Identification of two amino acids within E2 important for the pathogenicity of chimeric classical swine fever virus

Assessment of the Safety Profile of Chimeric Marker Vaccine against Classical Swine Fever: Reversion to Virulence Study

Chimeric marker vaccine candidates, vGPE-/PAPeV Erns and vGPE-/PhoPeV Erns, have been generated and their efficacy and capability to differentiate infected from vaccinated animals were confirmed in previous studies. The safety profile of the two chimeric marker vaccine candidates, particularly in the potential reversion to virulence, was evaluated. Each virus was administered to pigs with a dose equivalent to the vaccination dose, and pooled tonsil homogenates were subsequently inoculated into further pigs. Chimeric virus vGPE-/PAPeV Erns displayed the most substantial attenuation, achieving this within only two passages, whereas vGPE-/PhoPeV Erns was detectable until the third passage and disappeared entirely by the fourth passage. The vGPE- strain, assessed alongside, consistently exhibited stable virus recovery across each passage without any signs of increased virulence in pigs. In vitro assays revealed that the type I interferon-inducing capacity of vGPE-/PAPeV Erns was significantly higher than that of vGPE-/PhoPeV Erns and vGPE-. In conclusion, the safety profile of the two chimeric marker vaccine candidates was affirmed. Further research is essential to ensure the stability of their attenuation and safety in diverse pig populations.

Evolutionary-Related High- and Low-Virulent Classical Swine Fever Virus Isolates Reveal Viral Determinants of Virulence

Classical swine fever (CSF) has been eradicated from Western and Central Europe but remains endemic in parts of Central and South America, Asia, and the Caribbean. CSF virus (CSFV) has been endemic in Cuba since 1993, most likely following an escape of the highly virulent Margarita/1958 strain. In recent years, chronic and persistent infections with low-virulent CSFV have been observed. Amino acid substitutions located in immunodominant epitopes of the envelope glycoprotein E2 of the attenuated isolates were attributed to positive selection due to suboptimal vaccination and control. To obtain a complete picture of the mutations involved in attenuation, we applied forward and reverse genetics using the evolutionary-related low-virulent CSFV/Pinar del Rio (CSF1058)/2010 (PdR) and highly virulent Margarita/1958 isolates. Sequence comparison of the two viruses recovered from experimental infections in pigs revealed 40 amino acid differences. Interestingly, the amino acid substitutions clustered in E2 and the NS5A and NS5B proteins. A long poly-uridine sequence was identified previously in the 3' untranslated region (UTR) of PdR. We constructed functional cDNA clones of the PdR and Margarita strains and generated eight recombinant viruses by introducing single or multiple gene fragments from Margarita into the PdR backbone. All chimeric viruses had comparable replication characteristics in porcine monocyte-derived macrophages. Recombinant PdR viruses carrying either E2 or NS5A/NS5B of Margarita, with 36 or 5 uridines in the 3'UTR, remained low virulent in 3-month-old pigs. The combination of these elements recovered the high-virulent Margarita phenotype. These results show that CSFV evolution towards attenuated variants in the field involved mutations in both structural and non-structural proteins and the UTRs, which act synergistically to determine virulence.

Construction and efficacy of a new live chimeric C-strain vaccine with DIVA characteristics against classical swine fever

To develop the new classical swine fever (CSF) vaccine candidate with differentiating infected vaccinated animals (DIVA) characteristics, a chimeric CSF virus (CSFV) was constructed based on an infectious cDNA clone of the CSF vaccine C-strain. The 5'- and 3'-untranslated regions (UTRs) and partial E2 region (residues 690-860) of the C-strain were substituted with the corresponding regions of bovine viral diarrhoea virus (BVDV) to construct the chimeric cDNA clone pC/bUTRs-tE2. The chimeric virus rC/bUTRs-tE2 was generated by several passages of pC/bUTRs-tE2-transfected PK15 cells. Stable growth and genetic properties of rC/bUTRs-tE2 were obtained after 30 serial passages. Compared to parental rC/bUTRs-tE2 (1^st passage), two residue mutations (M834K and M979K) located in E2 in rC/bUTRs-tE2 P30 were observed. Compared to the C-strain, rC/bUTRs-tE2 exhibited unchanged cell tropism and decreased plaque-forming ability. Substituting the C-strain UTRs with the BVDV UTRs resulted in significantly increased viral replication in PK15 cells. Compared to CSFV E^rns-positive and BVDV tE2-negative antibody responses induced by the CSF vaccine C-strain, immunization of rabbits and piglets with rC/bUTRs-tE2 resulted in serological profiles of CSFV E^rns- and BVDV tE2-positive antibodies, which are used to serologically discriminate pigs that are clinically infected and vaccinated. Vaccination of piglets with rC/bUTRs-tE2 conferred complete protection against lethal CSFV challenge. Our results suggest that rC/bUTRs-tE2 is a promising new CSF marker vaccine candidate.

