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

Protection against the H1N1 influenza virus using self-assembled nanoparticles formed by lumazine synthase and bearing the M2e peptide

There is an urgent need for influenza vaccines that offer broad cross-protection. The highly conserved ectodomain of the influenza matrix protein 2 (M2e) is a promising candidate; however, its low immunogenicity can be addressed. In this study, we developed influenza vaccines using the Lumazine synthase (LS) platform. The primary objective of this study was to determine the protective potential of M2e proteins expressed on Lumazine synthase (LS) nanoparticles. M2e-LS proteins, produced through the E. coli system, spontaneously assemble into nanoparticles. The study investigated the efficacy of the M2e-LS nanoparticle vaccine in mice. Mice immunized with M2e-LS nanoparticles exhibited significantly higher levels of intracellular cytokines than those receiving soluble M2e proteins. The M2e-LS protein exhibited robust immunogenicity and provided 100% protection against cross-clade influenza.

Epidemiological investigation of Senecavirus A infection in pig herds in China from 2018 to 2021

Senecaviurs A (SVA) infection, an emerging infectious disease in pig populations, is characterized by vesicular lesions predominantly affecting the mouth, snout, and hooves of infected pigs, similar to the symptoms of Foot and Mouth Disease Virus (FMDV). This disease first spread into China in 2015, causing great panic in the pig breeding industry. To determine the prevalence of SVA in pig herds in China from 2018 to 2021, a total of 4,901 pig tissue samples were collected from 18 provinces, autonomous regions and municipalities (P.A.M.s) for epidemiological investigation, virus isolation and genetic analysis. In 2021, the individual positive rates (IPRs) from the perspective of spatial distribution in East China, South China, Central China, North China, Southwest China, Northwest China, and Northeast China were 0, 0, 1.69, 0.94, 11.70, 3.31 and 2.21%, respectively. The herd positive rates (HPRs) were 0, 0, 9.52, 9.09, 50.00, 7.69 and 23.08%. From the perspective of temporal distribution, the IPR showed an overall downwards trend from 2018 to 2021, with only a slight increase in 2020. Moreover, the HPR decreased from 36.63 to 10.07%. From the perspective of population distribution in 2021, the IPR (2.62%) and HPR (12.00%) in apparently healthy pig herds (slaughterhouses) were greater than those in non-healthy pig herds (2.10 and 5.13%, respectively), consistent with the results in 2019. To characterize the prevalent strains, 10 SVA strains isolated from positive samples in 2019 were clustered in Clades I and VII; SVA-FJ039-2019, SVA-HuN032-2019, SVA-GX011-2019, SVA-FJ036-2019, SVA-GXF011-2019 and SVA-GXF053-2019 were clustered in Clade I; and SVA-FJ018-2019, SVA-SD069-2019, SVA-SD072-2019, and SVA-SD074-2019 were clustered in Clade VII. In conclusion, until 2021, the prevalence of SVA in pig herds in China was still relatively high, the contaminated area was still large, and there were a number of hidden infections. In the future, the epidemic status of SVA in pig herds in China must be closely monitored and the prevention and control measures must be adjusted in a timely manner.

Identification of cis-acting replication element in VP2-encoding region of Senecavirus A genome

Picornavirus possesses one positive-sense, single-stranded RNA genome, in which a cis-acting replication element (cre) is located. The cre is a stem-loop structure that harbors a conserved AAACA motif within its loop region. This motif functions as a template for adding two U residues to the viral VPg, therefore generating a VPg-pUpU that is required for viral RNA synthesis. Senecavirus A (SVA) is an emerging picornavirus. Its cre has not been identified as yet. In the present study, one putative cre containing a typical AAACA motif was computationally predicted to exist within the VP2-encoding sequence of SVA. To test the role of this putative cre, 22 SVA cDNA clones with different point mutations in their cre-formed sequences were constructed in an attempt to rescue replication-competent SVAs. A total of 11 viruses were rescued from their individual cDNA clones, implying that some mutated cres exerted lethal impacts on SVA replication. To eliminate these impacts, an intact cre was artificially inserted into those SVA cDNA clones without ability of recovering virus. The artificial cre was proven to be able of compensating for some, but not all, defects caused by mutated cres, leading to successful recovery of SVAs. These results indicated that the putative cre of SVA was functionally similar to those of other picornaviruses, perhaps involved in the uridylylation of VPg.

