Comprehensive assessment of the genetics and virulence of tick-borne encephalitis virus strains isolated from patients with inapparent and clinical forms of the infection in the Russian Far East

Genetic polymorphisms in innate immunity genes influence predisposition to tick-borne encephalitis

Tick-borne encephalitis (TBE) is a neuroviral disease that ranges in severity from a mild febrile illness to a severe and life-threatening meningoencephalitis or encephalomyelitis. There is increasing evidence that susceptibility to tick-borne encephalitis virus (TBEV)-induced disease and its severity are largely influenced by host genetic factors, in addition to other virus- and host-related factors. In this study, we investigated the contribution of selected single nucleotide polymorphisms (SNPs) in innate immunity genes to predisposition to TBE in humans. More specifically, we investigated a possible association between SNPs rs304478 and rs303212 in the gene Interferon Induced Protein With Tetratricopeptide Repeats 1 (IFIT1), rs7070001 and rs4934470 in the gene Interferon Induced Protein With Tetratricopeptide Repeats 2 (IFIT2), and RIG-I (Retinoic acid-inducible gene I) encoding gene DDX58 rs311795343, rs10813831, rs17217280 and rs3739674 SNPs with predisposition to TBE in population of the Czech Republic, where TBEV is highly endemic. Genotypic and allelic frequencies for these SNPs were analyzed in 247 nonimmunized TBE patients and compared with 204 control subjects. The analysis showed an association of IFIT1 rs304478 SNP and DDX58 rs3739674 and rs17217280 SNPs with predisposition to TBE in the Czech population indicating novel risk factors for clinical TBE but not for disease severity. These results also highlight the role of innate immunity genes in TBE pathogenesis.

Tick-Borne Encephalitis Vaccine: Recommendations of the Advisory Committee on Immunization Practices, United States, 2023

Tick-borne encephalitis (TBE) virus is focally endemic in parts of Europe and Asia. The virus is primarily transmitted to humans by the bites of infected

Ixodes species ticks but can also be acquired less frequently by alimentary transmission. Other rare modes of transmission include through breastfeeding, blood transfusion, solid organ transplantation, and slaughtering of viremic animals. TBE virus can cause acute neurologic disease, which usually results in hospitalization, often permanent neurologic or cognitive sequelae, and sometimes death. TBE virus infection is a risk for certain travelers and for laboratory workers who work with the virus. In August 2021, the Food and Drug Administration approved Ticovac TBE vaccine for use among persons aged ≥1 year. This report summarizes the epidemiology of and risks for infection with TBE virus, provides information on the immunogenicity and safety of TBE vaccine, and summarizes the recommendations of the Advisory Committee on Immunization Practices (ACIP) for use of TBE vaccine among U.S. travelers and laboratory workers.

The risk for TBE for most U.S. travelers to areas where the disease is endemic is very low. The risk for exposure to infected ticks is highest for persons who are in areas where TBE is endemic during the main TBE virus transmission season of April–November and who are planning to engage in recreational activities in woodland habitats or who might be occupationally exposed. All persons who travel to areas where TBE is endemic should be advised to take precautions to avoid tick bites and to avoid the consumption of unpasteurized dairy products because alimentary transmission of TBE virus can occur. TBE vaccine can further reduce infection risk and might be indicated for certain persons who are at higher risk for TBE. The key factors in the risk-benefit assessment for vaccination are likelihood of exposure to ticks based on activities and itinerary (e.g., location, rurality, season, and duration of travel or residence). Other risk-benefit considerations should include 1) the rare occurrence of TBE but its potentially high morbidity and mortality, 2) the higher risk for severe disease among certain persons (e.g., older persons aged ≥60 years), 3) the availability of an effective vaccine, 4) the possibility but low probability of serious adverse events after vaccination, 5) the likelihood of future travel to areas where TBE is endemic, and 6) personal perception and tolerance of risk

ACIP recommends TBE vaccine for U.S. persons who are moving or traveling to an area where the disease is endemic and will have extensive exposure to ticks based on their planned outdoor activities and itinerary. Extensive exposure can be considered based on the duration of travel and frequency of exposure and might include shorter-term (e.g., <1 month) travelers with daily or frequent exposure or longer-term travelers with regular (e.g., a few times a month) exposure to environments that might harbor infected ticks. In addition, TBE vaccine may be considered for persons who might engage in outdoor activities in areas where ticks are likely to be found, with a decision to vaccinate made on the basis of an assessment of their planned activities and itinerary, risk factors for a poor medical outcome, and personal perception and tolerance of risk. In the laboratory setting, ACIP recommends TBE vaccine for laboratory workers with a potential for exposure to TBE virus

Activation of Early Proinflammatory Responses by TBEV NS1 Varies between the Strains of Various Subtypes

Tick-borne encephalitis (TBE) is an emerging zoonosis that may cause long-term neurological sequelae or even death. Thus, there is a growing interest in understanding the factors of TBE pathogenesis. Viral genetic determinants may greatly affect the severity and consequences of TBE. In this study, nonstructural protein 1 (NS1) of the tick-borne encephalitis virus (TBEV) was tested as such a determinant. NS1s of three strains with similar neuroinvasiveness belonging to the European, Siberian and Far-Eastern subtypes of TBEV were studied. Transfection of mouse cells with plasmids encoding NS1 of the three TBEV subtypes led to different levels of NS1 protein accumulation in and secretion from the cells. NS1s of TBEV were able to trigger cytokine production either in isolated mouse splenocytes or in mice after delivery of NS1 encoding plasmids. The profile and dynamics of TNF-α, IL-6, IL-10 and IFN-γ differed between the strains. These results demonstrated the involvement of TBEV NS1 in triggering an immune response and indicated the diversity of NS1 as one of the genetic factors of TBEV pathogenicity.

