion fetuses, and blood were collected from large-scale pig farms across 11 prefecture-level cities in Sichuan province between 2019 and 2020 for antigen detection and PRRS virus isolation. The antigen detection results indicated that the positive rate of HP-PRRSV (JXA1-Like strain) was 44.74% (51/114), NADC30-Like PRRSV was 17.54% (20/114), and classical PRRSV (VR2332-Like strain) was 37.72% (43/114). The predominant strain was HP-PRRSV. Positive samples were further inoculated into Marc-145 cells for virus isolation and identification, leading to the isolation of a new JXA1-Like PRRSV strain named SCSN2020. The strain was characterized by RT-qPCR, indirect immunofluorescence assay (IFA), plaque purification, electron microscopy, and whole genome sequencing. The total length of the viral genome was determined to be approximately 15,374 bp. A comparison of the SCSN2020 genome with VR2332 revealed that both strains had the same discontinuous 30-amino acid deletion on the Nsp2 gene. ORF5 genotyping classified the SCSN2020 strain as sublineage 8.7, with a whole genome sequence identity of 99.34% with JXA1. Furthermore, we evaluated the pathogenicity of the SCSN2020 strain in 28-day-old piglets and observed persistent fever from day 4 to day 10, weight loss started on day 7, dyspnea and severe lung lesions began started on day 14. The results of this study highlight the current PRRSV epidemic situation in Sichuan province and provide a scientific reference for subsequent prevention and control measures.

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.

Autophagy induced by Rab1a-ULK1 interaction promotes porcine reproductive and respiratory syndrome virus replication

Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus from the Nidovirales order, continues to be a threat to the swine industry worldwide causing reproductive failure and respiratory disease in pigs. Previous studies have demonstrated that autophagy plays a positive role in PRRSV replication. However, its mechanism is less clearly understood. Herein, we report first that the protein level of Rab1a, a member of the Ras superfamily of GTPases, is upregulated during PRRSV infection. Subsequently, we demonstrate that Rab1a enhances PRRSV replication through an autophagy pathway as evidenced by knocking down the autophagy-related 7 (ATG7) gene, the key adaptor of autophagy. Importantly, we reveal that Rab1a interacts with ULK1 and promotes ULK1 phosphorylation dependent on its GTP-binding activity. These data indicate that PRRSV utilizes the Rab1a-ULK1 complex to initiate autophagy, which, in turn, benefits viral replication. These findings further highlight the interplay between PRRSV replication and the autophagy pathway, deepening our understanding of PRRSV infection.

Molecular Characterization of the Nsp2 and ORF5s of PRRSV Strains in Sichuan China during 2012-2020

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that poses a serious threat to the global pig industry. Sichuan Province is one of the largest pig breeding provinces in China. There is a lack of reports on the continuous surveillance and systematic analysis of prevalent strains of PRRSV in Sichuan Province in recent years. To fill this gap, a total of 539 samples were collected from 13 breeding regions in Sichuan during 2012-2020. The detection result showed that the positive rate of PRRSV was 52.32% (282/539). The ORF5s and Nsp2 were obtained and further analyzed, with Chinese reference strains downloaded from the GenBank. Phylogenetic analysis showed that the PRRSV strains sequenced in this study belonged to PRRSV-1 and PRRSV-2 (lineage 1, 3, 5 and 8). In total, 168 PRRSV-2 strains were selected for ORF5 analyses, and these strains were classified into sub-lineage 8.7 (HP-PRRSV), sub-lineage 5.1 (classical PRRSV), sub-lineage 1.8 (NADC30-like), sub-lineage 1.5 (NADC34-like) and sub-lineage 3.5 (QYYZ-like), accounting for 60.71% (102/168), 11.31% (19/168), 18.45% (31/168), 2.97% (5/168) and 6.55% (11/168) of the total analyzed strains, respectively. The Nsp2 of identified PRRSV strains exhibited a nucleotide identity of 44.5-100%, and an amino acid identity of 46.82-100%. The ORF5 of the identified PRRSV strains exhibited a nucleotide identity of 81.3-100%, and an amino acid identity of 78.5-100%. A sequence analysis of ORF5 revealed that the mutation sites of GP5 were mainly concentrated in HVR1 and HVR2 and the virulence sites. In summary, the HP-PRRSV, NADC30-like PRRSV, Classic-PRRSV, QYYZ-like PRRSV, NADC34-like PRRSV and PRRSV-1 strains exist simultaneously in pigs in Sichuan. NADC30-like PRRSV was gradually becoming the most prevalent genotype currently in Sichuan province. This study suggested that PRRSV strains in Sichuan were undergoing genomic divergence.

CD163-Expressing Porcine Macrophages Support NADC30-like and NADC34-like PRRSV Infections

Porcine reproductive and respiratory syndrome virus (PRRSV) has a strict cell tropism. In addition to the primary alveolar macrophages, PRRSV is strictly cytotropic to African green monkey kidney cells, such as MARC-145 cells; however, MARC-145 cells are not infected by most NADC30-like and NADC34-like PRRSV strains. The essential scavenger receptor CD163 has been proved to mediate productive infection of PRRSV in various non-permissive cell lines. In this study, we systematically tested the porcine CD163 stably expressing 3D4/21 cells for infections with various PRRSV strains. The results showed that the porcine CD163-expressing macrophages support the infections of PRRSV2 of lineages 1, 5, and 8, as evidenced by Western blotting, immunofluorescence assay, quantitative PCR, and virus titration assay. Considering the current prevalence of NADC30-like and NADC34-like PRRSV2 of lineage 1 in China, the CD163-expressing macrophages are very useful for PRRSV research and disease management.

Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021

In the last decade, the emergence of QYYZ-like porcine reproductive and respiratory syndrome virus (PRRSV) has attracted increasing attention due to the high incidence of PRRSV mutation and recombination. However, the endemic status and genomic characteristics of the QYYZ-like strains are unclear. From 2018 to October 2021, 24 QYYZ-like PRRSV isolates were obtained from 787 PRRSV-positive clinical samples. Only one QYYZ-like positive sample was from a northern province, and the rest were from central and southern provinces. We selected 9 samples for whole-genome sequencing, revealing genome lengths of 15,008–15,316 nt. We retrieved all the available whole-genome sequences of QYYZ-like PRRSVs isolated in China from 2010 to 2021 (n = 28) from GenBank and analyzed them together with the new whole-genome sequences (n = 9). Phylogenetic tree analysis based on the ORF5 gene showed that all QYYZ-like PRRSV strains belonged to sublineage 3.5 but were clustered into three lineages (sublineage 1.8, sublineage 3.5, and sublineage 8.7) based on whole-genome sequences. Genomic sequence alignment showed that QYYZ-like strains, have characteristic amino acids insertions or deletions in the Nsp2 region (same as NADC30, JXA1 and QYYZ) and that thirteen strains also had additional amino acid deletions, mostly between 468 and 518 aa. Moreover, QYYZ-like strains (sublineage 3.5) have seven identical characteristic amino acid mutations in ORF5. Recombination analysis revealed that almost all QYYZ-like complete genome sequences (36/37) were products of recombination and mainly provided structural protein fragments (GP2-N) for the recombinant strains. Overall, QYYZ-like strains were mainly prevalent in central and southern China from 2018 to 2021, and these strains provided recombinant fragments in the PRRSV epidemic in China.

Genetic characterization and pathogenicity of a novel recombinant PRRSV from lineage 1, 8 and 3 in China failed to infect MARC-145 cells

The diversity of porcine reproductive and respiratory syndrome virus (PRRSV) in China is increasing rapidly along with mutation and recombination. Recombination could occur between inter- and intra-lineage of PRRSV, which accelerated the complexity of pathogenicity and cell tropism of the recombinant strain. In the present study, a novel PRRSV strain named HN-YL1711 was isolated from a pig farm suffering from severe respiratory difficulty in Henan province, China. The whole genomic sequence analysis indicated that the genome of HN-YL1711 was 15018 nt. It shared 86%, 87.3%, 88.1%, 91.1%, 84.2%, and 84.1% nucleotide similarities with PRRSVs VR2332, CH1a, JXA1, NADC30, QYYZ, and GM2, respectively. Based on phylogenetic analysis of Nsp2, ORF5 and complete genomes, HN-YL1711 was classified into lineage 1 of PRRSV. However, seven genomic break points were detected in recombination analysis, which indicated that the HN-YL1711 originated from multiple recombination among NADC30-like (major parent, lineage 1), JXA1-like (minor parent, lineage 8), and QYYZ-like (minor parent, lineage 3) PRRSV. Porcine alveolar macrophages (PAMs), 3D4/21-CD163 and MARC-145 cells were used to explore the viral adaptation of HN-YL1711. The results indicated that it could infect the PAMs but failed to infect MARC-145 cells. Challenge experiments showed that HN-YL1711 exhibits intermediate virulence in pigs, compared with HP-PRRSV JXA1 and LP-PRRSV CH1a. Taken together, our findings suggest that recombination remains an important factor in PRRSV evolution and that recombination further complicates the cell tropism and pathogenicity of PRRSV.

Emergence and spread of NADC34-like PRRSV in Southwest China

In recent years, NADC34-like PRRSV had a strong impact on the pig industry in the United States and Peru; it was also detected in northeastern China in 2017. In this study, we conducted a retrospective survey of NADC34-like PRRSV in Southwest China from 2016 to 2020. Five NADC34-like PRRSV strains were detected in samples and their whole genomes were sequenced, designated as CHSCMY-22019, CHSCYB-32020, CHSCMS-42020 and CHSCLS-22020. This is the first discovery and report of an NADC34-like PRRSV strain in Southwest China. Phylogenetic tree analysis based on the whole genome showed that the five NADC34-like PRRSV strains belonged to sub-lineage 1.5 of PRRV-2. They had 100 aa deletions in the Nsp2 hypervariable region of VR2332, located at 329 to 428 aa, similar to the US isolate IA/2014/NADC34. Recombination analysis showed that CHSCCD-42020 strain was the recombinant strain of QYYZ strain and IA/2014/NADC34 strain in China. The emergence of NADC34-like PRRSV strains in Southwest China indicates a potential threat to PRRS prevention and control in pigs. This study improves our understanding of the epidemic status and genetic variation of NADC34-like PRRSV strains in China. This article is protected by copyright. All rights reserved.

The Role of Pathology in the Diagnosis of Swine Respiratory Disease

The definition “porcine respiratory disease complex” (PRDC) is used to indicate the current approach for presenting respiratory pathology in modern pig farming. PRDC includes pneumonias with variable pictures, mixed with both aerogenous and hematogenous forms with variable etiology, often multimicrobial, and influenced by environmental and management factors. The notion that many etiological agents of swine respiratory pathology are ubiquitous in the airways is commonly understood; however, their isolation or identification is not always associable with the current pathology. In this complex context, lung lesions registered at slaughterhouse or during necropsy, and supplemented by histological investigations, must be considered as powerful tools for assigning a prominent role to etiologic agents. In recent years, the goal of colocalizing causative agents with the lesions they produce has been frequently applied, and valid examples in routine diagnostics are those that indicate pulmonary involvement during porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) infections.

