Construction of eGFP-Tagged Senecavirus A for Facilitating Virus Neutralization Test and Antiviral Assay

Translational selenium nanoparticles boost GPx1 activation to reverse HAdV-14 virus-induced oxidative damage

Human adenovirus (HAdV) can cause severe respiratory infections in immunocompromised patients, but its clinical treatment is seriously limited by side effects of drugs such as poor efficacy, low bioavailability and severe nephrotoxicity. Trace element selenium (Se) has been found will affect the disease progression of pneumonia, but its antivirus efficacy could be improved by speciation optimization. Therefore, herein we performed anti-HAdV effects of different Se speciation and found that lentinan (LNT)-decorated selenium nanoparticles (SeNPs) exhibited low cytotoxicity and excellent anti-HAdV antiviral activity. Furthermore, SeNPs@LNT reduced the HAdV infection-induced mitochondrial damage and excessive production of reactive oxygen species (ROS). It was also involved in the repair of host cell DNA damage and inhibition of viral DNA replication. SeNPs@LNT inhibited HAdV-induced apoptosis mainly by modulating the p53/Bcl-2 apoptosis signaling pathway. In vivo, SeNPs@LNT replenished Se by targeting the infected site through the circulatory system and was involved in the synthesis of Glutathione peroxidase 1 (GPx1). More importantly, GPx1 played an antioxidant and immunomodulatory role in alleviating HAdV-induced inflammatory cytokine storm and alleviating adenovirus pneumonia in Se-deficient mice. Collectively, this study provides a Se speciation of SeNPs@LNT with anti-HAdV activity, and demonstrate that SeNPs@LNT is a promising pharmaceutical candidate for the treatment of HAdV.

A recombinant Getah Virus expressing a GFP gene for rapid neutralization testing and antiviral drug screening assay

Getah virus (GETV) is a re-emerging mosquito-borne RNA virus that induces fever, hind limb edema, swollen submandibular lymph nodes, and urticaria in horses. In pigs, the virus often results in stillbirths among pregnant sows, and neurological symptoms leading to death in piglets. Currently, there are no specific treatments or drugs available for GETV infection. The use of reporter viruses to monitor viral replication and spread in real-time within infected cells and animals provides a powerful tool for targeting antiviral drugs throughout the viral life cycle. Their fluorescence-tracked characteristics greatly facilitate virus neutralization tests (VNTs). In this study, we engineered two recombinant viruses by inserting different reporter protein genes at the 3' end of the structural protein gene, an unreported location that can accommodate exogenous genes. The rGEEiLOV and rGEEGFP viruses demonstrated genetic stability for at least five passages and replicated at a rate similar to that of the parental virus in BHK-21 cells. The rGEEGFP virus facilitated viral neutralization testing. Additionally, we used the reporter virus rGEEGFP to confirm ivermectin, a broad-spectrum antiparasitic agent, as a potential inhibitor of GETV in vitro. Ivermectin appears to inhibit the early replication stages of the virus and can block cell-to-cell viral transmission. In conclusion, rGEEGFP holds significant potential for antiviral screening to identify specific inhibitors against GETV and for use in viral neutralization tests.

Construction and characterization of recombinant senecavirus A expressing secreted luciferase for antiviral screening

Senecavirus A (SVA) is a newly identified picornavirus associated with swine vesicular disease and neonatal mortality. The development of an SVA incorporating an exogenous reporter gene provides a powerful tool for viral research. In this study, we successfully constructed a recombinant SVA expressing Gaussia Luciferase (Gluc), termed rSVA-Gluc. The growth kinetics of rSVA-Gluc in BHK-21 cells were found to be comparable to those of the parental virus, and Gluc activity paralleled the virus growth curve. Genetic analysis revealed stable inheritance of the inserted reporter protein genes for at least six generations. We evaluated the utility of rSVA-Gluc in antiviral drug screening, and the results highlighted its potential as an effective tool for such purposes against SVA. DATA AVAILABILITY STATEMENT: The data that support the findings of this study are available on request from the corresponding author.