Y-shaped RNA Secondary Structure of a Noncoding Region in the Genomic RNA of Tick-Borne Encephalitis Virus Affects Pathogenicity

Tick-borne encephalitis virus (TBEV) is a zoonotic virus that causes encephalitis in humans. Various deletions have been reported in a variable region of the 3' untranslated region of the TBEV genome. In this study, we analyzed the role of a Y-shaped secondary structure in the pathogenicity of TBEV by using reverse genetics. Deletion of the structure increased the mortality rate of virus-infected mice but did not affect virus multiplication in cultured cells and organs. Our results indicated that the secondary structure is involved in the regulation of TBEV pathogenesis. This article is protected by copyright. All rights reserved.

IRE1-Mediated Unfolded Protein Response Promotes the Replication of Tick-Borne Flaviviruses in a Virus and Cell-Type Dependent Manner

Tick-borne flaviviruses (TBFV) can cause severe neurological complications in humans, but differences in tissue tropism and pathogenicity have been described for individual virus strains. Viral protein synthesis leads to the induction of the unfolded protein response (UPR) within infected cells. The IRE1 pathway has been hypothesized to support flavivirus replication by increasing protein and lipid biogenesis. Here, we investigated the role of the UPR in TBFV infection in human astrocytes, neuronal and intestinal cell lines that had been infected with tick-borne encephalitis virus (TBEV) strains Neudoerfl and MucAr-HB-171/11 as well as Langat virus (LGTV). Both TBEV strains replicated better than LGTV in central nervous system (CNS) cells. TBEV strain MucAr-HB-171/11, which is associated with gastrointestinal symptoms, replicated best in intestinal cells. All three viruses activated the inositol-requiring enzyme 1 (IRE1) pathway via the X-box binding protein 1 (XBP1). Interestingly, the neurotropic TBEV strain Neudoerfl induced a strong upregulation of XBP1 in all cell types, but with faster kinetics in CNS cells. In contrast, TBEV strain MucAr-HB-171/11 failed to activate the IRE1 pathway in astrocytes. The low pathogenic LGTV led to a mild induction of IRE1 signaling in astrocytes and intestinal cells. When cells were treated with IRE1 inhibitors prior to infection, TBFV replication in astrocytes was significantly reduced. This confirms a supporting role of the IRE1 pathway for TBFV infection in relevant viral target cells and suggests a correlation between viral tissue tropism and the cell-type dependent induction of the unfolded protein response.

The Pseudo-Circular Genomes of Flaviviruses: Structures, Mechanisms, and Functions of Circularization

The circularization of viral genomes fulfills various functions, from evading host defense mechanisms to promoting specific replication and translation patterns supporting viral proliferation. Here, we describe the genomic structures and associated host factors important for flaviviruses genome circularization and summarize their functional roles. Flaviviruses are relatively small, single-stranded, positive-sense RNA viruses with genomes of approximately 11 kb in length. These genomes contain motifs at their 5′ and 3′ ends, as well as in other regions, that are involved in circularization. These motifs are highly conserved throughout the Flavivirus genus and occur both in mature virions and within infected cells. We provide an overview of these sequence motifs and RNA structures involved in circularization, describe their linear and circularized structures, and discuss the proteins that interact with these circular structures and that promote and regulate their formation, aiming to clarify the key features of genome circularization and understand how these affect the flaviviruses life cycle.

Molecular and Genetic Bases of Inhibition of Tick-Borne Encephalitis Virus Replication by Eprosartan and Ribavirin

The antiviral activity of eprosartan (compound selected in silico) towards highly and low-virulent strains of tick-borne encephalitis virus was compared in vitro with activity of ribavirin. Study of the cytopathogenic activity of the virus on SPEV cells by ELISA, IFAT, and PCR showed similar results: both substances (eprosartan and ribavirin) promoted elimination of tick-borne encephalitis virus. Ribavirin exhibited intracellular inhibition towards both strains: the selectivity index for highly virulent Dal'negorsk strain was 160, for low-virulent Primorye-437 strain - 113. Eprosartan inhibited intracellular replication of Dal'negorsk strain (13.7) and less so that of Primorye-437 strain (2.9). The efficiency of virtual screening of the ligand (eprosartan) was demonstrated for highly virulent, but not low virulent tick-borne encephalitis strain.

Mechanisms of Protective Actions of Specific Antibodies against the Tick-Borne Encephalitis Virus

The protective mechanisms of specific antibodies against tick-borne encephalitis virus were demonstrated on in vitro model. The effect of specific IgG on tick-borne encephalitis virus was comprehensively assessed in virucidal, preventive, direct antiviral, and intracellular actions by ELISA and virus titration results. The IC₅₀ values were obtained for virucidal (3.8±0.7 U/ml), preventive (42.8±9.9 U/ml), direct antiviral (7.2±0.9 U/ml), and intracellular action (1.7±0.4 U/ml). During titration of the samples, complete elimination of the virus was observed at IgG concentration of 16 U/ml (virucidal), 320 U/ml (preventive), 32 U/ml (direct antiviral), and 8 U/ml (intracellular action). It was demonstrated that specific IgG produces a complex inhibitory effect on tick-borne encephalitis virus: it possesses both direct neutralizing activity on the virus and reduces its adsorption and intracellular replication.

