US20190255168A1

US20190255168A1 - Chimeric dengue virus e glycoproteins comprising mutant domain i and domain ii hinge regions

Info

Publication number: US20190255168A1
Application number: US16/146,996
Authority: US
Inventors: Aravinda M. De Silva; A. Ruklanthi De Alwis; Wahala M.P.B. Wahala; Ralph S. Baric; William B. Messer; James E. Crowe, Jr.; Scott A. Smith
Original assignee: University of North Carolina at Chapel Hill; Vanderbilt University
Current assignee: University of North Carolina at Chapel Hill; Vanderbilt University
Priority date: 2012-04-02
Filing date: 2018-09-28
Publication date: 2019-08-22
Also published as: CN108912215A; BR112014024612A2; CN104428312A; US9821050B2; US10117924B2; EP2834265A1; US20180125964A1; US20150328303A1; WO2013151764A1; EP2834265A4

Abstract

The present invention provides compositions and methods of use comprising a chimeric dengue virus E glycoprotein comprising a dengue virus E glycoprotein backbone, which comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region from a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone.

Description

STATEMENT OF PRIORITY

This application is a divisional of, and claims priority to, U.S. patent application Ser. No. 15/783,675, filed Oct. 13, 2017 (allowed), which is a divisional of U.S. patent application Ser. No. 14/390,312, filed Oct. 2, 2014, now U.S. Pat. No. 9,821,050, issued Nov. 21, 2017, which is a 35 USC § 371 national phase application of International Application Serial No. PCT/US2013/032367, filed Mar. 15, 2013, which claims the benefit under 35 U.S.C. § 119(e), of U.S. Provisional Application No. 61/619,247, filed Apr. 2, 2012, the entire contents of each of which are incorporated by reference herein.

STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, submitted under 37 C.F.R. § 1.821, entitled 5470-626TSDV2_ST25.txt, 24,934 bytes in size, generated on Sep. 26, 2018 and filed via EFS-Web, is provided in lieu of a paper copy. This Sequence Listing is hereby incorporated by reference into the specification for its disclosures.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under Grant No. U54 AI057157 awarded by the National Institutes of Health. The United States government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention is based, in part, on the discovery by the inventors of a novel complex, quaternary structure dengue virus epitope that spans adjacent E protein dimers in the assembled virus particle. Further, the inventors have demonstrated that antibodies directed against this epitope neutralize dengue virus infection. These findings have significant implications for the design and characterization of immunogenic compositions intended to produce an immune response to dengue virus.
In particular, the inventors have identified a dengue virus epitope that has a footprint that spans the hinge region between domains I and II of the E protein in one E protein homodimer. In some cases, this epitope extends into portions of domain III from an E protein in an adjacent homodimer, where both E proteins are in the same orientation within their respective homodimers.

BACKGROUND

Dengue is a mosquito-borne flavivirus that is spreading at an unprecedented rate and has developed into a major health and economic burden in over 50 countries. Even though infected individuals develop potent and long-lasting serotype-specific neutralizing antibodies (Abs), the epitopes engaged by human neutralizing Abs have not been identified. Here, we demonstrate that the dengue virus (DENV)-specific serum Ab response in humans consists of a large fraction of cross-reactive, poorly neutralizing Abs and a small fraction of serotype-specific, potently inhibitory Abs. Although many mouse-generated, strongly neutralizing monoclonal antibodies (MAbs) recognize epitopes that are present on recombinant DENV envelope (E) proteins, unexpectedly, the majority of neutralizing Abs in human immune sera bound to intact virions but not to the ectodomain of purified soluble E proteins. These conclusions with polyclonal Abs were confirmed with newly generated human MAbs derived from DENV-immune individuals. Two of three strongly neutralizing human MAbs bound to E protein epitopes that were preserved on the virion but not on recombinant E (rE) protein. It is proposed that humans produce Abs that neutralize DENV infection by binding a complex, quaternary structure epitope that is expressed only when E proteins are assembled on a virus particle. Mapping studies indicate that this epitope has a footprint that spans adjacent E protein dimers and includes residues at the hinge between domains I and II of E protein. These results have significant implications for the DENV Ab and vaccine field.