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.

A positively charged surface patch on the pestivirus NS3 protease module plays an important role in modulating NS3 helicase activity and virus production

Pestivirus nonstructural protein 3 (NS3) is a multifunctional protein with protease and helicase activities that are essential for virus replication. In this study, we used a combination of biochemical and genetic approaches to investigate the relationship between a positively charged patch on the protease module and NS3 function. The surface patch is composed of four basic residues, R50, K74 and K94 in the NS3 protease domain and H24 in the structurally integrated cofactor NS4A^PCS. Single-residue or simultaneous four-residue substitutions in the patch to alanine or aspartic acid had little effect on ATPase activity. However, single substitutions of R50, K94 or H24 or a simultaneous four-residue substitution resulted in apparent changes in the helicase activity and RNA-binding ability of NS3. When these mutations were introduced into a classical swine fever virus (CSFV) cDNA clone, a single substitution at K94 or a simultaneous four-residue substitution (Qua_A or Qua_D) impaired the production of infectious virus. Furthermore, the replication efficiency of the CSFV variants was partially correlated with the helicase activity of NS3 in vitro. Our results suggest that the conserved positively charged patch on NS3 plays an important role in modulating the NS3 helicase activity in vitro and CSFV production.

Comparison of the Pathogenicity of Classical Swine Fever Virus Subgenotype 2.1c and 2.1d Strains from China

Classical swine fever (CSF) caused by classical swine fever virus (CSFV) is a highly contagious and devastating disease. The traditional live attenuated C-strain vaccine is widely used to control disease outbreaks in China. Since 2000, subgenotype 2.1 has become dominant in China. Here, we isolated subgenotype 2.1c and 2.1d strains from CSF-suspected pigs. The genetic variations and pathogenesis of subgenotype 2.1c and 2.1d strains were investigated experimentally. We aimed to evaluate and compare the replication characteristics and clinical signs of subgenotype 2.1c and 2.1d strains with those of the typical highly virulent CSFV SM strain. In PK-15 cells, the three CSFV isolates exhibited similar replication levels but significantly lower replication levels compared with the CSFV SM strain. The experimental animal infection model showed that the pathogenicity of subgenotype 2.1c and 2.1d strains was less than that of the CSFV SM strain. According to the clinical scoring system, subgenotype 2.1c (GDGZ-2019) and 2.1d (HBXY-2019 and GXGG-2019) strains were moderately virulent. This study showed that the pathogenicity of CSFV field strains will aid in the understanding of CSFV biological characteristics and the related epidemiology.

P108 and T109 on E2 Glycoprotein Domain I Are Critical for the Adaptation of Classical Swine Fever Virus to Rabbits but Not for Virulence in Pigs

