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.

Immune evasion of porcine reproductive and respiratory syndrome virus through glycan shielding involves both glycoprotein 5 as well as glycoprotein 3.

Passive administration of porcine reproductive and respiratory syndrome virus (PRRSV) neutralizing antibodies (NAbs) can effectively protect pigs against PRRSV infection. However, after PRRSV infection, pigs typically develop a weak and deferred NAb response. One major reason for such a meager NAb response is the phenomenon of glycan shielding involving GP5, a major glycoprotein carrying one major neutralizing epitope. We describe here a type II PRRSV field isolate (PRRSV-01) that is highly susceptible to neutralization and induces an atypically rapid, robust NAb response in vivo. Sequence analysis shows that PRRSV-01 lacks two N-glycosylation sites, normally present in wild-type (wt) PRRSV strains, in two of its envelope glycoproteins, one in GP3 (position 131) and the other in GP5 (position 51). To determine the influence of these missing N-glycosylation sites on the distinct neutralization phenotype of PRRSV-01, a chimeric virus (FL01) was generated by replacing the structural genes of type II PRRSV strain FL12 cDNA infectious clone with those from PRRSV-01. N-glycosylation sites were reintroduced into GP3 and GP5 of FL01, separately or in combination, by site-directed mutagenesis. Reintroduction of the N-glycosylation site in either GP3 or GP5 allowed recovery of in vivo and in vitro glycan shielding capacity, with an additive effect when these sites were reintroduced into both glycoproteins simultaneously. Although the loss of these glycosylation sites has seemingly occurred naturally (presumably by passage through cell cultures), PRRSV-01 virus quickly regains these glycosylation sites through replication in vivo, suggesting that a strong selective pressure is exerted at these sites. Collectively, our data demonstrate the involvement of an N-glycan moiety located in GP3 in glycan shield interference.

Porcine reproductive and respiratory syndrome virus nonstructural protein 1beta modulates host innate immune response by antagonizing IRF3 activation.

Porcine reproductive and respiratory syndrome virus (PRRSV) infection of swine leads to a serious disease characterized by a delayed and defective adaptive immune response. It is hypothesized that a suboptimal innate immune response is responsible for the disease pathogenesis. In the study presented here we tested this hypothesis and identified several nonstructural proteins (NSPs) with innate immune evasion properties encoded by the PRRS viral genome. Four of the total ten PRRSV NSPs tested were found to have strong to moderate inhibitory effects on beta interferon (IFN-beta) promoter activation. The strongest inhibitory effect was exhibited by NSP1 followed by, NSP2, NSP11, and NSP4. We focused on NSP1alpha and NSP1beta (self-cleavage products of NSP1 during virus infection) and NSP11, three NSPs with strong inhibitory activity. All of three proteins, when expressed stably in cell lines, strongly inhibited double-stranded RNA (dsRNA) signaling pathways. NSP1beta was found to inhibit both IFN regulatory factor 3 (IRF3)- and NF-kappaB-dependent gene induction by dsRNA and Sendai virus. Mechanistically, the dsRNA-induced phosphorylation and nuclear translocation of IRF3 were strongly inhibited by NSP1beta. Moreover, when tested in a porcine myelomonocytic cell line, NSP1beta inhibited Sendai virus-mediated activation of porcine IFN-beta promoter activity. We propose that this NSP1beta-mediated subversion of the host innate immune response plays an important role in PRRSV pathogenesis.

Is the posterior cingulate cortex an on-off switch for tinnitus?: A comparison between hearing loss subjects with and without tinnitus.