SUMMARY OF THE INVENTION

Thus, the invention provides a dengue virus epitope (e.g., an isolated dengue virus epitope) that spans adjacent dengue virus E protein dimers and comprises the hinge region between domains I and II of a first E protein from a first E protein dimer and domain III of a second dengue virus E protein from a second E protein dimer.
The dengue virus epitope of the invention can be present in an intact virus particle (e.g., a killed or live attenuated virus particle or a recombinant dengue virus vector) or a virus-like particle (VLP), which may optionally be an intact dengue virus particle or dengue virus VLP.
Alternatively, dengue virus particles or VLPs can be processed, for example, chemically cross-linked and/or cleaved with protease to release the epitope from the viral coat and provide the epitope in a processed form.
The invention also provides isolated and/or recombinant polypeptides comprising a dengue virus E protein domain I and domain II hinge region, a peptide spacer, and at least a portion of a dengue virus E protein domain III. While not wishing to be bound by any theory of the invention, it appears that the epitope is formed between adjacent E protein homodimers because the E protein domain III is not in sufficiently close proximity within the same E protein molecule or even homodimer (see, e.g., FIG. 3). Thus, based on this knowledge, E proteins can be engineered in which the E protein domain III is brought into closer proximity to the E domain I/II hinge region, thereby providing an epitope formed within a single E protein molecule. Such an approach would be desirable from a standpoint of the manufacture and delivery of immunogenic compositions to produce an immune response to dengue virus, for example, as a soluble subunit immunogenic composition.
In further embodiments, the present invention provides a chimeric dengue virus E glycoprotein comprising a dengue virus E glycoprotein backbone, which comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region from a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone. The chimeric dengue virus E glycoprotein described herein can further comprise amino acid substitutions that introduce a dengue virus E glycoprotein domain III region from a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone.
Also provided herein is a chimeric flavivirus E glycoprotein comprising a flavivirus E glycoprotein backbone from a flavivirus that is not dengue virus, which comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region into the flavivirus E glycoprotein backbone. The chimeric flavivirus E glycoprotein described herein can further comprise amino acid substitutions that introduce a dengue virus E glycoprotein domain III region into the flavivirus E glycoprotein backbone.
Furthermore, the present invention provides a method of producing an immune response to a dengue virus in a subject, treating a dengue virus infection in a subject in need thereof, preventing a dengue virus infection in a subject and/or protecting a subject from the effects of dengue virus infection, such methods comprising administering to the subject an effective amount of an isolated dengue virus epitope of this invention, a polypeptide of this invention, an E glycoprotein of this invention, a flavivirus particle or VLP of this invention, a nucleic acid of this invention, a composition of this invention and any combination thereof.
In some embodiments, the epitopes, proteins, virus particles and/or VLPs of this invention can be readily used in diagnostic methods to determine if a subject produces an antibody that specifically binds to the native quaternary epitope, e.g., to determine if the subject has neutralizing antibodies. Such a diagnostic method finds use, for example, to determine the quality of the subject's immune response following natural infection with dengue virus and/or following administration of an immunogenic composition intended to produce an immune response to dengue virus (e.g., to determine if the immunogenic composition induces neutralizing antibodies that specifically bind to the native quaternary epitope on the virus).
A method is also provided herein of detecting a neutralizing antibody to a dengue virus, the method comprising the step of determining whether an antibody binds to an isolated dengue virus epitope of this invention, a polypeptide of this invention, an E glycoprotein of this invention and/or a flavivirus particle or VLP of this invention, wherein binding by the antibody to the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention detects a neutralizing antibody to a dengue virus.
Additionally provided herein is a method of identifying a neutralizing antibody to a dengue virus, the method comprising: (a) contacting an antibody with to an isolated dengue virus epitope of this invention, a polypeptide of this invention, an E glycoprotein of this invention and/or a flavivirus particle or VLP of this invention; and (b) determining if the antibody binds to the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention, wherein binding by the antibody to the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention identifies the antibody as a neutralizing antibody to a dengue virus.
The present invention further provides a method of identifying an immunogenic composition that induces a neutralizing antibody to a dengue virus in a subject, the method comprising: (a) contacting a biological sample from a subject that has been administered the immunogenic composition with an isolated dengue virus epitope of this invention, a polypeptide of this invention, an E glycoprotein of this invention and/or a flavivirus particle or VLP of this invention; (b) determining if the biological sample comprises an antibody that binds to the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention; and (c) identifying the immunogenic composition as inducing a neutralizing antibody to a dengue virus in the subject if the biological sample comprises an antibody that binds to the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention.
Also provided herein is a method of identifying an immunogenic composition that induces a neutralizing antibody to a dengue virus in a subject, the method comprising: (a administering an immunogenic composition comprising a dengue virus antigen to a subject in an amount effective to induce antibodies against the dengue virus antigen; (b) contacting a biological sample from the subject with an isolated dengue virus epitope of this invention, a polypeptide of this invention, an E glycoprotein of this invention and/or a flavivirus particle or VLP of this invention; (c) determining if the biological sample comprises an antibody that binds the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention; and (d identifying the immunogenic composition as inducing a neutralizing antibody to a dengue virus in the subject if the biological sample comprises an antibody that binds to the isolated dengue virus epitope of this invention, the polypeptide of this invention, the E glycoprotein of this invention and/or the flavivirus particle or VLP of this invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Binding and neutralization properties of primary DENV-immune sera depleted of total or cross-reactive DENV-binding Abs. (Panels A and B) Total DENV-specific Abs were removed from a DENV3 primary immune serum (e.g., subject 011) using polystyrene beads coated with purified DENV3 and tested for (Panel A) DENV binding and (Panel B) neutralization. The serum depleted with the homologous serotype did not bind to any of the four DENV viruses and failed to neutralize DENV3. Similar results were observed for four other primary immune sera (two DENV2 and two DENV3 sera) depleted with the homologous serotype responsible for infection. (Panels C-F) Primary DENV2 (Panels C and D) and DENV3 (Panels E and F) immune sera were depleted of cross-reactive Abs using beads coated with virus of heterologous serotype, and tested for DENV virus binding (Panels C and E) and neutralization of the homologous serotype (Panels D and F). Immune sera depleted of cross-reactive Abs contained type-specific Abs that bound to virus from the homologous serotype only Immune sera depleted of cross-reactive Abs were as potently neutralizing as undepleted or control depleted sera. Results presented here for cross-reactive antibody depletions are representative of data obtained with four primary DENV2 and three primary DENV3 human immune sera (See Table 1). *P<0.001 by unpaired student t-test of mean binding values.

FIG. 2: Binding and neutralization properties of primary DENV-immune sera depleted of rE-binding Abs. DENV rE from the homotypic strain was coupled covalently to agarose beads and incubated with the relevant DENV-immune sera to deplete DENV rE-specific Abs. (Panels A-B) Binding of immune sera to rE protein. (Panel A) Primary DENV2 and (Panel B) DENV3-immune sera were depleted with DENV2 and DENV3 rE protein respectively, and binding to rE protein from each of the four serotypes was measured by ELISA. Depletion with the rE from the homologous serotype led to a loss of binding to rE protein from each of the four serotypes. (Panel C) Successful removal of all rE-reactive Abs from sera (e.g., primary DENV3-immune subject 003) also was confirmed by Western blot analysis. Purified homotypic DENV virus (700 ng/well) and rE protein (500 ng/well) were electrophoresed, transferred to nitrocellulose membrane and probed with undepleted, control depleted or rE-depleted sera (at 1:1000 dilution). (Panels D-E) Neutralization of the homologous DENV virus by rE-depleted sera was measured using the U937+DC-SIGN flow cytometry-based assay. Homologous DENV neutralization by (Panel D) primary DENV2 (subject 031), (Panel E) primary DENV3 (subject 003); human immune sera depleted of rE-binding Abs was tested. No reduction in neutralization potency was observed following removal of rE-binding Abs from either of these two serum samples. A total of six primary immune sera were depleted of rE-binding Abs and tested (see Table 2). (Panel F) Non-human primates vaccinated with rE develop neutralizing Abs that can be depleted with rE antigen. Rhesus macaques (Macaca mulatta) were vaccinated and boosted with an alphavirus vector expressing DENV3 E ectodomain and sera were collected 10 weeks post-vaccination. Depletion of rE-binding Abs from sera of vaccinated animals (e.g., M630) removed greater than 98% (value estimated by comparing Neut₅₀values between control depleted and rE depleted) of the neutralizing Abs. Data is representative of two vaccinated rhesus macaque controls.