Inhibitory Activity of Scutellaria baicalensis Flavonoids against Tick-Borne Encephalitis Virus

We studied virus-inhibiting activity of Baikal skullcap (Scutellaria baicalensis) flavonoids against tick-borne encephalitis virus using various model schemes. The half-maximum cytotoxic concentration (CC₅₀) for the plant extract was found (363.9±58.6 μg/ml). Based on the CC₅₀ and IC₅₀, selective index (SI) was calculated for viricidal (53.4), preventive (50.5), and direct antiviral actions (39.1) and for-intracellular replication of the virus (40.4). Suppression of virus reproduction ≥2.0 lg TCID₅₀ was observed at extract concentration ≥5 μg/ml (viricidal effect), ≥11.2 μg/ml (preventive and direct antiviral effects), and ≥9 μg/ml (intracellular replication). Flavonoids of Baikal skullcap extract produced an in vitro inhibitory effect on tick-borne encephalitis virus due to their direct viricidal activity and direct inhibition of adsorption and intracellular replication of tick-borne encephalitis virus, which determines their value as highly effective antiviral drugs.

Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis?

Tick-borne encephalitis (TBE) is one of the most important viral zoonosis transmitted by the bite of infected ticks. In this study, all tick-borne encephalitis virus (TBEV) E gene sequences available in GenBank as of June 2019 with known date of isolation (n = 551) were analyzed. Simulation studies showed that a sample bias could significantly affect earlier studies, because small TBEV datasets (n = 50) produced non-overlapping intervals for evolutionary rate estimates. An apparent lack of a temporal signal in TBEV, in general, was found, precluding molecular clock analysis of all TBEV subtypes in one dataset. Within all subtypes and most of the smaller groups in these subtypes, there was evidence of many medium- and long-distance virus transfers. These multiple random events may play a key role in the virus spreading. For some groups, virus diversity within one territory was similar to diversity over the whole geographic range. This is best exemplified by the virus diversity observed in Switzerland or Czech Republic. These two countries yielded most of the known European subtype Eu3 subgroup sequences, and the diversity of viruses found within each of these small countries is comparable to that of the whole Eu3 subgroup, which is prevalent all over Central and Eastern Europe. Most of the deep tree nodes within all three established TBEV subtypes dated less than 300 years back. This could be explained by the recent emergence of most of the known TBEV diversity. Results of bioinformatics analysis presented here, together with multiple field findings, suggest that TBEV may be regarded as an emerging disease.

Comprehensive assessment of specific antibodies on infectious activity of tick-borne encephalitis virus

Vaccines for prophylactic immunization provide the most reliable and effective protection against the vast majority of infectious diseases. Tick-borne encephalitis (TBE) represents a high-priority medical issue at the territory of the Eurasian continent. Of great importance is assessing a role of distinct antibody titers especially low titers, observed quite often in vaccinated individuals, sometimes posing obstacles in determining a threshold of seropositivity as well as the level of specific protection against TBE virus. We aimed at obtaining data to assess antiviral activity of virus-specific antibodies with distinct titer levels based on the in vitro, ex vivo and in vivo experimental studies with a highly virulent Far-Eastern strain of tick-borne encephalitis virus. The in vitro, ex vivo and in vivo comprehensive experimental studies with a highly virulent Far-Eastern strain of tick-borne encephalitis virus (TBEV) were conducted and the dynamics of antiviral activity of virus-specific antibodies at variable titers (1:100–1:3200) was measured (timeframe ranged within 1–96 hours p.i.) to provide a rationale for evaluating the antiviral immune response. It was found that the in vitro experiments demonstrated that the IgG at 1:100 titer exerted a weak anti-TBEV neutralizing effect at all time-points examined. The IgG 1:400 titer caused a 2 log PFU/mL decline in TBEV Dal strain yield at 72 h post-infection, whereas at 1:3200 titer it completely suppressed TBEV replication throughout the observation period. The ex vivo experiments with blood serum obtained from vaccinated subjects demonstrating a range of TBEV antibody titers (sera from vaccinated individuals with varying anti-TBEV antibody titers) and in vivo (outinbred white mice) experiments revealed a delayed virus elimination for antibody titers at 1:100 and 1:200 as well as rapid virus elimination (1–2 days p.i.) for antibody titers greater than 1:400. Thus, antibody titer at 1:400 may be considered as the universal anti-TBEV protection threshold. In order to properly conclude regarding the revaccination schedule it is advised to start with testing blood serum for durability of anti-TBEV immune response. Subjects with TBEV antibody titers at 1:100 and 1:200 should be strongly recommended to undergo a mandatory revaccination. Such an approach is believed to be the most effective way toward enhancing efficacy of vaccine-mediated protection against TBE.