As the human brain works in a Bayesian manner to minimize uncertainty toward external stimuli, the deafferented brain may generate tinnitus in an attempt to fill in missing auditory information, e.g. due to hearing loss. However, not everybody with hearing loss develops tinnitus. Understanding the differences between people with hearing loss who develop tinnitus versus those who do not offers a unique opportunity to unravel critical brain areas involved in the generation of a phantom sound. In this study, we compared resting-state quantitative electroencephalography between hearing loss patients with (HL-T) and without tinnitus (HL-NT) to identify cortical oscillatory signatures that may reveal prerequisites for the selective development of tinnitus in subjects with hearing loss. We enrolled 65 subjects with HL-NT and 65 subjects with HL-T whose tinnitus handicap inventory scores were <16 (grade 1) to minimize the bias induced by distress-induced cortical activity changes. Subjects in the HL-T and HL-NT groups were matched in terms of the bilateral hearing threshold (0.25-8 kHz) using nearest neighbor method. Compared to the HL-NT group, the HL-T group showed significantly higher activity in the right parahippocampus for the beta 1 frequency band, in the left inferior parietal lobule (IPL) for the beta 2 frequency band, and in the right IPL for the beta 3- and gamma frequency bands. Functional connectivity analyses revealed that the HL-T group had significantly higher connectivity than the HL-NT group between both parahippocampal gyri and the right IPL for the delta frequency band, and between the left posterior cingulate cortex (PCC) and right IPL for the beta 2 frequency band. These results suggest that tinnitus may be perceived only if auditory memory stored in the parahippocampus is actively linked to the IPL-based "circuit breaker" system and the circuit breaker signal is connected to the PCC-based default mode network (DMN). Thus, when the circuit breaker system regards tinnitus secondary to peripheral deafferentation as a salient event and then the DMN regards tinnitus as a norm, subjects with hearing loss may consciously perceive tinnitus. The results of this study further refine the recently proposed Bayesian model and decipher the neurobiological mechanism of the selective development of tinnitus in subjects with hearing loss.

Estimating PM2.5 concentration of the conterminous United States via interpretable convolutional neural networks.

We apply convolutional neural network (CNN) model for estimating daily 24-h averaged ground-level PM2.5 of the conterminous United States in 2011 by incorporating aerosol optical depth (AOD) data, meteorological fields, and land-use data. Unlike some of the recent supervised learning-based approaches, which only utilized the predictors from the location of which PM2.5 value is estimated, we naturally aggregate predictors from nearby locations such that the spatial correlation among the predictors can be exploited. We carefully evaluate the performance of our method via overall, temporally-separated, and spatially-separated cross-validations (CV) and show that our CNN achieves competitive estimation accuracy compared to the recently developed baselines. Furthermore, we develop a novel predictor importance metric for our CNN based on the recent neural network interpretation method, Layerwise Relevance Propagation (LRP), and identify several informative predictors for PM2.5 estimation.

Protective humoral immune response induced by an inactivated porcine reproductive and respiratory syndrome virus expressing the hypo-glycosylated glycoprotein 5.

Porcine reproductive and respiratory syndrome (PRRS) causes significant economic losses to the swine industry worldwide. Although inactivated and live vaccines are commercially available for the control of PRRS, both types of vaccine have not always proven successful in terms of generating a protective immune response, particularly in the case of inactivated vaccines. In this study, we tested whether an inactivated vaccine could induce a humoral immune response to PRRS during a homologous challenge. Amino acid substitutions were introduced into glycoprotein (GP) 5 of the FL12 strain of the PRRS virus (PRRSV) using site-directed mutagenesis with a pFL12 infectious clone. The substitutions led to double deglycosylation in the putative glycosylation moieties on GP5. The mutant virus was subsequently inactivated with binary ethylenimine. The efficacy of the inactivated mutant virus was compared with that of the inactivated wild-type PRRSV. Only the inactivated mutant PRRSV induced serum neutralizing antibodies at six weeks post-vaccination. The group that was administered the inactivated mutant virus twice exhibited a significantly increased neutralizing antibody titer after a challenge with the virulent homologous strain and exhibited more rapid clearing of viremia compared to other groups, including the groups that were administered either the inactivated mutant or wild-type virus only once and the group that was administered the inactivated wild-type virus twice. Histopathological examination of lung tissue sections revealed that the group that was administered the inactivated mutant virus twice exhibited significantly thinner alveolar septa, whereas the thickness of the alveolar septa of the other groups were markedly increased due to lymphocyte infiltration. These results indicated that the deglycosylation of GP5 enhanced the immunogenicity of the inactivated mutant PRRSV and that twice administrations of the inactivated mutant virus conferred better protection against the homologous challenge. These findings suggest that the inactivated PRRSV that expresses a hypo-glycosylated GP5 is a potential inactivated vaccine candidate and a valuable tool for controlling PRRS for the swine industry.

