Pathogenicity and cross-reactive immune responses of a historical and a contemporary Senecavirus A strains in pigs

Identification of two conserved linear antigenic epitopes on the 2C protein of Senecavirus A

Senecavirus A (SVA) is a newly emerging picornavirus threatening the global swine industry, causing vesicular disease and neonatal mortality in pigs. The non-structural protein 2C of SVA is a multifunctional virulence factor. To provide robust tools for a comprehensive study of this protein's function, we successfully generated two monoclonal antibodies (mAbs; 1F9 and 6B4) by immunizing BALB/c mice with the prokaryotically expressed 2C protein as the immunogen. Indirect immunofluorescence assays confirmed that these mAbs specifically recognized the native 2C protein. Western blot analysis further substantiated their reactivity, revealing that the recognized epitopes are linear. Both 1F9 and 6B4 were characterized as IgG1/κ isotypes. Sequence analysis of the heavy and light chain variable regions showed that the framework and complementarity-determining region (CDR) sequences were entirely distinct between the two mAbs. The antigenic epitopes recognized by 1F9 and 6B4 were precisely mapped to amino acids 162DGYKGQF168 and 34LQAWINKE41, respectively, through the expression of a series of truncated forms of 2C protein. Amino acid sequence alignment of the 2C protein from global SVA strains in the GenBank database indicated that these epitopes are highly conserved. Molecular docking revealed that mAbs 1F9 and 6B4 bind to SVA 2C via hydrophobic interactions, hydrogen bonds, and salt bridges involving specific residues in their heavy and light chain CDRs. The successful development of these mAbs provides a powerful tool for the functional investigation of SVA 2C protein.

Evidence of vertical transmission of Senecavirus A in naturally infected sows

Senecavirus A (SVA) is a Picornaviridae RNA virus that causes vesicular disease (VD) and transitory neonatal losses in pigs. The major ways SVA is spread are by oral, nasal, and feces. Vertical transmission of SVA was investigated during a VD epidemic in a farrow-to-finish herd in Brazil. Vesicular lesions were observed on sows before farrowing and on piglets within 24 h of birth. Analyses included RT-qPCR, viral isolation, sequencing, and virus-neutralization assays on serum, vesicular fluid, colostrum, and milk. Five out of ten sows were viremic before farrowing, and 46.7% of tested piglets had high viral loads in the first 24 h after birth. Infectious virus was detected in colostrum and milk from one postnatal sow. Despite high levels of neutralizing antibodies (nAbs) in piglet serum, colostrum, and milk, piglets were not protected from viremia and clinical illness. These findings support the vertical and congenital transmission of SVA.

A rapid and visual detection assay for Senecavirus A based on recombinase-aided amplification and lateral flow dipstick

Background

Senecavirus A (SVA) is a newly pathogenic virus correlated with the acute death of piglets and vesicular lesions in pigs. The further prevalence of SVA will cause considerable economic damage to the global pig farming industry. Therefore, rapid and accurate diagnostic tools for SVA are crucial for preventing and controlling the disease.

Methods

We designed multiple primer pairs targeting the most conserved region of the SVA 3D gene and selected those with the highest specificity. Nfo-probes were subsequently developed based on the highest specificity primer pairs. Subsequently, the recombinase-assisted amplification (RAA) reaction was completed, and the reaction temperature and duration were optimized. The RAA amplicons were detected using a lateral flow device (LFD). Finally, a rapid and intuitive RAA-LFD assay was established against SVA.

Results

The SVA RAA-LFD assay can be performed under reaction conditions of 35°C within 17 minutes, with results observable to the naked eye. We then evaluated the performance of this method. It exhibited high specificity and no cross-reaction with the other common swine pathogens. The lowest detectable limits of this method for the plasmid of pMD18-SVA-3D, DNA amplification product, and viral were 3.86×101 copies/µL, 8.76×10-7 ng/µL, and 1×100.25 TCID50/mL, respectively. A total of 44 clinical samples were then tested using the RAA-LFD, PCR, and RT-qPCR methods. The results demonstrated a consistent detection rate between the RAA-LFD and RT-qPCR assays.

Conclusion

The SVA RAA-LFD assay developed in our study exhibits excellent specificity, sensitivity, and time-saving attributes, making it ideally suited for utilization in lack-instrumented laboratory and field settings.

TRIM5 inhibits the replication of Senecavirus A by promoting the RIG-I-mediated type I interferon antiviral response

Senecavirus A (SVA) is an emerging virus that poses a threat to swine herds worldwide. To date, the role of tripartite motif 5 (TRIM5) in the replication of viruses has not been evaluated. Here, TRIM5 was reported to inhibit SVA replication by promoting the type I interferon (IFN) antiviral response mediated by retinoic acid-inducible gene I (RIG-I). TRIM5 expression was significantly upregulated in SVA-infected cells, and TRIM5 overexpression inhibited viral replication and promoted IFN-α, IFN-β, interleukin-1beta (IL-1β), IL-6, and IL-18 expression. Conversely, interfering with the expression of TRIM5 had the opposite effect. Viral adsorption and entry assays showed that TRIM5 did not affect the adsorption of SVA but inhibited its entry. In addition, TRIM5 promoted the expression of RIG-I and RIG-I-mediated IFNs and proinflammatory cytokines, and this effect was also proven by inhibiting the expression of TRIM5. These findings expand the scope of knowledge on host factors inhibiting the replication of SVA and indicate that targeting TRIM5 may aid in the development of new agents against SVA.

