Over 50 million humans live in areas of potential exposure to tick-borne encephalitis virus (TBEV). The disease exhibits an estimated 16,000 cases recorded annually over 30 European and Asian countries. Conventionally, TBEV transmission to Ixodes spp. ticks occurs whilst feeding on viraemic animals. However, an alternative mechanism of non-viraemic transmission (NVT) between infected and uninfected ticks co-feeding on the same transmission-competent host, has also been demonstrated. Here, using laboratory-bred I. ricinus ticks, we demonstrate low and high efficiency NVT for TBEV strains Vasilchenko (Vs) and Hypr, respectively. These virus strains share high sequence similarity but are classified as two TBEV subtypes. The Vs strain is a Siberian subtype, naturally associated with I. persulcatus ticks whilst the Hypr strain is a European subtype, transmitted by I. ricinus ticks. In mammalian cell culture (porcine kidney cell line PS), Vs and Hypr induce low and high cytopathic effects (cpe), respectively. Using reverse genetics, we engineered a range of viable Vs/Hypr chimaeric strains, with substituted genes. No significant differences in replication rate were detected between wild-type and chimaeric viruses in cell culture. However, the chimaeric strain Vs[Hypr str] (Hypr structural and Vs non-structural genomic regions) demonstrated high efficiency NVT in I. ricinus whereas the counterpart Hypr[Vs str] was not transmitted by NVT, indicating that the virion structural proteins largely determine TBEV NVT transmission efficiency between ticks. In contrast, in cell culture, the extent of cpe was largely determined by the non-structural region of the TBEV genome. Chimaeras with Hypr non-structural genes were more cytotoxic for PS cells when compared with Vs genome-based chimaeras.

ABSTRACT A new flavivirus, Ecuador Paraiso Escondido virus (EPEV), named after the village where it was discovered, was isolated from sand flies ( Psathyromyia abonnenci , formerly Lutzomyia abonnenci ) that are unique to the New World. This represents the first sand fly-borne flavivirus identified in the New World. EPEV exhibited a typical flavivirus genome organization. Nevertheless, the maximum pairwise amino acid sequence identity with currently recognized flaviviruses was 52.8%. Phylogenetic analysis of the complete coding sequence showed that EPEV represents a distinct clade which diverged from a lineage that was ancestral to the nonvectored flaviviruses Entebbe bat virus, Yokose virus, and Sokoluk virus and also the Aedes -associated mosquito-borne flaviviruses, which include yellow fever virus, Sepik virus, Saboya virus, and others. EPEV replicated in C6/36 mosquito cells, yielding high infectious titers, but failed to reproduce either in vertebrate cell lines (Vero, BHK, SW13, and XTC cells) or in suckling mouse brains. This surprising result, which appears to eliminate an association with vertebrate hosts in the life cycle of EPEV, is discussed in the context of the evolutionary origins of EPEV in the New World. IMPORTANCE The flaviviruses are rarely (if ever) vectored by sand fly species, at least in the Old World. We have identified the first representative of a sand fly-associated flavivirus, Ecuador Paraiso Escondido virus (EPEV), in the New World. EPEV constitutes a novel clade according to current knowledge of the flaviviruses. Phylogenetic analysis of the virus genome showed that EPEV roots the Aedes -associated mosquito-borne flaviviruses, including yellow fever virus. In light of this new discovery, the New World origin of EPEV is discussed together with that of the other flaviviruses.

Tick-borne encephalitis virus (TBEV; family Flaviviridae, genus Flavivirus) is a complex of closely related arboviruses transmitted to humans and other vertebrates by infected Ixodes spp. ticks. The virions contain positive polarity single-stranded RNA (ssRNA) (∼ 11 kbp) enclosed in a core consisting of capsid protein surrounded by a lipid membrane containing envelope and membrane glycoproteins. Three-dimensional structural analysis has revealed the mechanism of the pH-dependent fusion between viral and endosomal membranes during entry into cells. After fusion, viral RNA is translated, producing a polyprotein of ∼ 3400 amino acids that is co-translationally processed into three structural and seven nonstructural proteins, the latter providing viral proteolytic and replicase functions. The mode of RNA replication is asymmetric and semiconservative and mediated by the interaction of 5′-and 3′-untranslated regions. Details of virion maturation have been resolved at the atomic level. These viruses circulate in the forests and on the sheep-rearing and goat-rearing hillsides of the Northern Hemisphere, using both viremic and nonviremic transmission strategies. The specific biological characteristics of different TBEVs and related viruses and their evolution and dispersal directly reflect the ecological requirements of the tick and its protracted life cycle. Human disease control in endemic regions relies primarily on the use of vaccines.