Genomic profile of eGFP-tagged senecavirus A subjected to serial plaque-to-plaque transfers

Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. This virus possesses a positive-sense, single-stranded RNA genome, approximately 7200 nt in length, composed of a single 5' untranslated region, encoding region and 3' untranslated region. In this study, a recombinant SVA tagged with enhanced green fluorescent protein (eGFP) sequence, rSVA-eGFP, was rescued from its cDNA clone using reverse genetics. The passage-5 (P5) rSVA-eGFP was totally subjected to 55 rounds of consecutive fluorescent plaque-to-fluorescent plaque (FP-FP) transfers, and one extra common passaging in vitro. The P61 viral stock was analyzed by next-generation sequencing. The result showed ten single-nucleotide mutations (SNMs) in the rSVA-eGFP genome, including nine transitions and only one transversion. The P61 progeny still showed a complete eGFP sequence, indicating no occurrence of copy-choice recombination within the eGFP region during serial FP-FP transfers. In other words, this progeny was genetically deficient in the recombination of eGFP sequence (RES), namely, an RES-deficient strain. Out of ten SNMs, three were missense mutations, leading to single-amino acid mutations (SAAMs): F15V in L protein, A74T in VP2, and E53R in 3D protein. The E53R was predicted to be spatially adjacent to the RNA channel of 3D protein, perhaps involved in the emergence of RES-deficient strain. In conclusion, this study uncovered a global landscape of rSVA-eGFP genome after serial FP-FP transfers, and moreover shed light on a putative SAAM possibly related to the RES-deficient mechanism.

Evaluation of packaging capacity at the genomic 2C/3A junction region in Porcine enterovirus G

Porcine enterovirus G (EV-G) is endogenous to most pig farming countries worldwide. Reports that a papain-like protease (PLP) gene has been naturally inserted into the 2C/3A junction region of the EV-G genome, has increased the potential public health threats from this virus. We constructed a full-length infectious cDNA clone of EV-G, CH/17GXQZ/2017, in order to determine the packaging capacity at the 2C/3A insertion site. Subsequently, recombinants viruses containing the coding tags, GFP, iLOV and His at the 2C/3A junction region, were synthesized. The infectious virus was successfully rescued only with the insertion of the His-tag, which displayed similar virological and molecular properties to its parental strain. This study determined the packaging capacity of the 2C/3A insertion site, and it provides a practical tool for studying the functions and pathogenic mechanisms of EV-G in pigs.

The 3' end of the coding region of senecavirus A contains a highly conserved sequence that potentially forms a stem-loop structure required for virus rescue

Senecavirus A (SVA) can cause a vesicular disease in swine. It is a positive-strand RNA virus belonging to the genus Senecavirus in the family Picornaviridae. Positive-strand RNA viruses possess positive-sense, single-stranded genomes whose untranslated regions (UTRs) have been reported to contain cis-acting RNA elements. In the present study, a total of 100 SVA isolates were comparatively analyzed at the genome level. A highly conserved fragment (HCF) was found to be located in the 3D sequence and to be close to the 3' UTR. The HCF was computationally predicted to form a stem-loop structure. Eight synonymous mutations can individually disrupt the formation of a single base pair within the stem region. We found that SVA itself was able to tolerate each of these mutations alone, as evidenced by the ability to rescue all eight single-site mutants from their individual cDNA clones, and all of them were genetically stable during serial passaging. However, the replication-competent SVA could not be rescued from another cDNA clone containing all eight mutations. The failure to recover SVA might be attributed to disruption of the predicted stem-loop structure, whereas introduction of a wild-type HCF into the cDNA clone with eight mutations still had no effect on virus recovery. These results suggest that the putative stem-loop structure at the 3' end of the 3D sequence is a cis-acting RNA element that is required for SVA growth.