The game between host antiviral innate immunity and immune evasion strategies of senecavirus A - A cell biological perspective

Innate immunity is the first line of the cellular host to defend against viral infection. Upon infection, viruses can be sensed by the cellular host's pattern recognition receptors (PRRs), leading to the activation of the signaling cascade and the robust production of interferons (IFNs) to restrict the infection and replication of the viruses. However, numerous cunning viruses have evolved strategies to evade host innate immunity. The senecavirus A (SVA) is a newly identified member of the Picornaviridae family, causing severe vesicular or ulcerative lesions on the oral mucosa, snout, coronary bands, and hooves of pigs of different ages. During SVA infection, the cellular host will launch the innate immune response and various physiological processes to restrict SVA. In contrast, SVA has evolved several strategies to evade the porcine innate immune responses. This review focus on the underlying mechanisms employed by SVA to evade pattern recognition receptor signaling pathways, type I interferon (IFN-α/β) receptor (IFNAR) signaling pathway, interferon-stimulated genes (ISGs) and autophagy, and stress granules. Deciphering the antiviral immune evasion mechanisms by SVA will enhance our understanding of SVA's pathogenesis and provide insights into developing antiviral strategies and improving vaccines.

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.

Genetic characterization and pathogenicity of a Eurasian avian-like H1N1 swine influenza reassortant virus

BACKGROUND

Swine influenza viruses (SIV), considered the "mixing vessels" of influenza viruses, posed a significant threat to global health systems and are dangerous pathogens. Eurasian avian-like H1N1(EA-H1N1) viruses have become predominant in swine populations in China since 2016.

METHODS

Lung tissue samples were obtained from pregnant sows with miscarriage and respiratory disease in Heilongjiang province, and pathogens were detected by Next-generation sequencing (NGS) and PCR. The nucleic acid of isolates was extracted to detect SIV by RT-PCR. Then, SIV-positive samples were inoculated into embryonated chicken eggs. After successive generations, the isolates were identified by RT-PCR, IFA, WB and TEM. The genetic evolution and pathogenicity to mice of A/swine/Heilongjiang/GN/2020 were analyzed.

RESULTS

The major pathogens were influenza virus (31%), Simbu orthobunyavirus (15%) and Jingmen tick virus (8%) by NGS, while the pathogen that can cause miscarriage and respiratory disease was influenza virus. The SIV(A/swine/Heilongjiang/GN/2020) with hemagglutination activity was isolated from lung samples and was successfully identified by RT-PCR, IFA, WB and TEM. Homology and phylogenetic analysis showed that A/swine/Heilongjiang/GN/2020 is most closely related to A/swine/Henan/SN/10/2018 and belonged to EA-H1N1. Pathogenicity in mice showed that the EA-H1N1 could cause lethal or exhibit extrapulmonary virus spread and cause severe damage to respiratory tracts effectively proliferating in lung and trachea.

CONCLUSION

A/swine/Heilongjiang/GN/2020 (EA-H1N1) virus was isolated from pregnant sows with miscarriage and respiratory disease in Heilongjiang province, China. Clinical signs associated with influenza infection were observed during 14 days with A/swine/Heilongjiang/GN/2020 infected mice. These data suggest that A/swine/Heilongjiang/GN/2020 (EA-H1N1) had high pathogenicity and could be systemic spread in mice.

