The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution

Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin-Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.

Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin

The main approach to preventing tick-borne encephalitis (TBE) is vaccination. Formaldehyde-inactivated TBE vaccines have a proven record of safety and efficiency but have never been characterized structurally with atomic resolution. We report a cryoelectron microscopy (cryo-EM) structure of the formaldehyde-inactivated TBE virus (TBEV) of Sofjin-Chumakov strain representing the Far-Eastern subtype. A 3.8 Å resolution reconstruction reveals the structural integrity of the envelope E proteins, specifically the E protein ectodomains. The comparative study shows a high structural similarity to the previously published structures of the TBEV European subtype strains Hypr and Kuutsalo-14. A fraction of inactivated virions exhibits asymmetric features including the deformations of the membrane profile. We propose that the heterogeneity is caused by inactivation and perform a local variability analysis on the small parts of the envelope protein shell to reveal membrane curvature features possibly induced by the inactivation. The results of this study will have implications for the design of novel vaccines against diseases caused by flaviviruses.

Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL

X-ray imaging of virus particles at the European XFEL could eventually allow their complete structures to be solved, potentially approaching the resolution of other structural virology methods. To achieve this ambitious goal with today's technologies, about 1 ml of purified virus suspension containing at least 1012 particles per millilitre is required. Such large amounts of concentrated suspension have never before been obtained for enveloped viruses. Tick-borne encephalitis virus (TBEV) represents an attractive model system for the development of enveloped virus purification and concentration protocols, given the availability of large amounts of inactivated virus material provided by vaccine-manufacturing facilities. Here, the development of a TBEV vaccine purification and concentration scheme is presented combined with a quality-control protocol that allows substantial amounts of highly concentrated non-aggregated suspension to be obtained. Preliminary single-particle imaging experiments were performed for this sample at the European XFEL, showing distinct diffraction patterns.

[Investigation of oncolytic potential of vaccine strains of yellow fever and tick-borne encephalitis viruses against glioblastoma and pancreatic carcinoma cell lines]

INTRODUCTION

Flaviviruses, possessing natural neurotropicity could be used in glioblastoma therapy using attenuated strains or as a delivery system for antitumor agents in an inactivated form.

OBJECTIVE

To investigate the sensitivity of glioblastoma and pancreatic carcinoma cell lines to vaccine strains of yellow fever and tick-borne encephalitis viruses.

MATERIALS AND METHODS

Cell lines: glioblastoma GL-6, T98G, LN-229, pancreatic carcinoma MIA RaCa-2 and human pancreatic ductal carcinoma PANC-1. Viral strains: 17D yellow fever virus (YF), Sofjin tick-borne encephalitis virus (TBEV). Virus concentration were determined by plaque assay and quantitative PCR. Determination of cell sensitivity to viruses by MTT assay.

RESULTS

17D YF was effective only against pancreatic carcinoma tumor cells MIA Paca-2 and had a limited effect against PANC-1. In glioblastoma cell lines (LN229, GL6, T98G), virus had no oncolytic effect and the viral RNA concentration fell in the culture medium. Sofjin TBEV showed CPE50 against MIA Paca-2 and a very limited cytotoxic effect against PANC-1. However, it had no oncolytic effect against glioblastoma cell lines (LN229, T98G and GL6), although virus reproduction continued in these cultures. For the GL6 glioblastoma cell line, the viral RNA concentration at the level with the infection dose was determined within 13 days, despite medium replacement, while in the case of the LN229 cell line, the virus concentration increased from 1 × 109 to 1 × 1010 copies/ml.

CONCLUSION

Tumor behavior in organism is more complex and is determined by different microenvironmental factors and immune status. In the future, it is advisable to continue studying the antitumor oncolytic and immunomodulatory effects of viral strains 17D YF and Sofjin TBEV using in vivo models.