Immunogenicity of an Inactivated Senecavirus A Vaccine with a Contemporary Brazilian Strain in Mice

Senecavirus A (SVA) is a picornavirus that is endemic in swine, causing a vesicular disease clinically indistinguishable from other vesicular diseases, like foot-and-mouth disease. The widespread viral circulation, constant evolution, and economic losses caused to the swine industry emphasize the need for measures to control the agent. In this study, we evaluated the immunogenicity of a whole-virus-inactivated vaccine using a representative contemporary Brazilian SVA strain in Balb/ByJ mice. The animals were vaccinated with two doses by an intramuscular route. The humoral response induced by the vaccination was evaluated by an in-house ELISA assay for IgG detection. The cellular response was assessed by flow cytometry after in vitro SVA stimulation in splenocyte cultures from vaccinated and non-vaccinated groups. Protection against SVA was assessed in the experimental groups following an oral challenge with the homologous virus. The vaccination induced high levels of IgG antibodies and the proliferation of CD45R/B220+sIgM+, CD3e+CD69+, and CD3e+CD4+CD44+CD62L- cells. These results indicate the immunogenicity and safety of the vaccine formulation in a murine model and the induction of humoral and cellular response against SVA.

Interfering factors in the diagnosis of Senecavirus A

BACKGROUND

Senecavirus A (SV-A) is an RNA virus that belongs to the genus Senecavirus within the family Picornaviridae. This study aimed to analyze factors that can influence the molecular diagnosis of Senecavirus A, such as oligonucleotides, RNA extraction methods, and RT-qPCR kits.

METHODS

Samples from suspected cases of vesicular disease in Brazilian pigs were analyzed for foot-and-mouth disease, swine vesicular disease, and vesicular stomatitis. All tested negative for these diseases but positive for SV-A. RT-qPCR tests were used, comparing different reagent kits and RNA extraction methods. Sensitivity and repeatability were evaluated, demonstrating efficacy in detecting SV-A in clinical samples.

RESULTS

In RNA extraction, significant reduction in Cq values was observed with initial dilutions, particularly with larger supernatant volumes. Trizol and Maxwell showed greater sensitivity in automated equipment protocols, though results varied in tissue tests. RT-qPCR kit comparison revealed differences in amplification using viral RNA but minimal differences with plasmid DNA. Sensitivity among methods was comparable, with slight variations in non-amplified samples. Repeatability tests showed consistent results among RT-qPCRs, demonstrating similarity between methods despite minor discrepancies in Cq values.

CONCLUSIONS

Trizol, silica columns, and semi-automated extraction were compared, as well as different RT-qPCR kits. The study found significant variations that could impact the final diagnosis.

Senecavirus A induces mitophagy to promote self-replication through direct interaction of 2C protein with K27-linked ubiquitinated TUFM catalyzed by RNF185

Senecavirus A (SVA) is a newly emerging picornavirus associated with swine vesicular lesions and neonatal mortality, threatening the global pig industry. Despite sustained efforts, the molecular mechanisms of SVA pathogenesis have not yet been fully elucidated. Here, we demonstrate for the first time that SVA infection can induce complete mitophagy in host cells, which depends on SVA replication. Mitophagy has been subsequently proven to promote SVA replication in host cells. Genome-wide screening of SVA proteins involved in inducing mitophagy showed that although VP2, VP3, 2C, and 3A proteins can independently induce mitophagy, only the 2C protein mediates mitophagy through direct interaction with TUFM (Tu translation elongation factor, mitochondrial). The glutamic acids at positions 196 and 211 of TUFM were shown to be two key sites for its interaction with 2C protein. Moreover, TUFM was discovered to interact directly with BECN1 and indirectly with the ATG12-ATG5 conjugate. Further experiments revealed that TUFM needs to undergo ubiquitination modification before being recognized by the macroautophagy/autophagy receptor protein SQSTM1/p62, and E3 ubiquitin ligase RNF185 catalyzes K27-linked polyubiquitination of TUFM through the interaction between RNF185's transmembrane domain 1 and TUFM to initiate SVA-induced mitophagy. The ubiquitinated TUFM is recognized and bound by SQSTM1, which in turn interacts with MAP1LC3/LC3, thereby linking the 2C-anchored mitochondria to the phagophore for sequestration into mitophagosomes, which ultimately fuse with lysosomes to achieve complete mitophagy. Overall, our results elucidated the molecular mechanism by which SVA induces mitophagy to promote self-replication and provide new insights into SVA pathogenesis.Abbreviations: aa: amino acid; Baf A1: bafilomycin A1; BHK-21: baby hamster kidney-21; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4',6-diamidino-2'-phenylindole; DMSO: dimethyl sulfoxide; EGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GST: glutathione S-transferase; HA: hemagglutinin; hpi: hours post-infection; hpt: hours post-transfection; IPTG: isopropyl β-D-1-thiogalactopyranoside; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; Mdivi-1: mitochondrial division inhibitor-1; MOI: multiplicity of infection; mRFP: monomeric red fluorescent protein; MS: mass spectrometry; ORF: open reading frame; PBS: phosphate-buffered saline; SD: standard deviation; SQSTM1/p62: sequestosome 1; ST: swine testis; SVA: Senecavirus A; TCID50: 50% tissue culture infectious dose; TIMM23: translocase of inner mitochondrial membrane 23; TM: transmembrane; TOMM20: translocase of outer mitochondrial membrane 20; TUFM: Tu translation elongation factor, mitochondrial; Ub: ubiquitin; UV: ultraviolet; VDAC1: voltage dependent anion channel 1; WT: wild-type; μg: microgram; μm: micrometer; μM: micromole.

Construction and characterization of a full-length infectious clone of an emerging senecavirus A strain

Senecavirus A (SVA) is an emerging virus that causes vesicular disease in pigs. Construction of a full-length SVA cDNA clone is crucial for understanding its replication and pathogenesis. Here, we successfully constructed a CMV-promoter-driven infectious cDNA clone of the SVA isolate SVA/GX/CH/2018, which we named rSVA GX01. Sequence comparison between the pSVA GX01 and the parental isolate (SVA/GX/CH/2018) revealed three single-nucleotide differences. Four-week-old piglets were experimentally infected with either the parental virus or the cloned virus. The results showed that the cloned rSVA GX01 displayed weak pathogenicity in 4-week-old pigs compared to the parental virus SVA CH-GX-01-2018. The infectious clone of SVA will serve as a valuable tool for studying the viral replication cycle and for functional analysis of the viral genome.

