Encephalitis Virus Strains Research Articles

Onset and duration of protective immunity to IA/IB and IE strains of Venezuelan equine encephalitis virus in vaccinated mice

Three vaccines developed for protection against IA/IB subtypes of Venezuelan equine encephalitis (VEE) virus were evaluated in mice for the ability to protect against systemic and mucosal challenges with a virulent virus of the IE subtype. The vaccines were the formaldehyde-inactivated C-84 and live attenuated TC-83 vaccines currently administered to people under investigational new drug (IND) status, and a new live attenuated vaccine candidate, V3526. V3526 was superior for inducing protection to VEE IA/IB within a week of vaccination, and protection persisted for at least a year. All three vaccines induced long-term clinical protection against peripheral or mucosal challenge with IE virus, with the mucosal immunity induced by attenuated vaccines lasting longer than that induced by the inactivated vaccine. These data show that the molecularly cloned V3526 vaccine induces equivalent or improved immunity to homologous and heterologous VEE viruses than the existing vaccines.

Tick-borne encephalitis virus strains of Western Siberia

Tick-borne encephalitis virus (TBEV) strains were isolated from ticks in Western Siberia for 12 years. Molecular hybridization of the 46 viral RNA with the TBEV cDNA and oligonucleotide probes revealed differences between the Siberian and Far Eastern strains. A comparison of the viral E gene fragment nucleotide sequence showed 89–98% homology between Siberian TBEV strains, whereas their similarity with strains from other populations was less than 83%. However, the viral E and NS1 glycoprotein antigenic structures appeared to be conservative because of the degenerate genetic code. This was shown by enzyme-linked immunosorbent assay with the corresponding monoclonal antibodies (MAb). The single exception was the MAb 17C3 against nonstructural glycoprotein NS1, which could distinguish Siberian from Far Eastern strains. Moreover, the neurovirulence differed between strains from the two natural populations. Lower neuroinvasiveness of the Siberian strains in comparison with Far Eastern Sofyin strain might be caused by both E and NS1 glycoprotein mutations.

Genetic variation of Japanese encephalitis virus in Taiwan.

A 280-nucleotide sequence from the capsid-premembrane (C/preM) gene region of 44 Japanese encephalitis (JE) virus strains isolated in Taiwan from mosquitoes from 1983 to 1994, and 3 strains, (Ling [1965], Chang [1965], and HV1 [1958]) isolated from human brain were analyzed by direct sequencing of reverse transcription-polymerase chain reaction (RT-PCR) amplified products and compared with the corresponding sequences of reference strains. The overall sequence homology of the 47 isolates was > or = 93.3%. Taking 12% nucleotide divergence as a cut-off value, all isolates fell into genotype 3, which included strains from Japan, China, the Philippines, Sri Lanka, India, and Nepal. High nucleotide homology was observed among isolates from different regions of Taiwan and different time periods; on the other hand, high variation existed among isolates from the same region and time period. Phylogenetic analysis showed that the 47 Taiwan isolates fell into three clusters. Twenty-five isolates formed cluster 1, 18 isolates cluster 2, and four isolates cluster 3. Isolates in cluster 1 showed greater (< or = 2.9%) intragroup divergence compared to those in cluster 2 (< or = 1.1%) or cluster 3 (< or = 0.7%). The majority of isolates from northern (73.3%) and central (60%) Taiwan belonged to cluster 1, whereas most isolates (66.7%) from southern Taiwan belonged to cluster 2. Comparison with other Asian JE virus strains showed that isolates of cluster 1 were more specific to Taiwan than isolates of cluster 2 and cluster 3.

Immunogenicity and protective efficacy of the current inactivated Japanese encephalitis vaccine against different Japanese encephalitis virus strains

Mouse brain-derived, inactivated Japanese encephalitis (JE) vaccine has been internationally used for many years. It is believed that this vaccine made a great contribution to the reduction of JE patients in several countries. Mouse brain-derived, Beijing-1 and Nakayama JE vaccines induce high levels of neutralizing antibodies. High levels of induced antibodies are maintained at least for 3–4 yr. The induced antibodies are cross-reactive to heterologous strains; however, the neutralizing antibody titers against heterologous strains are usually lower than those against homologous strains. Considering that both Nakayama and Beijing-1 JE vaccines showed high levels of protective efficacy in Taiwan and Thailand where strains other than Nakayama and Beijing-1 were circulating, we conclude that the current inactivated JE vaccine can induce high levels of protective immunity against heterologous JE virus strains.