FIG. 3: Epitope mapping of escape mutants generated from type-specific neutralizing hMAbs. (Panels A-C) Neutralization profiles of respective wild type (WT) and escape mutants against (Panel A) 1F4, (Panel B) 2D22 and (Panel C) 5J7. Neutralization escape by the mutant viruses was confirmed using the U937+DC-SIGN flow cytometry-based neutralization assay for 1F4 and 2D22, and by FRNT for 5J7. (Panels D-F) Display enlarged views indicating the positions of the original amino acids of the escape mutations on EDIII and EDI-EDII hinge region for 1F4 (Panel D), 2D22 (Panel E) and 5J7 (Panel F). Images were generated with DENV1, DENV2 and DENV3 E dimer structure respectively. The DENV2 and DENV3 E dimer structures (RCSB accession no. 1OAN and 1UZG respectively) (8, 9) were modeled using Swiss PDB viewer and Pymol to generate structures for DENV1 and DENV3 (Thai 95) E dimers. (Panel G) Alignment of E protein segments from DENV (SEQ ID NOS:1-3, 5-7, 9-11 and 13-15) and WNV (SEQ ID NOS:4, 8, 12 and 16) identified in the neutralizing hMAb binding epitope of CR4354. Mutations leading to escape from 1F4 (blue), 2D22 (green) or 5J7 (pink) are highlighted on relevant regions of the aligned DENV E protein sequences. A portion of the CR4354 epitope that overlaps with the corresponding DENV escape mutations described here is highlighted in bold on the aligned WNV (New York 2000) sequence. Panel H. The escape mutations were mapped on to the E polymeric structure generated for TBEV (RCSB accession no. 1K4R) (10). The position of escape mutations generated from 1F4, 2D22 and 5J7 are highlighted on the structure in blue (Gly274, K47), green (Arg323, His282, Asp362) and pink (Gln271, Asn272, i.e., residues surrounding the lysine insertion) respectively. The footprint of the anti-WNV CR4354 hMAb that spans E protein dimers is circled with a white line. Note that all escape mutations for 1F4, 2D22, and 5J7 fall within the CR4354 footprint. *Neut₅₀values for each escape mutant differed significantly from the respective WT virus (P<0.0001).

FIG. 4: Comparison of neutralization properties of primary DENV-immune human sera depleted with either one heterologous virus or all three heterologous viruses. (Panel A) Depletion of primary DENV2-immune sera (e.g., subject 019) with DENV3 virus, or DENV1, 3, and 4 viruses, had no statistically significant effect on the Neut₅₀against the homotypic virus, DENV2. (Panel B) Depletion of primary DENV3-immune sera (e.g., subject 003) with DENV2 virus or DENV1, 2 and 4 viruses, had no statistically significant effect on the Neut₅₀against DENV3. Data are representative of single experiments conducted in duplicate. The Neut₅₀values of undepleted, control depleted and cross-reactive depleted sera were compared for each serum using one-way ANOVA analysis followed by a Tukey's multiple comparison test at P<0.05.

FIG. 5: Confirmation of the DENV2 rE structure on the CnBr-activated beads using mouse MAbs. Mouse MAbs, 9F16 (E DIII-specific) (12), 4G2 (fusion loop-specific), DV2-30, DV2-46, and DV2-58 (dimer interface-specific) (11), and human mAbs, 2D22 (virus-specific) were incubated three consecutive times with either control beads or DENV2 rE-conjugated beads for 2 hrs at 37° C. The depleted samples were tested for binding to DENV2 rE by capture ELISA. (Panel A) All previously mapped mouse MAbs that bound epitopes on DENV rE protein were successfully depleted with rE protein covalently conjugated to beads. (Panel B) The virus-specific human mAb, 2D22, was not depleted by rE protein. Data are representative of individual experiments conducted in duplicate. *P<0.001 by unpaired student t-test of mean binding values.

FIG. 6: Titration of DENV rE quantities that were covalently conjugated to beads. CnBr-activated beads were mixed with varying quantities (i.e., 0, 0.02, 0.2, 2, 10, 20 and 40 μg/ml) of DENV2 and DENV3 rE protein, and then incubated with primary DENV2 (i.e., subject 001) and DENV3 (i.e., subject 003) sera respectively. The remaining supernatant was tested for the presence of homologous rE-binding antibodies by capture ELISA. The grey arrow represents the amount of rE added to beads during ensuing rE depletion experiments with immune sera.

FIG. 7: Binding properties of rE-depleted sera to the homotypic DENV virus. Removal of rE-binding antibodies from (Panel A) primary DENV2 and (Panel B) DENV3 sera resulted in a statistically significant (P<0.05) 45±7% decrease in binding (EC₅₀) to the homologous virus. Statistical analysis was conducted using a one way ANOVA. Data are representative of three primary DENV2 and three primary DENV3 human immune sera (See Table 5).

FIG. 8. Loss of function: 50% neutralization titers for primary monkey anti-DENV3 sera against DENV 4, DENV 3 and DENV 3 with DENV 4 hinge (3/4 Hinge). X axis shows virus and Y axis shows inverse serum dilution on a log scale. The higher the inverse dilution value the more potent the sera is against a particular virus. Three of the sera, 8F7, 3H3 and 2G5 clearly lose potency against DENV 3/4 hinge virus.

FIG. 9. Gain of function: 50% neutralization titers for primary monkey anti-DENV4 sera against DENV 4, DENV 3 and DENV 3 with DENV 4 hinge (3/4 Hinge). X axis shows virus and Y axis shows inverse serum dilution on a log scale. The higher the inverse dilution value the more potent the serum is against a particular virus. All four of the sera clearly gain potency against DENV 3/4 hinge virus.

FIG. 10. Gain and loss of function: 50% neutralization titers for primary human anti-DENV 3 sera and anti-DENV 4 against DENV 4, DENV 3 and DENV 3 with DENV 4 hinge (3/4 Hinge). X axis shows virus and Y axis shows inverse serum dilution on a log scale. The higher the inverse dilution value the more potent the sera is against a particular virus. The two primary DENV-3 sera clearly lost potency against DENV 3/4 hinge virus and the two primary DENV-4 sera clearly gain potency against DENV 3/4 hinge virus.