Characterization of a serologic marker candidate for development of a live-attenuated DIVA vaccine against porcine reproductive and respiratory syndrome virus.

DIVA (differentiating infected from vaccinated animals) vaccines have proven extremely useful for control and eradication of infectious diseases in livestock. We describe here the characterization of a serologic marker epitope, so-called epitope-M201, which can be a potential target for development of a live-attenuated DIVA vaccine against porcine reproductive and respiratory syndrome virus (PRRSV). Epitope-M201 is located at the carboxyl terminus (residues 161-174) of the viral M protein. The epitope is highly immunodominant and well-conserved among type-II PRRSV isolates. Rabbit polyclonal antibodies prepared against this epitope are non-neutralizing; thus, the epitope does not seem to contribute to the protective immunity against PRRSV infection. Importantly, the immunogenicity of epitope-M201 can be disrupted through the introduction of a single amino acid mutation which does not adversely affect the viral replication. All together, our results provide an important starting point for the development of a live-attenuated DIVA vaccine against type-II PRRSV.

Amino acid residues in the non-structural protein 1 of porcine reproductive and respiratory syndrome virus involved in down-regulation of TNF-α expression in vitro and attenuation in vivo.

Porcine reproductive and respiratory syndrome virus (PRRSV) suppresses tumor necrosis factor-alpha (TNF-α) production at both transcriptional and post-transcriptional levels by its non-structural proteins 1α and 1ß (Nsp1α and Nsp1ß). To identify the amino acid residues responsible for this activity, we generated several alanine substitution mutants of Nsp1α and Nsp1ß. Examination of the mutant proteins revealed that Nsp1α residues Gly90, Asn91, Arg97, Arg100 and Arg124 were necessary for TNF-α promoter suppression, whereas several amino acids spanning the entire Nsp1ß were found to be required for this activity. Two mutant viruses, with mutations at Nsp1α Gly90 or Nsp1ß residues 70-74, generated from infectious cDNA clones, exhibited attenuated viral replication in vitro and TNF-α was found to be up regulated in infected macrophages. In infected pigs, the Nsp1ß mutant virus was attenuated in growth. These studies provide insights into how PRRSV evades the effector mechanisms of innate immunity during infection.

Identification of amino acid residues important for anti-IFN activity of porcine reproductive and respiratory syndrome virus non-structural protein 1.

The non-structural protein 1 (nsp1) of porcine reproductive and respiratory syndrome virus is partly responsible for inhibition of type I interferon (IFN) response by the infected host. By performing alanine-scanning mutagenesis, we have identified amino acid residues in nsp1α and nsp1ß (the proteolytic products of nsp1) that when substituted with alanine(s) exhibited significant relief of IFN-suppression. A mutant virus (16-5A, in which residues 16-20 of nsp1ß were substituted with alanines) encoding mutant nsp1ß recovered from infectious cDNA clone was shown to be attenuated for growth in vitro and induced significantly higher amount of type I IFN transcripts in infected macrophages. In infected pigs, the 16-5A virus exhibited reduced growth at early times after infection but quickly regained wild type growth properties as a result of substitutions within the mutated sequences. The results indicate a strong selection pressure towards maintaining the IFN-inhibitory property of the virus for successful propagation in pigs.

Evaluation of monoclonal antibody-based immunohistochemistry for the detection of European and North American Porcine reproductive and respiratory syndrome virus and a comparison with in situ hybridization and reverse transcription polymerase chain reaction.