Sequencing of prototype viruses in the Venezuelan equine encephalitis antigenic complex

The 5′ nontranslated region (5′NTR) and nonstructural region nucleotide sequences of nine enzootic Venezuelan equine encephalitis (VEE) virus strains were determined, thus completing the genomic RNA sequences of all prototype strains. The full-length genomes, representing VEE virus antigenic subtypes I–VI, range in size from 11.3 to 11.5 kilobases, with 48–53% overall G+C contents. Size disparities result from subtype-related differences in the number and length of direct repeats in the C-terminal nonstructural protein 3 (nsP3) domain coding sequence and the 3′NTR, while G+C content disparities are attributable to strain-specific variations in base composition at the wobble position of the polyprotein codons. Highly-conserved protein components and one nonconserved protein domain constitute the VEE virus replicase polyproteins. Approximately 80% of deduced nsP1 and nsP4 amino acid residues are invariant, compared to less than 20% of C-terminal nsP3 domain residues. In two enzootic strains, C-terminal nsP3 domain sequences degenerate into little more than repetitive serine-rich blocks. Nonstructural region sequence information drawn from a cross-section of VEE virus subtypes clarifies features of alphavirus conserved sequence elements and proteinase recognition signals. As well, whole-genome comparative analysis supports the reclassification of VEE subtype-variety IF and subtype II viruses.

TC-83 vaccine protects against airborne or subcutaneous challenge with heterologous mouse-virulent strains of Venezuelan equine encephalitis virus

Vaccination with TC-83 virus produced solid protection against subcutaneous challenge with Venezuelan equine encephalitis (VEEV) viruses from homologous and heterologous serogroups, but breakthrough infection and disease occurred after airborne challenge. Breakthrough occurred more often with time after vaccination, and was more frequent with epizootic, homologous serogroup 1A/B viruses than with enzootic, heterologous serogroup viruses. A decrease in VEEV-specific IgA levels in the respiratory tract of vaccinated mice may explain the increased frequency of breakthrough with time after vaccination. However increased breakthrough with the highly virulent homologous serogroup 1A/B viruses (compared to less virulent viruses from heterologous serogroups) may be a consequence of their greater ability to invade the brain via the olfactory neuroepithelium and olfactory nerve.

Pathogenicity of tick-borne encephalitis virus isolated in Hokkaido, Japan in mouse model

The pathogenic characteristics of tick-borne encephalitis (TBE) virus strain (Oshima 5-10) isolated from a sentinel dog in Hokkaido, Japan, was compared by use of a mouse model with several inoculation routes to other strains of TBE virus (the Far Eastern subtype; Sofjin strain and the Western subtype; Hochosterwitz strain) and TBE complex virus (Langat virus; TP-21 strain). The degree of neuroinvasiveness of the strains in mice subcutaneously (s.c.) inoculated was Sofjin equaled Hochosterwitz which was greater than Oshima and TP-21, respectively. Neurovirulence, as determined after intracerebral inoculation was Sofjin>Oshima=Hochosterwitz>TP-21. Virus replication in the brains of mice s.c. or intracerebrally inoculated with Oshima strain was slower and of lower titer than that of Sofjin strain. Histopathological findings indicated that subarachnoid infiltration of mononuclear cells prior to necrosis of the cerebrum was characteristic in Oshima strain. These findings indicated that the Oshima strain possessed a pathogenic potential common to TBE viruses and is less virulent for mice as compared with the two other TBE strains examined.

Localizations of NS3 and E proteins in mouse brain infected with mutant strain of Japanese encephalitis virus.

Infection with a mutant Japanese encephalitis virus (JEV) strain RP-2ms showed reduced neurovirulence than wild type or RP-9 strains after inoculation in BALB/c mice. However, higher intracellular viral titer was detected in Rp-2ms infected cultured cells. Localizations of non-structural 3 (NS3) and envelope (E) proteins were demonstrated by immunocytochemistry. NS3 protein was primarily found in the pyramidal neurons in cerebrum, in the molecular and granular layers of cerebellum. Neither E nor NS3 protein was detected in Purkinje cells of the cerebellum. Immunoelectron microscopic observations showed that E and NS3 proteins were positive in JEV-induced membranous systems, mainly hypertrophic rough endoplasmic reticulum (rER) and membrane vesicle structure (MVS) but not smooth membrane structure. Virus particles were seen in the Golgi apparatus, rER, nuclear envelope, MVS and cytoplasmic vacuoles. Different mechanisms of intracellular trapping in vivo provide a possible basis for attenuation of RP-2ms strains of JEV.

