A ten years (2007–2016) retrospective serological survey for Seneca Valley virus infection in major pig producing states of Brazil

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.

The Establishment and Application of Indirect 3AB-ELISA for The Detection of Antibodies against Senecavirus A

Senecavirus A (SVA) is an emerging pathogen that negatively affects the pig industry in China. Affected animals present vesicular lesions which are indistinguishable from other vesicular diseases. To date, there is no commercial vaccine that can be used to control SVA infection in China. In this study, recombinant SVA 3AB, 2C, 3C, 3D, L and VP1 proteins are expressed by using a prokaryotic expression system. The kinetics of the presence and levels of SVA antibodies with SVA-inoculated pig serum show that 3AB has the best antigenicity. An indirect enzyme-linked immunosorbent assay (ELISA) is developed with the 3AB protein, exhibiting a sensitivity of 91.3% and no cross-reaction with serum antibodies against PRRSV, CSFV, PRV, PCV2 or O-type FMDV. Given the high sensitivity and specificity of this approach, a nine-year (2014–2022) retrospective and prospective serological study is conducted to determine the epidemiological profile and dynamics of SVA in East China. Although SVA seropositivity declined markedly from 2016 (98.85%) to 2022 (62.40%), SVA transmission continues in China. Consequently, the SVA 3AB-based indirect ELISA has good sensitivity and specificity and is suitable for viral detection, field surveillance and epidemiological studies.

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.

Development of an indirect ELISA using a novel linear epitope at the C-terminal region of the VP2 protein to specifically detect antibodies against Senecavirus A

BACKGROUND

Senecavirus A (SVA) is a pathogen that has recently caused porcine idiopathic vesicular disease (PIVD). The clinical signs are similar to those of foot-and-mouth disease, porcine vesicular disease, and vesicular stomatitis. Therefore, identification of SVA as a cause of PIVD is important to eliminate this emerging pathogen.

METHODS

In this study, an indirect ELISA based on the VP2 epitope (VP2-epitp-ELISA) was developed to detect antibodies directed against SVA.

RESULTS

A novel linear epitope (²⁷¹GLRNRFTTGTDEEQ²⁸⁴) was first identified at the C-terminus of the VP2 protein by epitope mapping. The diagnostic performance of VP2-epitp-ELISA was estimated by testing a panel of known background sera from swine. Under the optimum test conditions, when the cutoff value was 37%, the diagnostic sensitivity (Dn) and diagnostic specificity (Dp) of the assay were 91.13% and 91.17%, respectively. The accuracy of VP2-epitp-ELISA was validated and further compared with that of commercial diagnostic kits. The diagnostic results showed that VP2-epitp-ELISA did not cross-react with serum positive for other idiopathic vesicular diseases and had a concordance rate of 90.41% with the Swinecheck^® SVA bELISA.

CONCLUSIONS

These results indicate that VP2-epitp-ELISA is suitable for specific detection of antibodies against SVA in swine.

Senecavirus A seroprevalence and risk factors in United States pig farms

Senecavirus A (SVA) is a non-enveloped, single-stranded, positive-sense RNA virus belonging to the Picornaviridae family. Senecavirus A is constantly associated with outbreaks of vesicular disease in pigs and has been reported in several countries since its first large-scale outbreak in 2014. Senecavirus A's clinical disease and lesions are indistinguishable from other vesicular foreign animal diseases (FAD). Therefore, an FAD investigation needs to be conducted for every SVA case. For this reason, SVA has been attributed as the cause of an alarming increase in the number of yearly FAD investigations performed by the United States Department of Agriculture (USDA). The objectives of this study were to estimate the seroprevalence of SVA antibodies in breeding and growing pig farms in the United States and to determine the farm-level risk factors associated with seropositivity. A total of 5,794 blood samples were collected from 98 and 95 breeding and growing pig farms in 17 states. A farm characteristics questionnaire was sent to all farms, to which 80% responded. The responses were used to conduct logistic regression analyses to assess the risk factors associated with SVA seropositivity. The estimated farm-level seroprevalences were 17.3% and 7.4% in breeding and growing pig farms, respectively. Breeding farms had 2.64 times higher odds of SVA seropositivity than growing pig farms. One key risk factor identified in breeding farms was the practice of rendering dead animal carcasses. However, the adoption of a higher number of farm biosecurity measures was associated with a protective effect against SVA seropositivity in breeding farms.

