Epitope mapping of flavivirus glycoproteins

Structure of viral B-cell epitopes

Four categories of viral epitopes can be distinguished that have been designated cryptotopes, neotopes, metatopes and neutralization epitopes. Specific examples of each epitope type are presented and the methods used for locating their positions in viral proteins are described. The epitopes of four well-characterized viruses, namely poliovirus, foot-and-mouth disease virus, influenza virus and tobacco mosaic virus are briefly described.

Expression of the structural proteins of dengue 2 virus and yellow fever virus by recombinant vaccinia viruses

Vaccinia virus recombinants were constructed which contained cDNA sequences encoding the structural region of dengue 2 virus (PR159/S1 strain) or yellow fever virus (17D strain). The flavivirus cDNA sequences were expressed under the control of the vaccinia 7.5k early/late promotor. Cultured cells infected with these recombinants expressed immunologically reactive flavivirus structural proteins, precursor prM and E. These proteins appeared to be cleaved and glycosylated properly since they comigrated with the authentic proteins from dengue 2 virus- and yellow fever virus-infected cells. Mice immunized with the dengue/vaccinia recombinant showed a dengue-specific immune response that included low levels of neutralizing antibodies. Immunization of mice with the yellow fever/vaccinia recombinant was less effective at inducing an immune response to yellow fever virus and in only some of the mice were low titers of neutralizing antibodies produced.

Genome sequence of tick-borne encephalitis virus (Western subtype) and comparative analysis of nonstructural proteins with other flaviviruses

The genome sequence of tick-borne encephalitis (TBE) virus (Western subtype vaccine strain Neudoerfl) was determined. This extends the previously published sequence of the structural proteins to the nonstructural protein region and noncoding sequences at the 5'- and 3'-termini. The amino-termini of the individual proteins were assigned by comparison with other flavivirus sequences. Amino acid homology calculations between TBE virus and mosquito-borne flaviviruses were performed for all nonstructural proteins. An evolutionary tree based on protein NS1 is presented that reveals the molecular basis of relationships among flaviviruses. Tick-borne and mosquito-borne flaviviruses share a common hydrophilicity profile and also other features of their primary sequences, such as the presumably functional Gly-Asp-Asp sequence element within protein NS5. Other characteristics, such as the potential N-glycosylation sites of protein NS1 and a potential proteolytic cleavage site within protein NS4B, are conserved within the mosquito-borne group, but differ in the TBE virus sequence.

Synthetic peptides derived from the deduced amino acid sequence of the E-glycoprotein of Murray Valley encephalitis virus elicit antiviral antibody

We used computer analysis to study hydrophilicity, homology, surface accessibility, molecular flexibility, and secondary structure of the deduced amino acid sequence of the flavivirus envelope (E)-glycoprotein. Using the results, we modified the E-glycoprotein antigenic structure proposed by Nowak and Wengler (1987, Virology, 156, 127-137). Our model predicts considerable overlaps in the previously defined domains. We have prepared 11 synthetic peptides from the deduced amino acid sequence of the E-glycoprotein of Murray Valley encephalitis (MVE) virus and analyzed their immunogenicity. Peptides derived from the redefined R1 and R2 domains elicit antiviral antibody. Nine of these peptides are recognized by polyclonal antiviral antibodies; however, none are consistently recognized by monoclonal antibodies. Peptides derived from the R1 domain demonstrate MVE virus specificity, and 1 peptide elicited low-level virus neutralizing antibody. Spatial overlap of the domains was defined by competitive binding assays between antipeptide antisera and radioactive monoclonal antibodies. These results indicate that synthetic peptides aid in defining flavivirus antigenic structure, and may serve as possible type-specific diagnostic reagents.

Antigenic structure of the flavivirus envelope protein E at the molecular level, using tick-borne encephalitis virus as a model

A model of the tick-borne encephalitis virus envelope protein E is presented that contains information on the structural organization of this flavivirus protein and correlates epitopes and antigenic domains to defined sequence elements. It thus reveals details of the structural and functional characteristics of the corresponding protein domains. The localization of three antigenic domains (composed of 16 distinct epitopes) within the primary structure was performed by (i) amino-terminal sequencing of three immunoreactive fragments of protein E and (ii) sequencing the protein E-coding regions of seven antigenic variants of tick-borne encephalitis virus that had been selected in the presence of neutralizing monoclonal antibodies directed against the E protein. Further information about variable and conserved regions was obtained by a comparative computer analysis of flavivirus E protein amino acid sequences. The search for potential T-cell determinants revealed at least one sequence compatible with an amphipathic alpha-helix which is conserved in all flaviviruses sequenced so far. By combining these data with those on the location of disulfide bridges (T. Nowak and G. Wengler, Virology 156:127-137, 1987) and the structural characteristics of epitopes, such as dependency on conformation or on intact disulfide bridges or both, a model was established that goes beyond the location of epitopes in the primary sequence and reveals features of the folding of the polypeptide chain, including the generation of discontinuous protein domains.