The objective of the present study was to compare the ability of 2 monoclonal antibodies (mAbs; SDOW17 and SR30) to detect types 1 and 2 Porcine reproductive and respiratory syndrome virus (PRRSV) in formalin-fixed, paraffin-embedded (FFPE) lung tissues by immunohistochemistry (IHC) and to compare the immunohistochemical results with in situ hybridization (ISH) and reverse transcription nested polymerase chain reaction (RT-nPCR) detection techniques. Lungs from 30 experimentally infected pigs (15 pigs with each genotype of PRRSV) and 20 naturally infected pigs (10 pigs with each genotype of PRRSV) with types 1 and 2 PRRSV, respectively, were used for the IHC, ISH, and RT-nPCR analyses. The SR30 mAb-based IHC detected significantly more type 1 PRRSV-positive cells in the accessory and caudal lobes from the experimentally infected pigs at 7 (P = 0.025) and 14 (P = 0.018) days postinoculation, respectively, compared to the SDOW17 mAb-based IHC. The results demonstrated that SR30 mAb-based IHC is useful for detecting both types 1 and 2 PRRSV antigen in FFPE lung tissues.

A virulent strain of porcine reproductive and respiratory syndrome virus does not up-regulate interleukin-10 levels in vitro or in vivo.

Porcine reproductive and respiratory syndrome virus (PRRSV) causes reproductive failure and respiratory illness in infected pigs. It has been postulated that the ability of PRRSV to induce the anti-inflammatory cytokine interleukin-10 (IL-10) in macrophages of infected pigs would be important for PRRSV immunopathogenesis, although this property would be variable and might be dependent on the strain. Several strains were reported to induce IL-10 in infected macrophages while others would not. In this study, we analyzed the IL-10 expression during in vitro and in vivo infections by a well-characterized virulent strain of PRRSV, vFL12, which is derived from an infectious clone. Our results showed that the vFL12 strain did not up-regulate IL-10 at mRNA or protein levels in either infected macrophages or dendritic cells in vitro. Furthermore, immunofluorescence staining for IL-10 on tonsil sections of PRRSV-infected pigs did not produce any evidence of IL-10 induction in PRRSV-infected cells or in bystander cells of the lymphoid tissues. Hence, based on these results obtained with a well-characterized highly pathogenic PRRSV strain it may be concluded that the induction of IL-10 release is not a part of the PRRSV virulence mechanisms.

Glycosylation of minor envelope glycoproteins of porcine reproductive and respiratory syndrome virus in infectious virus recovery, receptor interaction, and immune response.

The role of N-glycosylation of the three minor envelope glycoproteins (GP2, GP3, and GP4) of porcine reproductive and respiratory syndrome virus (PRRSV) on infectious virus production, interactions with the receptor CD163, and neutralizing antibody production in infected pigs was examined. By mutation of the glycosylation sites in these proteins, the studies show that glycan addition at N184 of GP2, N42, N50 and N131 of GP3 is necessary for infectious virus production. Although single-site mutants of GP4 led to infectious virus production, mutation of any two sites in GP4 was lethal. Furthermore, the glycosylation of GP2 and GP4 was important for efficient interaction with CD163. Unlike PRRSVs encoding hypoglycosylated form of GP5 that induced significantly higher levels of neutralizing antibodies in infected piglets, PRRSVs encoding hypoglycosylated forms of GP2, GP3 or GP4 did not. These studies reveal the importance of glycosylation of these minor GPs in the biology of PRRSV.

Porcine reproductive and respiratory syndrome virus non-structural protein 1 suppresses tumor necrosis factor-alpha promoter activation by inhibiting NF-κB and Sp1.