Biotic factors contributing to the survival of tick-borne viruses in nature are poorly understood. Using tick-borne encephalitis virus (TBEV) and its principal European vector, Ixodes ricinus, we examined the relative roles of salivary gland infection, co-feeding transmission, and moulting in virus survival. Virus titres in the salivary glands increased after blood-feeding in a time- and dose-dependent manner. This was observed in ticks infected by inoculation but not in ticks infected by the natural route of co-feeding. Amplification of infection prevalence occurred via co-feeding. However, when larvae or nymphs subsequently moulted, the infection prevalence dramatically declined although this was not observed when ticks were infected by inoculation. Trans-stadial survival is a hitherto overlooked parameter that may contribute to the low incidence of TBEV infection in field-collected I. ricinus ticks.

RNA secondary structures in the 3'untranslated regions (3'UTR) of the viruses of the family Flaviviridae, previously identified as essential (promoters) or beneficial (enhancers) for replication, have been analysed. Duplicated enhancer elements are revealed as a global feature in the evolution of the 3'UTR of distantly related viruses within the genera Flavivirus and Pestivirus. For the flaviviruses, duplicated structures occur in the 3'UTR of all four distantly related ecological virus subgroups (tick-borne, mosquito-borne, no known vector and insect-specific flaviviruses (ISFV). RNA structural differences distinguish tick-borne flaviviruses with discrete pathogenetic characteristics. For Aedes- and Culex-associated ISFV, secondary RNA structures with different conformations display numerous short ssRNA direct repeats, exposed as loops and bulges. Long quadruplicate regions comprise almost the entire 3'UTR of Culex-associated ISFV. Extended duplicated sequence and associated RNA structures were also discovered in the 3'UTR of pestiviruses. In both the Flavivirus and Pestivirus genera, duplicated RNA structures were localized to the enhancer regions of the 3'UTR suggesting an adaptive role predominantly in wild-type viruses. We propose sequence reiteration might act as a scaffold for dimerization of proteins involved in assembly of viral replicase complexes. Numerous nucleotide repeats exposed as loops/bulges might also interfere with host immune responses acting as a molecular sponge to sequester key host proteins or microRNAs.

В настоящее время выделяют 3 субтипа вируса клещевого энцефалита (ВКЭ, род Flavivirus, сем. Fla-viviridae): Западно-Европейский (ассоциирован с клещом I. ricinus), Сибирский и Дальневосточный (ассоциированы с таежным клещом I. persulcatus). Одним из основных путей циркуляции ВКЭ в природе является невиремическая трансмиссия вируса между зараженными и незараженными клещами во время совместного питания на одном прокормителе. Ранее было обнаружено, что эффективность невиремической трансмиссии между клещами I. ricinus типового штамма Западно-Европейского субтипа «Hypr» (Hypr) составляет 60 %, в то время как для типового штамма Сибирского субтипа «Васильченко» (Vs) – только 5 %. Для установления вирусных детерминант, определяющих эффективность трансмиссии мы создали ряд рекомбинантных вирусов с взаимозамененными генами структурных (str) и неструктурных (ns) белков. Рекомбинантный вирус Hypr[str]Vs[ns] обладал 70 % эффективностью невиремической трансмиссии. Введение отдельных структурных генов штамма Hypr в ифекционный клон Vs также увеличивало эффективность трансмиссии до 33 %. Таким образом, нами показано, что эффективность невиремической трансмиссии ВКЭ определяется, прежде всего, свойствами структурных белков вируса.

There are 3 subtypes of tick-borne encephalitis virus (TBEV) distinguished, at present time: European (EU), Siberian (SIB) and Far Eastern (FE). The former one is associated with Ixodes ricinus tick, whereas the latter two - with I. persulcatus. The circulation of TBEV in nature is mediated by the non-viraemic transmission, between infected and. uninfected ticks co-feeding on the same hosts and. it was shown that transmission rate of «Hypr» strain (EU subtype) is much higher than rate of «Vasilchenko» strain (SIB subtype) - 60 and 5 % respectively. To reveal the viral determinants of transmission efficacy, we constructed the series of recombinant viruses with gradually exchanged genes coding structural (str) and. non-structural (ns) viral proteins. The recombinant virus Hypr[str]Vs[ns] achieved the rate of non-viraemic transmission of 70 %. The introduction of separate structural genes of Hypr into Vs infectious clone has enhanced the transmission efficacy as well, though not to such extent as entire structural region but up to 33 % only. Thus, it was shown that efficacy of non-viraemic transmission of TBEV depends from properties of viral structural proteins mainly.

