De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Molecular Analysis of Classical Swine Fever Virus Associated Field Infections Evidence Novel CSFV Sub Genotype in Tamil Nadu, Southern India

Classical swine fever (CSF) is an endemic and major viral infection of Indian swine husbandry, contributing to great economic losses with multiple genotypes associated with vast clinical and subclinical outcomes. Molecular detection and genotyping of CSF virus directly from field samples has great application in disease monitoring and control measures hence this study aimed to isolate and characterize CSFV genotypes circulating in southern states of India. Fifty-seven porcine post-mortem tissues (lymph nodes, spleens, livers, lungs, and kidneys) collected from pigs suspected of systemic infections and sudden death with the history of live attenuated CSF vaccination from different regions of Tamil Nadu were used in this study. An NS5B gene based CSFV specific RT-PCR screening confirmed CSFV positivity in 7% (4/57) of samples with a specific amplicon of 449 bp. Further molecular screening for other viral co-infections such as PCV2, PPV and PRRSV done by specific individual PCR assays to all the samples. Non-involvement of above screened three viral pathogens in all four field samples which showed positivity for CSFV confirming CSFV as primary pathogen. Two RT-PCR positive samples (TNI-4 and CHNL-2) selected randomly and sequenced. Aligned contig sequences of both samples were subjected to BLAST homology search and phylogentic characterization. BLAST study of TNI-4 sequence revealed 99% sequence identity with Indian CSFV sequences of genotype 1 and CHNL-2 showed 98% sequence identity with Indian CSFV sequences of genotype 2. Phylogenetic analysis of the TNI-4 and CHNL-2 sequences obtained in this study along with 38 published CSFV sequences consisting of all 5 new genotypes and 14 sub genotypes through the Maximum Likelihood tree method in MEGA 11 revealed that TNI-4 clustering together with 1.7 sub genotypes and CHNL-2 clustering together with 2.2 sub genotypes. TNI-4 and CHNL-2 partial NS5B gene sequences obtained in this study deposited in the GenBank database under accession numbers of MW822568 and MW822569 respectively. The study is the first to report CSF infections associated with the newer 1.7 sub genotype in Tamil Nadu, southern India. It is possible that vaccination could affect the genetic diversity of the CSFV through recombination and point mutations for immune evasion.

Proline to Threonine Mutation at Position 162 of NS5B of Classical Swine Fever Virus Vaccine C Strain Promoted Genome Replication and Infectious Virus Production by Facilitating Initiation of RNA Synthesis

The 3′untranslated region (3′UTR) and NS5B of classical swine fever virus (CSFV) play vital roles in viral genome replication. In this study, two chimeric viruses, vC/SM3′UTR and vC/b3′UTR, with 3′UTR substitution of CSFV Shimen strain or bovine viral diarrhea virus (BVDV) NADL strain, were constructed based on the infectious cDNA clone of CSFV vaccine C strain, respectively. After virus rescue, each recombinant chimeric virus was subjected to continuous passages in PK-15 cells. The representative passaged viruses were characterized and sequenced. Serial passages resulted in generation of mutations and the passaged viruses exhibited significantly increased genomic replication efficiency and infectious virus production compared to parent viruses. A proline to threonine mutation at position 162 of NS5B was identified in both passaged vC/SM3′UTR and vC/b3′UTR. We generated P162T mutants of two chimeras using the reverse genetics system, separately. The single P162T mutation in NS5B of vC/SM3′UTR or vC/b3′UTR played a key role in increased viral genome replication and infectious virus production. The P162T mutation increased vC/SM3′UTR_P162T replication in rabbits. From RNA-dependent RNA polymerase (RdRp) assays in vitro, the NS5B containing P162T mutation (NS5B_P162T) exhibited enhanced RdRp activity for different RNA templates. We further identified that the enhanced RdRp activity originated from increased initiation efficiency of RNA synthesis. These findings revealed a novel function for the NS5B residue 162 in modulating pestivirus replication.

Molecular detection and seroprevalence of classical swine fever virus from 2016 to 2018 in pigs of Mizoram, India

Classical swine fever (CSF) is a fatal endemic disease of pig population of North eastern India in particular and India in general. Present study revealed molecular detection of CSFV and seroprevalence of the disease in pig population of Mizoram, India during 2016–2018. Serum samples from apparently healthy, unvaccinated pigs were collected in collaboration with the State Animal Husbandry and Veterinary Department, Mizoram and a total of 594 serum samples from 7 districts were subjected to detection of CSFV specific antibodies by indirect ELISA. A total of 206 (34.68%) serum samples were positive for CSFV antibodies by ELISA. District wise, Saiha district showed highest seroprevalence of the disease followed by Kolasib and Serchhip. Apart from this, during the same time period, CSFV suspected samples received in the Department of Veterinary Microbiology consisting of 269 serum samples, 10 whole blood and 83 tissue samples obtained from 8 districts of Mizoram were subjected to detection of NS5b and E2 mRNA transcripts by nRT-PCR of which a total of 42 (11.60%) samples including serum (5.58%), tissues (27.71%) and whole blood (40%) were positive for the NS5b and E2 mRNA transcripts, specific for CSFV. District wise analysis revealed that Aizawl has the highest percentage of positive samples of CSFV followed by Saiha and Lawngtlai district.