Tick-borne encephalitis virus: molecular determinants of neuropathogenesis of an emerging pathogen

Tick-borne encephalitis virus (TBEV) is a zoonotic agent causing severe encephalitis. The transmission cycle involves the virus, the Ixodes tick vector, and a vertebrate reservoir, such as small mammals (rodents, or shrews). Humans are accidentally involved in this transmission cycle. Tick-borne encephalitis (TBE) has been a growing public health problem in Europe and Asia over the past 30 years. The mechanisms involved in the development of TBE are very complex and likely multifactorial, involving both host and viral factors. The purpose of this review is to provide an overview of the current literature on TBE neuropathogenesis in the human host and to demonstrate the emergence of common themes in the molecular pathogenesis of TBE in humans. We discuss and review data on experimental study models and on both viral (molecular genetics of TBEV) and host (immune response, and genetic background) factors involved in TBE neuropathogenesis in the context of human infection.

Correlation of Severity of Human Tick-Borne Encephalitis Virus Disease and Pathogenicity in Mice

We compared 2 tick-borne encephalitis virus strains isolated from 2 different foci that cause different symptoms in tick-borne encephalitis patients, from neurologic to mild gastrointestinal symptoms. We compared neuroinvasiveness, neurovirulence, and proinflammatory cytokine response in mice and found unique differences that contribute to our understanding of pathogenesis.

Tick-borne encephalitis in Europe and Russia: Review of pathogenesis, clinical features, therapy, and vaccines

Tick-borne encephalitis (TBE) is an illness caused by tick-borne encephalitis virus (TBEV) infection which is often limited to a febrile illness, but may lead to very aggressive downstream neurological manifestations. The disease is prevalent in forested areas of Europe and northeastern Asia, and is typically caused by infection involving one of three TBEV subtypes, namely the European (TBEV-Eu), the Siberian (TBEV-Sib), or the Far Eastern (TBEV-FE) subtypes. In addition to the three main TBEV subtypes, two other subtypes; i.e., the Baikalian (TBEV-Bkl) and the Himalayan subtype (TBEV-Him), have been described recently. In Europe, TBEV-Eu infection usually results in only mild TBE associated with a mortality rate of <2%. TBEV-Sib infection also results in a generally mild TBE associated with a non-paralytic febrile form of encephalitis, although there is a tendency towards persistent TBE caused by chronic viral infection. TBE-FE infection is considered to induce the most severe forms of TBE. Importantly though, viral subtype is not the sole determinant of TBE severity; both mild and severe cases of TBE are in fact associated with infection by any of the subtypes. In keeping with this observation, the overall TBE mortality rate in Russia is ∼2%, in spite of the fact that TBEV-Sib and TBEV-FE subtypes appear to be inducers of more severe TBE than TBEV-Eu. On the other hand, TBEV-Sib and TBEV-FE subtype infections in Russia are associated with essentially unique forms of TBE rarely seen elsewhere if at all, such as the hemorrhagic and chronic (progressive) forms of the disease. For post-exposure prophylaxis and TBE treatment in Russia and Kazakhstan, a specific anti-TBEV immunoglobulin is currently used with well-documented efficacy, but the use of specific TBEV immunoglobulins has been discontinued in Europe due to concerns regarding antibody-enhanced disease in naïve individuals. Therefore, new treatments are essential. This review summarizes available data on the pathogenesis and clinical features of TBE, plus different vaccine preparations available in Europe and Russia. In addition, new treatment possibilities, including small molecule drugs and experimental immunotherapies are reviewed. The authors caution that their descriptions of approved or experimental therapies should not be considered to be recommendations for patient care.

Comparative Analysis of NS5 Protein for Tick Borne Encephalitis Virus Strains in three Virus Subtypes

Non-structural protein 5 (NS5) of tick-borne encephalitis virus is an enzyme which is responsible for a copying of viral RNA, and it has a strong structural similarity to RNA polymerases of another RNA virus families. The strains of the virus are separated into three subtypes, which differ by specific mutations in virus proteins, including NS5 protein. The methods of structural bioinformatics allow to construct a model of NS5 protein for several strains of the virus.

The paper presents the comparative analysis of sequences and structures of NS5 protein, for three subtypes of the tick-borne encephalitis virus. The segments of protein were identified where the highest difference between subtypes and within subtypes is observed. These segments, where most of the mutations are accumulated, are located in methyltransferase domain, in the inter-domain interface, and in the three subdomains of polymerase domain. The association between the locations of mutations in NS5 protein and the flexibility of a protein backbone was observed using normal mode analysis. Namely, the most important mutations are located in the parts of protein where the amplitude of synchronous oscillations estimated using normal mode analysis is the highest: in the second zinc binding pocket within polymerase domain, in the N-terminal extension within inter-domain interface, and around an active site of methyltransferase domain.

[Phylogenetic analysis and distribution of far eastern tick-borne encephalitis virus subtype (Flaviridae, Flavirus, TBEV-FE) from Asia.]

To date, a lot of data on molecular genetic characteristics of different tick-borne encephalitis virus strains has appeared. Only on the basis of the E protein genome, sequences of about 1,500 TBEV strains were registered in GenBank.

PURPOSE

The purpose of the work - revision and comparative analysis of data on complete genomes sequences of the Far Eastern subtype of TBE virus strains distributed in the Asian part of Eurasian continent.

MATERIAL AND METHODS

The data on the complete genomes of 84 strains of TBEV isolated in Asia were used; phylogenetic analysis was performed.