The objective of this study was to identify porcine reproductive and respiratory syndrome virus (PRRSV)-encoded proteins that are responsible for the inhibition of TNF-α expression and the mechanism(s) involved in this phenomenon. Using a TNF-α promoter reporter system, the non-structural protein 1 (Nsp1) was found to strongly suppress the TNF-α promoter activity. Such inhibition takes place especially at the promoter's proximal region. Both Nsp1α and Nsp1ß, the two proteolytic fragments of Nsp1, were shown to be involved in TNF-α promoter suppression. Furthermore, using reporter plasmids specific for transcription factors (TFs) that bind to TNF-α promoter, Nsp1α and Nsp1ß were demonstrated to inhibit the activity of the TFs that bind CRE-κB(3) and Sp1 elements respectively. Subsequent analyses showed that Nsp1α moderately inhibits NF-κB activation and that Nsp1ß completely abrogates the Sp1 transactivation. These findings reveal one of the important mechanisms underlying the innate immune evasion by PRRSV during infection.

Localization of porcine reproductive and respiratory syndrome virus in mammary glands of experimentally infected sows.

We investigated the localization of porcine reproductive and respiratory syndrome virus (PRRSV) in the mammary glands of experimentally infected sows using reverse transcription PCR and immunohistochemistry. Six pregnant sows were inoculated intranasally with PRRSV three weeks prior to the predicted farrowing date. The six PRRSV-infected sows and two uninfected negative control sows remained clinically healthy and farrowed normally. Milk samples were collected from all sows on lactation days 1, 2, and 3. PRRSV was detected in milk as early as lactation day 1 in all of the PRRSV-infected sows, but not in the uninfected sows. PRRSV antigen was detected by immunohistochemistry in macrophage-like cells in the alveolar lumina of the mammary glands and in other tissues. Our results show that PRRSV is shed in the milk of infected sows, and that PRRSV antigen is present in the mammary glands of experimentally infected sows.

Characterization of canine oral papillomavirus by histopathological and genetic analysis in Korea.

In August 2008, forty dogs out of 400 developed oral warts in a breeding farm in Korea. Canine oral papilloma infection is a common disease in dogs. However, there has been no report of an outbreak of canine oral papillomavirus (COPV) in a group of dogs or in dog breeding farms in Korea, and the genetic analysis of COPV in Korea has yet to be performed. This study diagnosed canine oral papilloma from the oral samples of these dogs based on histopathological examination and immunohistochemistry. Polymerase chain reaction was applied to amplify the corresponding products using preexisting primer sets for COPV and a universal human papillomavirus targeting L1 gene. Further genetic analysis of the major viral capsid gene L1 confirms the sequences of Korean COPV, which shows a close relationship to previously reported COPV. This study describes the histopathological and immunohistochemical characteristics of canine oral papilloma in a group of breeding dogs in Korea and discloses the complete L1 gene sequences of Korean COPV.

Identification of virulence determinants of porcine reproductive and respiratory syndrome virus through construction of chimeric clones.

In order to determine virulence associated genes in porcine reproductive and respiratory syndrome virus (PRRSV), a series of chimeric viruses were generated where specific genomic regions of a highly virulent PRRSV infectious clone (FL12) were replaced with their counterparts of an attenuated vaccine strain (Prime Pac). Initial genome-wide scanning using a sow reproductive failure model indicated that non-structural (ORF 1a and 1b) and structural (ORF2-7) genomic regions appear to be sites where virulence determinants of PRRSV may reside. These results thus confirm the multigenic character of PRRSV virulence. Additional chimeras containing each individual structural ORFs (2 through 7) of Prime Pac and ORF5 of Neb-1 (parental strain of Prime Pac) within the FL12 backbone were generated and tested individually for further mapping of virulence determinants. Our results allow to conclude that NSP3-8 and ORF5 are the location of major virulence determinants, while other virulence determinants may also be contained in NSP1-3, NSP10-12 and ORF2.

Development of a porcine reproductive and respiratory syndrome virus differentiable (DIVA) strain through deletion of specific immunodominant epitopes.