A Review on Pathological and Diagnostic Aspects of Emerging Viruses—Senecavirus A, Torque teno sus virus and Linda Virus—In Swine

Simple Summary

Worldwide demand for food is expected to increase due to population growth and swine accounts for more than one-third of meat produced worldwide. Several factors affect the success of livestock production systems, including animal disease control. Despite the importance of infectious diseases to animal health and the productivity of the global swine industry, pathogens of swine, in particular emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, have gained limited interest. We performed a systematic analysis of the literature, with a focus on the main macroscopical and histological findings related to those viruses to fill the gap and highpoint these potentially hazardous pathogens.

Abstract

Swine production represents a significant component in agricultural economies as it occupies over 30% of global meat demand. Infectious diseases could constrain the swine health and productivity of the global swine industry. In particular, emerging swine viral diseases are omnipresent in swine populations, but the limited knowledge of the pathogenesis and the scarce information related to associated lesions restrict the development of data-based control strategies aimed to reduce the potentially great impact on the swine industry. In this paper, we reviewed and summarized the main pathological findings related to emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, suggesting a call for further multidisciplinary studies aimed to fill this lack of knowledge and better clarify the potential role of those viral diseases in swine pathology.

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.

Transcriptome Analyses of Senecavirus A-Infected PK-15 Cells: RIG-I and IRF7 Are the Important Factors in Inducing Type III Interferons

Senecavirus A (SVA) is a new type of virus related to swine vesicular disease, which results in enormous economic losses worldwide. At present, the host transcriptional responses to SVA infection, host-SVA interactions, and the mechanism of SVA in innate immune modulation are not well understood. This study explores the gene expression profiles of PK-15 cells at 0, 6, 12, 18, 24, 36 h SVA post-infection by RNA sequencing. Our analysis identified 61, 510, 1,584, 2,460, and 2,359 differentially expressed genes (DEGs) in the comparison groups S6 vs. Control, S12 vs. Control, S18 vs. Control, S24 vs. Control, S36 vs. Control, respectively. The reproducibility and repeatability of the results were validated by RT-qPCR, and all DEGs exhibited expression patterns consistent with the RNA-seq results. According to GO enrichment analysis and KEGG pathway analysis of DEGs in different periods after SVA infection, we found that SVA infection significantly modified the host cell gene-expression patterns and the host cells responded in highly specific manners, including response to signal reception and transmission, external biotic stimulus, response to the virus and host immune defense response. Notably, we observed the specific induction of type III interferon IFN-λ1 and IFN-λ3, which indicated that type III interferon plays an important antiviral function in PK-15 cells. Furthermore, our results showed that SVA might be recognized by RIG-I/MDA-5 receptors first after infecting PK-15 cells and then activates downstream IRF7-mediated signaling pathways, causing an increase in the expression of type III interferon. This study could provide important insights into the modulation of host metabolism during SVA infection and provide a strong theoretical basis for a better understanding of the pathogenic mechanism and immune escape mechanism of SVA.

Evaluation of immunogenicity and protective efficacy of a novel Senecavirus A strain-based inactivated vaccine in mice

Senecavirus A (SVA) is an emerging picornavirus associated with porcine idiopathic vesicular disease (PIVD), which is clinically indistinguishable from foot-and-mouth disease and other vesicular diseases in pigs. In recent years, the wide spread of SVA has caused huge economic losses to the world's pig industry. However, there are no vaccines currently available to prevent and control the infection of SVA due to the extensive diversity of SVA isolates and high cost of the pig model for vaccine evaluation. In the present study, a novel SVA CH-HNCY-2019 strain with unique amino-acid mutations in VP1, VP3 and 3C was isolated from the central part of China. A mouse model was proposed to for evaluation of the immunogenicity and protective efficacy of the inactivated CH-HNCY-2019 vaccine. The results indicated that one dose immunization of 107TCID50 inactivated CH-HNCY-2019 vaccine in mice induced a high titer of neutralizing antibody and complete protection. After challenging with the homologous virus, no viral RNA or histopathological damages were detected in the heart, liver, spleen, lung, kidney, intestine and brain tissues of the immunized mice. However, viral RNA and different degrees of histopathological damages were observed in all corresponding tissues of the unimmunized mice. In summary, the present study proved that mouse is a candidate animal model for the primary evaluation of the immunogenicity and protection efficacy of SVA vaccines for the first time. In addition, the inactivated SVA CH-HNCY-2019 vaccine was immunogenic and could protect mice against homologous viral challenges.