Porcine reproductive and respiratory syndrome virus genetic variability a management and diagnostic dilemma

As genetic analysis becomes less expensive, more comprehensive diagnostics such as whole genome sequencing (WGS) will become available to the veterinary practitioner. The WGS elucidates more about porcine reproductive and respiratory syndrome virus (PRRSV) beyond the traditional analysis of open reading frame (ORF) 5 Sanger sequencing. The veterinary practitioner will require a more complete understanding of the mechanics and consequences of PRRSV genetic variability to interpret the WGS results. More recently, PRRSV recombination events have been described in the literature. The objective of this review is to provide a comprehensive outlook for swine practitioners that PRRSV mutates and recombines naturally causing genetic variability, review the diagnostic cadence when suspecting recombination has occurred, and present theory on how, why, and where industry accepted management practices may influence recombination. As practitioners, it is imperative to remember that PRRS viral recombination is occurring continuously in swine populations. Finding a recombinant by diagnostic analysis does not ultimately declare its significance. The error prone replication, mutation, and recombination of PRRSV means exact clones may exist; but a quasispecies swarm of variable strains also exist adding to the genetic diversity. PRRSV nonstructural proteins (nsps) are translated from ORF1a and ORF1b. The arterivirus nsps modulate the hosts' immune response and are involved in viral pathogenesis. The strains that contribute the PRRSV replicase and transcription complex is driving replication and possibly recombination in the quasispecies swarm. Furthermore, mutations favoring the virus to evade the immune system may result in the emergence of a more fit virus. More fit viruses tend to become the dominant strains in the quasispecies swarm. In theory, the swine management practices that may exacerbate or mitigate recombination include immunization strategies, swine movements, regional swine density, and topography. Controlling PRRSV equates to managing the quasispecies swarm and its interaction with the host. Further research is warranted on the frequency of recombination and the genome characteristics impacting the recombination rate. With a well-defined understanding of these characteristics, the clinical implications from recombination can be detected and potentially reduced; thus, minimizing recombination and perhaps the emergence of epidemic strains.

Glyceraldehyde-3-Phosphate Dehydrogenase Restricted in Cytoplasmic Location by Viral GP5 Facilitates Porcine Reproductive and Respiratory Syndrome Virus Replication via Its Glycolytic Activity

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important endemic swine pathogens, causing enormous losses in the global swine industry. Commercially available vaccines only partially prevent or counteract the virus infection and correlated losses. PRRSV's replication mechanism has not been well understood. In this study, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was screened to bind with the viral major envelope glycoprotein 5 (GP5) after PRRSV infection. The interacting sites are located within a 13-amino-acid (aa) region (aa 93 to 105) of GP5 and at Lys227 of GAPDH. Interestingly, viral GP5 restricts the translocation of GAPDH from the cytoplasm to the nucleus. Moreover, cytoplasmic GAPDH facilitates PRRSV replication by virtue of its glycolytic activity. The results suggest that PRRSV GP5 restricts GAPDH to the nucleus and exploits its glycolytic activity to stimulate virus replication. The data provide insight into the role of GAPDH in PRRSV replication and reveal a potential target for controlling viral infection. IMPORTANCE PRRSV poses a severe economic threat to the pig industry. PRRSV GP5, the major viral envelope protein, plays an important role in viral infection, pathogenicity, and immunity. However, interactions between GP5 and host proteins have not yet been well studied. Here, we show that GAPDH interacts with GP5 through binding a 13-aa sequence (aa 93 to 105) in GP5, while GP5 interacts with GAPDH at the K277 amino acid residue of GAPDH. We demonstrate that GP5 interacts with GAPDH in the cytoplasm during PPRSV infection, inhibiting GAPDH entry into the nucleus. PRRSV exploits the glycolytic activity of GAPDH to promote viral replication. These results enrich our understanding of PRRSV infection and pathogenesis and open a new avenue for antiviral prevention and PRRSV treatment strategies.

Molecular Characterization of the Nsp2 and ORF5 (ORF5a) Genes of PRRSV Strains in Nine Provinces of China During 2016-2018

Porcine reproductive and respiratory syndrome virus (PRRSV) causes a highly contagious disease and brings huge economic losses to commercial pork production worldwide. PRRSV causes severe reproductive failure in sows and respiratory distress in piglets. To trace the evolution of PRRSV in pigs with respiratory diseases in some regions of China, 112 samples were collected from nine provinces in China during 2016–2018. All samples were detected by RT-PCR and analyzed by the Nsp2/ORF5 (ORF5a)-genes-phylogeny. Sequence analysis and recombination analysis were conducted on the Nsp2/ORF5 (ORF5a) genes of the identified strain in the study. The RT-PCR result shown that the positive rate of PRRSV was 50.89% (57/112). Phylogenetic analysis showed that the identified PRRSV strains were all NA genotype and belonged to lineage 1, 3, and 8. The Nsp2 gene of identified PRRSV strains exhibited nucleotide homologies of 53.0 ~ 99.8%, and amino acid homologies of 46.8 ~ 99.7%. The ORF5 gene of identified PRRSV strains exhibited nucleotide homologies of 82.4 ~ 100%, and amino acid homologies of 79.6 ~ 100%. Sequence analysis revealed that a discontinuous 30-amino-acid deletion (positions 481 and 533–561) and a 131-amino-acid discontinuity deletion (positions 323–433, 481, and 533–551) in Nsp2 of PPRSV isolates; all identified strains in this study may be wild strains, and most identified strains may be highly virulent strains. Sequence analysis of ORF5 and ORF5a revealed that the mutation sites of GP5 were mainly concentrated in the signal peptide and epitopes region, while the mutation sites of ORF5a were mainly concentrated in the transmembrane and the intramembrane region. The recombination analysis indicated that there may be multiple recombination regions in identified strains, and the recombination pattern was more complex. This study showed that the prevalent PRRSV strain in some regions of China was still HP-PRRSV, while NADC30 strain also occupied a certain proportion; different types of PRRSV strains showed different patterns and variation in China. This study suggested that the monitoring of PRRSV prevalence and genetic variation should be further strengthened.