There are 3 subtypes of tick-borne encephalitis virus (TBEV) distinguished, at present time: European (EU), Siberian (SIB) and Far Eastern (FE). The former one is associated with Ixodes ricinus tick, whereas the latter two with I. persulcatus. The circulation of TBEV in nature is mediated by the non-viraemic transmission, between infected and. uninfected ticks co-feeding on the same hosts and. it was shown that transmission rate of «Hypr» strain (EU subtype) is much higher than rate of «Vasilchenko» strain (SIB subtype) 60 and 5 % respectively. To reveal the viral determinants of transmission efficacy, we constructed the series of recombinant viruses with gradually exchanged genes coding structural (str) and. non-structural (ns) viral proteins. The recombinant virus Hypr[str]Vs[ns] achieved the rate of non-viraemic transmission of 70 %. The introduction of separate structural genes of Hypr into Vs infectious clone has enhanced the transmission efficacy as well, though not to such extent as entire structural region but up to 33 % only. Thus, it was shown that efficacy of non-viraemic transmission of TBEV depends from properties of viral structural proteins mainly.

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem-loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents.

Background: Tick-borne encephalitis virus (TBEV) is transmitted to humans by Ixodid ticks causing >10,000 cases of disease annually. The risk of human infection relates to the efficiency of virus transmission between infected and uninfected ticks. Here we identify specific mutations in the viral envelope protein that affect transmission efficiency of TBEV between ticks. Methods: The genomes of 4 field isolates of TBEV deficient in haemagglutination, were sequenced and recreated by site-directed mutagenesis, in a TBEV infectious clone. They were then compared with the wild-type infectious clone in mice, porcine kidney PS cells and adult and nymphal I. ricinus ticks. Results: Sequence analysis revealed unique amino acid substitutions D67G, E122G or D277A in the envelope glycoprotein. Each mutation resulted in an increase of net charge and hydrophobicity on the virion surface. When introduced individually into the TBEV infectious clone (IC), each substitution inhibited haemagglutination and reduced mouse neuroinvasiveness from 65% to 15-30%. Antibody production in infected mice was 1.5-3 times lower for IC-E122G and IC-D277A suggesting lower levels of viraemia and/or deficient immune stimulation induced by these viruses. All mutants demonstrated delayed growth in PS cells during the first 24hpi; however, mutant IC-D67G exhibited significantly better growth characteristics than IC-E122G and IC-D277A. The reproduction of IC-E122G and IC-D277A in fasting ticks was similar to that of control HA positive virus whereas the titres of IC-D67G were significantly lower (2.5-3 vs. 1-2 log10PFU/ml, respectively). In feeding ticks, the titre of IC-E122G increased approximately 1000-fold and IC-D277A and IC-D67G - approximately 300-fold, whereas for control virus the increase was about 10-fold. Non-viraemic transmission efficiency from infected to uninfected ticks was increased by each individual substitution in nymphal I. ricinus (Figure 1). Figure 1 Tick-to-tick transmission rate (clear bars) is expressed as the proportion of infected I.ricinus nymphs. Black triangles show the average virus titres in individually infected recipient nymphs as determined by plaque assay. Conclusion: We hypothesize that the mechanism of adaptation of TBEV to its host utilizes the shift of charge/hydrophobicity at several critical aminoacid residues exposed on the virion surface. This shift results in different biological consequences depending on the localisation of certain aminoacid residue. The results provide valuable information concerning the maintenance in nature and the emergence of pathogenic variants of TBEV. Abstracts for SupplementInternational Journal of Infectious DiseasesVol. 14Preview Full-Text PDF Open Archive

Epidemics of tick-borne encephalitis involving thousands of humans occur annually in the forested regions of Europe and Asia. Despite the importance of this disease, the underlying basis for the development of encephalitis remains undefined. Here, we prove the key role of CD8+ T-cells in the immunopathology of tick-borne encephalitis, as demonstrated by prolonged survival of SCID or CD8−/− mice, following infection, when compared with immunocompetent mice or mice with adoptively transferred CD8+ T-cells. The results imply that tick-borne encephalitis is an immunopathological disease and that the inflammatory reaction significantly contributes to the fatal outcome of the infection.