Reporter Coxsackievirus A5 Expressing iLOV Fluorescent Protein or Luciferase Used for Rapid Neutralizing Assay in Cells and Living Imaging in Mice

Coxsackievirus A5 (CV-A5) is a re-emerging enterovirus that causes hand, foot, and mouth disease in children under five years of age. CV-A5-M14-611 is a mouse-adapted strain that can infect orally and lead to the death of 14-day-old mice. Here, recombinants based on CV-A5-M14-611 were constructed carrying three reporter genes in different lengths. Smaller fluorescent marker proteins, light, oxygen, voltage sensing (iLOV), and nano luciferase (Nluc) were proven to be able to express efficiently in vitro. However, the recombinant with the largest insertion of the red fluorescence protein gene (DsRed) was not rescued. The construction strategy of reporter viruses was to insert the foreign genes between the C-terminus of VP1 and the N-terminus of 2A genes and to add a 2A protease cleavage domain at both ends of the insertions. The iLOV-tagged or Nluc-tagged recombinants, CV-A5-iLOV or CV-A5-Nluc, exhibited a high capacity for viral replication, genetic stability in cells and pathogenicity in mice. They were used to establish a rapid, inexpensive and convenient neutralizing antibody assay and greatly facilitated virus neutralizing antibody titration. Living imaging was performed on mice with CV-A5-Nluc, which exhibited specific bioluminescence in virus-disseminated organs, while fluorescence induced by CV-A5-iLOV was weakly detected. The reporter-gene-tagged CV-A5 can be used to study the infection and mechanisms of CV-A5 pathogenicity in a mouse model. They can also be used to establish rapid and sensitive assays for detecting neutralizing antibodies.

Cells at early and late stages of infection with Senecavirus A: Comparative analysis of N6-methyladenosine modification on mRNAs

Infection with Senecavirus A (SVA) causes differential phenotypes in cells. In this study, cells were inoculated with SVA for culture. At 12 and 72 h post infection, cells were independently harvested for high-throughput RNA sequencing, and further methylated RNA immunoprecipitation sequencing. The resultant data were comprehensively analyzed for mapping N⁶-methyladenosine (m⁶A)-modified profiles of SVA-infected cells. More importantly, m⁶A-modified regions were identified in the SVA genome. A dataset of m⁶A-modified mRNAs was generated for screening out differentially m⁶A-modified mRNAs, further subjected to a series of in-depth analyses. This study not only showed statistical differentiation of m⁶A-modified sites between two SVA-infected groups, but also demonstrated that SVA genome, as a positive-sense, single-stranded mRNA, itself could be modified through the m⁶A pattern. Out of the six samples of SVA mRNAs, only three were identified to be m⁶A-modified, implying that the epigenetic effect might not be a crucial driving force for SVA evolution.

A putative wild-type or wild-type-like hairpin structure is required within 3' untranslated region of Senecavirus A for virus replication

The 3' untranslated region (UTR) of Senecavirus A (SVA) was predicted to harbor two hairpin structures, hairpin-I and -II. The former is composed of two internal loops, one terminal loop and three stem regions; the latter comprises one internal loop, one terminal loop and two stem regions. In this study, we constructed a total of nine SVA cDNA clones, which contained different point mutations within a stem-formed motif in the hairpin-I or -II, for rescuing replication-competent viruses. Only three mutants were successfully rescued and moreover genetically stable during at least five serial passages. Computer-aided prediction showed these three mutants bearing either a wild-type or a wild-type-like hairpin-I in their individual 3' UTRs. Neither wild-type nor wild-type-like hairpin-I could be computationally predicted to exist in 3' UTRs of the other six unviable "viruses". The results suggested that the wild-type or wild-type-like hairpin-I was necessary in the 3' UTR for SVA replication.

The porcine piRNA transcriptome response to Senecavirus a infection

Introduction

Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. PIWI-interacting RNAs (piRNAs) are a class of small Ribonucleic Acids (RNAs) that have been found in mammalian cells in recent years. However, the expression profile of piRNAs in the host during SVA infection and their roles are poorly understood.

Methods

Here, we found the significant differential expression of 173 piRNAs in SVA-infected porcine kidney (PK-15) cells using RNA-seq and 10 significant differentially expressed (DE) piRNAs were further verified by qRT-PCR.

Results

GO annotation analysis showed that metabolism, proliferation, and differentiation were significantly activated after SVA infection. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that significant DE piRNAs were mainly enriched in AMPK pathway, Rap1 pathway, circadian rhythm and VEGF pathway. It was suggested that piRNAs may regulated antiviral immunity, intracellular homeostasis, and tumor activities during SVA infection. In addition, we found that the expression levels of the major piRNA-generating genes BMAL1 and CRY1 were significantly downregulated after SVA infection.