Estimated quantity of swine virus genomes based on quantitative PCR analysis in spray-dried porcine plasma samples collected from multiple manufacturing plants

This survey was conducted to estimate the incidence and level of potential viral contamination in commercially collected porcine plasma. Samples of spray dried porcine plasma (SDPP) were collected over a 12- month period from eight spray drying facilities in Spain, England, Northern Ireland, Brazil, Canada, and the United States. In this survey, viral load for several porcine pathogens including SVA, TGEV, PRRSV (EU and US strains), PEDV, PCV-2, SIV, SDCoV and PPV were determined by qPCR. Regression of Ct on TCID₅₀ of serial diluted stock solution of each virus allowed the estimate of potential viral level in SDPP and unprocessed liquid plasma (using typical solids content of commercially collected porcine plasma). In this survey SVA, TGEV or SDCoV were not detected in any of the SDPP samples. Brazil SDPP samples were free of PRRSV and PEDV. Samples of SDPP from North America primarily contained the PRRSV-US strain while the European samples contained the PRRSV-EU strain (except for one sample from each region containing a relatively low estimated level of the alternative PRRSV strain). Estimated viral level tended to be in the range from <1.0 log₁₀ TCID₅₀ to <2.5 log₁₀ TCID₅₀. Estimated level of SIV was the exception with a very low incidence rate but higher estimated viral load <3.9 log₁₀ TCID₅₀. In summary, the incidence of potential viral contamination in commercially collected porcine plasma was variable and estimated virus level in samples containing viral DNA/RNA was relatively low compared with that occurring at the peak viremia during an infection for all viruses or when considering the minimal infectious dose for each of them.

Infectious dose of Senecavirus A in market weight and neonatal pigs

Foot-and-mouth disease virus (FMDV) is a picornavirus that produces a highly transmissible vesicular disease that can devastate meat and dairy production to such an extent that FMDV-free countries commit significant economic resources to maintain their FMDV-free status. Senecavirus A (SVA), also a picornavirus, causes vesicular disease in swine that is indistinguishable from FMDV. Since 2015, SVA outbreaks have been reported around the world requiring FMDV-free countries to investigate these cases to rule out FMDV. Understanding the pathogenesis of the SVA and its ability to transmit to naïve populations is critical to formulating control and prevention measures, which could reduce FMDV investigations. The primary objective of this study was to determine the infectious dose of SVA in market weight and neonatal pigs. A 2011 SVA isolate was serially hundred-fold diluted to create four challenge inoculums ranging from 106.5 to 100.5 TCID50/ml. Four market weight pigs individually housed were intranasally inoculated with 5 mL of each dose (n = 16). Serial ten-fold dilutions were used to create 6 challenge inoculums ranging from 105.5 to 100.5 TCID50/ml for neonatal pigs. Again, four animals in individual housing were challenged orally with 2 mL of each dose (n = 24). Detection of SVA by PCR in collected samples and/or neutralizing antibody response was utilized to classify an animal as infected. The minimum infectious dose for this study in market weight animals was 1,260 TCID50/ml (103.1 TCID50/ml) and for neonates it was 316 TCID50/ml (102.5 TCID50/ml). Knowledge of the infectious dose of SVA can guide biosecurity and disinfection measures to control the spread of SVA.

Evaluation of Immunoreactivity and Protection Efficacy of Seneca Valley Virus Inactivated Vaccine in Finishing Pigs Based on Screening of Inactivated Agents and Adjuvants

Seneca Valley virus (SVV), also known as Senecavirus A (SVA), is a non-enveloped and single-strand positive-sense RNA virus, which belongs to the genus of Senecavirus within the family Picornaviridae. Porcine idiopathic vesicular disease (PIVD) caused by SVV has frequently been prevalent in America and Southeast Asia (especially in China) since the end of 2014, and has caused continuing issues. In this study, an SVV strain isolated in China, named SVV LNSY01-2017 (MH064435), was used as the stock virus for the preparation of an SVV-inactivated vaccine. The SVV culture was directly inactivated using binary ethyleneimine (BEI) and β-propiolactone (BPL). BPL showed a better effect as an SVV inactivator, according to the results of pH variation, inactivation kinetics, and the detection of VP1 content during inactivation. Then, SVV inactivated by BPL was subsequently emulsified using different adjuvants, including MONTANIDE^TM ISA 201 VG (ISA 201) and MONTANIDE^TM IMG 1313 VG N (IMS 1313). The immunoreactivity and protection efficacy of the inactivated vaccines were then evaluated in finishing pigs. SVV-BPL-1313 showed a better humoral response post-immunization and further challenge tests post-immunization showed that both the SVV-BPL-201 and SVV-BPL-1313 combinations could resist challenge from a virulent SVV strain. The SVV LNSY01-2017-inactivated vaccine candidate developed here represents a promising alternative to prevent and control SVV infection in swine.