Sequence of the structural proteins of tick-borne encephalitis virus (western subtype) and comparative analysis with other flaviviruses

Tick-borne encephalitis (TBE) virus (Western subtype strain Neudoerfl) was cloned and the sequence of 2450 nucleotides of the 5'-terminal region of the genome was determined. By amino acid sequencing and sequence comparisons with other flaviviruses the amino-termini of the structural proteins and protein NS1 were localized. Sequence homologies with other flaviviruses were determined and corresponded well to the established serological classification system of the Flavivirus family. N-Glycosylation sites were found to be conserved to a large extent among members of the same serological subgroup, but not between members of different subgroups. Hydrophilicity plots and sequence comparisons revealed that the TBE virus capsid protein exhibited features distinct from all other flaviviruses. Additionally, the capsid protein coding region of another natural isolate of TBE virus (strain ZZ-9) was sequenced in order to analyze why the capsid protein of this strain exhibited a significantly faster migration rate on SDS-polyacrylamide gels than other TBE virus strains.

Murray Valley encephalitis virus field strains from Australia and Papua New Guinea: studies on the sequence of the major envelope protein gene and virulence for mice

We have compared the nucleotide sequence of the gene encoding the major envelope (E) protein of a number of Murray Valley encephalitis virus (MVE) isolates from Australia and Papua New Guinea (PNG). The isolates, from widely separated geographic regions, were from four fatal human cases, a heron, and six mosquito pools and covered a period of 25 years. The sequences of the Australian strains were notable for their similarity, showing not more than 1.7% nucleotide sequence divergence in pairwise comparisons. There was 6.8% divergence in the E gene between the two available strains from PNG, and 9-10% divergence between each of the PNG strains and the Australian prototype. These data are consistent with previous conclusions based on HaeIII restriction digest analysis of cDNA to virion RNA (M. Lobigs, I. D. Marshall, R. C. Weir, and L. Dalgarno, 1986, Aust. J. Exp. Biol. Med. Sci. 64, 571-585). We conclude that a single MVE genetic type exists in Australia. Separate foci of MVE evolution appear to exist in PNG, generating greater strain variation. For all MVE isolates the deduced length of the E protein was 501 amino acids. The E protein differed at no more than three positions between any two Australian strains. The PNG strains differed from the Australian strains at 6-11 residues depending on the virus pair. Differences in amino acid sequence did not occur at a position corresponding to a previously demonstrated neutralization determinant in yellow fever virus (M. Lobigs, L. Dalgarno, J. J. Schlesinger, and R. C. Weir, 1987, Virology 161, 474-478). Thus selection for neutralization resistance may not be a major evolutionary pressure in the field situation. In comparisons between the E protein amino acid sequence of the prototype strain and those of a number of other MVE strains, 7 out of 14 differences were at residues seen at the corresponding position for Japanese encephalitis virus (JE), consistent with the close serological relationship of MVE and JE. Five Australian MVE strains and two from PNG were tested for virulence by comparing LD50 values after intraperitoneal and intracranial inoculation of 21-day-old mice; all strains were virulent by this test.

Location of a neutralization determinant in the E protein of yellow fever virus (17D vaccine strain)

The location of a major antigenic determinant involved in the neutralization of a flavivirus, yellow fever virus (YF), has been defined in terms of its position in the amino acid sequence of the E protein. Neutralization escape variants of the 17D vaccine strain of YF were selected with two neutralizing monoclonal antibodies. Nucleotide sequencing of the envelope protein genes (E and M) of the variants showed that in each variant there was a single nucleotide change in the E gene leading to a nonconservative amino acid substitution in the E protein at position 71 or 72. The changes are in a region of the E protein which is hydrophilic, rich in cysteine residues, and not conserved between flavivirus subgroups. Since the selecting monoclonal antibodies neutralize attenuated 17D and virulent Asibi strains of YF with equal efficiency (J. J. Schlesinger, M. W. Brandriss, and T. P. Monath, 1983, Virology 125, 8-17), it can be concluded that the neutralization determinant defined for 17D YF is also present in Asibi YF.