First assessment of weeks-to-negative processing fluids in breeding herds after a Senecavirus A outbreak

Senecavirus A (SVA) causes vesicular disease in swine and has been responsible for a rampant increase in the yearly number of foreign animal disease investigations conducted in the United States. Diagnostic investigations for SVA are typically performed by sampling animals individually, which is labor-intensive and stressful. Developing an alternative aggregate sampling method would facilitate the detection of this virus at the population level. In a preliminary study, SVA was detected in processing fluids (PF) collected in a breeding herd before and after outbreak detection. The objective of this study was to estimate the average number of weeks PF remain SVA-positive after an SVA outbreak. Ten farrow-to-wean breeding herds volunteered to participate in this studyby longitudinally collecting PF samples after an SVA outbreak was detected and submitting samples for RT-rtPCR testing. The PF samples from the 10 farms were SVA-positive for an average of 11.8 weeks after the outbreak. Here, we show that testing of PF may be a cost-effective method to detect SVA and help halt its spread in SVA-endemic regions.

Development and Evaluation of a Competitive Enzyme-Linked Immunosorbent Assay Based on Swine Monoclonal Antibodies for Detecting Neutralizing Antibodies against Senecavirus A

Senecavirus A (SVA) is an emerging viral pathogen related to vesicular disease and neonatal mortality in swine, which results in enormous economic losses to the global swine industry. The clinical signs of SVA are indistinguishable from those of other vesicular diseases, such as foot-and-mouth disease, which is an economically devastating animal disease. Therefore, development of a rapid, sensitive, and specific diagnostic method for the detection of SVA infection is critical for the prevention and control of SVA and would help to rule out other exotic diseases. In this study, two whole-porcine anti-SVA antibodies (1M5 and 1M25) were produced using single B cell antibody technology. 1M5 and 1M25 possessed neutralizing activity against SVA but recognized different conformational epitopes that depended on the intact virion. Using 1M5 as the capture antibody and biotinylated 1M25 as the detection antibody, a reliable and rapid competitive enzyme-linked immunosorbent assay for detecting neutralizing antibodies (NAC-ELISA) against SVA was developed. Receiver-operating characteristic curve analysis showed that the sensitivity and specificity of the assay were 98.11% and 100%, respectively, with a cutoff percent inhibition value of 45%. The NAC-ELISA was specific for detecting SVA-specific antibodies, without cross-reactivity to other virus-infected sera. The results of the NAC-ELISA showed a strong agreement with the results of the virus neutralization test. Therefore, the NAC-ELISA developed in this study represents a sensitive, specific, and reliable tool for the detection of SVA-specific antibodies, which is applicable for serodiagnosis and serological surveillance of SVA and is conducive to the prevention and control of SVA. IMPORTANCE Senecavirus A (SVA) is an emerging picornavirus related to vesicular disease and neonatal mortality in swine, which results in enormous economic losses worldwide. Additionally, the clinical characteristics of the disease are indistinguishable from those of other vesicular diseases, such as foot-and-mouth disease. Therefore, developing tools for rapidly and accurately detecting SVA infection is critical and urgent. In this study, two porcine-derived monoclonal antibodies against SVA were generated, and a competitive ELISA for the detection of neutralizing antibodies (NAC-ELISA) against SVA was successfully developed using these two porcine monoclonal antibodies. The NAC-ELISA was SVA specific with no cross-reactivity to other related pathogens and had high sensitivity, specificity, and reproducibility for detecting SVA-specific antibody. Therefore, the NAC-ELISA developed in this study may be of great value as a simple and reliable tool for serodiagnosis or surveillance of SVA and may facilitate the prevention and control of SVA.

Modeling senecavirus a replication in immortalized porcine alveolar macrophages triggers a robust interferon-mediated immune response that conversely constrains viral replication

Senecavirus A (SVA) is a newly emerging causative agent of vesicular diseases in swine characterized with wide genetic diversity and rapid evolution. The lack of immunologically active cell culture model impedes the study of SVA-specific innate immunity. Here, an immortalized porcine alveolar macrophages 3D4/21 strongly and productively supported replication of two SVA strains. To elaborate global and dynamic host immune response, we demonstrated that 3D4/21 intrinsically expressed canonical ISGs which were important for pre-empting viral infection. Moreover, 3D4/21 were constitutively abundant in RIG-I-like receptors (RLRs) RIG-I and MDA5 necessary for sensing RNA virus infection, thereby enabling 3D4/21 cells to establish persistent and efficient antiviral status, in particular the most dramatic and sustained expression of type I/II interferons and inflammatory and innate immune genes critical for constraining SVA replication. Our study reveals a pivotal regulatory connection between virus and host that points to the SVA pathogenesis and potential vaccine development.

The Evolution and Global Spatiotemporal Dynamics of Senecavirus A

Recurrent outbreaks of senecavirus A (SVA)-associated vesicular disease have led to a large number of infected pigs being culled and has caused considerable economic losses to the swine industry. Although SVA was discovered 2 decades ago, knowledge about the evolutionary and transmission histories of SVA remains unclear. Herein, we performed an integrated analysis of the recombination, phylogeny, selection, and spatiotemporal dynamics of SVA. Phylogenetic analysis demonstrated that SVA diverged into two main branches, clade I (pre-2007 strains) and clade II (post-2007 strains). Importantly, analysis of selective strength showed that clade II was evolving under relaxed selection compared with clade I. Positive selection analysis identified 27 positive selective sites, most of which are located on the outer surface of capsid protomer or on the important functional domains of nonstructure proteins. Bayesian phylodynamics suggested that the estimated time to the most recent common ancestor of SVA was around 1986, and the estimated substitution rate of SVA was 3.3522 × 10-3 nucleotide substitutions/site/year. Demographic history analysis revealed that the effective population size of SVA has experienced a gradually increasing trend with slight fluctuation until 2017 followed by a sharp decline. Notably, Bayesian phylogeographic analysis inferred that Brazil might be the source of SVA's global transmission since 2015. In summary, these data illustrated that the ongoing evolution of SVA drove the lineage-specific innovation and potentially phenotypically important variation. Our study sheds new light on the fundamental understanding of SVA evolution and spread history. IMPORTANCE Recurrent outbreaks and global epidemics of senecavirus A-associated vesicular disease have caused heavy economic losses and have threatened the development of the pig industry. However, the question of where the virus comes from has been one of the biggest puzzles due to the stealthy nature of the virus. Consequently, tracing the source, evolution, and transmission pattern of SVA is a very challenging task. Based on the most comprehensive analysis, we revealed the origin time, rapid evolution, epidemic dynamics, and selection of SVA. We observed two main genetic branches, clade I (pre-2007 strains) and clade II (post-2007 strains), and described the epidemiological patterns of SVA in different countries. We also first identified Brazil as the source of SVA's global transmission since 2015. Findings in this study provide important implications for the control and prevention of the virus.