Genome variability of classical swine fever virus during the 2018-2020 epidemic in Japan

Although RNA viruses exhibit extensive sequence diversity, the mutation rate must be limited to ensure protein functions that maintain the viral life cycle. Here, we compared the whole genome sequences of 150 isolates of classical swine fever virus (CSFV), obtained from a single epidemic that occurred in Japan during 2018-2020. After the detection of the first case, the disease spread among both farm pigs and wild boars and caused severe impact on the pig industry. To evaluate the diversification of the CSFV genome that eliminated mutations negatively affecting viral transmission, the substitution sets inherited by at least two isolates were separately evaluated as shared single nucleotide variants (SNVs) or shared single amino acid variants (SAVs). Comparisons of 12 protein-coding regions indicated that the percentages of SNVs and SAVs in the multifunctional nonstructural protein NS3 were the lowest, and shared SAVs were not detected in another nonstructural protein, NS4A. This demonstrated purifying negative selection suppressing changes in the protein sequences of NS3 and NS4A during virus transmission in the field. In contrast, a high possibility of nonsynonymous substitution among shared SNVs was detected only in genes encoding the secreted protein E^rns and the nonstructural protein NS2, suggesting positive selection during the epidemic. Mapping of shared SAVs to the three-dimensional structure of E^rns revealed that shared SAVs were not present in the substrate-binding sites but were instead localized to the peripheral region of the protein. These data will support efforts toward the development of diagnostic methods, recombinant vaccines, and antiviral agents targeting conserved and indispensable viral genes.

Crystal Structure of Classical Swine Fever Virus NS5B Reveals a Novel N-Terminal Domain

Classical swine fever virus (CSFV) is the cause of classical swine fever (CSF). Nonstructural protein 5B (NS5B) is an RNA-dependent RNA polymerase (RdRp) that is a key enzyme initiating viral RNA replication by a de novo mechanism. It is also an attractive target for the development of anti-CSFV drugs. To gain a better understanding of the mechanism of CSFV RNA synthesis, here, we solved the first crystal structure of CSFV NS5B. Our studies show that the CSFV NS5B RdRp contains the characteristic finger, palm, and thumb domains, as well as a unique N-terminal domain (NTD) that has never been observed. Mutagenesis studies on NS5B validated the importance of the NTD in the catalytic activity of this novel RNA-dependent RNA polymerase. Moreover, our results shed light on CSFV infection.IMPORTANCE Pigs are important domesticated animals. However, a highly contagious viral disease named classical swine fever (CSF) causes devastating economic losses. Classical swine fever virus (CSFV), the primary cause of CSF, is a positive-sense single-stranded RNA virus belonging to the genus Pestivirus, family Flaviviridae Genome replication of CSFV depends on an RNA-dependent RNA polymerase (RdRp) known as NS5B. However, the structure of CSFV NS5B has never been reported, and the mechanism of CSFV replication is poorly understood. Here, we solve the first crystal structure of CSFV NS5B and analyze the functions of the characteristic finger, palm, and thumb domains. Additionally, our structure revealed the presence of a novel N-terminal domain (NTD). Biochemical studies demonstrated that the NTD of CSFV NS5B is very important for RdRp activity. Collectively, our studies provide a structural basis for future rational design of anti-CSFV drugs, which is critically important, as no effective anti-CSFV drugs have been developed.

Pathology and molecular diagnosis of classical swine fever in Mizoram

AIM

Clinical histopathological and molecular diagnosis of classical swine fever disease in pigs of Mizoram.

MATERIALS AND METHODS

Totally, 31 clinically suspected pigs from 6 districts of Mizoram were examined, and clinical symptoms were recorded. Detailed post mortem examination of all the 31 dead animals was conducted, and gross changes were recorded. Tissue samples were collected for histopathological examination and molecular diagnosis. The collected tissues (tonsil, lymph nodes, spleen) were also processed for RNA extraction. Reverse transcription polymerase chain reaction (RT-PCR) was performed to detect the specific gene fragments of classical swine fever virus (CSFV).

RESULTS

Clinical examination of all the 31 suspected pigs revealed typical clinical signs of CSF. All the animals also showed typical gross and microscopic lesions of CSF. RT-PCR on tissue samples amplified the 421bp, 449bp and 735bp region of 5´NCR, non-structural protein 5B and E(rns) gene regions of CSFV, respectively. Nested PCR for internal region of E2 gene also amplified the expected product of 271bp using PCR product of whole E2 region as template DNA.

CONCLUSION

CSF is highly endemic disease in Mizoram. The viral strains circulating in this region are highly virulent. The disease can be diagnosed specifically using RT-PCR.