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.

N-Linked Glycosylation on Anthrax Toxin Receptor 1 Is Essential for Seneca Valley Virus Infection

Seneca Valley virus (SVV) is a picornavirus with potency in selectively infecting and lysing cancerous cells. The cellular receptor for SVV mediating the selective tropism for tumors is anthrax toxin receptor 1 (ANTXR1), a type I transmembrane protein expressed in tumors. Similar to other mammalian receptors, ANTXR1 has been shown to harbor N-linked glycosylation sites in its extracellular vWA domain. However, the exact role of ANTXR1 glycosylation on SVV attachment and cellular entry was unknown. Here we show that N-linked glycosylation in the ANTXR1 vWA domain is necessary for SVV attachment and entry. In our study, tandem mass spectrometry analysis of recombinant ANTXR1-Fc revealed the presence of complex glycans at N166, N184 in the vWA domain, and N81 in the Fc domain. Symmetry-expanded cryo-EM reconstruction of SVV-ANTXR1-Fc further validated the presence of N166 and N184 in the vWA domain. Cell blocking, co-immunoprecipitation, and plaque formation assays confirmed that deglycosylation of ANTXR1 prevents SVV attachment and subsequent entry. Overall, our results identified N-glycosylation in ANTXR1 as a necessary post-translational modification for establishing stable interactions with SVV. We anticipate our findings will aid in selecting patients for future cancer therapeutics, where screening for both ANTXR1 and its glycosylation could lead to an improved outcome from SVV therapy.

Infectious recombinant Senecavirus A expressing novel reporter proteins

Senecavirus A (SVA) is an emerging picornavirus that has been associated with vesicular disease and neonatal mortality in swine. The construction of SVA virus carrying foreign reporter gene provides a powerful tool in virus research. However, it is often fraught with rescuing a recombinant picornavirus harboring a foreign gene or maintaining the stability of foreign gene in the virus genome. Here, we successfully generated recombinant SVA GD05/2017 viruses (V-GD05-clone) expressing the green fluorescent protein (iLOV), red fluorescent protein (RFP), or NanoLuc luciferase (Nluc). These recombinant viruses have comparable growth kinetics to the parental virus. Genetic stability analysis indicated that V-GD05-iLOV was highly stable in retaining iLOV gene for more than 10 passages, while V-GD05-RFP and V-GD05-Nluc lost the foreign genes in five passages. In addition, high-intensity fluorescent signals were found in the V-GD05-RFP- and V-GD05-iLOV-infected cells by fluorescence observation and flow cytometry analysis, and the luciferase activity assay could quantitatively monitor the replication of V-GD05-Nluc. In order to identify the porcine cell receptor for SVA, anthrax toxin receptor 1 (ANTXR1) was knocked out or overexpressed in the ST-R cells. The ANTXR1 knock-out cells lost the ability for SVA infection, while overexpression of ANTXR1 significantly increased the cell permissivity. These results confirmed that ANTXR1 was the receptor for SVA to invade porcine cells as reported in the human cells. Overall, this study suggests that these SVA reporter viruses will be useful tools in elucidating virus pathogenesis and developing control measures. KEY POINTS: • We successfully generated SVA viruses expressing the iLOV, RFP, or Nluc. • The iLOV was genetically stable in the V-GD05-iLOV genome over ten passages. • ANTXR1 was the receptor for SVA to invade porcine cells.