Advances in the differential molecular diagnosis of vesicular disease pathogens in swine

Foot-and-mouth disease virus (FMDV), Senecavirus A (SVA) and swine vesicular disease virus (SVDV) are members of the family Picornaviridae, which can cause similar symptoms - vesicular lesions in the tissues of the mouth, nose, feet, skin and mucous membrane of animals. Rapid and accurate diagnosis of these viruses allows for control measures to prevent the spread of these diseases. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR are traditional and reliable methods for pathogen detection, while their amplification reaction requires a thermocycler. Isothermal amplification methods including loop-mediated isothermal amplification and recombinase polymerase amplification developed in recent years are simple, rapid and do not require specialized equipment, allowing for point of care diagnostics. Luminex technology allows for simultaneous detection of multiple pathogens. CRISPR-Cas diagnostic systems also emerging nucleic acid detection technologies which are very sensitivity and specificity. In this paper, various nucleic acid detection methods aimed at vesicular disease pathogens in swine (including FMDV, SVA and SVDV) are summarized.

Evolving role of seneca valley virus and its biomarker TEM8/ANTXR1 in cancer therapeutics

Oncolytic viruses have made a significant inroad in cancer drug development. Numerous clinical trials are currently investigating oncolytic viruses both as single agents or in combination with various immunomodulators. Oncolytic viruses (OV) are an integral pillar of immuno-oncology and hold potential for not only delivering durable anti-tumor responses but also converting “cold” tumors to “hot” tumors. In this review we will discuss one such promising oncolytic virus called Seneca Valley Virus (SVV-001) and its therapeutic implications. SVV development has seen seismic evolution over the past decade and now boasts of being the only OV with a practically applicable biomarker for viral tropism. We discuss relevant preclinical and clinical data involving SVV and how bio-selecting for TEM8/ANTXR1, a negative tumor prognosticator can lead to first of its kind biomarker driven oncolytic viral cancer therapy.

The third wave of Seneca Valley virus outbreaks in pig herds in southern Brazil

Seneca Valley virus (SVV) is the only representative member of the Senecavirus genus of the Picornaviridae family. Since 2014, SVV has been identified as a causative agent of vesicular disease outbreaks in pigs of different ages from Brazil, the USA, Canada, China, Thailand, Colombia, Vietnam, and India. From May 2020, several pig herds, from the Brazilian states Parana and Santa Catarina reported vesicular disease in different pig categories. This study aimed to report the third wave of SVV outbreaks in pig herds in southern Brazil. A total of 263 biological samples from 150 pigs in 18 pig herds were evaluated. The samples were obtained from pigs with clinical signs of vesicular disease (n = 242) and asymptomatic animals (n = 21). Seneca Valley virus RNA was detected in 96 (36.5%) of the biological samples evaluated, with 89 samples from symptomatic and 7 from asymptomatic pigs. The data show that asymptomatic pigs, but in viremia, are possible sources of infection and can act as carriers and possibly spreaders of SVV to the herd. In this study, we report the third wave of vesicular disease outbreaks caused by SVV in different categories of pigs from herds located in southern Brazil.

Senecavirus A: Frequently asked questions

Senecavirus A (SVA) has been demonstrated to be a causative agent for vesicular disease in swine. It is clinically indistinguishable from other agents that cause vesicular disease such as foot-and-mouth disease virus (FMDV), which is a reportable foreign animal disease (FAD). Thus, an investigation is initiated to rule out FMDV every time a vesicle is observed. Senecavirus A has now been reported across the Americas and Asia, and it appears the ecology of this virus has changed from sporadic infections to an endemic disease in some areas. In addition to vesicular disease, there have also been reports of increased neonatal mortality on affected sow farms. Knowledge about the pathogenesis of SVA in swine can provide many benefits to the swine industry. Understanding how long the virus can be detected in various sample types after infection can aide in choosing the correct samples to collect for diagnosis. In addition, the duration of virus shedding can help determine measures to control virus spread between animals. Prevention of SVA infection and disease with an efficacious vaccine could improve swine welfare, minimize SVA transmission, and reduce the burden of FAD investigations.

Comparative Proteomic Analysis Reveals Mx1 Inhibits Senecavirus A Replication in PK-15 Cells by Interacting with the Capsid Proteins VP1, VP2 and VP3

As an emergent picornavirus pathogenic to pigs, Senecavirus A (SVA) can replicate in pig kidneys and proliferates well in porcine kidney epithelial PK-15 cells. Here, tandem mass tags (TMT) labeling coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS) was used to analyze the proteome dynamic changes in PK-15 cells during SVA infection. In total, 314, 697 and 426 upregulated differentially expressed proteins (DEPs) and 131, 263 and 342 downregulated DEPs were identified at 12, 24 and 36 hpi, respectively. After ensuring reliability of the proteomic data by quantitative PCR and Western blot testing of five randomly selected DEPs, Mx1, eIF4E, G6PD, TOP1 and PGAM1, all the DEPs were subjected to multiple bioinformatics analyses, including GO, COG, KEGG and STRING. The results reveal that the DEPs were mainly involved in host innate and adaptive immune responses in the early and middle stages of SVA infection, while the DEPs mainly participated in various metabolic processes in the late stage of infection. Finally, we demonstrated that Mx1 protein exerts antiviral activity against SVA by interacting with VP1 and VP2 proteins dependent on its GTPase, oligomerization and interaction activities, while Mx1 interacts with VP3 only depending on its oligomerization activity. Collectively, our study provides valuable clues for further investigation of SVA pathogenesis.