The availability of a DIVA (differentiating infected from vaccinated animals) vaccine is very important for the control and eradication of endemic infectious diseases such as porcine reproductive and respiratory syndrome (PRRS). Previous studies in our laboratory identified several B-cell linear epitopes consistently recognized by convalescent sera obtained from pigs infected with a North American porcine reproductive and respiratory syndrome virus (PRRSV) strain. To ascertain if one or more of these immunodominant epitopes can be used as the basis of DIVA differentiation, we selected two epitope markers previously identified on the non-structural protein 2 (PRRSV NSP2, predictably the viral protein most likely to tolerate large deletions). The choice of these epitopes was primarily based on their immunodominance and their deletion were performed along the backbone of the wild-type cDNA infectious clone (FL12). We were able to successfully rescue a mutant that fulfilled the requirements for a DIVA marker strain, such as: efficient growth of the deletion mutant in vitro and in vivo and induction of specific seroconversion as measured by a commercial ELISA kit, with absence of a marker-specific peptide-ELISA response in 100% (n=15) of the inoculated animals. In summary, our results provide proof of concept that DIVA PRRSV vaccines can potentially be developed by deletion of individual "marker" immunodominant epitopes.

Infectious clone-derived viruses from virulent and vaccine strains of porcine reproductive and respiratory syndrome virus mimic biological properties of their parental viruses in a pregnant sow model.

Understanding of the molecular basis of virulence and attenuation of porcine reproductive and respiratory syndrome virus (PRRSV) is important for the development of a safe and efficacious vaccine. Prime Pac (PP) is an attenuated vaccine strain of PRRSV which is being used in our laboratories as a source of gene(s) for the generation of chimeric constructs in the background of a highly virulent PRRSV derived from an infectious clone (FL12) to examine the molecular determinants of virulence and attenuation. To facilitate these studies, we generated a full-length cDNA clone of the PP vaccine strain by serially replacing the genomic fragments of the FL12 with the corresponding regions from the PP strain. The virus rescued from this newly assembled cDNA clone (PP18) exhibited in vitro growth properties and in vivo apathogenic characteristics of the parental PP virus. Using pregnant sows as the experimental model of reproductive pathogenesis, we have been able to unequivocally demonstrate the clearly contrasting phenotypes of the virulent and the attenuated viruses derived from the infectious clones (FL12 and PP18). The development of an infectious clone derived from a bona fide attenuated PRRSV vaccine strain should significantly facilitate ongoing studies to determine the molecular basis of virulence and attenuation.

Influence of N-linked glycosylation of porcine reproductive and respiratory syndrome virus GP5 on virus infectivity, antigenicity, and ability to induce neutralizing antibodies.

Porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 5 (GP5) is the most abundant envelope glycoprotein and a major inducer of neutralizing antibodies in vivo. Three putative N-linked glycosylation sites (N34, N44, and N51) are located on the GP5 ectodomain, where a major neutralization epitope also exists. To determine which of these putative sites are used for glycosylation and the role of the glycan moieties in the neutralizing antibody response, we generated a panel of GP5 mutants containing amino acid substitutions at these sites. Biochemical studies with expressed wild-type (wt) and mutant proteins revealed that the mature GP5 contains high-mannose-type sugar moieties at all three sites. These mutations were subsequently incorporated into a full-length cDNA clone. Our data demonstrate that mutations involving residue N44 did not result in infectious progeny production, indicating that N44 is the most critical amino acid residue for infectivity. Viruses carrying mutations at N34, N51, and N34/51 grew to lower titers than the wt PRRSV. In serum neutralization assays, the mutant viruses exhibited enhanced sensitivity to neutralization by wt PRRSV-specific antibodies. Furthermore, inoculation of pigs with the mutant viruses induced significantly higher levels of neutralizing antibodies against the mutant as well as the wt PRRSV, suggesting that the loss of glycan residues in the ectodomain of GP5 enhances both the sensitivity of these viruses to in vitro neutralization and the immunogenicity of the nearby neutralization epitope. These results should have great significance for development of PRRSV vaccines of enhanced protective efficacy.