Genomic characteristics and pathogenicity of a new recombinant strain of porcine reproductive and respiratory syndrome virus

Recombination is an important phenomenon that accelerates evolution and enriches the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV). Recombinant PRRSV isolates sometimes have different genetic backgrounds. In this study, we report a recombinant PRRSV (SD-YL1712) isolated from a pig farm. The genome of SD-YL1712 is 15,014 nucleotides in length, and its nucleotide and amino acid sequence conservation is higher than that of PRRSV strain JXA1 except within the NSP2 region. The NSP2 region of SDYL1712 shares the highest nucleotide (85.9%) and amino acid (84.1%) sequence identity with PRRSV strain NADC30. SD-YL1712 was found to contain a characteristic 131-amino-acid deletion in the NSP2 region. Two recombination breakpoints were detected at nt 2134 and nt 3958 within the NSP2 region, which revealed that SD-YL1712 originated from a recombination event between NADC30-like and HP-PRRSV-derived MLV-like strains. Interestingly, SD-YL1712 had an additional deletion at position 586, similar to that found in strain TJnh1501. Moreover, the pathogenicity of strain SD-YL1712 was found to be similar to that of HP-PRRSV JXA1, which was higher than that of the CH1a strain. Further analysis indicated that SD-YL1712 might be a transitional intermediate in the evolution of TJbd1401 to TJnh1501.

Epidemiology investigation of PRRSV discharged by faecal and genetic variation of ORF5

To obtain more information of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) transmission via faeces in/between farms, 360 swine faecal samples were randomly collected from different farms in China from 2017 to 2019. Sixty-two ORF5 genes were amplified by PCR from 120 positive samples identified by real-time RT-PCR and further characterized by sequencing. Phylogenetic analysis based on the ORF5 gene revealed that these strains can be divided into four lineages: lineage 1 (NADC30-like), lineage 3 (QYYZ-like), lineage 5.1 (VR2332-like) and lineage 8.7 (JXA1-like), with 62.9% (39/62) NADC30-like virus, 21% (13/62) QYYZ-like virus, 1.6% (1/62) VR2332-like virus and 14.5% (9/62) for JAX1-like virus. In particular, 14 PRRSVs including lineage 1, 5.1 and 8.7 can be isolated from 120 positive faecal samples, which further suggests that faecal transmission may be an important factor in the spread of PRRSV in farms. Full-length genome sequencing analysis showed that 14 isolates share 83.1%-97.7% homology with each other and 82.3%-96.1% identity with NADC30, 83.2%-99.7% with VR2332, 79.6%-87.2% with QYYZ and 82.6%-98.9% with JXA1 and CH-1a, and only 60.1%-60.7% with LV. Recombination events were observed in the six out of 14 strains. Collectively, the data of this study are useful for understanding the spread of PRRSV via faeces. Additionally, the virus was isolated from positive faecal samples, suggesting that faecal transmission may be an important factor in the spread of PRRSV in farms.

Porcine reproductive and respiratory syndrome virus Nsp4 cleaves ZAP to antagonize its antiviral activity

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important pathogens impacting the global swine industry. PRRSV has been recognized to modulate the host immune response through a number of mechanisms. In our previous study, we found that over-expression of ZAP, a zinc finger antiviral protein of host, could suppress PRRSV replication, but how PRRSV escape the restriction of ZAP under natural conditions was still unknown. In this study, We found PRRSV infection significantly down-regulate the endogenous ZAP protein expression in Marc-145 cells. And PRRSV nonstructural protein 4 (Nsp4), a 3C-like serine proteinase, was screened to be responsible for ZAP reduction. Nsp4 could cleave ZAP, depending on its protease activity. The anti-PRRSV activity of ZAP was antagonized by Nsp4 in Marc-145 cells. In addition, we identified a unique amino acid, serine 180 of Nsp4 was required for efficient degradation of ZAP, and the mutation at residue 180 could decrease the ability of recombinant PRRSV to degrade ZAP. Those findings reveal a manner of PRRSV Nsp4 antagonizing the antiviral activity of ZAP, and shed light on a new strategy evolved by PRRSV to escape the host defense.

Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) From 1996 to 2017 in China

Porcine reproductive and respiratory syndrome (PRRS) is one of the most devastating diseases of the global swine industry. The causative agent porcine reproductive and respiratory syndrome virus (PRRSV) was first isolated in China in 1996 and has evolved quickly during the last two decades. To fully understand virus diversity, epidemic situation in the field, and make future predictions, a total of 365 PRRSV strains were used for evolution and genome analysis in which 353 strains were isolated from mainland China. The results showed that high diversity was found among PRRSV isolates. Total PRRSV isolates could be divided into eight subgroups. Among these subgroups strains, Original HP-PRRSV, NADC30-like, and Intermediate PRRSV were the major epidemic PRRSV strains circling in the field and would play a major role in PRRS epidemic in the future. Deletions, insertions, and recombinations have occurred frequently in the PRRSV genome. Deletions were the main driving force of viral evolution before 2006 and may also contribute further to the virus' evolution in a relatively closed or low strain diversity circumstance. The recombinant strains could be divided into three groups: the Inner group, Extensional group, and Propagating group. The evolutionary directions of the isolates in the Extensional and Propagating groups have changed, and the routes of recombination in the Propagating group were analyzed and sorted into three types. The increases in recombinant strains and high rates of recombination in recent years indicate that recombination has played a very important role in the virus' evolution. Isolates, which incorporate the advantages of their parental strains, will influence PRRSV evolution and make adverse effects on PRRS control in the future.

Molecular and Cellular Mechanisms for PRRSV Pathogenesis and Host Response to Infection

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PRRSV has evolved to arm with various strategies to modify host antiviral response.

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Viral modulation of homeostatic cellular processes provides favorable conditions for PRRSV survival during infection.