Prolonged Viability of Senecavirus A in Exposed House Flies (Musca domestica)

House flies (Musca domestica) are often present in swine farms worldwide. These flies utilize animal secretions and waste as a food source. House flies may harbor and transport microbes and pathogens acting as mechanical vectors for diseases. Senecavirus A (SVA) infection in pigs occurs via oronasal route, and animals shed high virus titers to the environment. Additionally, SVA possesses increased environmental resistance. Due to these reasons, we investigated the tenacity of SVA in house flies. Five groups of flies, each composed of ten females and ten males, were exposed to SVA, titer of 10^9.3 tissue culture infectious dose (TCID₅₀/mL). Groups of male and female flies were collected at 0, 6, 12, 24, and 48 h post-exposure. For comparison purposes, groups of flies were exposed to Swinepox virus (SwPV). Infectious SVA was identified in all tested groups. Successful isolation of SVA demonstrated the titers varied between 10^6.8 and 10^2.8 TCID₅₀/mL in female groups and varied from 10^5.85 to 10^3.8 TCID₅₀/mL in male groups. In contrast, infectious SwPV was only detected in the female group at 6 h. The significant SVA infectious titer for prolonged periods of time, up to 48 h, indicates a potential role of flies in SVA transmission.

Development of a VP2-based real-time fluorescent reverse transcription recombinase-aided amplification assay to rapidly detect Senecavirus A

Senecavirus A (SVA), a newly emergent picornavirus correlated with sudden neonatal mortality and vesicular lesions in pigs, has had a considerable impact on the global pig farming industry. Timely and dependable detection of SVA is helpful in preventing the further spread of this pathogenic virus. In the current study, a real-time fluorescent reverse transcription recombinase-aided amplification (rRT-RAA) assay, which targets the most conserved region within the VP2 gene of SVA, was developed and evaluated for SVA detection. The detection limit for this assay was tested to be 1.185 50% tissue culture infective dose (TCID₅₀ ) of SVA RNA per reaction at a 95% confidence interval, which is comparable to that of a previously published rRT-PCR assay for SVA. The testing results of the rRT-RAA assay were very reproducible and repeatable, with inter- and intra-assay coefficient of variation values less than 7.0%. In addition, the established rRT-RAA assay displayed excellent specificity for SVA detection without cross-reaction with other clinically important swine pathogenic viruses. The diagnostic performance of rRT-RAA was evaluated using 189 clinical swine samples, which were detected in parallel using the reference rRT-PCR assay. The results showed that 146 and 151 samples tested positive for SVA by rRT-RAA and rRT-PCR, respectively. The overall agreement between both assays was 97.4% (184/189) with a kappa value of 0.927 (p < .001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R² = 0.9192, p < .0001). Taken together, our newly established rRT-RAA assay is a powerful and time-saving diagnostic tool for SVA detection in clinical samples. This article is protected by copyright. All rights reserved.

Stability of Senecavirus A in animal feed ingredients and infection following consumption of contaminated feed

Animal feed and feed ingredients have recently been investigated as sources of pathogen introduction to farms and as a potential source of infection to animals post-consumption of contaminated feed. Survival of several viruses for a prolonged period has been demonstrated in feed. Here, we determined the rate of decay of Senecavirus A (SVA) in swine feed ingredients as a function of time and temperature and established half-life estimates for the virus. Select feed ingredients were spiked with a constant amount of SVA (10⁵ median tissue culture infectious dose 50) and incubated at 4, 15 and 30°C for up to 91 days. Virus viability and the presence of viral RNA were assessed in samples collected over time. At the three different temperatures investigated, dried distillers' grains with solubles (DDGS) and soybean meal (SBM) provided the most stable matrices for SVA, resulting in half-lives of 25.6 and 9.8 days, respectively. At 30°C, SVA was completely inactivated in all feed ingredients and in the control sample, which did not contain a feed matrix. Although virus infectivity was lost, viral RNA remained stable and at consistent levels throughout the experimental period. Additionally, the ability of SVA to infect swine via ingestion of contaminated feed was investigated in 3-week-old, weaned pigs. Animals were provided complete feed spiked with three concentrations of SVA (10⁵ , 10⁶ and 10⁷ per 200 g of feed) and allowed to naturally consume the contaminated feed. This procedure was repeated for three consecutive days. Infection of pigs through consumption of contaminated feed was confirmed by virus neutralization assay and the detection of SVA in serum, feces and in the tonsil of exposed animals by real-time reverse transcriptase PCR. Our findings demonstrate that feed matrices are able to extend the survival of SVA, protecting the virus from decay. Additionally, we demonstrated that consumption of contaminated feed can lead to productive SVA infection.

Seneca Valley virus induces immunodepressionin suckling piglets by selective apoptosis of B lymphocytes

Seneca Valley virus (SVV) is the causative agent of an emerging infectious vesicular disease in swine that is clinically indistinguishable from other vesicular diseases of swine. This study utilized healthy suckling piglets (control) and SVV-naturally infected suckling piglets to determine the effects of SVV on lymphoid tissues and determined the SVV RNA load by quantitative RT-PCR (qRT-PCR). Furthermore, immunohistochemistry (IHC) analyses were performed to quantify the expression of T and B cell lymphocytes, natural killer cells, cleaved caspase 3, and ki-67. The main histopathologic finding in the infected group was severe lymphoid depletion. The highest average of SVV RNA load by qRT-PCR (Log10 genomic copies/g of tissue) occurred at the spleen (8.54 ± 0.8), followed by the tonsils (8.04 ± 1.42), and mesenteric lymph nodes (6.90 ± 1.42). The IHC analyses revealed that there was an increased in cellular apoptosis with concomitant reduction in the proliferation of B cells. The results from this study have demonstrated that SVV-infected piglets exhibited decreased lymphocyte density probably due to lymphoid apoptosis, affecting particularly B-cells lymphocytes.