Development and analysis of a tick-borne encephalitis virus infectious clone using a novel and rapid strategy

In less than 1 month we have constructed an infectious clone of attenuated tick-borne encephalitis virus (strain Vasilchenko) from 100 μl of unpurified virus suspension using long high fidelity PCR and a modified bacterial cloning system. Optimization of the 3′ antisense primer concentration was essential to achieve PCR synthesis of an 11 kb cDNA copy of RNA from infectious virus. A novel system utilising two antisense primers, a 14-mer for reverse transcription and a 35-mer for long PCR, produced high yields of genomic length cDNA. Use of low copy number Able™ K cells and an incubation temperature of 28°C increased the genetic stability of cloned cDNA. Clones containing 11 kb cDNA inserts produced colonies of reduced size, thus providing a positive selection system for full length clones. Sequencing of the infectious clone emphasised the improved fidelity of the method compared with conventional PCR and cloning methods. A simple and rapid strategy for genetic manipulation of the infectious clone is also described. These developments represent a significant advance in recombinant technology and should be applicable to positive stranded RNA viruses which cannot easily be purified or genetically manipulated.

Attenuation of Japanese Encephalitis Virus by Selection of Its Mouse Brain Membrane Receptor Preparation Escape Variants

Six variants of Japanese encephalitis (JE) virus strain P3 were selected for resistance to binding to mouse brain membrane receptor preparations (MRP). All but one of these MRP escape (MRPR) variants were significantly attenuated in mice for both neuroinvasiveness (>200-fold) and neurovirulence (>500-fold) compared to their parent virus. Attenuated mouse brain MRPRvariants could be detected in the sera of mice following either intracerebral (i.c.) or intraperitoneal inoculation, whereas virus was detected only in brains of mice following ic inoculation. Immunization of mice with MRPRs induced neutralizing antibodies and protected mice against challenge with wild-type JE virus. A common amino acid mutation was found in the envelope (E) protein gene of all attenuated mouse brain MRPRvariants at residue E-306 compared to P3 virus grown in mosquito C6-36 cells or plaque purified and amplified in monkey kidney Vero cells. This amino acid is putatively responsible for attenuation due to alteration in binding of JE virus to its cell receptor in mouse brain. The methodology developed in this study has general applicability to the attenuation of virulence of viruses and to the identification of agents that will block amino acids in a viral attachment protein(s) that interacts with cell receptors.

Genus-specific detection of alphaviruses by a semi-nested reverse transcription-polymerase chain reaction.

A reverse transcription-polymerase chain reaction (RT-PCR) was developed for the genus-specific detection of alphaviruses. Based on the available published sequences, degenerate primers were designed to ensure hybridization to a conserved region within the nonstructural protein 1 gene of all alphavirus species. The expected 434-basepair (bp) cDNA fragment was amplified from all 27 alphavirus species by using RNA extracted from 200 microl of infected cell culture supernatant. In addition, eight strains of Venezuelan equine encephalitis (VEE) virus and 10 strains of Sindbis virus were amplified. The viral origin of the amplicons was confirmed by restriction enzyme analysis and comparison with the expected cleavage pattern based on published sequence data. The PCR products of alphavirus species with thus far unknown nucleotide composition were sequenced. About 120 nucleotides downstream of the forward primer, a region showing sufficient homology for the design of another forward primer was found and used in a semi-nested PCR. The expected 310-bp semi-nested fragment was demonstrated for all viruses investigated. The sensitivity of the RT-PCR was about 1,200 plaque-forming units (PFU) for VEE virus reference strain Trinidad donkey. The detection limit after the semi-nested PCR was 1.2 PFU. The sensitivity was not hampered by the presence of human serum, thus making this test suitable for an application in viremic individuals. Chikungunya virus RNA was amplified from infected mouse brain tissue by the described RT-PCR assay. Our data suggest that the semi-nested RT-PCR may be applied as a highly sensitive alternative to virus isolation in the rapid screening and diagnosis of alphavirus infections, including post-mortem diagnosis. Phylogenetic analysis of the amplicon sequence data identified six genotypes within the Alphavirus genus.