Isolation and phylogenomic analysis of two Senecavirus A isolates in Sichuan Province, 2018

In our study, we isolated and characterised two new Senecavirus A (SVA) isolates in Sichuan Province, China. Phylogenetic analysis of both the SVA full-length genomes and the VP1 genes revealed that the two new SVA isolates are more closely related to previous Chinese strains and US strains. The most variable isolate, SVV-SC-01, showed a significant difference from previous SVA strains, and it was identified as a recombinant using several algorithms. Study findings indicate that the SVA virus in China is constantly evolving and new SVA variants may have emerged. Hence, we must take effective measures to prevent further spread of SVA. This report provides evidence that SVA infection of pigs has occurred in Sichuan Province, and the results will contribute to our understanding of the genetic characteristics and recombinant events of SVA in China.

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.

Seroprevalence of Senecavirus A in sows and grower-finisher pigs in major swine producing-states in the United States

Senecavirus A (SVA) is a single-stranded RNA virus in the family Picornaviridae. Recently, SVA has been associated with idiopathic vesicular disease and increased neonate mortality outbreaks in the United States, Brazil, China, Colombia, and Thailand, with increasing incidence since 2014. Indirect detection by antibody detection methods, including indirect immunofluorescence assay (IFA), virus neutralization assay, and competitive or indirect enzyme-linked immunosorbent assays (ELISAs), have been reported in clinical and experimental trials. The objective of this study was to determine the seroprevalence of SVA in nonclinical affected herds in the United States. Individual samples were collected from 3654 and 2433 clinically healthy grower-finisher pigs and sows, respectively, from 219 unique commercial swine production sites. SVA seroprevalence was evaluated by SVA rVP1 ELISA and SVA IFA. The estimated seroprevalence for grower-finisher pigs and sows was 12.2% and 34.0%, respectively. The herd prevalence was 42.7% for grower-finisher farms and 75.8% for sow farms. The SVA rVP1 ELISA and SVA IFA exhibited a fair (sows) and moderate (grower-finisher) agreement at the herd level, while a fair agreement was observed at the individual level for both pig categories evaluated. The McNemar's test was significant at the individual and herd level (p <  0.05). In this study, we demonstrated the presence of SVA IgG antibodies in pigs from clinically healthy grower-finisher and sow herds. These results suggest that SVA is circulating subclinically in sow farms and grower-finisher pig farms in major swine producing-states in the United States.

Isolation and phylogenetic analysis of an emerging Senecavirus A in China, 2017

Senecavirus A (SVA), which is associated with porcine vesicular disease and high mortality in neonatal piglets, is a small non-enveloped RNA virus and a member of Picornaviridae family. An emerging SVA strain, named SVA CH/FuJ/2017, was isolated from vesicular liquid and vesicular lesion tissue from piglets with vesicular disease in Fujian province, China. In our study, the complete genome sequence of SVA CH/FuJ/2017 strain has been determined. The viral genome was 7285 nt in length. The homology analysis indicated that the gene sequences of polyprotein and VP1 in SVA CH/FuJ/2017 shared highest nucleotide identities with American SVA isolates; and polyprotein showed the highest similarity with American SVA isolates. The phylogenetic analysis based on polyprotein and VP1 nucleotide sequences indicated that SVA CH/FuJ/2017 was closely related to American SVA isolates. The results revealed that the novel SVA strain was closely related to those SVA strains that were isolated in America. Hence, the retrospective study is important for tracing the probable origin of China SVA strains.

Review of Seneca Valley Virus: A Call for Increased Surveillance and Research

Seneca Valley virus (SVV) has recently caused many vesicular diseases in pigs in different regions and countries. As a newly causative agent of porcine vesicular disease, SVV has evolved and spread quickly. It causes clinical signs similar to those of foot-and-mouth disease and results in significant economic losses. An increasing number of SVV outbreaks were reported in 2016 and 2017 in Brazil, United States, and China. However, few diagnostic methods have been established and no commercial vaccine has been available until now. Therefore, more attention needs to be paid to SVV, and urgent surveillance should be performed to prevent the spread of this virus. Although recent research has shed some light on SVV, there are still many aspects of the virus and the disease that are not yet fully understood, and many questions need to be resolved. This review presents current knowledge concerning SVV infection, epidemiology, pathogenicity, immune response, and diagnostic methods. This information will aid the design and adoption of effective prevention and control strategies to counter this viral pathogen.