FIG. 11. Alignment of E glycoprotein sequences of dengue virus serotypes and other flaviviruses. (SEQ ID NOS:17-22)

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based, in part on the unexpected discovery that epitope regions that define a DENV serotype can be transferred into or created in chimeric molecules. Thus, in one embodiment, the present invention provides a chimeric dengue virus E glycoprotein comprising a dengue virus E glycoprotein backbone, which comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region from a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone. In some embodiments, the chimeric dengue virus E glycoprotein described herein above can further comprise amino acid substitutions that introduce a dengue virus E glycoprotein domain III region from a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone. In such embodiments, the dengue virus E glycoprotein backbone can be from dengue virus serotype 1, dengue virus serotype 2, dengue virus serotype 3 or dengue virus serotype 4.
Furthermore, the domain I and domain II hinge region of the chimeric dengue virus E glycoprotein of this invention can be from dengue virus serotype 1, dengue virus serotype 2, dengue virus serotype 3 or dengue virus serotype 4.
In embodiments wherein the chimeric dengue virus E glycoprotein comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region E and further comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain III region, the domain 1 and domain II hinge region and the domain III region can be from dengue virus serotype 1, dengue virus serotype 2, dengue virus serotype 3 or dengue virus serotype 4.
In additional embodiments, of this invention, a chimeric flavivirus E glycoprotein is provided, said chimeric flavivirus E glycoprotein comprising a flavivirus E glycoprotein backbone from a flavivirus that is not dengue virus, which comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region into the flavivirus E glycoprotein backbone. In some embodiments, the chimeric flavivirus E glycoprotein can further comprise amino acid substitutions that introduce a dengue virus E glycoprotein domain III region into the flavivirus E glycoprotein backbone.
In some embodiments, the flavivirus E glycoprotein backbone can be from any flavivirus, including but not limited to, yellow fever virus (YFV), Japanese encephalitis virus (JEV) or West Nile virus (WNV).
Furthermore, the domain I and domain II hinge region of the chimeric flavivirus E glycoprotein of this invention can be from dengue virus serotype 1, dengue virus serotype 2, dengue virus serotype 3 or dengue virus serotype 4.
In embodiments wherein the chimeric flavivirus E glycoprotein comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain I and domain II hinge region E and further comprises amino acid substitutions that introduce a dengue virus E glycoprotein domain III region, the domain 1 and domain II hinge region and the domain III region can be from dengue virus serotype 1, dengue virus serotype 2, dengue virus serotype 3 or dengue virus serotype 4.
The present invention also provides a flavivirus particle or virus like particle (VLP) comprising the chimeric dengue virus E glycoprotein or chimeric flavivirus E glycoprotein of this invention.
In addition, the present invention provides an isolated nucleic acid encoding the chimeric dengue virus E glycoprotein or the chimeric flavivirus E glycoprotein of this invention, as well as an isolated nucleic acid encoding the isolated dengue virus epitope of this invention, an isolated nucleic acid encoding the polypeptide of this invention, an isolated nucleic acid encoding the flavivirus particle, VLP or viral coat of the chimeric flavivirus of this invention.
Further provided herein is a composition comprising the isolated dengue virus epitope this invention, the polypeptide of this invention, the chimeric VLP of this invention, the chimeric dengue virus E glycoprotein or chimeric flavivirus E glycoprotein of this invention, the flavivirus particle or VLP of this invention, the nucleic acid of this invention and any combination thereof, in a pharmaceutically acceptable carrier.
The dengue virus E glycoprotein domain I and domain II hinge region makes up a conformational epitope that induces the production of neutralizing antibodies. All or part of the domain III region of the E glycoprotein can be included to form a conformational epitope that induces the production of neutralizing antibodies.
The term “dengue virus E protein domain I and domain II hinge region” and similar terms would be understood in the art to include the three-dimensional interface between domain I and II in the dengue virus E glycoprotein and, optionally, the adjacent amino acid residues. In addition, those skilled in the art will appreciate that certain amino acid residues in the hinge region may facilitate proper folding and presentation of the epitope, even if they do not form part of the epitope per se. In representative embodiments, the dengue virus E protein domain I and domain II hinge region comprises, consists essentially of, or consists of amino acid positions 47-59, 124-133, 199-222 and/or 206-228 of the E protein of dengue virus serotype 3 (DENV3; e.g., GenBank® Database Accession No. JQ411814) or the corresponding positions of the E protein of other dengue viruses (e.g., dengue virus serotypes 1 (DENV1; e.g., GenBank® Database Accession No. U88535), 2 (DENV2; e.g., GenBank® Database Accession No. NC_001474) or DENV4; full E glycoprotein sequences are shown in FIG. 11 and corresponding amino acid numbers are provided in Table 6).
The term “at least a portion of a dengue virus E protein domain III” and similar terms refer to those portions of E protein domain III that form part of the epitope as well as those amino acid residues that facilitate proper folding and presentation of the epitope, even if they do not form part of the epitope per se. In representative embodiments, the dengue virus E protein domain III comprises, consists essentially of, or consists of amino acid positions 305-308, 323-325, 359-362 and/or 389-390 of the E protein of dengue virus serotype 3 or the corresponding positions of the E protein of other dengue viruses (e.g., dengue virus serotypes 1 (DENV1), 2 (DENV2) or DENV4; full E glycoprotein sequences are shown in FIG. 11 and corresponding amino acid numbers are provided in Table 6).
Thus, the present invention provides a chimeric dengue virus E glycoprotein comprising a DENV1 domain I and domain II hinge region in a DENV2, DENV3 or DENV4 E glycoprotein backbone. Also provided is a chimeric dengue virus E glycoprotein comprising a DENV1 domain I and domain II hinge region as well as a domain III region in a DENV2, DENV3 or DENV4 E glycoprotein backbone. Further provided is a chimeric dengue virus E glycoprotein comprising a DENV3 domain I and domain II hinge region in a DENV1, DENV2 or DENV4 E glycoprotein backbone. Also provided is a chimeric dengue virus E glycoprotein comprising a DENV3 domain I and domain II hinge region as well as a domain III region in a DENV1, DENV2 or DENV4 E glycoprotein backbone. Further provided is a chimeric dengue virus E glycoprotein comprising a DENV4 domain I and domain II hinge region in a DENV1, DENV2 or DENV3 E glycoprotein backbone. Also provided is a chimeric dengue virus E glycoprotein comprising a DENV4 domain I and domain II hinge region as well as a domain III region in a DENV1, DENV2 or DENV3 E glycoprotein backbone. Production of these chimeras can be carried out by introducing some (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) or all of the amino acid substitutions identified in Table 6. Not every amino acid identified in Table 6 is required to be substituted to produce a chimeric protein of this invention. For example, in some embodiments further substitutions and/or omission of substitutions of about 1, 2, 3, 4 or 5 amino acids at either end of the contiguous amino acid sequences identified in Table 6 as the respective epitope regions can be included in production of a chimera of this invention. The number of substitutions necessary to produce the desired conformational epitope can be readily determined by one of ordinary skill in the art according to the teachings herein and according to protocols well known in the art.