Ultrastructure and Localization of E Proteins in Cultured Neuron Cells Infected with Japanese Encephalitis Virus

A unique structure andin situlocalization of E proteins were demonstrated in cultured neurons infected with neurovirulent and aneurovirulent strains of local Japanese encephalitis virus (JEV). Dilated rough endoplasmic reticulum (rER) containing smooth membrane structures (SMS) was continuous with the outer membrane of the nuclear envelope. These membranes were found to be connected to unique dense bodies, membrane vesicle structures (MVS). Thede novoformation of SMS, annulate lamellae, and the appearance of MVS indicated proliferation of the membranous system in response to JEV infection. E proteins were possibly assembled in the virions in the nuclear envelope or rER or on the plasma membrane. The interconnections between MVS, rER, and the nuclear envelope and immunogold labeling of E proteins on the MVS provided strong evidence that MVS serve as a reservoir of JEV components during virus assembly.

Statistical analysis of the envelope gene and the prM region of Japanese encephalitis virus: Evidence suggestive of positive selection

The variation in nucleotide sequence observed in the envelope (E) gene and the prM (precursor of M protein) region of different strains of Japanese encephalitis virus (JEV) was analysed. Presence of selective forces acting on these regions was investigated by computing the relative rates of synonymous (Ks) and nonsynonymous (Ka) substitutions. The ratioKs/Ka was used as an indicator of the overall selective constraints on the amino acid sequence of JEV proteins. The possibility that different regions of the gene may be subject to varying selective pressures was tested by dividing the gene into three regions and estimating theKs/Ka ratio for each region. On the basis of analysis of a limited number (17) of strains of JEV, evidence suggestive of positive selection acting on certain regions of the E gene of the virus, and in some cases on the entire gene, was obtained. Analysis ofKa diversity in the prM region of 46 JEV strains grouped into three genotypes revealed that strains included in genotype II were more heterogeneous than strains belonging to genotype I, while the differences between meanKa values for genotypes I and III and genotypes II and III were not statistically significant. Analysis of host-specific heterogeneity in the prM region revealed that pig isolates were more Xa-diverse than human isolates.

Infectious cDNA clones of tick-borne encephalitis virus European subtype prototypic strain Neudoerfl and high virulence strain Hypr.

Infectious cDNA clones of two strains of tick-borne encephalitis (TBE) virus, i.e. European subtype prototypic strain Neudoerfl and the closely related but more virulent strain Hypr, were constructed. The recombinant constructs consisted of cDNAs stably inserted into the bacterial plasmid pBR322 under the control of T7 promoter elements. The genome of TBE virus strain Neudoerfl was successfully cloned, both as a full-length cDNA and as two partial cDNAs. In the case of strain Hypr, the genome is represented by two cDNA clones corresponding to the 5'- and 3'-terminal halves of the genome. Highly infectious RNAs can be produced from the full-length cDNA clone or from the partial clones ligated in vitro to form full-length cDNA templates prior to T7 transcription. The biological properties of the recombinant progeny viruses, including virulence characteristics, were indistinguishable from the corresponding parent virus strains. Thus, the described infectious cDNA clones represent a useful and reliable experimental system for the specific mutagenesis of TBE virus.

Sexual transmission of tick-borne encephalitis virus in laboratory mice

Mating of males infected with tick-borne encephalitis virus (strain Sofyin) with intact females results in a marked decrease in the weight of embryos and an almost threefodl increase in embryonal mortality. Viral RNA was identified by the polymerase chain reaction in embryonal tissues of 2 out of 11 litters. In one case the infection of the progeny was confirmed by biological test.

Genotypes of Japanese encephalitis virus isolated in three states in Malaysia.

Two hundred forty nucleotides from the pre-membrane gene region of 12 Japanese encephalitis virus (JEV) strains isolated from three different regions of Malaysia from 1993 to 1994 were sequenced and compared with each other and with the JEV strains from different geographic areas in Asia. These 12 Malaysian isolates were classified into two genotypes. The four JEV strains isolated from Sarawak in 1994 and the four JEV strains isolated from Sepang, Selangor in 1993 were classified into one genotype that included earlier isolated strains from Malaysia (JE-827 from Sarawak in 1968 and WTP/70/22 from Kuala Lumpur in 1970). The four JEV strains from Ipoh, Perak in 1994 were classified into another genotype that included JEV strains isolated from northern Thailand and Cambodia. In an earlier report, 10 JEV strains from Sabak Bernam, Selangor in 1992 were classified into the largest genotype that included strains isolated in temperate regions such as Japan, China, and Taiwan. The data indicate that at least three genotypes of JEV have been circulating in Malaysia.