A virulent and pathogenic infectious clone of Senecavirus A

Senecavirus A (SVA) is a picornavirus that circulates in swine populations worldwide causing vesicular disease (VD) in affected animals. Here we developed a reverse genetics system for SVA based on the well-characterized wild-type SVA strain SD15-26 (wt SVA SD15-26). The full-length cDNA genome of SVA was cloned into a plasmid under a T7 RNA polymerase promoter. Following in vitro transcription, the genomic viral RNA was transfected into BHK-21 cells and rescue of infectious virus (rSVA SD15-26) was shown by inoculation of highly susceptible H1299 cells. In vitro characterization of the rSVA SD15-26 showed similar replication properties and protein expression levels as the wt SVA SD15-26. A pathogenesis study was conducted in 15-week-old finishing pigs to evaluate the pathogenicity and infection dynamics of the rSVA SD15-26 virus in comparison to the wt SVA SD15-26. Animals from both rSVA- and wt SVA SD15-26-inoculated groups presented characteristic SVA clinical signs (lethargy and lameness) followed by the development of vesicular lesions on the snout and/or feet. The clinical outcome of infection, including disease onset, severity and duration was similar in rSVA- and the wt SVA SD15-26-inoculated animals. All animals inoculated with rSVA or with wt SVA SD15-26 presented a short-term viremia, and animals from both groups shed similar amounts of virus in oral and nasal secretion, and faeces. Our data demonstrates that the rSVA SD5-26 clone is fully virulent and pathogenic in pigs, presenting comparable pathogenesis and infection dynamics to the wt SVA SD15-26 strain. The infectious clone generated here is a useful platform to study virulence determinants of SVA, and to dissect other aspects of SVA infection biology, pathogenesis and persistence.

Comparison of historical and contemporary isolates of Senecavirus A

Senecavirus A (SVA) was discovered as a cell culture contaminant in 2002, and multiple attempts to experimentally reproduce disease were unsuccessful. Field reports of porcine idiopathic vesicular disease (PIVD) cases testing PCR positive for SVA in addition to outbreaks of PIVD in Brazil and the United States in 2015 suggested SVA was a causative agent, which has now been consistently demonstrated experimentally. Ease of experimental reproduction of disease with contemporary strains of SVA raised questions concerning the difficulty of reproducing vesicular disease with historical isolates. The following study was conducted to compare the pathogenicity of SVA between historical and contemporary isolates in growing pigs. Six groups of pigs (n = 8) were intranasally inoculated with the following SVA isolates: SVV001/2002, CAN/2011, HI/2012, IA/2015, NC/2015, SD/2015. All isolates induced vesicular disease in at least half of the inoculated pigs from each group. All pigs replicated virus as demonstrated by serum and/or swab samples positive for SVA by quantitative PCR. Pig sera tested by virus neutralization assay demonstrated cross-neutralizing antibodies against all viruses utilized in the study. Cross-neutralizing antibodies from pigs inoculated with historical isolates were lower than those pigs that were inoculated with contemporary isolates. Phylogenetic analysis revealed two clades with SVV001/2002 being in a separate clade compared to the other five isolates. Although differences in the infection kinetics and sequences of these six isolates were found, clinical presentation of vesicular disease was similar between both historical and contemporary isolates.

Comprehensive review on immunopathogenesis, diagnostic and epidemiology of Senecavirus A

Senecavirus A (SVA), formerly known as Seneca Valley virus, is a single-strand, positive-sense RNA virus in the family Picornaviridae. This virus has been associated with recent outbreaks of vesicular disease (SVA-VD) and epidemic transient neonatal losses (ETNL) in several swine-producing countries. The clinical manifestation of and lesion caused by SVA are indistinguishable from other vesicular diseases. Pathogenicity studies indicate that SVA could regulate the host innate immune response to facilitate virus replication and the spread of the virus to bystander cells. SVA infection can induce specific humoral and cellular responses that can be detected within the first week of infection. However, SVA seems to produce persistent infection, and the virus can be shed in oral fluids for a month and detected in tissues for approximately two months after experimental infection. SVA transmission could be horizontal or vertical in infected herds of swine, while positive animals can also remain subclinical. In addition, mice seem to act as reservoirs, and the virus can persist in feed and feed ingredients, increasing the risk of introduction into naïve farms. Besides the pathological effects in swine, SVA possesses cytolytic activity, especially in neoplastic cells. Thus, SVA has been evaluated in phase II clinical trials as a virotherapy for neuroendocrine tumors. The goal of this review is summarize the current SVA-related research in pathogenesis, immunity, epidemiology and advances in diagnosis as well as discuses current challenges with subclinical/persistent presentation.

Pathogenesis of a senecavirus a isolate from swine in shandong Province, China

Senecavirus A (SVA), previously called Seneca Valley virus, can cause vesicular lesions in sows and a sharp decline in neonatal piglet production. In this study, a SVA strain was isolated from a pig herd in Shandong Province in China and identified as SVV-CH-SD. The full genome was 7286 nucleotides (nt) in length and contained a single open reading frame (ORF) of 6546 nt, encoding a 2182 amino acid (aa). A phylogenetic analysis showed that the isolate shares highest sequence homology (98.52 %) with SVA strain USA-GBI26-2015. A genetic comparison of virulent and weakly virulent SVA strains showed that some amino acid residues may be associated with virulence. Animal challenge experiments showed that 90-100-day-old pigs inoculated with SVV-CH-SD intraorally and intranasally, intranasally, or intramuscularly developed low fever, blisters, and lameness. They had similar levels of neutralizing antibodies against SVA and viral loads in the serum and organs at 28 days post-CHallenge. However, 30-35- and 55-65-day-old pigs challenged with SVV-CH-SD showed no clinical signs, although anti-SVA neutralizing antibodies were detected. Our findings provide useful data for studying the pathogenesis and transmission of SVA in pigs.