Flaviviruses in AntiTumor Therapy

Oncolytic viruses offer a promising approach to tumor treatment. These viruses not only have a direct lytic effect on tumor cells but can also modify the tumor microenvironment and activate antitumor immunity. Due to their high pathogenicity, flaviviruses have often been overlooked as potential antitumor agents. However, with recent advancements in genetic engineering techniques, an extensive history with vaccine strains, and the development of new attenuated vaccine strains, there has been a renewed interest in the Flavivirus genus. Flaviviruses can be genetically modified to express transgenes at acceptable levels, and the stability of such constructs has been greatly improving over the years. The key advantages of flaviviruses include their reproduction cycle occurring entirely within the cytoplasm (avoiding genome integration) and their ability to cross the blood-brain barrier, facilitating the systemic delivery of oncolytics against brain tumors. So far, the direct lytic effects and immunomodulatory activities of many flaviviruses have been widely studied in experimental animal models across various types of tumors. In this review, we delve into the findings of these studies and contemplate the promising potential of flaviviruses in oncolytic therapies.

Size Distribution of Inactivated Tick-Borne Encephalitis Virus Particles Revealed by a Comprehensive Physicochemical Approach

Tick-borne encephalitis virus (TBEV) is an enveloped RNA virus, a member of the genus Flavivirus (family Flaviviridae). Here, we provide a detailed analysis of the size and structure of the inactivated TBEV vaccine strain Sofjin-Chumakov. Four analytical methods were used to analyze individual TBEV particles—negative staining TEM, cryo-EM, atomic force microscopy (AFM), and nanoparticle tracking analysis (NTA). All methods confirmed that the particles were monodisperse and that their mean size was ~50 nm. Cryo-EM data allowed us to obtain a 3D electron density model of the virus with clearly distinguishable E protein molecules. STEM-EELS analysis detected phosphorus in the particles, which was interpreted as an indicator of RNA presence. Altogether, the described analytical procedures can be valuable for the characterization of inactivated vaccine virus samples.

Inactivated tick-borne encephalitis vaccine elicits several overlapping waves of T cell response

The development and implementation of vaccines have been growing exponentially, remaining one of the major successes of healthcare over the last century. Nowadays, active regular immunizations prevent epidemics of many viral diseases, including tick-borne encephalitis (TBE). Along with the generation of virus-specific antibodies, a highly effective vaccine should induce T cell responses providing long-term immune defense. In this study, we performed longitudinal high-throughput T cell receptor (TCR) sequencing to characterize changes in individual T cell repertoires of 11 donors immunized with an inactivated TBE vaccine. After two-step immunization, we found significant clonal expansion of both CD4⁺ and CD8⁺ T cells, ranging from 302 to 1706 vaccine-associated TCRβ clonotypes in different donors. We detected several waves of T cell clonal expansion generated by distinct groups of vaccine-responding clones. Both CD4⁺ and CD8⁺ vaccine-responding T cell clones formed 17 motifs in TCRβ sequences shared by donors with identical HLA alleles. Our results indicate that TBE vaccination leads to a robust T cell response due to the production of a variety of T cell clones with a memory phenotype, which recognize a large set of epitopes.

Vaccine building ‘kit’: combining peptide bricks to elicit a desired immune response without adding an adjuvant

Protein nanoparticles (NPs) can be used as vaccine platforms for target antigen presentation. Aim: To conduct a proof-of-concept study to demonstrate that an effective NP platform can be built based on a short self-assembling peptide (SAP) rather than a large self-assembling protein. Materials & methods: SUMO-based protein fusions (SFs) containing an N-terminal SAP and a C-terminal antigen were designed, expressed in Escherichia coli and purified. The structure was investigated by electron microscopy. The antibody response was tested in mice after two adjuvant-free immunizations. Results: Renatured SFs form fiber-like NPs with the antigen exposed on the surface and induce a significant antibody response with a remarkably high target-to-platform ratio. Conclusion: The platform is effective and has considerable potential for modification toward various applications, including vaccine development.