RESULTS AND DISCUSSION

it was shown that variants of the TBEV of the Far Eastern subtype are circulating here and form three separate clusters (Sofjin, Senzhang- и Shkotovo-like strains). Sofjin strain (Sofjin-1953, Sofjin-Chumakov, Sofjin-KSY) was considered to be the reference for Far Eastern TBE virus subtype strains and a cluster of Sofjin-like strains. Sofjin-like strains were not found in China and Japan, but widely distributed throughout the area of Primorsky and Khabarovsk krai. The group of Senzhang-like strains was distributed in China, Eastern Siberia, Khabarovsk krai and northern Primorsky krai, but was not found in Japan (Hokkaido). According to molecular genetic characteristics the youngest and more genetically homogeneous group was the Shkotovo-like strains, isolated in the southern part of Primorsky krai, however not found on Hokkaido Island (Japan).

CONCLUSION

revision of the complete genome characteristics of TBEV strains revealed the features of micro-evolutionary process of viral populations in the Asian part of Eurasia, show the individual affection of strains to certain territories, as well as detect random finds of such strains in the territories of other natural foci.

Immunogenicity and Protective Activity of a Chimeric Protein Based on the Domain III of the Tick-Borne Encephalitis Virus E Protein and the OmpF Porin of Yersinia pseudotuberculosis Incorporated into the TI-Complex

Tick-borne encephalitis (TBE) is a widespread, dangerous infection. Unfortunately, all attempts to create safe anti-TBE subunit vaccines are still unsuccessful due to their low immunogenicity. The goal of the present work was to investigate the immunogenicity of a recombinant chimeric protein created by the fusion of the EIII protein, comprising domain III and a stem region of the tick-borne encephalitis virus (TBEV) E protein, and the OmpF porin of Yersinia pseudotuberculosis (OmpF-EIII). Adjuvanted antigen delivery systems, the tubular immunostimulating complexes (TI-complexes) based on the monogalactosyldiacylglycerol from different marine macrophytes, were used to enhance the immunogenicity of OmpF-EIII. Also, the chimeric protein incorporated into the most effective TI-complex was used to study its protective activity. The content of anti-OmpF-EIII antibodies was estimated in mice blood serum by enzyme-linked immunosorbent assay (ELISA). To study protective activity, previously immunized mice were infected with TBEV strain Dal’negorsk (GenBank ID: FJ402886). The animal survival was monitored daily for 21 days. OmpF-EIII incorporated into the TI-complexes induced about a 30–60- and 5–10-fold increase in the production of anti-OmpF-EIII and anti-EIII antibodies, respectively, in comparison with the effect of an individual OmpF-EIII. The most effective vaccine construction provided 60% protection. Despite the dramatic effect on the specific antibody titer, the studied TI-complex did not provide a statistically significant increase in the protection of OmpF-EIII protein. However, our results provide the basis of the future search for approaches to design and optimize the anti-TBEV vaccine based on the OmpF-EIII protein.

Viral Determinants of Virulence in Tick-Borne Flaviviruses

Tick-borne flaviviruses have a global distribution and cause significant human disease, including encephalitis and hemorrhagic fever, and often result in neurologic sequelae. There are two distinct properties that determine the neuropathogenesis of a virus. The ability to invade the central nervous system (CNS) is referred to as the neuroinvasiveness of the agent, while the ability to infect and damage cells within the CNS is referred to as its neurovirulence. Examination of laboratory variants, cDNA clones, natural isolates with varying pathogenicity, and virally encoded immune evasion strategies have contributed extensively to our understanding of these properties. Here we will review the major viral determinants of virulence that contribute to pathogenesis and influence both neuroinvasiveness and neurovirulence properties of tick-borne flaviviruses, focusing particularly on the envelope protein (E), nonstructural protein 5 (NS5), and the 3′ untranslated region (UTR).

Complete Genomic Characterization of Three Tick-Borne Encephalitis Viruses Detected Along the China-North Korea Border, 2011

Tick-borne encephalitis virus (TBEV) causes neurological infections with serious sequelae in Europe and Northeast Asia. In China, the major epidemic areas are along the borders with Russia and North Korea. Although several TBEV isolates have been reported, the biological characteristics of the Chinese strains, especially those along the China-North Korea border, are unclear. In this study, we detected seven TBEV fragment sequences in 602 adult Dermacentor silvarum collected in the Changbai Mountain area of Jilin Province on the China-North Korea border and characterized the genome of three TBEV strains (JLCB11-08, JLCB11-35, and JLCB11-40). These three TBEV strains belong to the TBEV-Far Eastern (TBEV-FE) genotype and clustered most closely with the Svetlogorie and Kavalerovo strains from Russia. In addition, the TBEV strains from Northeast China clustered geographically within the TBEV-FE subtype branch. These findings will facilitate further research on the distinct genetic groupings of TBEV strains in China.

A new subtype of eastern tick-borne encephalitis virus discovered in Qinghai-Tibet Plateau, China