Discussion

This suggests that SVA may affect circadian rhythm and promote apoptosis by inhibiting the major piRNA-generating genes BMAL1 and CRY1. The piRNA transcriptome in PK-15 cells has never been reported before, and this study will further the understanding of the piRNA regulatory mechanisms underlying SVA infections.

Inhibition of HAdV-14 induced apoptosis by selenocystine through ROS-mediated PARP and p53 signaling pathways

BACKGROUND

Human Adenovirus (HAdV) can cause severe respiratory symptoms in people with low immunity and there is no targeted treatment for adenovirus infection. Anti-adenoviral drugs have high clinical significance for inhibiting adenovirus infection. Selenium (Se) plays an important role in anti-oxidation, redox signal transduction, and redox homeostasis. The excellent biological activity of Se is mainly achieved by being converted into selenocystine (SeC). Se participates in the active sites of various selenoproteins in the form of SeC. The ability of SeC to resist the virus has raised high awareness due to its unique antioxidative activity in recent years. The antiviral ability of the SeC was determined by detecting the infection rate of the virus in the cells.

METHODS

The experiment mainly investigated the antiviral mechanism of SeC by locating the virus in the cell, detecting the generation of ROS, observing the DNA status of the cell, and monitoring the mitochondrial membrane potential.

RESULTS

In the present study, SeC was designed to resist A549 cells infections caused by HAdV-14. SeC could prevent HAdV-14 from causing cell apoptosis-related to DNA damage. SeC significantly inhibited ROS generation and protect the cells from oxidative damage induced by ROS against HAdV-14. SeC induced the increase of antiviral cytokines such as IL-6 and IL-8 by activating the Jak2 signaling pathway, and repaired DNA lesions by suppressing ATR, p53, and PARP signaling pathways.

CONCLUSION

SeC might provide an effective selenium species with antiviral properties for the therapies against HAdV-14.

Only fourteen 3'-end poly(A)s sufficient for rescuing Senecavirus A from its cDNA clone, but inadequate to meet requirement of viral replication

Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-strand RNA that has 5' and 3' untranslated regions. There is a poly(A) tail at the 3' end of viral genome. Although the number of poly(A)s is variable, the length of poly(A) tail generally has the minimum nucleotide limit for picornaviral replication. To identify a range limit of poly(A)s for SVA recovery, five SVA cDNA clones, separately containing 25, 20, 15, 10 and 5 poly(A)s, were constructed for rescuing viruses. Replication-competent SVAs could be rescued from the first three cDNA clones, implying the range limit of poly(A)s was (A)₁₅ to (A)₁₀. To recognize the precise limit, four extra cDNA clones, separately containing 14, 13, 12 and 11 poly(A)s, were constructed to rescue SVAs further. The replication-competent SVA was rescued only from the poly(A)₁₄-containing plasmid, indicating that the precise limit was poly(A)₁₄ at the 3' end of cDNA clone for SVA recovery. The rescued SVA was serially passaged in cells. The passage-5 and -10 progenies were independently subjected to the analysis of 3'-rapid amplification of cDNA ends. Both progenies showed their own poly(A) tails far more than 14 (A)s, implying extra (A)s added to the poly(A)₁₄ sequence during viral passaging. It can be concluded that fourteen (A)s are sufficient for rescuing a replication-competent SVA from its cDNA clone, but inadequate for maintaining viral propagation in cells.

Infectious Recombinant Senecavirus A Expressing p16INK4A Protein

Senecavirus A (SVA) is an oncolytic RNA virus, and it is the ideal oncolytic virus that can be genetically engineered for editing. However, there has not been much exploration into creating SVA viruses that carry antitumor genes to increase their oncolytic potential. The construction of SVA viruses carrying antitumor genes that enhance oncolytic potential has not been fully explored. In this study, a recombinant SVA-CH-01-2015 virus (p15A-SVA-clone) expressing the human p16^INK4A protein, also known as cell cycle-dependent protein kinase inhibitor 2A (CDKN2A), was successfully rescued and characterized. The recombinant virus, called SVA-p16, exhibited similar viral replication kinetics to the parent virus, was genetically stable, and demonstrated enhanced antitumor effects in Ishikawa cells. Additionally, another recombinant SVA virus carrying a reporter gene (iLOV), SVA-iLOV, was constructed and identified using the same construction method as an auxiliary validation. Collectively, this study successfully created a new recombinant virus, SVA-p16, that showed increased antitumor effects and could serve as a model for further exploring the antitumor potential of SVA as an oncolytic virus.