Comparison of the Pathogenicity of Two Different Branches of Senecavirus a Strain in China

Senecavirus A (SVA), an emerging infectious disease, is associated with the porcine idiopathic vesicular disease. Here, the pathogenesis of different strains of SVA was investigated in growing-finishing pigs. We aimed to evaluate the replication characteristics, virus particle morphology, clinical signs, and vesicular lesions in comparison with two different strains of SVA. The animals were infected with SVA HB-CH-2016 or CH/AH-02/2017 by intranasal routes (3 mL, 10⁹TCID₅₀/mL) and monitored daily for 14 days post-inoculation (dpi) for clinical signs and vesicular lesions. Viremia or viral shedding was detected in the blood, fecal swab, and nasal swab samples. Results showed no distinct differences in plaque size, replication ability, and characteristic virions between SVA HB-CH-2016 and CH/AH-02/2017 strains. Animal experimental results showed that both SVA CH/AH-02/2017 and SVA HB-CH-2016 could infect pigs. However, an obvious difference in the pathogenicity and dynamics of infection was observed between SVA HB-CH-2016 and CH/AH-02/2017 strains. The pathogenesis of SVA CH/AH-02/2017 was similar to that of published results of USA strains, whereas the SVA HB-CH-2016 strain had low pathogenicity to pigs. Clinical signs and vesicular lesions were observed in SVA CH/AH-02/2017-infected pigs. Additionally, the different branches of SVA should be capable of inducing broad cross-reactive neutralizing antibodies, which play an important role in clearing the SVA virus. This study of animal models for SVA infection will be beneficial to develop vaccines and antivirals.

Genetic diversity and evolution of the emerging picornavirus Senecavirus A

Senecavirus A (SVA) is an emerging picornavirus that causes vesicular disease (VD) in swine. The virus has been circulating in swine in the United Stated (USA) since at least 1988, however, since 2014 a marked increase in the number of SVA outbreaks has been observed in swine worldwide. The factors that led to the emergence of SVA remain unknown. Evolutionary changes that accumulated in the SVA genome over the years may have contributed to the recent increase in disease incidence. Here we compared full-genome sequences of historical SVA strains (identified before 2010) from the USA and global contemporary SVA strains (identified after 2011). The results from the genetic analysis revealed 6.32 % genetic divergence between historical and contemporary SVA isolates. Selection pressure analysis revealed that the SVA polyprotein is undergoing selection, with four amino acid (aa) residues located in the VP1 (aa 735), 2A (aa 941), 3C (aa 1547) and 3D (aa 1850) coding regions being under positive/diversifying selection. Several aa substitutions were observed in the structural proteins (VP1, VP2 and VP3) of contemporary SVA isolates when compared to historical SVA strains. Some of these aa substitutions led to changes in the surface electrostatic potential of the structural proteins. This work provides important insights into the molecular evolution and epidemiology of SVA.

A Novel Live Attenuated Vaccine Candidate Protects Against Heterologous Senecavirus A Challenge

Senecavirus A (SVA) is an emerging picornavirus causing vesicular disease (VD) clinically indistinguishable from foot-and-mouth disease (FMD) in pigs. Currently there are no vaccines currently available for SVA. Here we developed a recombinant SVA strain (rSVAm SacII) using reverse genetics and assessed its immunogenicity and protective efficacy in pigs. In vivo characterization of the rSVAm SacII strain demonstrated that the virus is attenuated, as evidenced by absence of lesions, decreased viremia and virus shedding in inoculated animals. Notably, while attenuated, rSVA mSacII virus retained its immunogenicity as high neutralizing antibody (NA) responses were detected in inoculated animals. To assess the immunogenicity and protective efficacy of rSVA mSacII, 4-week-old piglets were sham-immunized or immunized with inactivated or live rSVA mSacII virus-based formulations. A single immunization with live rSVA mSacII virus via the intramuscular (IM) and intranasal (IN) routes resulted in robust NA responses with antibodies being detected between days 3-7 pi. Neutralizing antibody responses in animals immunized with the inactivated virus via the IM route were delayed and only detected after a booster on day 21 pi. Immunization with live virus resulted in recall T cell proliferation (CD4⁺, CD8⁺, and CD4⁺/CD8⁺ T cells), demonstrating efficient stimulation of cellular immunity. Notably, a single dose of the live attenuated vaccine candidate resulted in protection against heterologous SVA challenge, as demonstrated by absence of overt disease and reduced viremia, virus shedding and viral load in tissues. The live attenuated vaccine candidate developed here represents a promising alternative to prevent and control SVA in swine.

Persistent Infection and Transmission of Senecavirus A from Carrier Sows to Contact Piglets

Senecavirus A (SVA) is a picornavirus that causes acute vesicular disease (VD), that is clinically indistinguishable from foot-and-mouth disease (FMD), in pigs. Notably, SVA RNA has been detected in lymphoid tissues of infected animals several weeks following resolution of the clinical disease, suggesting that the virus may persist in select host tissues. Here, we investigated the occurrence of persistent SVA infection and the contribution of stressors (transportation, immunosuppression, or parturition) to acute disease and recrudescence from persistent SVA infection. Our results show that transportation stress leads to a slight increase in disease severity following infection. During persistence, transportation, immunosuppression, and parturition stressors did not lead to overt/recrudescent clinical disease, but intermittent viremia and virus shedding were detected up to day 60 postinfection (p.i.) in all treatment groups following stress stimulation. Notably, real-time PCR and in situ hybridization (ISH) assays confirmed that the tonsil harbors SVA RNA during the persistent phase of infection. Immunofluorescence assays (IFA) specific for double-stranded RNA (dsRNA) demonstrated the presence of double-stranded viral RNA in tonsillar cells. Most importantly, infectious SVA was isolated from the tonsil of two animals on day 60 p.i., confirming the occurrence of carrier animals following SVA infection. These findings were supported by the fact that contact piglets (11/44) born to persistently infected sows were infected by SVA, demonstrating successful transmission of the virus from carrier sows to contact piglets. Results here confirm the establishment of persistent infection by SVA and demonstrate successful transmission of the virus from persistently infected animals.IMPORTANCE Persistent viral infections have significant implications for disease control strategies. Previous studies demonstrated the persistence of SVA RNA in the tonsil of experimentally or naturally infected animals long after resolution of the clinical disease. Here, we showed that SVA establishes persistent infection in SVA-infected animals, with the tonsil serving as one of the sites of virus persistence. Importantly, persistently infected carrier animals shedding SVA in oral and nasal secretions or feces can serve as sources of infection to other susceptible animals, as evidenced by successful transmission of SVA from persistently infected sows to contact piglets. These findings unveil an important aspect of SVA infection biology, suggesting that persistently infected pigs may function as reservoirs for SVA.