In some embodiments, the present invention provides a chimeric flavivirus E glycoprotein in which amino acid substitutions are made to introduce a dengue virus epitope into a flavivirus E glycoprotein from a flavivirus that is not a dengue virus. Nonlimiting examples of flaviviruses that can be used include yellow fever virus (YFV) (e.g., GenBank® Database Accession No. JX503529) Japanese encephalitis virus (JEV) (e.g., GenBank® Database Accession No. U14163), West Nile virus (WNV) (e.g., GenBank® Database Accession No. DQ211652) and any other flavivirus now known or later identified. Thus, the present invention provides, for example a chimeric flavivirus E glycoprotein comprising a DENV1, DENV2, DENV3, or DENV4 domain I and domain II hinge region in a YFV, JEV or WNV E glycoprotein backbone. Also provided is a chimeric dengue virus E glycoprotein comprising a DENV1, DENV2, DENV3 or DENV4 domain I and domain II hinge region as well as a domain III region in a YFV, JEV or WNV E glycoprotein backbone.
In other embodiments, “at least a portion of a dengue virus E protein domain III” (and similar terms) comprises, consists essentially of, or consists of at least about 6, 8, 10, 12, 15, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids, optionally contiguous amino acids, and/or less than about 12, 15, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids, optionally contiguous amino acids, including any combination of the foregoing as long as the lower limit is less than the upper limit.
In representative embodiments, the peptide spacer comprises, consists of, or consists essentially of about 1, 2, 3 or less, 4 or less, 5 or less, 6 or less, 7 or less, 8 or less, 9 or less, 10 or less, 11 or less, 12 or less, 13 or less, 14 or less, 15 or less, 16 or less, 17 or less, 18 or less, 19 or less, 20 or less, 25 or less, 30 or less, 35 or less, 40 or less, 45 or less, 50 or less, 55 or less, 60 or less, 70 or less, 80 or less, 90 or less or 100 or less amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 1 to about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 3 to about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 4 to about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 5 to about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 10 to about 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 15 to about 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids. In embodiments, the peptide spacer comprises, consists of, or consists essentially of about 20 to about 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90 or 100 amino acids.
In embodiments, the spacer brings the E protein domain I/II hinge region and the domain III region involved in the quaternary epitope about 10 or less, 15 or less, 20 or less, 25 or less, 30 or less, 35 or less, 40 or less, 45 or less, 50 or less, 60 or less or 70 or less angstroms apart. In embodiments, the spacer brings the E protein domain hinge region and the domain III region involved in the quaternary epitope about 10 to 20, 25, 30, 35, 40, 45, 50, 60 or 70 angstroms apart. In embodiments, the spacer brings the E protein domain I/II hinge region and the domain III region involved in the quaternary epitope about 15 to 25, 30, 35, 40, 45, 50, 60 or 70 angstroms apart. In embodiments, the spacer brings the E protein domain I/II hinge region and the domain III region involved in the quaternary epitope about 20 to 30, 35, 40, 45, 50, 60 or 70 angstroms apart. In embodiments, the spacer brings the E protein domain I/II hinge region and the domain III region involved in the quaternary epitope about 25 to 35, 40, 45, 50, 60 or 70 angstroms apart. In embodiments, the spacer brings the E protein domain I/II hinge region and the domain III region involved in the quaternary epitope about 30 to 40, 45, 50, 60 or 70 angstroms apart. In embodiments, the spacer brings the E protein domain I/II hinge region and the domain III region involved in the quaternary epitope about 35 to 45, 50, 60 or 70 angstroms apart.
The peptide spacer can be derived in whole or in part from a native E protein, or can be partially or wholly synthetic.
In embodiments, the peptide spacer forms a secondary structure, e.g., a beta-sheet, beta-barrel and/or an alpha helical structure. In embodiments, the peptide spacer comprises one or more disulfide bonds (e.g., cystine residues).
It is known in the art that many attempts to produce dengue virus vaccines result in the production of non-neutralizing antibodies, which may increase the likelihood of pathology upon subsequence exposure to natural infection or vaccine. Another approach to provide an engineered epitope is to deliver all or a portion of the dengue virus E protein incorporated into another flavivirus particle or VLP. In representative embodiments, the heterologous flavivirus is West Nile virus or Yellow Fever virus. Portions of the E protein can be grafted into the E protein of the heterologous flavivirus backbone, e.g., to reduce the generation of non-neutralizing dengue virus antibodies to non-neutralizing epitopes present in the dengue virus E protein and/or other dengue virus structural proteins.
Thus, a chimeric flavivirus or chimeric flavivirus VLP can present the quaternary dengue virus epitope in proper conformation while reducing the generation of non-neutralizing antibodies to other portions of the dengue virus E protein and/or other structural proteins that are not presented in the chimeric flavivirus or flavivirus VLP.
Thus, as another aspect, the invention provides a chimeric flavivirus particle or chimeric flavivirus VLP comprising a chimeric flavivirus E protein, the chimeric flavivirus E protein comprising a dengue virus E protein domain I and domain II hinge region and at least a portion of the dengue virus E protein domain III. In embodiments of the invention, the dengue virus E protein region(s) are substituted for the corresponding region(s) of the heterologous flavivirus E protein. In embodiments, amino acid sequences from the dengue virus prM protein and/or the dengue virus C protein are not incorporated into the chimeric flavivirus or chimeric flavivirus VLP.
In some embodiments of the invention the individual and conformational epitopes of the flavivirus E glycoprotein or dengue virus E glycoprotein can be presented on a synthetic backbone or support structure so that the epitopes within the synthetic backbone or support structure mimic the conformation and arrangement of the epitopes within the structure of the E glycoprotein, virus particle or VLP.
In still further embodiments of the invention, the present invention provides peptide mimitopes (see, Meloen et al. (2000) J. Mol. Recognit. 13, 352-359) that mimic the individual and conformational epitopes of the E glycoproteins of the invention. Mimitopes may be identified using any technique known in the art, such as by surface stimulation, random peptide libraries or phage display libraries, using an antibody or antibodies to the individual and conformational epitopes of the E glycoproteins of the invention.
The invention further provides a nucleic acid (e.g., isolated nucleic acid) encoding a dengue virus epitope or a polypeptide of the invention.
The invention further provides a nucleic acid (e.g., an isolated nucleic acid) encoding a chimeric flavivirus VLP or a viral coat of a chimeric flavivirus particle of the invention.
Also provided are vectors encoding the nucleic acids of the invention.
Also provided are cells comprising the vectors, nucleic acids, dengue virus epitopes, polypeptides, chimeric flavivirus VLPs or chimeric flavivirus particles of the invention.
The invention also provides immunogenic compositions comprising the cells, vectors, nucleic acids, dengue virus epitopes, polypeptides, chimeric flavivirus VLPs or chimeric flavivirus particles of the invention. In embodiments, the immunogenic composition is monovalent. In embodiments, the immunogenic composition is multivalent (e.g., tetravalent) for dengue virus serotypes DEN1, DEN2, DEN 3 and/or DEN4.