Pathogenicity of Seneca Valley virus in pigs and detection in Culicoides from an infected pig farm

Background

Porcine vesicular disease is caused by the Seneca Valley virus (SVV), it is a novel Picornaviridae, which is prevalent in several countries. However, the pathogenicity of SVV on 5–6 week old pigs and the transmission routes of SVV remain unknown.

Methods

This research mainly focuses on the pathogenicity of the CH-GX-01-2019 strain and the possible vector of SVV. In this study, 5–6 week old pigs infected with SVV (CH-GX-01-2019) and its clinical symptoms (including rectal temperatures and other clinical symptoms) were monitored, qRT-PCR were used to detect the viremia and virus distribution. Neutralization antibody assay was set up during this research. Mosquitoes and Culicoides were collected from pigsties after pigs challenge with SVV, and SVV detection within mosquitoes and Culicoides was done via RT-PCR.

Results

The challenged pigs presented with low fevers and mild lethargy on 5–8 days post infection. The viremia lasted more than 14 days. SVV was detected in almost all tissues on the 14th day following the challenge, and it was significantly higher in the hoofs (vesicles) and lymph nodes in comparison with other tissues. Neutralizing antibodies were also detected and could persist for more than 28 days, in addition neutralizing antibody titers ranged from 1:128 to 1:512. Mosquitoes and Culicoides were collected from the pigsty environments following SVV infection. Although SVV was not detected in the mosquitoes, it was present in the Culicoides, however SVV could not be isolated from the positive Culicoides.

Conclusions

Our work has enriched the knowledge relating to SVV pathogenicity and possible transmission routes, which may lay the foundation for further research into the prevention and control of this virus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-021-01679-w.

The Insufficient Activation of RIG-I-Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells

Seneca Valley virus (SVV) or commonly known as senecavirus A, is one of the picornavirus that is associated with vesicular disease and neonatal mortality in swine herds. Our previous study found that SVV replicates extremely faster in porcine Instituto Biologico-Rim Suino-2 (IBRS-2) cells than that in porcine kidney-15 (PK-15) cells. However, the underlying mechanism remains unknown. In this study, we comprehensively compared the expression features between IBRS-2 cells and PK-15 cells in response to SVV infection by an unbiased high-throughput quantitative proteomic analysis. We found that the innate immune response–related pathways were efficiently activated in PK-15 cells but not in IBRS-2 cells during SVV infection. A large amount of interferon (IFN)-stimulated genes were induced in PK-15 cells. In contrast, no IFN-stimulated genes were induced in IBRS-2 cells. Besides, we determined similar results in the two cell lines infected by another porcine picornavirus foot-and-mouth disease virus. Further study demonstrated that the Janus kinase signal transducer and activator of transcription signaling pathway was functioning properly in both IBRS-2 and PK-15 cells. A systematic screening study revealed that the aberrant signal transduction from TANK-binding kinase 1 to IFN regulatory factor 3 in the retinoic acid–inducible gene I–like receptor signaling pathway in IBRS-2 cells was the fundamental cause of the different innate immune response manifestation and different viral replication rate in the two cell lines. Together, our findings determined the different features of IBRS-2 and PK-15 cell lines, which will help for clarification of the pathogenesis of SVV. Besides, identification of the underlying mechanisms will provide new targets and an insight for decreasing the viral clearance rate and probably improve the oncolytic effect by SVV in cancer cells.

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Divergent innate immune responses were triggered by SVV in IBRS-2 and PK-15 cells.

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SVV induced higher levels of type I IFN in PK-15 cells than in IBRS-2 cells.

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IBRS-2 cell line has an aberrant RLR pathway but an intact type I IFN pathway.