The classical swine fever virus (CSFV) live attenuated vaccine C-strain is adaptive to rabbits and attenuated in pigs, in contrast with the highly virulent CSFV Shimen strain. Previously, we demonstrated that P108 and T109 on the E2 glycoprotein (E2^P108-T109) in domain I (E2^DomainI) rather than R132, S133, and D191 in domain II (E2^DomainII) determine C-strain's adaptation to rabbits (ATR) (Y. Li, L. Xie, L. Zhang, X. Wang, C. Li, et al., Virology 519:197-206, 2018). However, it remains elusive whether these critical amino acids affect the ATR of the Shimen strain and virulence in pigs. In this study, three chimeric viruses harboring E2^P108-T109, E2^DomainI, or E2^DomainII of C-strain based on the non-rabbit-adaptive Shimen mutant vSM-HCLVE^rns carrying the E^rns glycoprotein of C-strain were generated and evaluated. We found that E2^P108-T109 or E2^DomainI but not E2^DomainII of C-strain renders vSM-HCLVE^rns adaptive to rabbits, suggesting that E2^P108-T109 in combination with the E^rns glycoprotein (E2^P108-T109-E^rns) confers ATR on the Shimen strain, creating new rabbit-adaptive CSFVs. Mechanistically, E2^P108-T109-E^rns of C-strain mediates viral entry during infection in rabbit spleen lymphocytes, which are target cells of C-strain. Notably, pig experiments showed that E2^P108-T109-E^rns of C-strain does not affect virulence compared with the Shimen strain. Conversely, the substitution of E2^DomainII and E^rns of C-strain attenuates the Shimen strain in pigs, indicating that the molecular basis of the CSFV ATR and that of virulence in pigs do not overlap. Our findings provide new insights into the mechanism of adaptation of CSFV to rabbits and the molecular basis of CSFV adaptation and attenuation.IMPORTANCE Historically, live attenuated vaccines produced by blind passage usually undergo adaptation in cell cultures or nonsusceptible hosts and attenuation in natural hosts, with a classical example being the classical swine fever virus (CSFV) lapinized vaccine C-strain, which was developed by hundreds of passages in rabbits. However, the mechanism of viral adaptation to nonsusceptible hosts and the molecular basis for viral adaptation and attenuation remain largely unknown. In this study, we demonstrated that P108 and T109 on the E2 glycoprotein together with the E^rns glycoprotein of the rabbit-adaptive C-strain confer adaptation to rabbits on the highly virulent CSFV Shimen strain by affecting viral entry during infection but do not attenuate the Shimen strain in pigs. Our results provide vital information on the different molecular bases of CSFV adaptation to rabbits and attenuation in pigs.

Development of a marker vaccine candidate against classical swine fever based on the live attenuated vaccine C-strain

Classical swine fever (CSF) is a highly contagious and economically damaging disease. Classical swine fever virus (CSFV) lapinized vaccine C-strain against CSF worldwide lacks the capacity for the serological differentiation between infected and vaccinated animals (DIVA). To develop a marker C-strain complying with the DIVA principle, we generated and evaluated mutants rHCLV-E2F117A, rHCLV-E2G119A, and rHCLV-E2P122A, which harbor the single amino acid mutation at ¹¹⁷F, ¹¹⁹G or ¹²²P of the monoclonal antibody HQ06-recognized epitope on the E2 glycoprotein in rabbits and pigs. Viral intravenous administration demonstrated that all the mutants retain the phenotype of C-strain in rabbits, including fever response induction and replication in the spleen. Notably, the HQ06-recognized epitope did not react with the antibodies induced by rHCLV-E2P122A in rabbits, in contrast with C-strain and other two mutants. Intramuscular administration of rHCLV-E2P122A in pigs induced anti-CSFV neutralizing antibodies but not antibodies against the HQ06-recognized epitope at 28 days post-inoculation. Collectively, our data demonstrate that rHCLV-E2P122A is a promising marker vaccine candidate against CSF.

Impact of a Live Attenuated Classical Swine Fever Virus Introduced to Jeju Island, a CSF-Free Area

Here, we examine the effects of LOM(Low virulence of Miyagi) strains isolated from pigs (Jeju LOM strains) of Jeju Island, where vaccination with a live attenuated classical swine fever (CSF) LOM vaccine strain was stopped. The circulation of the Jeju LOM strains was mainly caused by a commercial swine erysipelas (Erysipelothrix rhusiopathiae) vaccine mixed with a LOM vaccine strain, which was inoculated into pregnant sows of 20 pig farms in 2014. The Jeju LOM strain was transmitted to 91 pig farms from 2015 to 2018. A histopathogenic investigation was performed for 25 farms among 111 farms affected by the Jeju LOM strain and revealed pigs infected with the Jeju LOM strain in combination with other pathogens, which resulted in the abortion of fetuses and mortality in suckling piglets. Histopathologic examination and immunohistochemical staining identified CSF-like lesions. Our results also confirm that the main transmission factor for the Jeju LOM strain circulation is the vehicles entering/exiting farms and slaughterhouses. Probability estimates of transmission between cohabiting pigs and pigs harboring the Jeju LOM strain JJ16LOM-YJK08 revealed that immunocompromised pigs showed horizontal transmission (r = 1.22). In a full genome analysis, we did not find genetic mutation on the site that is known to relate to pathogenicity between Jeju LOM strains (2014–2018) and the commercial LOM vaccine strain. However, we were not able to determine whether the Jeju LOM strain (2014–2018) is genetically the same virus as those of the commercial LOM vaccine due to several genetic variations in structure and non-structure proteins. Therefore, further studies are needed to evaluate the pathogenicity of the Jeju LOM strain in pregnant sow and SPF pigs and to clarify the characteristics of Jeju LOM and commercial LOM vaccine strains.