The invention encompasses methods of producing an immune response to a dengue virus in a subject, the method comprising administering to the subject an effective amount of a dengue virus epitope, a polypeptide, a chimeric flavivirus VLP or chimeric flavivirus particle, nucleic acid, vector, cell or immunogenic composition of the invention.
Further, the present invention can advantageously be practiced to induce an immune response against one, two, three or all four of DEN1, DEN2, DEN3 and DEN4. It is well-known in the art that effective and safe multivalent dengue vaccines have been a challenge to design because of the problem of interference among serotypes. For example, the immune response may be predominantly directed against only some of the target serotypes. Multiple vaccinations are then required to try to achieve a response against all serotypes; however, in the case of dengue virus, this approach can be dangerous because repeated administrations to a subject with pre-existing antibodies can lead to dengue hemorrhagic fever.
A still further aspect of the invention is a method of treating a dengue virus infection, comprising administering to the subject an effective amount of a dengue virus epitope, a polypeptide, a chimeric flavivirus VLP or chimeric flavivirus particle, nucleic acid, vector, cell, or immunogenic composition of the invention.
A still further aspect of the invention is a method of preventing a dengue virus infection, comprising administering to the subject an effective amount of a dengue virus epitope, a polypeptide, a chimeric flavivirus VLP or chimeric flavivirus particle, nucleic acid, vector, cell, or immunogenic composition of the invention.
A still further aspect of the invention is a method of protecting a subject from the effects of dengue virus infection, comprising administering to the subject an effective amount of a dengue virus epitope, a polypeptide, a chimeric flavivirus VLP or chimeric flavivirus particle, nucleic acid, vector, cell, or immunogenic composition of the invention.
The invention can also be practiced to identify antibodies that bind (e.g., specifically bind) to the quaternary dengue virus epitope, e.g., to identify neutralizing antibodies to a dengue virus. For example, the invention can be employed as a diagnostic to qualitatively determine if a vaccine candidate is inducing neutralizing antibodies. In general, due to the abundance of non-neutralizing antibodies induced by many candidate dengue virus vaccines, antibody titers alone without further characterization of the antibody specificity provides incomplete information.
In representative embodiments, the invention provides a method of detecting a neutralizing antibody to a dengue virus, the method comprising the step of determining whether an antibody binds to a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention, wherein binding by the antibody to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus indicates that the antibody is a neutralizing antibody to a dengue virus.
In further representative embodiments, the invention provides a method of identifying a neutralizing antibody to a dengue virus, the method comprising: (a) contacting an antibody to a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention; and (b) determining if the antibody binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus; wherein binding by the antibody to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus indicates that the antibody is a neutralizing antibody to a dengue virus.
The invention also provides a method of identifying a neutralizing antibody to a dengue virus, the method comprising: (a) contacting an antibody to a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention; (b) determining if the antibody binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus; and (c) identifying the antibody as a neutralizing antibody to a dengue virus if the antibody binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus.
Still further, the invention provides a method of identifying an immunogenic composition that induces a neutralizing antibody to a dengue virus in a subject, the method comprising the step of determining whether a biological sample obtained from a subject that has been administered the immunogenic composition comprises an antibody that binds to a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention, wherein if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus, it indicates that the immunogenic composition induces a neutralizing antibody to a dengue virus in the subject.
The invention also provides a method of identifying an immunogenic composition that induces a neutralizing antibody to a dengue virus in a subject, the method comprising: (a) contacting a biological sample from a subject that has been administered the immunogenic composition with a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention; and (b) determining if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus; wherein if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus, it indicates that the immunogenic composition induces a neutralizing antibody to a dengue virus in the subject.
In yet another embodiment, the invention provides a method of identifying an immunogenic composition that induces a neutralizing antibody to a dengue virus in a subject, the method comprising: (a) contacting a biological sample from a subject that has been administered the immunogenic composition with a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention; (b) determining if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus; and (c) identifying the immunogenic composition as inducing a neutralizing antibody to a dengue virus in the subject if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus.
In other representative embodiments, the invention provides a method of identifying an immunogenic composition that induces a neutralizing antibody to a dengue virus in a subject, the method comprising: (a) administering an immunogenic composition comprising a dengue virus antigen to a subject in an amount effective to induce antibodies against the dengue virus antigen; (b) contacting a biological sample from the subject with a dengue virus epitope, a polypeptide, or a chimeric VLP or chimeric flavivirus of the invention; (c) determining if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or chimeric flavivirus; and (d) identifying the immunogenic composition as inducing a neutralizing antibody to a dengue virus in the subject if the biological sample comprises an antibody that binds to the dengue virus epitope, the polypeptide, the chimeric VLP or the chimeric flavivirus.
There are four serotypes of dengue virus (DEN1, DEN2, DEN3 and DEN4). Within each serotype there are a number of different strains or genotypes. The dengue virus antigens and epitopes of the invention can be derived from any dengue virus, including all serotypes, strains and genotypes, now known or later identified.
In embodiments of the invention, the dengue virus is UNC1017 strain (DEN1), West Pacific 74 strain (DEN1), S16803 strain (DEN2), UNC2005 strain (DEN2), UNC3001 strain (DEN3), UNC3043 (DEN3 strain 059.AP-2 from Philippines, 1984), UNC3009 strain (DEN3, D2863, Sri Lanka 1989), UNC3066 (DEN3, strain 1342 from Puerto Rico 1977), CH53489 strain (DEN3), UNC4019 strain (DEN4), or TVP-360 (DEN4).
In embodiments of the invention, an “immunogenically active fragment” of a dengue virus polypeptide (e.g., the E protein, or the EDI, EDII or EDIII domain) comprises, consists essentially of or consists of at least about 6, 8, 10, 12, 15, 20, 30, 50, 75, 100, 125, 150, 200, 250, 300, 350, 400, 450 or more amino acids, optionally contiguous amino acids, and/or less than about 495, 475, 450, 425, 400, 350, 300, 250, 200, 150, 100, 75 or 50 amino acids, optionally contiguous amino acids, including any combination of the foregoing as long as the lower limit is less than the upper limit, and the “immunogenically active fragment” induces an immune response (e.g., IgG and/or IgA that react with the native antigen), optionally a protective immune response, against dengue virus in a host and induces the production of antibodies that specifically bind to the quaternary dengue virus epitope newly identified by the inventors.
The term “epitope” as used herein means a specific amino acid sequence that, when present in the proper conformation, provides a reactive site for an antibody (e.g., B cell epitope) or T cell receptor (e.g., T cell epitope).