Tick-borne encephalitis virus (TBEV) has been classified into three subtypes, namely the European (Eu-TBEV), Far Eastern (FE-TBEV), and Siberian (Sib-TBEV). In this study, we discovered a new subtype of TBEV in wild rodent Marmota himalayana in Qinghai-Tibet Plateau in China, proposed as subtype Himalayan (Him-TBEV). Two complete genomes of TBEV were obtained from respiratory samples of 200 marmots. The phylogenetic analysis using the E protein and polyprotein demonstrated that the two strains of Him-TBEV formed an independent branch, separated from Eu-TBEV, Sib-TBEV, and FE-TBEV. The nomenclature of Him-TBEV as a new subtype was also supported by comparative analysis using nucleotide and amino acid sequences of E protein and polyprotein. For E protein, The Him-TBEV showed 82.6–84.6% nucleotide identities and 92.7–95.0% amino acid identities with other three subtypes. For polyprotein, the Him-TBEV showed 83.5–85.2% nucleotide identities and 92.6–94.2% amino acids identities with other three subtypes. Furthermore, of 69 amino acid substitutions profiles detected in complete polyprotein of 112 strains of TBEV, Him-TBEV subtype displayed unique amino acids in the 36 positions. Notably, for the subtype-specific amino acid position 206 of E protein, Him-TBEV shared the Val with Eu-TBEV, but differed from FE-TBEV and Sib-TBEV. The evolutionary analysis with BEAST suggested that Him-TBEV diverged from other subtypes of eastern TBEV group about 2469 years ago. It should be mentioned that Qinghai-Tibet Plateau in China is the plague endemic region where Marmota himalayana is the primary host. The public health significance of discovery of Him-TBEV in Marmota himalayana must be carefully evaluated.

Identification and analysis of host proteins that interact with the 3'-untranslated region of tick-borne encephalitis virus genomic RNA

Tick-borne encephalitis virus (TBEV) causes severe neurological disease, but the pathogenetic mechanism is unclear. The conformational structure of the 3'-untranslated region (UTR) of TBEV is associated with its virulence. We tried to identify host proteins interacting with the 3'-UTR of TBEV. Cellular proteins of HEK293T cells were co-precipitated with biotinylated RNAs of the 3'-UTR of low- and high-virulence TBEV strains and subjected to mass spectrometry analysis. Fifteen host proteins were found to bind to the 3'-UTR of TBEV, four of which-cold shock domain containing-E1 (CSDE1), spermatid perinuclear RNA binding protein (STRBP), fragile X mental retardation protein (FMRP), and interleukin enhancer binding factor 3 (ILF3)-bound specifically to that of the low-virulence strain. An RNA immunoprecipitation and pull-down assay confirmed the interactions of the complete 3'-UTRs of TBEV genomic RNA with CSDE1, FMRP, and ILF3. Partial deletion of the stem loop (SL) 3 to SL 5 structure of the variable region of the 3'-UTR did not affect interactions with the host proteins, but the interactions were markedly suppressed by deletion of the complete SL 3, 4, and 5 structures, as in the high-virulence TBEV strain. Further analysis of the roles of host proteins in the neurologic pathogenicity of TBEV is warranted.

A database of human genes and a gene network involved in response to tick-borne encephalitis virus infection

BACKGROUND

Tick-borne encephalitis is caused by the neurotropic, positive-sense RNA virus, tick-borne encephalitis virus (TBEV). TBEV infection can lead to a variety of clinical manifestations ranging from slight fever to severe neurological illness. Very little is known about genetic factors predisposing to severe forms of disease caused by TBEV. The aims of the study were to compile a catalog of human genes involved in response to TBEV infection and to rank genes from the catalog based on the number of neighbors in the network of pairwise interactions involving these genes and TBEV RNA or proteins.

RESULTS

Based on manual review and curation of scientific publications a catalog comprising 140 human genes involved in response to TBEV infection was developed. To provide access to data on all genes, the TBEVhostDB web resource ( http://icg.nsc.ru/TBEVHostDB/ ) was created. We reconstructed a network formed by pairwise interactions between TBEV virion itself, viral RNA and viral proteins and 140 genes/proteins from TBEVHostDB. Genes were ranked according to the number of interactions in the network. Two genes/proteins (CCR5 and IFNAR1) that had maximal number of interactions were revealed. It was found that the subnetworks formed by CCR5 and IFNAR1 and their neighbors were a fragments of two key pathways functioning during the course of tick-borne encephalitis: (1) the attenuation of interferon-I signaling pathway by the TBEV NS5 protein that targeted peptidase D; (2) proinflammation and tissue damage pathway triggered by chemokine receptor CCR5 interacting with CD4, CCL3, CCL4, CCL2. Among nine genes associated with severe forms of TBEV infection, three genes/proteins (CCR5, IL10, ARID1B) were found to have protein-protein interactions within the network, and two genes/proteins (IFNL3 and the IL10, that was just mentioned) were up- or down-regulated in response to TBEV infection. Based on this finding, potential mechanisms for participation of CCR5, IL10, ARID1B, and IFNL3 in the host response to TBEV infection were suggested.

CONCLUSIONS

A database comprising 140 human genes involved in response to TBEV infection was compiled and the TBEVHostDB web resource, providing access to all genes was created. This is the first effort of integrating and unifying data on genetic factors that may predispose to severe forms of diseases caused by TBEV. The TBEVHostDB could potentially be used for assessment of risk factors for severe forms of tick-borne encephalitis and for the design of personalized pharmacological strategies for the treatment of TBEV infection.