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.

Translation of Senecavirus A polyprotein is initiated from the IRES-proximal initiation codon

To clarify whether Senecavirus A (SVA) has the potential of alternative translation, an extra G residue was inserted into an SVA cDNA clone, resultantly generating an "AUGAUG" motif. The second AUG is the authentic SVA initiation codon, whereas the first AUG is a putative one. Subsequently, eighteen nucleotides were inserted one by one between AUG and AUG for reconstructing cDNA clones. The test of virus recovery showed that three replication-competent SVAs, whose AUG/AUG-flanked sequences were not multiples of three nucleotides, were successfully rescued from their individual cDNA clones. The wild-type SVA possesses a UUUUU motif within the polyprotein-encoding region. Sanger sequencing showed that these three replication-competent SVAs harbored one or two extra U residues in the UUUUU motif, implying that polyprotein translation was initiated from the putative AUG, and the authentic AUG would be inactivated. This is probably attributed to the lack of ribosome scanning along an SVA genome.

The 5′-end motif of Senecavirus A cDNA clone is genetically modified in 36 different ways for uncovering profiles of virus recovery

Senecavirus A (SVA) is an emerging picornavirus. Its genome is one positive-sense, single-stranded RNA. The viral protein (VPg) is covalently linked to the extreme 5′ end of the SVA genome. A complex hairpin-pseudoknot-hairpin (HPH) RNA structure was computationally predicted to form at the 5′ end of the SVA genome. A total of three extra “U” residues (UUU) served as a linker between the HPH structure and the VPg, causing putative UUU–HPH formation at the extreme 5′ end of the SVA genome. It is unclear how the UUU–HPH structure functions. One SVA cDNA clone (N0) was constructed previously in our laboratory. Here, the N0 was genetically tailored for reconstructing a set of 36 modified cDNA clones (N1 to N36) in an attempt to rescue replication-competent SVAs using reverse genetics. The results showed that a total of nine viruses were successfully recovered. Out of them, five were independently rescued from the N1 to N5, reconstructed by deleting the first five nucleotides (TTTGA) one by one from the extreme 5′ end of N0. Interestingly, these five viral progenies reverted to the wild-type or/and wild-type-like genotype, suggesting that SVA with an ability to repair nucleotide defects in its extreme 5′ end. The other four were independently rescued from the N26 to N29, containing different loop-modifying motifs in the first hairpin of the HPH structure. These four loop-modifying motifs were genetically stable after serial passages, implying the wild-type loop motif was not a high-fidelity element in the first hairpin during SVA replication. The other genetically modified sequences were demonstrated to be lethal elements in the HPH structure for SVA recovery, suggesting that the putative HPH formation was a crucial cis-acting replication element for SVA propagation.

Tolerance of Senecavirus A to Mutations in Its Kissing-Loop or Pseudoknot Structure Computationally Predicted in 3′ Untranslated Region

Senecavirus A (SVA) is an emerging virus that belongs to the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense and single-stranded RNA, containing two untranslated regions (UTRs). The 68-nt-long 3′ UTR is computationally predicted to possess two higher-order RNA structures: a kissing-loop interaction and an H-type-like pseudoknot, both of which, however, cannot coexist in the 3′ UTR. In this study, we constructed 17 full-length SVA cDNA clones (cD-1 to -17): the cD-1 to -7 contained different point mutations in a kissing-loop-forming motif (KLFM); the cD-8 to -17 harbored one single or multiple point mutations in a pseudoknot-forming motif (PFM). These 17 mutated cDNA clones were independently transfected into BSR-T7/5 cells for rescuing recombinant SVAs (rSVAs), named rSVA-1 to −17, corresponding to cD-1 to −17. The results showed that the rSVA-1, -2, -3, -4, -5, -6, -7, -9, -13, and -15 were successfully rescued from their individual cDNA clones. Moreover, all mutated motifs were genetically stable during 10 viral passages in vitro. This study unveiled viral abilities of tolerating mutations in the computationally predicted KLFM or PFMs. It can be concluded that the putative kissing-loop structure, even if present in the 3′ UTR, is unnecessary for SVA replication. Alternatively, if the pseudoknot formation potentially occurs in the 3′ UTR, its deformation would have a lethal effect on SVA propagation.