Portions of a given polypeptide that include a B-cell epitope can be identified using any number of epitope mapping techniques that are known in the art. (See, e.g., Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66, Glenn E. Morris, Ed., 1996, Humana Press, Totowa, N.J.). For example, linear epitopes can be determined by, e.g., concurrently synthesizing large numbers of peptides on solid supports, the peptides corresponding to portions of the protein molecule, and reacting the peptides with antibodies while the peptides are still attached to the supports. Such techniques are known in the art and described in, e.g., U.S. Pat. No. 4,708,871; Geysen et al. (1984) Proc. Natl. Acad. Sci. USA 81:3998-4002; Geysen et al. (1986) Molec. Immunol. 23:709-715.
Similarly, conformational epitopes can be readily identified by determining spatial conformation of amino acids such as by, e.g., x-ray crystallography and 2-dimensional nuclear magnetic resonance. Antigenic regions of proteins can also be identified using standard antigenicity and hydropathy plots, such as those calculated using, e.g., the Omiga version 1.0 software program available from the Oxford Molecular Group. This computer program employs the Hopp/Woods method (Hopp et al., Proc. Natl. Acad. Sci USA (1981) 78:3824-3828) for determining antigenicity profiles and the Kyte-Doolittle technique (Kyte et al., J. Mol. Biol. (1982) 157:105-132) for hydropathy plots.
Generally, T-cell epitopes that are involved in stimulating the cellular arm of a subject's immune system are short peptides of about 8-25 amino acids. A common way to identify T-cell epitopes is to use overlapping synthetic peptides and analyze pools of these peptides, or the individual ones, that are recognized by T cells from animals that are immune to the antigen of interest, using, for example, an enzyme-linked immunospot assay (ELISPOT). These overlapping peptides can also be used in other assays such as the stimulation of cytokine release or secretion, or evaluated by constructing major histocompatibility (MHC) tetramers containing the peptide. Such immunogenically active fragments can also be identified based on their ability to stimulate lymphocyte proliferation in response to stimulation by various fragments from the antigen of interest.
The present invention can be practiced for prophylactic, therapeutic and/or diagnostic purposes. In addition, the invention can be practiced to produce antibodies for any purpose, such as diagnostic or research purposes, or for passive immunization by transfer to another subject.
The present invention further provides a kit comprising one or more compositions of this invention. It would be well understood by one of ordinary skill in the art that the kit of this invention can comprise one or more containers and/or receptacles to hold the reagents (e.g., antibodies, antigens, nucleic acids) of the kit, along with appropriate buffers and/or diluents and/or other solutions and directions for using the kit, as would be well known in the art. Such kits can further comprise adjuvants and/or other immunostimulatory or immunomodulating agents, as are well known in the art.
The compositions and kits of the present invention can also include other medicinal agents, pharmaceutical agents, carriers, diluents, immunostimulatory cytokines, etc. Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art.
Administration to a subject can be by any route known in the art. As non-limiting examples, the route of administration can be by inhalation (e.g., oral and/or nasal inhalation), oral, buccal (e.g., sublingual), rectal, vaginal, topical (including administration to the airways), intraocular, transdermal, by parenteral (e.g., intramuscular [e.g., administration to skeletal muscle], intravenous, intra-arterial, intraperitoneal and the like), subcutaneous (including administration into the footpad), intradermal, intrapleural, intracerebral, and/or intrathecal routes.
The epitopes, polypeptides, VLPs and viral vectors of the invention can be delivered per se or by delivering a nucleic acid (e.g., DNA) that encodes the same.
Immunomodulatory compounds, such as immunomodulatory chemokines and cytokines (preferably, CTL inductive cytokines) can be administered concurrently to a subject.
Cytokines may be administered by any method known in the art. Exogenous cytokines may be administered to the subject, or alternatively, a nucleic acid encoding a cytokine may be delivered to the subject using a suitable vector, and the cytokine produced in vivo. In particular embodiments, a viral adjuvant expresses the cytokine.
In embodiments of the invention, multiple dosages (e.g., two, three or more) of a composition of the invention can be administered without detectable pathogenicity (e.g., Dengue Shock Syndrome/Dengue Hemorrhagic Fever).
In embodiments of the invention, the multivalent vaccines of the invention do not result in immune interference, e.g., a balanced immune response is induced against all antigens presented. In embodiments of the invention, the balanced response results in protective immunity against DEN1, DEN2, DEN3 and DEN4.
In embodiments of the invention, the multivalent vaccine can be administered to a subject that has anti-dengue maternal antibodies present.
It should be appreciated that the invention can be embodied in different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the invention to those skilled in the art.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.
As used herein, “a,” “an” or “the” can mean one or more than one. For example, “a” cell can mean a single cell or a multiplicity of cells.
Also as used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).
The term “about,” as used herein when referring to a measurable value such as an amount of dose (e.g., an amount of a fatty acid) and the like, is meant to encompass variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified amount.
As used herein, the transitional phrase “consisting essentially of” means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim, “and those that do not materially affect the basic and novel characteristic(s)” of the claimed invention. See, In re Herz, 537 F.2d 549, 551-52, 190 U.S.P.Q. 461, 463 (CCPA 1976) (emphasis in the original); see also MPEP § 2111.03. Thus, the term “consisting essentially of” when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”
As used herein, the term “nucleic acid” encompasses both RNA and DNA, including cDNA, genomic DNA, synthetic (e.g., chemically synthesized) DNA and chimeras of RNA and DNA. The nucleic acid may be double-stranded or single-stranded. The nucleic acid may be synthesized using nucleotide analogs or derivatives (e.g., inosine or phosphorothioate nucleotides). Such nucleotides can be used, for example, to prepare nucleic acids that have altered base-pairing abilities or increased resistance to nucleases.
As used herein, the term “polypeptide” encompasses both peptides and proteins (including fusion proteins), unless indicated otherwise.
A “fusion protein” is a polypeptide produced when two heterologous nucleotide sequences or fragments thereof coding for two (or more) different polypeptides not found fused together in nature are fused together in the correct translational reading frame.
A “recombinant” nucleic acid, polynucleotide or nucleotide sequence is one produced by genetic engineering techniques.
A “recombinant” polypeptide is produced from a recombinant nucleic acid, polypeptide or nucleotide sequence.
As used herein, an “isolated” polynucleotide (e.g., an “isolated nucleic acid” or an “isolated nucleotide sequence”) means a polynucleotide at least partially separated from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polynucleotide. Optionally, but not necessarily, the “isolated” polynucleotide is present at a greater concentration (i.e., is enriched) as compared with the starting material (e.g., at least about a two-fold, three-fold, four-fold, ten-fold, twenty-fold, fifty-fold, one-hundred-fold, five-hundred-fold, one thousand-fold, ten thousand-fold or greater concentration). In representative embodiments, the isolated polynucleotide is at least about 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more pure.