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PRRSV modulation of cellular processes includes pathways for interferons, apoptosis, microRNAs, cytokines, autophagy, and viral genome recombination.

Porcine reproductive and respiratory syndrome virus (PRRSV) has caused tremendous amounts of economic losses to the swine industry for more than three decades, but its control is still unsatisfactory. A significant amount of information is available for host cell-virus interactions during infection, and it is evident that PRRSV has evolved to equip various strategies to disrupt the host antiviral system and provide favorable conditions for survival. The current study reviews viral strategies for modulations of cellular processes including innate immunity, apoptosis, microRNAs, inflammatory cytokines, and other cellular pathways.

Genetic characterization of a novel recombinant PRRSV2 from lineage 8, 1 and 3 in China with significant variation in replication efficiency and cytopathic effects

There are four major porcine reproductive and respiratory syndrome virus 2 (PRRSV2) lineages circulating in China based on classification system, including lineages 1 (NADC30-like), 3 (QYYZ-like), 5.1 (VR2332-like) and 8 (JXA1-like/CH-1a-Like), which leads to the potential recombination. In the present study, a novel variant of PRRSV2 strain named JS18-3 was isolated from piglets suffering severe breathing difficulties in Jiangsu Province of China in 2018. Full-length genome analysis indicated that JS18-3 shared 86.5%, 87.9%, 84.2%, 82.2% and 86.4% nucleotide similarity with PRRSVs CH-1a, JXA1, VR2332, QYYZ and NADC30, respectively. 4871-6635 of JS18-3 shared the highest identity of 99.3% in nucleotide sequence with HP-PRRSV representative strain JXA1 indicating ongoing evolution to HP-PRRSV. JS18-3 was classified into classical lineage 8 of PRRSV2 based on phylogenetic analysis of complete genome and ORF5. Genomic break points in structural (ORF3) and non-structural (NSP2, NSP3) regions of genomes were detected in recombination analysis. JS18-3 is a recombinant isolate from lineages 8, 1 and 3. Replication enhancement and severe cytopathic effects caused by JS18-3 were observed in Marc-145 cells and porcine alveolar macrophages (PAMs) as compared to JX07, a typical strain of lineage 8. Pathogenicity results indicated that piglets inoculated with JS18-3 presented persistent fever, dyspnoea, serious microscopic lung lesions and lymph node congestion. The study suggests that lineage 8 of PRRSV2 is involved in continuing evolution by genetic recombination and mutation leading to outbreaks in vaccinated pigs in China.

Efficacy Evaluation of Two Commercial Vaccines Against a Recombinant PRRSV2 Strain ZJnb16-2 From Lineage 8 and 3 in China

From 2010, novel recombinant lineage 3 of porcine reproductive and respiratory syndrome virus 2 (PRRSV2) has continuously emerged China, which has brought about clinical outbreaks of the disease. Previously, a PRRSV2 strain named ZJnb16-2 was identified as a recombinant virus from lineage 8 and 3. In this study, two modified-live vaccines VR2332 MLV and HuN4-F112, which belong to lineage 5 and 8 respectively, were used for efficacy evaluation against the challenge of ZJnb16-2. Piglets vaccinated with HuN4-F112 exhibited temporary fever, higher average daily weight gain, and mild clinical signs as compared to VR2332 MLV vaccinated and unvaccinated piglets upon ZJnb16-2 challenge. Both vaccines could inhibit virus replication in piglets at 21days post challenge (DPC). Cross-reactivity of interferon (IFN)-γ secreting cells against ZJnb16-2 were detected in both vaccinated piglets. The number of IFN-γ secreting cells against ZJnb16-2 in the vaccination group exhibited sustaining elevation after challenge. Results demonstrated that both vaccines provided partial protection against ZJnb16-2 infection. A cross-neutralization antibody against ZJnb16-2 was not detected in any vaccinated piglet before challenge. A low neutralizing antibody titer against ZJnb16-2 was detected after challenge. Besides, all the vaccinated piglets suffered from different degrees of lung pathological lesions, indicating neither VR2332 MLV nor HuN4-F112 provided full protection against ZJnb16-2. This study provides valuable guidelines to control the recombinant virus from lineage 8 and 3 infection with MLV vaccines in the field.

Therapeutic effect of Xanthohumol against highly pathogenic porcine reproductive and respiratory syndrome viruses

The infection by porcine reproductive and respiratory syndrome virus (PRRSV) has a severe impact on the world swine industry. However, commercially available vaccines provide only incomplete protection against this disease. Thus, novel approaches to control PRRSV infection are essential for the robust and sustainable swine industry. In our previous study, Xanthohumol (Xn), a prenylated flavonoid extracted for hops (Humulus lupulus L), was screened from 386 natural products to inhibit PRRSV proliferation and alleviate oxidative stress induced by PRRSV via the Nrf2-HMOX1 axis in Marc-145 cells. In this study, we furtherly found that Xn could inhibit PRRSV different sub-genotype strains infection with a low IC₅₀ value in porcine primary alveolar macrophages (PAMs). In addition, it caused decreased expression of interleukin (IL)-1β, IL-6, IL-8, and tumor necrosis factor-α in PAMs infected with PRRSV or treated with lipopolysaccharide. Animal challenge experiments showed that Xn effectively alleviated clinical signs, lung pathology, and inflammatory responses in lung tissues of pigs induced by highly pathogenic PRRSV infection. The results demonstrate that Xn is a promising therapeutic agent to combat PRRSV infections.