Characteristics of far eastern strains of tick-borne encephalitis virus

A comparative study of biological, molecular and genetic characteristics of a collection of ten strains of tick-borne encephalitis virus (TBEV) isolated in Primorsky Krai before 1960 and stored in a lyophilized state for a prolonged period (over 65 years) is presented. The collection includes the Sofjin strain isolated from the brain of a fatal case in Primorsky Krai in 1937 and transferred to the Scientific Research Institute of Epidemiology and Microbiology (Vladivostok) in 1953. All lyophilized viral strains demonstrated great preservation and high infectious activity in the model of 2-day-old non-inbred mice. Whole-genome sequencing showed that all strains belong to the Far East TBEV subtype, comprising three clusters of Sofjin-, Oshima- and Senzhang-like strains. We show that SofjinPYB, Sofjin (Vector) and Sofjin-HO strains form a separate branch of the phylogenetic tree and are closely related to Khabarovsk-Obor-4, but not to the original Sofjin strain. The Sofjin-1953, Sofijin-Chumakov, SofjinKSY and SofjinCDC strains are genetically close to each other and can be used as reference strains for comparative analysis of the tick-borne encephalitis virus population.

Molecular Mechanisms of Interaction Between Human Immune Cells and Far Eastern Tick-Borne Encephalitis Virus Strains

Although studies have established that immune mechanisms are important in controlling tick-borne encephalitis virus (TBEV) infection, the interactions of different TBEV strains with cells of innate and adaptive immunity are not well understood. In this study, the ability of two Far Eastern subtype TBEV strains (Dal'negorsk and Primorye-183) with various degrees of pathogenicity for humans to modulate the expression of membrane molecules differently on human immune cells were investigated using a whole-blood flow cytometry-based assay. The whole-blood samples (from 10 healthy donors) were infected with TBEV strains and analyzed for the virus binding to the blood cells, as well as expression of adhesion (CD11b and ICAM-1) and activation (CD69, CD25, CD95) molecules on the surfaces of monocytes, granulocytes, natural killer (NK) cells, and T-lymphocytes (CD4+, CD8+) at selected times (3, 6, and 24 h post-infection). It was found that the highly pathogenic Dal'negorsk strain penetrated rapidly and was actively replicated in the blood cells, inducing downregulation of CD11b, ICAM-1, and CD69 on monocytes and a significant decrease of NK cells expressing CD69, CD25, CD95, and CD8 T-lymphocytes expressing CD69 compared with the mock-infected cells. The nonpathogenic Primorye-183 strain penetrated slowly and was replicated in the blood cells, but caused a significant increase in the adhesion and activation of molecule expression to trigger innate defense mechanisms and enable the rapid elimination of the virus from the organism. Thus, TBEV-induced activation or suppression of adhesion and activation receptors expression form an essential part of fundamental virus properties, that is, virulence and pathogenicity.

Virulence of tick-borne encephalitis virus is associated with intact conformational viral RNA structures in the variable region of the 3'-UTR

Tick-borne encephalitis virus (TBEV) is maintained between ticks and mammals in nature and causes severe neurological disease in human. However, the mechanism of viral pathogenicity is unknown. Previously, we showed that the deletion in the variable region of the 3'-untranslated region (UTR) is involved in the pathogenicity of the strains from the Far-Eastern subtype of TBEV. To investigate the detailed function of the variable region, we constructed recombinant TBEV with partial deletions in the region. In a mouse model, the partial deletions drastically increased the virulence of the virus, with no effect on virus multiplication in mouse brain. Furthermore, the mutations did not affect the production of subgenomic flavivirus RNA from the 3'-UTR, and the induction of interferon (IFN) and IFN-stimulated genes. These data suggested that the conformational structure of the variable region is associated with the pathogenicity of the Far-Eastern subtype of TBEV. These findings provide a foundation for further research to identify the pathogenic mechanisms of TBEV.

Louping ill virus (LIV) in the Far East

This study focused on finding, culturing, and identifying the biological and genetic characteristics of three louping ill virus (LIV) strains in the south of the Russian Far East. The Primorye-155-77 and Primorye-20-79 virus strains were isolated from Ixodes persulcatus ticks, and the Primorye-185-91 strain was isolated from the blood of a person after a tick bite. According to the hemagglutination and neutralization tests, Primorye-155-77, Primorye-20-79 and Primorye-185-91 had weak reactivity with antibodies in an antiserum against tick-borne encephalitis virus. In Primorye-155-77 and Primorye-20-79, the sequences of the 5' ends of the 2456-nucleotide-long viral RNA including the 5' untranslated region (UTR) and genes of the capsid protein, prM protein and envelope E protein were determined. The complete genome sequence of Primorye-185-91 was determined. The E protein gene of the Negishi strain differed from those of three analyzed strains, as there were mutations resulting in the replacement of three amino acids: Ala163Thr, Asp193Asn and Ala313Thr. The homology of Primorye-185-91 to LIV 369/T2 was 97.57 %, and to the Penrith strain, it was 98.36 %. Phylogenetic analysis showed that Primorye-155-77, Primorye-20-79 and Primorye-185-91 are related to LI/A and LI/K strains isolated in England and Scotland and to the Negishi strain; these strains have a common progenitor. Negishi-like strains were represented by one subtype of louping ill virus, i.e. the British subtype (LIV-Brit). The possibility is discussed of a single introduction of the virus to the Far Eastern region (Japan and Primorsky Krai) from a single natural locus more than 50 years ago.