Classical swine fever virus C-strain with eight mutation sites shows enhanced cell adaptation and protects pigs from lethal challenge

Control of classical swine fever (CSF) in developing countries is achieved by immunization with attenuated vaccines, such as the lapinized C-strain vaccine that has been widely used in China. However, C-strain has relatively low growth rate in cell cultures, thus affecting productivity of the vaccine for the industry. In this study, eight amino acid residues were mutated on the C-strain backbone, resulting in a cell-adapted strain Cmut8. The mutant strain exhibited rapid growth with titer of about 100 fold higher than its parental C-strain. The mutation sites located at structural proteins E^rns and E2 contributed more to cell adaptation than those located in non-structural proteins. Sera collected from pigs inoculated with Cmut8 and C-strain at the same dose showed similar antibody levels and neutralization titers. Pigs inoculated with different doses of Cmut8 (low, medium and high) and with C-strain offered full protection against challenge with a virulent strain, shown as absence of fever and other symptoms, marginal low levels of viral load, and no obvious gross pathological changes in major organs. Unvaccinated control pigs challenged with the virulent strain showed high fever from day 2 post-challenge and apparent clinical symptoms with two deaths. Viral load were markedly elevated in these control pigs after challenge. The pigs inoculated with high dose of Cmut8 did not show fever or other typical CSF symptoms, and no apparent pathological changes were observed in major organs. Besides, the Cmut8 strain did not induce typical fever response in rabbits. These results demonstrate that the cell-adapted Cmut8 strain remains non-pathogenic to the weaned pigs, provides full protection and could be a good candidate vaccine strain for improved yield at lower cost.

Uncoupling of Protease trans-Cleavage and Helicase Activities in Pestivirus NS3

The nonstructural protein NS3 from the Flaviviridae family is a multifunctional protein that contains an N-terminal protease and a C-terminal helicase, playing essential roles in viral polyprotein processing and genome replication. Here we report a full-length crystal structure of the classical swine fever virus (CSFV) NS3 in complex with its NS4A protease cofactor segment (PCS) at a 2.35-Å resolution. The structure reveals a previously unidentified ∼2,200-Ų intramolecular protease-helicase interface comprising three clusters of interactions, representing a "closed" global conformation related to the NS3-NS4A cis-cleavage event. Although this conformation is incompatible with protease trans-cleavage, it appears to be functionally important and beneficial to the helicase activity, as the mutations designed to perturb this conformation impaired both the helicase activities in vitro and virus production in vivo Our work reveals important features of protease-helicase coordination in pestivirus NS3 and provides a key basis for how different conformational states may explicitly contribute to certain functions of this natural protease-helicase fusion protein.IMPORTANCE Many RNA viruses encode helicases to aid their RNA genome replication and transcription by unwinding structured RNA. Being naturally fused to a protease participating in viral polyprotein processing, the NS3 helicases encoded by the Flaviviridae family viruses are unique. Therefore, how these two enzyme modules coordinate in a single polypeptide is of particular interest. Here we report a previously unidentified conformation of pestivirus NS3 in complex with its NS4A protease cofactor segment (PCS). This conformational state is related to the protease cis-cleavage event and is optimal for the function of helicase. This work provides an important basis to understand how different enzymatic activities of NS3 may be achieved by the coordination between the protease and helicase through different conformational states.