Pathogenicity of two Chinese Seneca Valley virus (SVV) strains in pigs

Seneca Valley virus (SVV) has been identified as the causative agent of SVV-associated vesicular disease (SAVD). To investigate the pathogenicity of two newly isolated SVV strains (GD-S5/2018 and GD04/2017) in China, experimental infections of pigs were performed. In pig experiments, both SVV strains successfully infected all animals, evidenced by presence of virus shedding and robust protective antibody responses. SVV GD-S5/2018 infection resulted in characteristic clinical signs, and ulcerative lesions on the tongue and gums. However, SVV GD04/2017 did not cause any clinical symptoms except depression in pigs during the experiment. Taken together, these results demonstrate that SVV GD-S5/2018 is a virulent strain for pigs, whereas SVV GD04/2017 is nearly avirulent. The established animal models for SVV infection will be utilized to dissect the immunity and pathogenesis, and develop vaccines and antivirals.

Development and evaluation of a real-time RT-PCR and a field-deployable RT-insulated isothermal PCR for the detection of Seneca Valley virus

Background

Seneca Valley virus (SVV) has emerged in multiple countries in recent years. SVV infection can cause vesicular lesions clinically indistinguishable from those caused by other vesicular disease viruses, such as foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), vesicular stomatitis virus (VSV), and vesicular exanthema of swine virus (VESV). Sensitive and specific RT-PCR assays for the SVV detection is necessary for differential diagnosis. Real-time RT-PCR (rRT-PCR) has been used for the detection of many RNA viruses. The insulated isothermal PCR (iiPCR) on a portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, SVV rRT-PCR and RT-iiPCR were developed and validated.

Results

Neither the SVV rRT-PCR nor the RT-iiPCR cross-reacted with any of the vesicular disease viruses (20 FMDV, two SVDV, six VSV, and two VESV strains), classical swine fever virus (four strains), and 15 other common swine viruses. Analytical sensitivities of the SVV rRT-PCR and RT-iiPCR were determined using serial dilutions of in vitro transcribed RNA as well as viral RNA extracted from a historical SVV isolate and a contemporary SVV isolate. Diagnostic performances were further evaluated using 125 swine samples by two approaches. First, nucleic acids were extracted from the 125 samples using the MagMAX™ kit and then tested by both RT-PCR methods. One sample was negative by the rRT-PCR but positive by the RT-iiPCR, resulting in a 99.20% agreement (124/125; 95% CI: 96.59–100%, κ = 0.98). Second, the 125 samples were tested by the taco™ mini extraction/RT-iiPCR and by the MagMAX™ extraction/rRT-PCR system in parallel. Two samples were positive by the MagMAX™/rRT-PCR system but negative by the taco™ mini/RT-iiPCR system, resulting in a 98.40% agreement (123/125; 95% CI: 95.39–100%, κ = 0.97). The two samples with discrepant results had relatively high C_T values.

Conclusions

The SVV rRT-PCR and RT-iiPCR developed in this study are very sensitive and specific and have comparable diagnostic performances for SVV RNA detection. The SVV rRT-PCR can be adopted for SVV detection in laboratories. The SVV RT-iiPCR in a simple field-deployable system could serve as a tool to help diagnose vesicular diseases in swine at points of need.

Senecavirus A 3C Protease Mediates Host Cell Apoptosis Late in Infection

Senecavirus A (SVA), an oncolytic picornavirus used for cancer treatment in humans, has recently emerged as a vesicular disease (VD)-causing agent in swine worldwide. Notably, SVA-induced VD is indistinguishable from foot-and-mouth disease (FMD) and other high-consequence VDs of pigs. Here we investigated the role of apoptosis on infection and replication of SVA. Given the critical role of the nuclear factor-kappa B (NF-κB) signaling pathway on modulation of cell death, we first assessed activation of NF-κB during SVA infection. Results here show that while early during infection SVA induces activation of NF-κB, as evidenced by nuclear translocation of NF-κB-p65 and NF-κB-mediated transcription, late in infection a cleaved product corresponding to the C-terminus of NF-κB-p65 is detected in infected cells, resulting in lower NF-κB transcriptional activity. Additionally, we assessed the potential role of SVA 3C protease (3Cpro) in SVA-induced host-cell apoptosis and cleavage of NF-κB-p65. Transient expression of SVA 3Cpro was associated with cleavage of NF-κB-p65 and Poly (ADP-ribose) polymerase (PARP), suggesting its involvement in virus-induced apoptosis. Most importantly, we showed that while cleavage of NF-κB-p65 is secondary to caspase activation, the proteolytic activity of SVA 3Cpro is essential for induction of apoptosis. Experiments using the pan-caspase inhibitor Z-VAD-FMK confirmed the relevance of late apoptosis for SVA infection, indicating that SVA induces apoptosis, presumably, as a mechanism to facilitate virus release and/or spread from infected cells. Together, these results suggest an important role of apoptosis for SVA infection biology.