Senecavirus A- and Non-Infected Cells at Early Stage of Infection: Comparative Metabolomic Profiles

Senecavirus A (SVA), classified into the genus Senecavirus in the family Picornaviridae, causes an infectious disease in pigs. This virus can efficiently replicate in some non-pig-derived cells, such as the BHK cell line and its derivative (BSR-T7/5 cell line). We had recovered a wild-type SVA from its cDNA clone previously, and then uncovered the proteomic profile of SVA-infected BSR-T7/5 cells at 12 h post inoculation (hpi). In order to explore the cellular metabolomics further, the SVA-inoculated BSR-T7/5 cell monolayer was collected at 12 hpi for assay via liquid chromatography-tandem mass spectrometry (LC-MS/MS). The resultant data set was comprehensively analyzed using bioinformatics tools. A total of 451 metabolites were identified using in-house and public databases. Out of these metabolites, sixty-one showed significantly differential values (p value < 0.05). The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was used to analyze metabolic pathways of the significantly differential metabolites. There were eighty-one identified KEGG pathways, out of which twenty-seven showed their p values < 0.05. The pyrimidine metabolism revealed the minimum p value and the maximum number of significantly differential metabolites, implying the pyrimidine played a key role in cellular metabolism after SVA infection. SVA replication must rely on the cellular metabolism. The present study on metabolomics would shed light on impacts of SVA-induced multiple interactions among metabolites on cells or even on natural hosts.

Construction and Generation of a Recombinant Senecavirus a Stably Expressing the NanoLuc Luciferase for Quantitative Antiviral Assay

Senecavirus A (SVA), also known as Seneca Valley virus, is a recently emerged picornavirus that can cause swine vesicular disease, posing a great threat to the global swine industry. A recombinant reporter virus (rSVA-Nluc) stably expressing the nanoluciferase (Nluc) gene between SVA 2A and 2B was developed to rapidly detect anti-SVA neutralizing antibodies and establish a high-throughput screen for antiviral agents. This recombinant virus displayed similar growth kinetics as the parental virus and remained stable for more than 10 passages in BHK-21 cells. As a proof-of-concept for its utility for rapid antiviral screening, this reporter virus was used to rapidly quantify anti-SVA neutralizing antibodies in 13 swine sera samples and screen for antiviral agents, including interferons ribavirin and interferon-stimulated genes (ISGs). Subsequently, interfering RNAs targeting different regions of the SVA genome were screened using the reporter virus. This reporter virus (rSVA-Nluc) represents a useful tool for rapid and quantitative screening and evaluation of antivirals against SVA.

Impacts of single nucleotide deletions from the 3' end of Senecavirus A 5' untranslated region on activity of viral IRES and on rescue of recombinant virus

The 5' untranslated region (UTR) of Senecavirus A (SVA) harbors an internal ribosome entry site (IRES), in which a pseudoknot structure is upstream of start codon AUG. Wild-type SVAs have a highly conserved 13-nt-sequence between the pseudoknot stem II (PKS-II)-forming motif and the AUG. In this study, a single nucleotide was deleted one by one from the 13-nt-sequence within a wild-type SVA minigenome. The result showed that neither mono- nor multi-nucleotide deletions abolished the IRES activity. Furthermore, a single nucleotide was deleted one by one from the 13-nt-sequence within a full-length SVA cDNA clone. The result indicated that nucleotide-deleting SVAs could be rescued from 1- to 5-nt-deleting cDNA clones, whereas only the 1- and 2-nt-deleting viruses were genetically stable during nine serial passages in vitro. Additionally, only the 1-nt-deleting SVA showed similar growth kinetics to that of the wild-type virus, suggesting that the pseudoknot-AUG distance was crucial for SVA replication.