Xanthohumol inhibits PRRSV proliferation and alleviates oxidative stress induced by PRRSV via the Nrf2-HMOX1 axis

Porcine reproductive and respiratory syndrome virus (PRRSV) is a prevalent and endemic swine pathogen that causes significant economic losses in the global swine industry. Commercial vaccines provide limited protection against this virus, and no highly effective therapeutic drugs are yet available. In this study, we first screened a library of 386 natural products and found that xanthohumol (Xn), a prenylated flavonoid found in hops, displayed high anti-PRRSV activity by inhibiting PRRSV adsorption onto and internalization into cells. Transcriptome sequencing revealed that Xn treatment stimulates genes associated with the antioxidant response in the nuclear factor-erythroid 2-related factor 2 (Nrf2) signalling pathway. Xn causes increased expression of Nrf2, HMOX1, GCLC, GCLM, and NQO1 in Marc-145 cells. The action of Xn against PRRSV proliferation depends on Nrf2 in Marc-145 cells and porcine alveolar macrophages (PAMs). This finding suggests that Xn significantly inhibits PRRSV proliferation and decreases viral-induced oxidative stress by activating the Nrf2–HMOX1 pathway. This information should be helpful for developing a novel prophylactic and therapeutic strategy against PRRSV infection.

High-frequency mutation and recombination are responsible for the emergence of novel porcine reproductive and respiratory syndrome virus in northwest China

Porcine reproductive and respiratory syndrome (PRRS) is one of the most highly infectious diseases in the pig industry, resulting in enormous economic losses worldwide. In this study, a PRRS virus (PRRSV) strain was isolated from primary porcine alveolar macrophage cells in Xinjiang in northwest China. This new strain was sequenced and designated as XJzx1-2015, and its sequence was then compared to those of other representative PRRSV strains from around the world. Complete genomic characterisation showed that the full-length nucleotide sequence of XJzx1-2015 exhibited low-level similarity to NB/04 (91.6%), JXA1 (90.5%), CH-1a (90.2%), VR-2332 (86.9%), QYYZ (85.7%), and JL580 (82.2%), with the highest similarity to HK13 (91.7%) sequence identity. Nonstructural protein 2 (NSP2) and glycosylated protein (GP) 2 of XJzx1-2015 had deletions of five and two amino acids, respectively, corresponding to strain VR-2332 positions 475-479 and 173-174. Phylogenetic analysis based on complete genome sequences showed that XJzx1-2015 and four other strains from China formed a new subgenotype closely related to other sublineage 8.7 (JXA1-like) strains belonging to the North American genotype. However, phylogenetic analysis based on NSP2 and GP5 showed that XJzx1-2015 clustered with sublineage 8.7 (JXA1-like, CH-1a-like) and lineage 3 (QYYZ-like) strains, respectively. Recombination analysis indicated that XJzx1-2015 is an intersubgenotype recombinant of CH-1a-like and QYYZ-like strains. Overall, our findings demonstrate that XJzx1-2015 is a novel PRRSV strain with a significantly high frequency of mutation and a recombinant between lineage 3 and sublineage 8.7 identified in northwest China. These results provide important insights into PRRSV evolution.

Phylogeography, phylodynamics and the recent outbreak of lineage 3 porcine reproductive and respiratory syndrome viruses in China

Novel highly pathogenic porcine reproductive and respiratory syndrome viruses (PRRSVs) have attracted increasing attention owing to their continual high emergence and recent re-emergence. Recently, lineage 3 PRRSVs, belonging to the type 2 viruses, with novel characteristics and increased virulence have been continuously re-emerging in China, thereby posing a great threat to pig farming. However, available information about lineage 3 is limited. Here, we carried out molecular epidemiological investigations for PRRSV surveillance in most regions of China from 2007 to 2017. More than 3,000 samples were obtained, amounting to 73 sequences of lineage 3 viruses. The origin, demographic history and spread pattern of lineage 3 PRRSVs were investigated combining with the database globally. Phylogeography and phylodynamic analyses within a Bayesian statistical framework revealed that lineage 3 viruses originated in Taiwan. Followed by subsequent propagation to different areas and geography, it dichotomized into two endemic clusters. South China has become an epicentre for these viruses, which diffused into China's interiors in recent years. Furthermore, viral dispersal route analysis revealed the risk of viral diffusion. Overall, the origin, epidemic history and geographical evolution of lineage 3 PRRSVs were comprehensively analysed in this study. In particular, the epicentre of southern China and the diffusion routines of the viruses are highlighted in this study, and the possible continuous transmission of the novel lineages poses the biggest threat to pig farmers.

Emergence of two novel recombinant porcine reproductive and respiratory syndrome viruses 2 (lineage 3) in Southwestern China

The lineage 3 of porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) was first reported in mainland China in 2010 and it has spread rapidly in recent years. Here, two novel lineage 3 strains of PRRSV-2 were isolated from diseased pigs in Southwestern China during 2017-2018, and were designated as GZgy17 and SCya18. The complete genomes of the two isolates were then determined, and sequence alignment revealed that GZgy17 had the same discontinuous 30-amino acid (aa) deletion in NSP2 as JXA1, while SCya18 contained the discontinuous 131-aa deletion in NSP2 identical to that of NADC30, when compared to the strain VR-2332. Notably, GZgy17 contained an additional 19-aa deletion in NSP2, and SCya18 had a unique 3-nt deletion in its 3'UTR. Homology and phylogenetic analysis showed that GZgy17 and SCya18 shared low nucleotide homology (91.2-92.0%) with QYYZ and were classified into a new cluster of lineage 3 strains based on ORF5 genotyping. Recombination analyses revealed that GZgy17 and SCya18 both originated from a SH/CH/2016-like (lineage 3) strain and had recombined with a JXA1-like (lineage 8) and a NADC30-like (lineage 1) strain, respectively. Furthermore, we compared the virulence of the two strains in 4-week-old piglets. The results showed that GZgy17 caused mortality rates of 20% and exhibited higher pathogenicity in piglets compared to SCya18. Our findings suggest that recombination might be responsible for the variations in pathogenicity of lineage 3 strains of PRRSV-2 and highlight the importance of surveillance of this lineage in China.