Coupled PCR-restriction enzyme analysis for rapid identification of structural gene relationships among strains of eastern equine encephalitis virus

We have used restriction endonuclease digestion analysis of polymerase chain reaction (PCR)-amplified gene regions to rapidly examine individual structural gene relationships among field isolates of estern equine encephalitis (EEE) virus. The E1 + (E1 gene plus 292 nucleotides 3′ of the coding region), E2, and C gene regions from North American (NA) variety and the E1 and C gene regions of South American (SA) variety viruses were successfully amplified by RT-PCR using a single primer set for each locus. The products were then digested with a panel of restriction endonucleases and the resulting DNA fragments electrophoretically compared. Our findings revealed marked similarity among the E1 + and the E2 gene restriction patterns, respectively, of most NA strains. In contrast, the restriction patterns exhibited by the E1 + gene of SA strains differed substantially from those of NA strains and also appeared more heterogeneous. The digestion patterns of the C gene were generally similar for all strains of the virus examined. These results thus demonstrate that EEE viral E1 + and C structural gene sequences can be amplified from an assortment of both NA and SA varieties of the virus by RT-PCR using a single primer set per locus, and that both varietal and individual isolate distinctions can be identified by comparison of subsequent restriction digestion patterns. This technique should prove useful as an epidemiological tool for rapid identification of EEE isolates from clinical and field specimens, and as a rapid screen for alterations within structural gene regions.

Phylogenetic analysis of the envelope gene of Japanese encephalitis virus

Variation among Japanese encephalitis virus (JEV) strains has been documented in a number of studies by employing a variety of techniques like HI, NT, CF, RNA fingerprinting and sequencing of prM region. We report the complete envelope (E) gene sequence and the deduced amino acid sequence of four strains of JEV from the Indian subcontinent. These sequences were compared with published E gene sequences of 16 strains of JEV. Pairwise comparisons of the E gene nucleotide and deduced amino acid sequences of these strains indicated an overall sequence conservation. A majority of the differences in the four strains were located in domain A and domain C (Mandl et al., 1989). Phylogenetic analysis of the E gene sequences by a variety of tree building methods identified four clusters. Viral groupings did not correspond to geographic origin, isolation host or virulence. Evidence for positive selection operating on some strains belonging to different clusters was obtained.

Characterization and complete genome sequences of high- and low- virulence variants of tick-borne encephalitis virus.

The entire genomic sequences of two strains (Hypr and 263) of the flavivirus tick-borne encephalitis (TBE) virus differing in virulence from the prototypic strain Neudoerfl were determined. Strain Hypr is a human isolate of TBE virus with a high laboratory passage history which exhibits a significantly higher neuro-invasiveness in mice compared to the prototype strain. Strain 263 is a low-passage tick-isolate with a temperature-sensitive and attenuated phenotype. Except for the heterogeneous 3' non-coding regions strains Hypr and 263 share, respectively, 97.2% and 97.6% nucleotide sequence identity with strain Neudoerfl, and differ by a total of 42 and 36 amino acids from the prototypic strain. Of these, only 12 amino acids for each of the two strains represent non-conservative differences unique to an individual strain and some of these are located at positions highly conserved among flaviviruses. Based on these observations, the potential biological significance of particular sequence differences is discussed in the context of the current knowledge about molecular determinants of flavivirus virulence.

Passage of Japanese encephalitis virus in HeLa cells results in attenuation of virulence in mice

Of four wild-type strains (Nakayama-original, SA14, 826309 and Beijing-1) of Japanese encephalitis (JE) virus that were passaged six times in HeLa cells (HeLa p6), two (Nakayama-original and 826309) became attenuated for mice. In the case of strain Nakayama-original, the virulence for mice was markedly reduced and attenuation was retained on passage in primary chicken embryo fibroblast, LLC-MK2 and C6/36 cells. The binding of non-HeLa-passaged Nakayama virus to mouse brain membrane receptor preparations could be differentiated from binding by Nakayama HeLa p6 virus, suggesting that the envelope (E) protein is involved in the attenuated phenotype. Both of the attenuated viruses can be distinguished from the virulent non-HeLa-passaged parental viruses by examination with E protein reactive vaccine and wild-type-specific monoclonal antibodies (MAbs). The vaccine-specific MAb V23, which is only reactive with the SA14 series of live vaccine viruses, recognized the HeLa cell-attenuated Nakayama-original and 826309 viruses, whereas two wild-type-specific MAbs (MAbs K13 and K39) lost reactivity. Comparison of the nucleotide sequences of the structural protein genes of the 826309 and Nakayama-original virulent parent and attenuated HeLa p6 viruses revealed that the viruses differed by 37 and 46 nucleotides coding for eight and nine amino acid mutations, respectively. However, other than one amino acid in the E protein, the membrane and E protein amino acid sequences of the two attenuated HeLa p6 viruses were identical.