Evervac: phase I/II study of immunogenicity and safety of a new adjuvant-free TBE vaccine cultivated in Vero cell culture

Approximately 10,000 cases of tick-borne encephalitis (TBE), a serious disease of the central nervous system caused by tick-borne encephalitis virus (TBEV), are registered worldwide every year. Vaccination against TBE remains the most essential measure of preventing the disease. Unlike available TBE vaccines, a new inactivated lyophilized candidate vaccine Evervac is produced in Vero continuous cell culture and its final formulation does not include aluminum-based adjuvants. To study the safety and immunogenicity of Evervac, healthy adults 18-60 y of age were immunized twice at 30-d intervals. The study was single-blind, randomized, comparative, controlled, and was conducted in TBE-endemic areas. The commercial lyophilized vaccine TBE-Moscow was used as a comparison treatment. The subjects were observed for incidence, severity, and duration of adverse reactions. It was shown that the severity of local and systemic reactions in the Evervac vaccine group was mild to moderate. There were no significant differences in the incidence of adverse reactions between the Evervac and TBE-Moscow vaccine groups. Immunization with Evervac produced a significant increase in geometric mean titer (GMT) of anti-TBEV antibodies in both initially seronegative and seropositive recipients. The seroconversion rate for the initially seronegative recipients was 69% (GMT = 1:214) after the first dose and reached 100% after the second dose. In these parameters, there were no significant differences between the study and control vaccine groups. Thus, the adjuvant-free Vero-based vaccine Evervac was well tolerated, had low reactogenicity, induced a pronounced immune response, and was overall non-inferior to the commercial adjuvanted TBE vaccine used as a control.

Comparison of the Immunogenicity and Safety of Two Pediatric TBE Vaccines Based on the Far Eastern and European Virus Subtypes

Up to 10,000 cases of tick-borne encephalitis are registered annually, 20% of which occur in children under 17 years of age. A comparison of the immunogenicity and safety between a new pediatric Tick-E-Vac vaccine based on the TBEV strain Sofjin and FSME-IMMUN Junior vaccine was performed in the Sverdlovsk region. The vaccine strains differ from strains of the Siberian subtype of TBEV that dominates in the region. The study was performed on 163 children aged 1 to 15, who received one of the vaccines according to either a conventional or rapid vaccination schedule. Immunogenicity was assessed based on the seroprotection rates and titers of virus-neutralizing antibodies. There were no significant differences in either the immunogenicity or reactogenicity of the pediatric vaccines based on strains of the Far Eastern or European subtypes of TBEV. Under both vaccination schedules, 30 days after the second injection, seroprotection rates were 100% for Tick-E-Vac and greater than 95% for FSME-IMMUN Junior, while the geometric mean titer of TBEV-neutralizing antibodies was at least 2,4 log10 (1 : 250) for either vaccine. Fourteen days after the second injection according to the rapid schedule, seroprotection rates were significantly lower, ranging from 50% to 63% regardless of the vaccine used. The observed adverse reactions were mild or moderate for both vaccines under both vaccination schedules, with total adverse event rates of less than 25%. Reactogenicity was not associated with the gender or age of the recipients. There were no statistically significant differences in the incidence of adverse reactions between the group of subjects who were baseline seronegative or seropositive. However, 14 days after the second vaccine injection according to the rapid schedule, a statistically significant difference in nAbs titers was identified between groups of children with and without reported reactions.

Experimental Evaluation of the Protective Efficacy of Tick-Borne Encephalitis (TBE) Vaccines Based on European and Far-Eastern TBEV Strains in Mice and in Vitro

Tick-borne encephalitis (TBE), caused by the TBE virus (TBEV), is a serious public health threat in northern Eurasia. Three subtypes of TBEV are distinguished. Inactivated vaccines are available for TBE prophylaxis, and their efficacy to prevent the disease has been demonstrated by years of implication. Nevertheless, rare TBE cases among the vaccinated have been registered. The present study aimed to evaluate the protective efficacy of 4 TBEV vaccines against naturally circulating TBEV variants. For the first time, the protection was evaluated against an extended number of phylogenetically distinct TBEV strains isolated in different years in different territories. The protective effect did not strongly depend on the infectious dose of the challenge virus or the scheme of vaccination. All vaccines induced neutralizing antibodies in protective titers against the TBEV strains used, although the vaccines varied in the spectra of induced antibodies and protective efficacy. The protective efficacy of the vaccines depended on the individual properties of the vaccine strain and the challenge virus, rather than on the subtypes. The neutralization efficiency appeared to be dependent not only on the presence of antibodies to particular epitopes and the amino acid composition of the virion surface but also on the intrinsic properties of the challenge virus E protein structure.