Emergence of Two different recombinant PRRSV strains with low neutralizing antibody susceptibility in China

PRRSV causes major economic loss in global swine industry. 41 of 131 (31.29%) tissue samples collected from pig farms in central and east China from 2016 to 2017 were confirmed as PRRSV positive in RT-PCR. Base on phylogenetic analysis for ORF5 and ORF6, 3 isolates closely related to QYYZ strain form a new subgroup IV, while 3 other ones were clustered into subgroup III, represented by NADC30. Numerous amino acid substitutions involved in viral neutralization susceptibility were identified in GP5 among these isolates. Two emerging PRRSV strains (ZJnb16-2, SDbz16-2) were successfully isolated and sequenced. ZJnb16-2 was identified as a recombinant virus between strain QYYZ and JXA1 while SDbz16-2 was an inter-subgenotype recombinant virus of strains NADC30 and JXA1. As shown in the pathogenicity evaluation in piglets, ZJnb16-2 is highly pathogenic while SDbz16-2 is mild. Hyper-immune sera against major vaccine strains HUN4-F112 and JK-100 failed to neutralize either ZJnb16-2 or SDbz16-2. Only 0.8–2.0% of pig serum samples which were confirmed as PRRSV-positive with commercial ELISA kits presented neutralization reactivity against either ZJnb16-2 or SDbz16-2. The study confirmed that the viral genomic recombination contributes to the emergence of new pathogenic PRRSVs in China, which may escape from the protective immunity elicited by the conventional vaccines, highlighting the necessity in updates of vaccine strains and the need for a universal vaccine against PRRSV.

Emergence of novel recombination lineage 3 of porcine reproductive and respiratory syndrome viruses in Southern China

Lineage 3 of porcine reproductive and respiratory syndrome viruses, which belong to North America type 2, has a long epidemic history in China. The novel lineage 3 viruses constantly emerging in recent years are characterized by a high detection rate and significant pathogenicity. In this study, we investigated the prevalence of lineage 3 in southern China and selected two isolated strains for genome and virulence analyses. A cross-sectional epidemiology investigation indicated that the prevalence of lineage 3 antigens was 35.68% (95% CI: 27.6-44.3%) among 227 samples collected from over 100 infected farms from January 2016 to July 2017 in southern China. Two novel isolates of lineage 3 were selected. After 20 passages, Marc-145 cells were not susceptible to those viruses. Full-length genome analysis indicated that the two strains share 95.2% homology with each other and 95.7%-96.2% with highly pathogenic porcine reproductive and respiratory syndrome viruses (HP-PRRSVs; JXA1-like strain, lineage 8.7). Phylogenetic and molecular evolutionary results showed that for the two isolates, HP-PRRSV provides most of the ORF1 gene. Animal experiment revealed discrepancies in virulence between the strains. Although challenge resulted in 100% morbidity, the isolate carrying most of the HP-PRRSV ORF1 caused severe clinical symptoms and 40% mortality, whereas the other isolate containing part of the ORF1 gene caused no mortality. Overall, these findings suggest that lineage 3 viruses might be commonly circulating in most of southern China. Frequent recombination events within HP-PRRSVs of this lineage with changing virulence could represent potential threats to the pig industry.

Characterization of newly emerged NADC30-like strains of porcine reproductive and respiratory syndrome virus in China

Different strains of porcine reproductive and respiratory syndrome virus (PRRSV) have emerged and circulated in different regions of mainland China since 1996, particularly after 2006. In 2012, NADC30-like PRRSV was first isolated in Henan Province. By 2016, it had spread to most provinces in China. In the present study, the whole genomes (excluding the poly(A) tails) of 13 newly emerged NADC30-like PRRSV strains were sequenced and analyzed. Furthermore, the pathogenicity of SD53-1603, one of the 13 PRRSV strains, was assessed. Phylogenetic analysis showed that these 13 newly emerged NADC30-like PRRSV strains, together with some reference strains, formed a new subgroup (subgroup 5), characterized by a predicted 131-amino-acid deletion in the nonstructural protein (NSP) 2. However, low levels of whole-genome similarity and a wide variety of recombination patterns complicated the classification of the NADC30-like PRRSV isolates. Interestingly, almost all of the recombination breakpoints found in these 13 PRRSV isolates and other NADC30-like PRRSV isolates occurred in genes encoding NSPs and/or minor structural proteins. In addition, piglets infected with the newly emerged NADC30-like strain SD53-1603 displayed clear clinical respiratory symptoms and underwent typical pathological changes. The findings may be useful for elucidating the characteristics and epidemic status of NADC30-like PRRSV in China.

Genetic Characterization and Pathogenicity of a Novel Recombined Porcine Reproductive and Respiratory Syndrome Virus 2 among Nadc30-Like, Jxa1-Like, and Mlv-Like Strains

Recombination among porcine reproductive and respiratory syndrome viruses (PRRSVs), coupled with point mutations, insertions, and deletions occurring in the genome, is considered to contribute to the emergence of new variants. Here, we report the complete genome sequences of a PRRSV field strain, designated SCN17, isolated from a RespPRRS MLV-vaccinated piglet in China in 2017. Sequence alignment revealed that SCN17 had discontinuous 131-amino acid (111 + 1 + 19-aa) deletion in the NSP2-coding region identical to that of NADC30 when compared to VR-2332. Notably, the strain, SCN17, contained an additional 1-aa deletion in NSP2, a 1-aa deletion in ORF5, and a unique 3-nt deletion in the 3′-UTR. Phylogenetic analysis showed that SCN17 clustered into NADC30-like lineage based on ORF5 genotyping, whereas it belonged to an inter-lineage between the NADC30-like and VR-2332-like lineages as established based on the full-length genome. Importantly, the SCN17 was identified as a novel virus recombined between a NADC30-like (moderately pathogenic), a JXA1-like (highly pathogenic), and an attenuated vaccine strain, RespPRRS MLV (parental strain VR-2332). Furthermore, we tested its pathogenicity in piglets. SCN17 infection caused a persistent fever, moderate interstitial pneumonia, and increased the viremia and antibody levels in the inoculated piglets. Of note, all SCN17-infected piglets survived throughout the study. The new virus was showed to be a moderately virulent isolate and have lower pathogenicity than HP-PRRSV strain, SCwhn09CD. Our results provide evidence for the continuing evolution of PRRSV field strain by genetic recombination and mutation leading to outbreaks in the vaccinated pig populations in China.