Motif mutations in pseudoknot stem I upstream of start codon in Senecavirus A genome: Impacts on activity of viral IRES and on rescue of recombinant virus

Senecavirus A (SVA), formerly known as Seneca Valley virus, is classified into the genus Senecavirus in the family Picornaviridae. Mature virion harbors an approximately 7 300-nt-long, positive-sense, and single-stranded RNA genome, which contains 5' and 3' untranslated regions (UTRs). Internal ribosome entry site (IRES) is identified in the SVA 5' UTR, and includes a RNA pseudoknot upstream of the start codon. This pseudoknot contains two stem structures, pseudoknot stem I and II (PKS-I and -II). The PKS-I is composed of two base-paired motifs (PKS-Ia and -Ib), between which there is an unpaired spacing (UpS). We reported previously that motif mutation in the PKS-II did not abolish the IRES activity, but interfered with SVA recovery from cDNA clone. In this study, we constructed five SVA minigenomes with point mutations in the PKS-I motif. Dual-luciferase reporter assay showed that motif mutations in PKS-I did not significantly interfere with the IRES activity to initiate protein expression. Correspondingly, we constructed five SVA cDNA clones with point mutations in the PKS-I motif. These genetically modified cDNA clones were separately transfected into BSR-T7/5 cells in attempting to rescue competent SVAs. However, only two viruses, namely PKS-Ia- and UpS-mutated recombinants, could be recovered from their individual cDNA clones. It can be concluded that the PKS-Ib is indispensable for viral growth.

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.

Rescue of dual reporter-tagged parainfluenza virus 5 as tool for rapid screening of antivirals in vitro

Parainfluenza virus 5 (PIV5) belongs to the genus Orthorubulavirus in the family Paramyxoviridae. PIV5 can infect a range of mammals, but induce mild or even unobservable clinical signs in some animals, except kennel cough in dogs. It is also able to infect a variety of cell lines, but causes minimal or even invisible cytopathic effects on many cells. Sometimes, owing to neither observable cytopathic effects in vitro nor typical clinical signs in vivo, the PIV5 is not easily usable for screening antiviral drugs. To solve this issue, we used reverse genetics to recover a dual reporter-tagged recombinant PIV5 that could simultaneously express enhanced green fluorescence protein (eGFP) and NanoLuc® luciferase (NLuc) in virus-infected cells. Both reporters were genetically stable during twenty serial passages of virus in MDBK cells. The eGFP allowed us to observe virus-infected MDBK cells in real time, and moreover the NLuc made it possible to quantify the degree of viral replication for determining antiviral activity of a given drug. Subsequently, the recombinant PIV5 was used for antiviral assays on five common drugs, i.e., ribavirin, apigenin, 1-adamantylamine hydrochloride, moroxydine hydrochloride and tea polyphenol. The results showed that only the ribavirin had an anti-PIV5 effect in MDBK cells. This study proposed a novel method for rapid screening (or prescreening) of anti-PIV5 drugs.

Comparative Proteomic Profiling: Cellular Metabolisms Are Mainly Affected in Senecavirus A-Inoculated Cells at an Early Stage of Infection

Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. SVA can cause vesicular disease and epidemic transient neonatal losses in pigs. This virus efficiently propagates in some non-pig-derived cells, like the baby hamster kidney (BHK) cell line and its derivate (BSR-T7/5). Conventionally, a few proteins or only one protein is selected for exploiting a given mechanism concerning cellular regulation after SVA infection in vitro. Proteomics plays a vital role in the analysis of protein profiling, protein-protein interactions, and protein-directed metabolisms, among others. Tandem mass tag-labeled liquid chromatography-tandem mass spectrometry combined with the parallel reaction monitoring technique is increasingly used for proteomic research. In this study, this combined method was used to uncover separately proteomic profiles of SVA- and non-infected BSR-T7/5 cells. Furthermore, both proteomic profiles were compared with each other. The proteomic profiling showed that a total of 361 differentially expressed proteins were identified, out of which, 305 and 56 were upregulated and downregulated in SVA-infected cells at 12 h post-inoculation, respectively. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that cellular metabolisms were affected mainly in SVA-inoculated cells at an early stage of infection. Therefore, an integrated metabolic atlas remains to be explored via metabolomic methods.