Tick-borne encephalitis virus (TBEV) causes human epidemics across Eurasia. Clinical manifestations range from inapparent infections and fevers to fatal encephalitis but the factors that determine disease severity are currently undefined. TBEV is characteristically a hemagglutinating (HA) virus; the ability to agglutinate erythrocytes tentatively reflects virion receptor/fusion activity. However, for the past few years many atypical HA-deficient strains have been isolated from patients and also from the natural European host tick, Ixodes persulcatus. By analysing the sequences of HA-deficient strains we have identified 3 unique amino acid substitutions (D67G, E122G or D277A) in the envelope protein, each of which increases the net charge and hydrophobicity of the virion surface. Therefore, we genetically engineered virus mutants each containing one of these 3 substitutions; they all exhibited HA-deficiency. Unexpectedly, each genetically modified non-HA virus demonstrated increased TBEV reproduction in feeding Ixodes ricinus, not the recognised tick host for these strains. Moreover, virus transmission efficiency between infected and uninfected ticks co-feeding on mice was also intensified by each substitution. Retrospectively, the mutation D67G was identified in viruses isolated from patients with encephalitis. We propose that the emergence of atypical Siberian HA-deficient TBEV strains in Europe is linked to their molecular adaptation to local ticks. This process appears to be driven by the selection of single mutations that change the virion surface thus enhancing receptor/fusion function essential for TBEV entry into the unfamiliar tick species. As the consequence of this adaptive mutagenesis, some of these mutations also appear to enhance the ability of TBEV to cross the human blood-brain barrier, a likely explanation for fatal encephalitis. Future research will reveal if these emerging Siberian TBEV strains continue to disperse westwards across Europe by adaptation to the indigenous tick species and if they are associated with severe forms of TBE.

Here, we analyze the complete coding sequences of all recognized tick-borne flavivirus species, including Gadgets Gully, Royal Farm and Karshi virus, seabird-associated flaviviruses, Kadam virus and previously uncharacterized isolates of Kyasanur Forest disease virus and Omsk hemorrhagic fever virus. Significant taxonomic improvements are proposed, e.g. the identification of three major groups (mammalian, seabird and Kadam tick-borne flavivirus groups), the creation of a new species (Karshi virus) and the assignment of Tick-borne encephalitis and Louping ill viruses to a unique species (Tick-borne encephalitis virus) including four viral types (i.e. Western Tick-borne encephalitis virus, Eastern Tick-borne encephalitis virus, Turkish sheep Tick-borne encephalitis virus and Louping ill Tick-borne encephalitis virus). The analyses also suggest a complex relationship between viruses infecting birds and those infecting mammals. Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages.

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Flavivirus replication is mediated by interactions between complementary ssRNA sequences of the 5'- and 3'-termini that form dsRNA cyclisation stems or panhandles, varying in length, sequence and specific location in the mosquito-borne, tick-borne, non-vectored and non-classified flaviviruses. In this manuscript we manually aligned the flavivirus 5'UTRs and adjacent capsid genes and revealed significantly more homology than has hitherto been identified. Analysis of the alignments revealed that the panhandles represent evolutionary remnants of a long cyclisation domain that probably emerged through duplication of one of the UTR termini.

Previously, it was shown that the 3' untranslated region (3'UTR) of Kamiti River virus (KRV) is nearly twice as long as the 3'UTR of other flaviviruses (1208 nucleotides compared with 730 nucleotides for the longest 3'UTR of any virus in the Tick-borne encephalitis virus species). Additionally, KRV and the closely related Cell fusing agent virus (CFAV) were shown to contain two short, almost perfect repeat sequences of 67 nucleotides. However, the construction of a robust comparative nucleotide alignment has now revealed that the double-length 3'UTR and the direct repeats resulted from the virtually complete duplication of a primordial KRV 3'UTR. We also propose that the CFAV 3'UTR was derived from a KRV-like precursor sequence with a large deletion that nevertheless preserved the two direct repeat sequences. These data provide new insights into the evolution of the flavivirus 3'UTR.

Full-length genomic sequences from six DENV-2 isolates sampled at different times during a dengue outbreak that occurred in Cuba in 1997 were determined. Phylogenetic analysis indicated that these isolates fall into the “American/Asian” genotype. Genome analysis revealed strong conservation of the structural proteins and the non-coding regions (5′ NCR and 3′ NCR). Nucleotide substitutions were observed in non-structural genes and most notably in the NS5 gene. There was a clear pattern of virus evolution during the epidemic; the earliest isolates sampled differed from those sampled later by amino acid replacements in the NS1 and NS5 proteins, although there was no evidence that these represented escape mutants. Further studies are therefore required to define the functional role of amino acid replacements observed and their possible relation to disease severity.