In vitro inhibition of CSFV replication by multiple siRNA expression

Classical swine fever (CSF) is a highly contagious viral disease of pigs which causes major economic losses worldwide. No specific drug is currently available for the effective treatment of CSFV infection; however, RNA interference (RNAi) has been applied successfully to inhibit the replication of human and other animal viruses. In this study, three effective siRNAs targeting NS3 of CSFV were selected. siNS3-2 targeting NS3 gene was chosen for further experimentation, while siN1 and siN2 targeting N^pro gene, and siNS5B targeting NS5B gene describe previously. Single, double and quadruple anti-CSFV siRNA expression plasmids, with loxp sites at each end of the selectable marker genes, were constructed and analyzed using the same promoters or four different promoters, targeting N^pro, NS3 and NS5B genes of CSFV. Results indicate that single or multiple siRNA expression plasmids can efficiently inhibit CSFV replication and that inhibition was markedly stronger when multiple siRNAs were expressed targeting different genes of CSFV. Since RNAi applied to anti-CSFV research, this study provides anti-CSFV methods by single and multiple siRNA expression which can target most viral isolates of different subtypes and prevent viral escape. It also provides a basis for development of CSFV-resistant transgenic pigs.

A multiplex RT-PCR assay for the rapid and differential diagnosis of classical swine fever and other pestivirus infections

Classical swine fever is a highly contagious viral disease causing severe economic losses in pig production almost worldwide. All pestivirus species can infect pigs, therefore accurate and rapid pestivirus detection and differentiation is of great importance to assure control measures in swine farming. Here we describe the development and evaluation of a novel multiplex, highly sensitive and specific RT-PCR for the simultaneous detection and rapid differentiation between CSFV and other pestivirus infections in swine. The universal and differential detection was based on primers designed to amplify a fragment of the 5' non-coding genome region for the detection of pestiviruses and a fragment of the NS5B gene for the detection of classical swine fever virus. The assay proved to be specific when different pestivirus strains from swine and ruminants were evaluated. The analytical sensitivity was estimated to be as little as 0.89TCID(50). The assay analysis of 30 tissue homogenate samples from naturally infected and non-CSF infected animals and 40 standard serum samples evaluated as part of two European Inter-laboratory Comparison Tests conducted by the European Community Reference Laboratory, Hanover, Germany proved that the multiplex RT-PCR method provides a rapid, highly sensitive, and cost-effective laboratory diagnosis for classical swine fever and other pestivirus infections in swine.

In vitro inhibition of classical swine fever virus replication by siRNAs targeting Npro and NS5B genes

Classical swine fever (CSF) is a highly contagious disease of pigs, which causes important economic losses worldwide. In the present study, the specific effect of RNA interference on the replication of CSF virus (CSFV) was explored. Three species of small interfering RNA (siRNA), targeting different regions of CSFV Npro and NS5B genes, were prepared by in vitro transcription. After transfection of PK-15 cells with each of the siRNAs followed by infection with CSFV, the viral proliferation within the cells was examined by indirect immunofluorescence microscopy. At 72 h post-infection, only a few siRNA-treated cells were positive for viral antigen staining, while most untreated virus-infected cells were positive. Treatment with the siRNAs caused a 4-12-fold reduction in viral genome copy number as assessed by real time RT-PCR. Transfection with the siRNAs also suppressed the production of infectious virus by up to 467-fold as assessed by TCID50 assay. These results suggested that the three species of siRNAs can efficiently inhibit CSFV genome replication and infectious virus production, with the inhibition persisting for 72-84 h.

Imidazo[4,5-c]pyridines inhibit the in vitro replication of the classical swine fever virus and target the viral polymerase

Selective inhibitors of the replication of the classical swine fever virus (CSFV) may have the potential to control the spread of the infection in an epidemic situation. We here report that 5-[(4-bromophenyl)methyl]-2-phenyl-5H-imidazo[4,5-c]pyridine (BPIP) is a highly potent inhibitor of the in vitro replication of CSFV. The compound resulted in a dose-dependent antiviral effect in PK(15) cells with a 50% effective concentration (EC(50)) for the inhibition of CSFV Alfort(187) (subgroup 1.1) of 1.6+/-0.4 microM and for CSFV Wingene (subgroup 2.3) 0.8+/-0.2 microM. Drug-resistant virus was selected by serial passage of the virus in increasing drug-concentration. The BPIP-resistant virus (EC(50): 24+/-4.0 microM) proved cross-resistant with VP32947 [3-[((2-dipropylamino)ethyl)thio]-5H-1,2,4-triazino[5,6-b]indole], an unrelated earlier reported selective inhibitor of pestivirus replication. BPIP-resistant CSFV carried a T259S mutation in NS5B, encoding the RNA-dependent RNA-polymerase (RdRp). This mutation is located near F224, a residue known to play a crucial role in the antiviral activity of BPIP against bovine viral diarrhoea virus (BVDV). The T259S mutation was introduced in a computational model of the BVDV RdRp. Molecular docking of BPIP in the BVDV polymerase suggests that T259S may have a negative impact on the stacking interaction between the imidazo[4,5-c]pyridine ring system of BPIP and F224.