The nature of replication of tick-borne encephalitis virus strains isolated from residents of the Russian Far East with inapparent and clinical forms of infection

We describe the biological properties and molecular characteristics of complete genomes of 33 tick-borne encephalitis virus (TBEV) strains that induced different forms of infection, from inapparent to severe focal ones resulting in fatal outcome. Hemagglutinating activity of Oshima-like strains was higher at pH 5.8, while activity of Sofjin- and Senhzang-like strains were higher at pH 6.2 and 6.8, respectively. We determined susceptibility of porcine kidney (PK) cell cultures to these TBEV strains by cytopathic effect (CPE), plaque formation, and size of plaques. The clinical TBEV strains had higher virus titers both in tissue culture infectious dose 50(TCID50) and in plaque-forming unit (PFU) titers and larger plaques than the inapparent strains. A comparison of virus multiplication kinetics by PFU in culture fluid with kinetics of ELISA antigen and hemagglutinin accumulation suggested a different mechanism of interaction between these virus strains and PK cells at the initial stage of cell infection.

The relationship between the structure of the tick-borne encephalitis virus strains and their pathogenic properties

Tick-borne encephalitis virus (TBEV) is transmitted to vertebrates by taiga or forest ticks through bites, inducing disease of variable severity. The reasons underlying these differences in the severity of the disease are unknown. In order to identify genetic factors affecting the pathogenicity of virus strains, we have sequenced and compared the complete genomes of 34 Far-Eastern subtype (FE) TBEV strains isolated from patients with different disease severity (Primorye, the Russian Far East). We analyzed the complete genomes of 11 human pathogenic strains isolated from the brains of dead patients with the encephalitic form of the disease (Efd), 4 strains from the blood of patients with the febrile form of TBE (Ffd), and 19 strains from patients with the subclinical form of TBE (Sfd). On the phylogenetic tree, pathogenic Efd strains formed two clusters containing the prototype strains, Senzhang and Sofjin, respectively. Sfd strains formed a third separate cluster, including the Oshima strain. The strains that caused the febrile form of the disease did not form a separate cluster. In the viral proteins, we found 198 positions with at least one amino acid residue substitution, of which only 17 amino acid residue substitutions were correlated with the variable pathogenicity of these strains in humans and they authentically differed between the groups. We considered the role of each amino acid substitution and assumed that the deletion of 111 amino acids in the capsid protein in combination with the amino acid substitutions R16K and S45F in the NS3 protease may affect the budding process of viral particles. These changes may be the major reason for the diminished pathogenicity of TBEV strains. We recommend Sfd strains for testing as attenuation vaccine candidates.

Variable region of the 3' UTR is a critical virulence factor in the Far-Eastern subtype of tick-borne encephalitis virus in a mouse model

Tick-borne encephalitis virus (TBEV) is a major arbovirus that causes thousands of cases of severe neurological illness in humans annually. However, virulence factors and pathological mechanisms of TBEV remain largely unknown. To identify the virulence factors, we constructed chimeric viruses between two TBEV strains of the Far-Eastern subtype, Sofjin-HO (highly pathogenic) and Oshima 5-10 (low pathogenic). The replacement of the coding region for the structural and non-structural proteins from Sofjin into Oshima showed a partial increase of the viral pathogenicity in a mouse model. Oshima-based chimeric viruses with the variable region of the 3' UTR of Sofjin, which had a deletion of 207 nt, killed 100 % of mice and showed almost the same virulence as Sofjin. Replacement of the variable region of the 3' UTR from Sofjin into Oshima did not increase viral multiplication in cultured cells and a mouse model at the early phase of viral entry into the brain. At the terminal phase of viral infection in mice, the virus titre of the Oshima-based chimeric virus with the variable region of the 3' UTR of Sofjin reached a level identical to that of Sofjin and showed a similar histopathological change in the brain tissue. This is the first report to show that the variable region of the 3' UTR is a critical virulence factor in mice. These findings encourage further study to understand the mechanisms of the pathogenicity of TBEV, and to develop preventative and therapeutic strategies for tick-borne encephalitis.

Surveillance of tick-borne encephalitis virus in wild birds and ticks in Tomsk city and its suburbs (Western Siberia)

To study the role of wild birds in the transmission of tick borne encephalitis virus (TBEV), we investigated randomly captured wild birds bearing ixodid ticks in a very highly endemic TBE region located in Tomsk city and its suburbs in the south of Western Siberia, Russia. The 779 wild birds representing 60 species were captured carrying a total of 841 ticks, Ixodes pavlovskyi Pom., 1946 (n=531), Ixodes persulcatus P. Sch., 1930 (n=244), and Ixodes plumbeus Leach. 1815 (n=66). The highest average number of ticks per bird in a particular species was found for the fieldfare (Turdus pilaris Linnaeus, 1758) (5.60 ticks/bird) and the tree pipit (Anthus trivialis Linnaeus, 1758) (13.25 ticks/bird). Samples from wild birds and ticks collected in highly endemic periods from 2006 to 2011 were tested for the TBEV markers using monoclonal modified enzyme immunoassay (EIA) and RT-PCR. TBEV RNA and antigen were found in 9.7% and 22.8% samples collected from wild birds, respectively. TBEV markers were also detected in 14.1% I. persulcatus ticks, 5.2% I. pavlovskyi, and 4.2% I. plumbeus ticks collected from wild birds. Two TBEV strains were also isolated on PKE (pig kidney embryo) cells from fieldfare and Blyth's reed warbler (Acrocephalus dumetorum Blyth, 1849). Sequencing of 5'-NCR of TBEV revealed that all TBEV isolates belong to Far Eastern (dominate) and Siberian genotypes. Several phylogenetic subgroups included TBEV sequences novel for the Tomsk region. Our data suggest that wild birds are potential disseminators of TBEV, TBEV-infected ixodid ticks, and possibly other tick-borne infections.