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TBK1-mediated antiviral signal transduction was dysfunctional in IBRS-2 cells.

Isolation and evolutionary analysis of Senecavirus A isolates from Guangdong province, China

Senecavirus A (SVA), an emerging swine pathogen, has been reported in many provinces of China since the first outbreak in 2015 in Guangdong province. In this study, 10 lymph nodes positive for SVA, collected between 2018 and 2019 from slaughterhouses in Guangdong province, were subjected to virus isolation. Rapid and evident cytopathic effects (CPEs) were observed in SVA-infected PK-15 cells, including shrinking, rounding and detaching, with peak titers being reached at 24 h post infection (hpi). Electron microscopy showed that SVA particles are spherical and approximately 30 nm in diameter, and exist as crystalline lattices in cytoplasm revealed by ultra-thin sectioning. Phylogenetic analysis based on the whole genome sequences of all available isolates showed that SVA globally can be divided into two groups with each being further divided into two subgroups (Ia-b and IIa-b), and with the Guangdong isolates obtained here and other Chinese strains belonging to subgroups IIa and IIb. Evolutionary analysis showed that the mean substitution rate of SVA was 2.696 × 10^-3 per site per year based on whole genomic sequences, with subgroup IIb isolates having evolved faster than those of subgroup IIa. Analysis of efficient population size showed that the outbreak point of SVA worldwide occurred at the end of 2013 with that of subgroup IIb, the current dominant group, in mid 2014.

Preliminary Evaluation of Protective Efficacy of Inactivated Senecavirus A on Pigs

Senecavirus A (SVA), formerly known as Seneca Valley virus (SVV), causes vesicular symptoms in adult pigs and acute death of neonatal piglets. This pathogen has emerged in major swine producing countries around the world and caused significant economic losses to the pig industry. Thus, it is necessary to develop strategies to prevent and control SVA infection. Herein, an SVA strain (named GD-ZYY02-2018) was isolated from a pig herd with vesicular symptoms in Guangdong province of China in 2018. The present study aimed to carry out the phylogenetic analysis of the GD-ZYY02-2018 strain, determine its pathogenicity in finishing pigs, and assess the protective efficacy of the inactivated GD-ZYY02-2018 strain against virus challenge. The results of phylogenetic analysis showed that the SVA GD-ZYY02-2018 strain belonged to the USA-like strains and had a close genetic relationship with recent Chinese SVA strains. Animal challenge experiment showed that 100-day-old pigs inoculated intranasally with SVA GD-ZYY02-2018 strain developed vesicular lesion, low fever, viremia, and virus shedding in feces. The immunization challenge experiment showed that pigs vaccinated with inactivated GD-ZYY02-2018 strain could produce a high titer of anti-SVA neutralizing antibody and no vesicular lesion, fever, viremia, and virus shedding in feces was observed in vaccinated pigs after challenge with GD-ZYY02-2018 strain, indicating that inactivated GD-ZYY02-2018 could protect finishing pigs against the challenge of homologous virus. In conclusion, preliminary results indicated that inactivated GD-ZYY02-2018 could be used as a candidate vaccine for in-depth research and might be conducive to the prevention and control of SVA infection.

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.

A 5-Year Review of Senecavirus A in China since Its Emergence in 2015

Senecavirus A (SVA), previously known as Seneca Valley virus, is classified into the genus Senecavirus in the family Picornaviridae. This virus can cause vesicular disease and epidemic transient neonatal losses in swine. Typical clinical signs include vesicular and/or ulcerative lesions on the snout, oral mucosa, coronary bands and hooves. SVA emerged in Guangdong Province of China in 2015, and thereafter gradually spread into other provinces, autonomous regions and municipalities (P.A.M.s). Nowadays more than half of the P.A.M.s have been affected by SVA, and asymptomatic infection has occurred in some areas. The phylogenetic analysis shows that China isolates are clustered into five genetic branches, implying a fast evolutionary speed since SVA emergence in 2015. This review presented current knowledge concerning SVA infection in China, including its history, epidemiology, evolutionary characteristics, diagnostics and vaccines.