Adaptions of field PRRSVs in Marc-145 cells were determined by variations in the minor envelope proteins GP2a-GP3

The recent rapid evolution of PRRSVs has resulted in certain biological characteristic changes, such as the fact that an increasing number of field PRRSVs can be isolated from PAMs but not from Marc-145 cells. In this study, we first isolated Marc-145-unadaptive field PRRSV strains from PAMs; sequence analysis showed that these PRRSVs belong to the HP-PRRSV (lineage 8) branch or NADC30-Like (lineage 1) branch. We further found major variations in ORF2-4 regions. To explore the viral adaptation mechanisms in detail, we constructed a full-length cDNA clone of MY-376, a Marc-145-unadaptive PRRSV. Construction of serially chimeric viruses of HuN4-F112 (a Marc-145-adaptive strain) and MY-376 demonstrated that variation in the minor envelope protein (GP2a and GP3) complex is a main determinant of PRRSV tropism for Marc-145 cells.

Whole Genome Analysis of Two Novel Type 2 Porcine Reproductive and Respiratory Syndrome Viruses with Complex Genome Recombination between Lineage 8, 3, and 1 Strains Identified in Southwestern China

Recombination among porcine reproductive and respiratory syndrome viruses (PRRSVs) is thought to contribute to the emergence of new PRRSV variants. In this study, two newly emerged PRRSV strains, designated SCcd16 and SCya17, are isolated from lung tissues of piglets in Southwestern China. Genome comparative analysis reveals that SCcd16/SCya17 exhibit 93.1%/93.2%, 86.9%/87.0%, 85.3%/85.7%, and 83.6%/82.0% nucleotide similarity to PRRSVs JXA1, VR-2332, QYYZ and NADC30, respectively. They only exhibit 44.8%/45.1% sequence identity with LV (PRRSV-1), indicating that both emergent strains belong to the PRRSV-2 genotype. Genomic sequence alignment shows that SCcd16 and SCya17 have the same discontinuous 30-amino acid (aa) deletion in Nsp2 of the highly pathogenic Chinese PRRSV strain JXA1, when compared to strain VR-2332. Notably, SCya17 shows a unique 5-nt deletion in its 3’-UTR. Phylogenetic analysis shows that both of the isolates are classified in the QYYZ-like lineage based on ORF5 genotyping, whereas they appear to constitute an inter-lineage between JXA1-like and QYYZ-like lineages based on their genomic sequences. Furthermore, recombination analyses reveal that the two newly emerged PRRSV isolates share the same novel recombination pattern. They have both likely originated from multiple recombination events between lineage 8 (JXA1-like), lineage 1 (NADC30-like), and lineage 3 (QYYZ-like) strains that have circulated in China recently. The genomic data from SCcd16 and SCya17 indicate that there is on going evolution of PRRSV field strains through genetic recombination, leading to outbreaks in the pig populations in Southwestern China.

Two Residues in NSP9 Contribute to the Enhanced Replication and Pathogenicity of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus

Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) possesses greater replicative capacity and pathogenicity than classical PRRSV. However, the factors that lead to enhanced replication and pathogenicity remain unclear. In our study, an alignment of all available full-length sequences of North American-type PRRSVs (n = 204) revealed two consistent amino acid mutations that differed between HP-PRRSV and classical PRRSV and were located at positions 519 and 544 in nonstructural protein 9. Next, a series of mutant viruses with either single or double amino acid replacements were generated from HP-PRRSV HuN4 and classical PRRSV CH-1a infectious cDNA clones. Deletion of either of the amino acids led to a complete loss of virus viability. In both Marc-145 and porcine alveolar macrophages, the replicative efficiencies of mutant viruses based on HuN4 were reduced compared to the parent, whereas the replication level of CH-1a-derived mutant viruses was increased. Plaque growth assays showed clear differences between mutant and parental viruses. In infected piglets, the pathogenicity of HuN4-derived mutant viruses, assessed through clinical symptoms, viral load in sera, histopathology examination, and thymus atrophy, was reduced. Our results indicate that the amino acids at positions 519 and 544 in NSP9 are involved in the replication efficiency of HP-PRRSV and contribute to enhanced pathogenicity. This study is the first to identify specific amino acids involved in PRRSV replication or pathogenicity. These findings will contribute to understanding the molecular mechanisms of PRRSV replication and pathogenicity, leading to better therapeutic and prognostic options to combat the virus.IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS), caused by porcine reproductive and respiratory syndrome virus (PRRSV), is a significant threat to the global pig industry. Highly pathogenic PRRSV (HP-PRRSV) first emerged in China in 2006 and has subsequently spread across Asia, causing considerable damage to local economies. HP-PRRSV strains possess a greater replication capacity and higher pathogenicity than classical PRRSV strains, although the mechanisms that underlie these characteristics are unclear. In the present study, we identified two mutations in HP-PRRSV strains that distinguish them from classical PRRSV strains. Further experiments that swapped the two mutations in an HP-PRRSV strain and a classical PRRSV strain demonstrated that they are involved in the replication efficiency of the virus and its virulence. Our findings have important implications for understanding the molecular mechanisms of PRRSV replication and pathogenicity and also provide new avenues of research for the study of other viruses.