Classical swine fever virus nonstructural protein p7 modulates infectious virus production

The classical swine fever virus (CSFV) nonstructural protein p7 is crucial for virus production, yet precisely how the p7 modulates this process is unclear. In this study, we first identified the interactions of p7 with E2 and NS2. The key binding regions of both p7 and NS2 mapped to the first transmembrane (TM1) domain of two proteins. Three amino acid substitutions in the TM1 region of p7 (p7^{TDI18/19/20AAA}, p7^{EVV21/22/23AAA} and p7^{YFY25/26/30AAA}) impaired infectious virus production and reduced the interaction of p7 with the NS2 protein. The E2p7 processing and mature p7, but not the E2p7 precursor, are essential for infectious virus production. Bicistronic mutants (pSM/E2/IRES) with single substitutions at residues 1 to 9 of p7 exhibited a significantly increased infectious CSFV titer compared to their counterparts in the context of pSM. Viral genomic RNA copies of the mutants exhibited similar levels compared with the wt CSFV. Our results demonstrated that CSFV p7 and its precursor E2p7 modulate viral protein interactions and infectious virus production without influencing viral RNA replication.

Recombinant Swinepox Virus Expressing Glycoprotein E2 of Classical Swine Fever Virus Confers Complete Protection in Pigs upon Viral Challenge

Classical swine fever (CSF) is a highly contagious and serious viral disease that affects the pig industry worldwide. The glycoprotein E2 of the classical swine fever virus (CSFV) can induce neutralizing antibodies, and it is widely used for novel vaccine development. To explore the development of a vaccine against CSFV infections, the gene of glycoprotein E2 was inserted into the swinepox virus (SPV) genome by homologous recombination. The culture titers of rSPV-E2 remained at about 4.3 × 10⁶ TCID₅₀ for more than 60 passages in PK15 and swine testis cell lines. The rSPV-E2 could not be replicated in Vero, MDBK or other non-porcine cell lines. After two to three passages, the SPV specific gene of rSPV-E2 could not been detected in the non-porcine cell culture. To evaluate the immunogenicity of rSPV-E2, 20 CSFV seronegative minipigs were immunized with rSPV-E2, a commercial C-strain vaccine, wild-type SPV (wtSPV; negative control), or PBS (a no-challenge control). After challenge with CSFV, pigs in the rSPV-E2-immunized group showed significantly shorter fever duration compared with the wtSPV-treated group (P < 0.05). E2-specific antibodies in the rSPV-E2-immunized group increased dramatically after vaccination and increased continuously over time. CSFV genomic copies in the serum of rSPV-E2-immunized pigs were significantly less compared with the wtSPV-treated group at all time points after challenge (P < 0.01). Significant reduction in gross lung lesion scores, histopathological liver, spleen, lung, and kidney lesion scores were noted in the rSPV-E2-immunized group compared with the wtSPV-treated group (P < 0.01). The results suggested that the recombinant rSPV-E2 provided pigs with significant protection from CSFV infections; thus, rSPV-E2 offers proof of principle for the development of a vaccine for the prevention of CSFV infections in pigs.

Efficacy evaluation of the C-strain-based vaccines against the subgenotype 2.1d classical swine fever virus emerging in China

Classical swine fever (CSF) is a devastating infectious disease of pigs caused by classical swine fever virus (CSFV). The disease has been controlled following extensive vaccination with the lapinized attenuated vaccine C-strain for decades in China. However, frequent CSF outbreaks occurred recently in a large number of C-strain-vaccinated pig farms in China and a new subgenotype 2.1d of CSFV has been reported to be responsible for the outbreaks. Here we analyzed the molecular variations and antigenic differences among the C-strain-based commercial vaccines of different origins from different manufacturers in China, and reevaluated the vaccines against the emerging subgenotype 2.1d strain of CSFV. The results showed that the C-strain adapted to the continuous ST cell line (C_ST) contain a unique M290K variation on the E2 protein, compared to those of primary BT cells (C_BT) or rabbit origin (C_RT) and the traditional C-strain sequences available in the GenBank database. Serum neutralization test revealed the antigenic differences between C_ST and C_BT or C_RT. Notably, the neutralizing titers of porcine anti-C-strain sera against the CSFV isolate of subgenotype 2.1d were significantly lower than those against C-strain or Shimen strain. The C-strain-vaccinated, subgenotype 2.1d HLJZZ2014 strain-challenged pigs did not show any clinical signs and all survived. However, these pigs displayed mild pathological and histological lesions, and the CSFV viral RNA was detected in the various tissue and blood samples. Taken together, the C-strain-based vaccines of different origins showed molecular variations and antigenic differences, and could provide clinical but not pathological and virological protection against the subgenotype 2.1d CSFV emerging in China. Further investigation is needed to comprehensively assess the efficacy of C-strain of different doses against the subgenotype 2.1d CSFV.