Stem II-disrupting pseudoknot does not abolish ability of Senecavirus A IRES to initiate protein expression, but inhibits recovery of virus from cDNA clone

Senecavirus A (SVA) is classified into the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded and nonsegmented RNA, approximately 7300 nucleotides in length. A picornaviral genome is essentially an mRNA, which, albeit unmodified with 5' cap structure, can still initiate protein expression by the internal ribosome entry site (IRES). The SVA genome contains a hepatitis C virus-like IRES, in which a pseudoknot structure plays an important role in initiating protein expression. In this study, we constructed a set of SVA (CH-LX-01-2016 strain) minigenomes with all combinations of point mutations in its pseudoknot stem II (PKS-II). The results showed that any combination of point mutations could not significantly interfere with the IRES to initiate protein expression. Further, we constructed a full-length SVA cDNA clone, in which the PKS-II-forming cDNA motif was subjected to site-directed mutagenesis for totally disrupting the PKS-II formation in IRES. Such a modified SVA cDNA clone was transfected into BSR-T7/5 cells, consequently demonstrating that the PKS-II-disrupting IRES interfered neither with protein expression nor with antigenome replication, whereas a competent SVA could not be rescued from the cDNA clone. It was speculated that the mutated motif possibly disrupted a packaging signal for virion assembly, therefore causing the failure of SVA rescue.

Rescue of Senecavirus A to uncover mutation profiles of its progenies during 80 serial passages in vitro

Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. In this study, a China SVA isolate (CH-LX-01-2016) was rescued from its cDNA clone, and then identified by RT-PCR, indirect immunofluorescence assay and mass spectrometry. The rescued SVA could separately induce typical plaque formations and cytopathic effects in cell monolayers. In order to uncover its evolutionary dynamics, the SVA was subjected to eighty serial passages in vitro. Its progenies per ten passages were analyzed by next-generation sequencing (NGS). The NGS analyses showed that neither sequence-deleting nor -inserting phenotype was detectable in eight progenies, within which a total of forty-one intra-host single-nucleotide variations (SNVs) arose with passaging. Almost all SNVs were identified as the single-nucleotide polymorphism with mixture of two nucleotides. SNVs led to eighteen nonsynonymous mutations, out of which sixteen could directly reflect their own frequencies of amino acid mutation, due to only one SNV occurring in their individual codons. Compared with its parental virus without passaging, the passage-80 SVA progeny had formed a viral quasispecies, as evidenced by a total of twenty-eight SNVs identified in it.

Recovery of NanoLuc Luciferase-Tagged Canine Distemper Virus for Facilitating Rapid Screening of Antivirals in vitro

Canine distemper virus (CDV), belonging to the genus Morbillivirus in the family Paramyxoviridae, is a highly contagious pathogen, affecting various domestic, and wild carnivores. Conventional methods are too cumbersome to be used for high-throughput screening of anti-CDV drugs. In this study, a recombinant CDV was rescued using reverse genetics for facilitating screening of anti-CDV drug in vitro. The recombinant CDV could stably express the NanoLuc® luciferase (NLuc), a novel enzyme that was smaller and “brighter” than others. The intensity of NLuc-catalyzed luminescence reaction indirectly reflected the anti-CDV effect of a certain drug, due to a positive correlation between NLuc expression and virus propagation in vitro. Based on such a characteristic feature, the recombinant CDV was used for anti-CDV assays on four drugs (ribavirin, moroxydine hydrochloride, 1-adamantylamine hydrochloride, and tea polyphenol) via analysis of luciferase activity, instead of via conventional methods. The result showed that out of these four drugs, only the ribavirin exhibited a detectable anti-CDV effect. The NLuc-tagged CDV would be a rapid tool for high-throughput screening of anti-CDV drugs.

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.