Immunogenicity and safety of the adult tbe vaccine «tick-e-vac»

About 3,000 cases of TBE are registered annually in the Russian Federation. Vaccination is the main way to prevent the tick-borne encephalitis disease. Comparative study of the reactogenicity and immunogenicity of a new vaccine «Tick-E-Vac» was held. Volunteers aged from 16 years old were twice immunized with the vaccines «Tick-E-Vac» or «Encevir» derived from strains of Far East subtype of TBE virus, according to standard and emergency schemes. The clinical study was randomized, comparative, blind, and controlled. The frequency, intensity, time of occurrence, and duration of local and general reactions had been recorded. The titers of antiviral antibodies in ELISA had been determined to assess the immunological efficacy of vaccination. According to the results of the clinical study, the severity of local and general reactions in initial seronegative recipients was weak or moderate. The symptoms were usually manifested within 1-2 days after injection and persisted for not more than 4 days, after which time the symptoms disappeared. There was no statistically significant difference in the reactogenicity of the vaccines after the first and after the second injection. The reactogenicity also did not depend on the gender of recipients. After the first immunization, the level of seroprotection was not less than 43%; the average geometric titer of antibodies (GTA), not less than 1:200. After the second injection, the level of seroprotection reached 90-100%; GTA, not less than 1:500. The data on the reactogenicity and immunogenicity to the original seropositive recipients is not significantly different from the data for the initial seronegative recipients. The data indicate weak reactogenicity of the vaccines «Tick-E-Vac» and «Encevir». Double vaccination with an interval of 14 or 30 days leads to the formation of expressed immune response. Thus, differences in the level of seroprotection and in antiviral titers in the cases of the standard and emergency vaccination schedules are not statistically significant. The correlation between the development in recipients of local and general symptoms and the immunological efficacy of the vaccines has not been identified.

[Vaccines based on the Far-Eastern and European strains induce the neutralizing antibodies against all known tick-borne encephalitis virus subtypes]

Serum of children aged 1 to 16 obtained in the course of clinical trials conducted in the sverdlovsk region in 2011 was used to study the post-vaccination immunity. Children were immunized twice with vaccines against the tick-borne encephalitis (TBE) Tick-E-Vak on the basis of the strain sofjin of the Far-Eastern subtype and FSME-IMMUN Junior based on the neudorfl strain of the european subtype. According to the plaque reduction neutralization test (PRNT), both vaccines have a high immunogenicity: after 30 days since two-time vaccination in the sera of 100% of children immunized with the vaccine Tick-E-Vak and in the 95% of children immunized with the vaccine FSME-IMMUN Junior antibodies (AT) against strain sofjin were identified in protective titers, whereas 24.5% and 21.4% of children, respectively, had antibody titers higher than 1:10000. selected sera of recipients with titers from 1:25 to 1:1000 were examined in the PRNT in a single experiment using the sofjin (Far-Eastern subtype), absettarov (European subtype) and Vasilchenko (Siberian subtype) strains. The two vaccines induced AT against the representatives of all three subtypes.

Genetic description of a tick-borne encephalitis virus strain Sofjin with the longest history as a vaccine strain

Vaccines based on the strain Sofjin of the Far-Eastern tick-borne encephalitis virus (TBEV) subtype have been used for TBE prophylaxis for over 50 years in Russia and neighboring countries. On the wide territory, where all known TBEV subtypes are circulating, the cultural, purified, concentrated, inactivated TBE vaccine Moscow has been shown to be safe and efficacious in a massive immunization. In the present work, we describe the genome of the vaccine strain Sofjin. We have shown that it differs from TBEV strains previously published with the name “Sofjin”. Moreover, we have shown the stability of the virus during the vaccine manufacturing process on the molecular level.

Exploring of primate models of tick-borne flaviviruses infection for evaluation of vaccines and drugs efficacy

Tick-borne encephalitis virus (TBEV) is one of the most prevalent and medically important tick-borne arboviruses in Eurasia. There are overlapping foci of two flaviviruses: TBEV and Omsk hemorrhagic fever virus (OHFV) in Russia. Inactivated vaccines exist only against TBE. There are no antiviral drugs for treatment of both diseases. Optimal animal models are necessary to study efficacy of novel vaccines and treatment preparations against TBE and relative flaviviruses. The models for TBE and OHF using subcutaneous inoculation were tested in Cercopithecus aethiops and Macaca fascicularis monkeys with or without prior immunization with inactivated TBE vaccine. No visible clinical signs or severe pathomorphological lesions were observed in any monkey infected with TBEV or OHFV. C. aethiops challenged with OHFV showed massive hemolytic syndrome and thrombocytopenia. Infectious virus or viral RNA was revealed in visceral organs and CNS of C. aethiops infected with both viruses; however, viremia was low. Inactivated TBE vaccines induced high antibody titers against both viruses and expressed booster after challenge. The protective efficacy against TBE was shown by the absence of virus in spleen, lymph nodes and CNS of immunized animals after challenge. Despite the absence of expressed hemolytic syndrome in immunized C. aethiops TBE vaccine did not prevent the reproduction of OHFV in CNS and visceral organs. Subcutaneous inoculation of M. fascicularis with two TBEV strains led to a febrile disease with well expressed viremia, fever, and virus reproduction in spleen, lymph nodes and CNS. The optimal terms for estimation of the viral titers in CNS were defined as 8-16 days post infection. We characterized two animal models similar to humans in their susceptibility to tick-borne flaviviruses and found the most optimal scheme for evaluation of efficacy of preventive and therapeutic preparations. We also identified M. fascicularis to be more susceptible to TBEV than C. aethiops.

A synthetic peptide based on the NS1 non-structural protein of tick-borne encephalitis virus induces a protective immune response against fatal encephalitis in an experimental animal model

Linear immunogenic peptides corresponding to amino acid sequences from the NS1 non-structural protein from tick-borne encephalitis virus (strain Sophyin) were predicted using established algorithms and synthesized. Of the 12 peptides predicted, 11 were able to induce peptide-specific antibodies in BALB/c mice but only 1 of these 11 was able to induce antibodies, which reacted with the native protein in a radio-immune precipitation assay. This peptide corresponds to amino acids 37--55, and forms one of the predicted structurally conserved alpha helices of the virus NS1 protein. It was able to protect 60% of animals against lethal challenge with the homologous highly pathogenic tick-borne encephalitis virus strain, and adoptive transfer experiments indicated the involvement of the antibodies induced by this peptide in its protective activity in mice.

Vaccinia virus recombinant expressing gene of tick-borne encephalitis virus non-structural NS1 protein elicits protective activity in mice

A vaccinia virus recombinant containing the non-structural tick-borne encephalitis virus (TBEV) NS1 gene was developed. The recombinant expressed native dimeric form of the NS1 protein in infected cells and protected mice against lethal infection with TBEV.

A monoclonal antibody that recognizes the predicted tick-borne encephalitis virus E protein fusion sequence blocks fusion

The fusion motif of tick-borne encephalitis virus E protein has been predicted to be located within its conserved region (98-120). Results are presented to demonstrate that non-neutralizing monoclonal antibody which recognizes a synthetic peptide corresponding to residues 98-113 of the E protein sequence can block the fusion of the virus particles with artificial membranes.

pH-dependent fusion of tick-borne encephalitis virus with artificial membranes

pH-dependent fusion of TBE virus with artificial membranes was effective at slightly acidic pH with maximum at 6.4. The influence of various changes in E protein conformation on fusion process was studied.