An “isolated” polypeptide means a polypeptide that is at least partially separated from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polypeptide. Optionally, but not necessarily, the “isolate” polypeptide is present at a greater concentration (i.e., is enriched) as compared with the starting material (e.g., at least about a two-fold, three-fold, four-fold, ten-fold, twenty-fold; fifty-fold, one-hundred-fold, five-hundred-fold, one thousand-fold, ten thousand-fold or greater concentration). In representative embodiments, the isolated polypeptide is at least about 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more pure.
Furthermore, an “isolated” cell is a cell that has been partially or completely separated from other components with which it is normally associated in nature. For example, an isolated cell can be a cell in culture medium and/or a cell in a pharmaceutically acceptable carrier.
The terms “immunogen” and “antigen” are used interchangeably herein and mean any compound (including polypeptides) to which a cellular and/or humoral immune response can be directed. In particular embodiments, an immunogen or antigen can induce a protective immune response against the effects of dengue virus infection.
“Effective amount” as used herein refers to an amount of a vector, nucleic acid, epitope, polypeptide, cell, composition or formulation of the invention that is sufficient to produce a desired effect, which can be a therapeutic and/or beneficial effect. The effective amount will vary with the age, general condition of the subject, the severity of the condition being treated, the particular agent administered, the duration of the treatment, the nature of any concurrent treatment, the pharmaceutically acceptable carrier used, and like factors within the knowledge and expertise of those skilled in the art. As appropriate, an “effective amount” in any individual case can be determined by one of ordinary skill in the art by reference to the pertinent texts and literature and/or by using routine experimentation.
The term “immunogenic amount” or “effective immunizing dose,” as used herein, unless otherwise indicated, means an amount or dose sufficient to induce an immune response (which can optionally be a protective response) in the treated subject that is greater than the inherent immunity of non-immunized subjects. An immunogenic amount or effective immunizing dose in any particular context can be routinely determined using methods known in the art.
The terms “vaccine,” “vaccination” and “immunization” are well-understood in the art, and are used interchangeably herein. For example, the terms vaccine, vaccination or immunization can be understood to be a process or composition that increases a subject's immune reaction to an immunogen (e.g., by providing an active immune response), and therefore its ability to resist, overcome and/or recover from infection (i.e., a protective immune response).
By the term “treat,” “treating” or “treatment of” (and grammatical variations thereof) it is meant that the severity of the subject's condition is reduced, at least partially improved or ameliorated and/or that some alleviation, mitigation or decrease in at least one clinical symptom is achieved and/or there is a delay in the progression of the disease or disorder. In representative embodiments, the term “treat,”, “treating” or “treatment of” (and grammatical variations thereof) refer to a reduction in the severity of viremia and/or a delay in the progression of viremia, with or without other signs of clinical disease.
A “treatment effective” amount as used herein is an amount that is sufficient to treat (as defined herein) the subject. Those skilled in the art will appreciate that the therapeutic effects need not be complete or curative, as long as some benefit is provided to the subject.
The term “prevent,” “preventing” or “prevention of” (and grammatical variations thereof) refer to prevention and/or delay of the onset and/or progression of a disease, disorder and/or a clinical symptom(s) in a subject and/or a reduction in the severity of the onset and/or progression of the disease, disorder and/or clinical symptom(s) relative to what would occur in the absence of the methods of the invention. In representative embodiments, the term “prevent,”, “preventing” or “prevention of” (and grammatical variations thereof) refer to prevention and/or delay of the onset and/or progression of viremia in the subject, with or without other signs of clinical disease. The prevention can be complete, e.g., the total absence of the disease, disorder and/or clinical symptom(s). The prevention can also be partial, such that the occurrence of the disease, disorder and/or clinical symptom(s) in the subject and/or the severity of onset and/or the progression is less than what would occur in the absence of the present invention.
A “prevention effective” amount as used herein is an amount that is sufficient to prevent (as defined herein) the disease, disorder and/or clinical symptom in the subject. Those skilled in the art will appreciate that the level of prevention need not be complete, as long as some benefit is provided to the subject.
The efficacy of treating and/or preventing dengue virus infection by the methods of the present invention can be determined by detecting a clinical improvement as indicated by a change in the subject's symptoms and/or clinical parameters (e.g., viremia), as would be well known to one of skill in the art.
Unless indicated otherwise, the terms “protect,” “protecting,” “protection” and “protective” (and grammatical variations thereof) encompass both methods of preventing and treating dengue virus infection in a subject, whether against one or multiple strains, genotypes or serotypes of dengue virus.
The terms “protective” immune response or “protective” immunity as used herein indicates that the immune response confers some benefit to the subject in that it prevents or reduces the incidence and/or severity and/or duration of disease or any other manifestation of infection. For example, in representative embodiments, a protective immune response or protective immunity results in reduced viremia, whether or not accompanied by clinical disease. Alternatively, a protective immune response or protective immunity may be useful in the therapeutic treatment of existing disease.
An “active immune response” or “active immunity” is characterized by “participation of host tissues and cells after an encounter with the immunogen. It involves differentiation and proliferation of immunocompetent cells in lymphoreticular tissues, which lead to synthesis of antibody or the development of cell-mediated reactivity, or both.” Herbert B. Herscowitz, Immunophysiology: Cell Function and Cellular Interactions in Antibody Formation, in IMMUNOLOGY: BASIC PROCESSES 117 (Joseph A. Bellanti ed., 1985). Alternatively stated, an active immune response is mounted by the host after exposure to immunogens by infection or by vaccination. Active immunity can be contrasted with passive immunity, which is acquired through the “transfer of preformed substances (antibody, transfer factor, thymic graft, interleukin-2) from an actively immunized host to a non-immune host.” Id.
A “subject” of the invention includes any animal susceptible to dengue virus infection. Such a subject is generally a mammalian subject (e.g., a laboratory animal such as a rat, mouse, guinea pig, rabbit, primates, etc.), a farm or commercial animal (e.g., a cow, horse, goat, donkey, sheep, etc.), or a domestic animal (e.g., cat, dog, ferret, etc.). In particular embodiments, the subject is a primate subject, a non-human primate subject (e.g., a chimpanzee, baboon, monkey, gorilla, etc.) or a human. Subjects of the invention can be a subject known or believed to be at risk of infection by dengue virus. Alternatively, a subject according to the invention can also include a subject not previously known or suspected to be infected by dengue virus or in need of treatment for dengue virus infection.
Subjects may be treated for any purpose, such as for eliciting a protective immune response or for eliciting the production of antibodies in that subject, which antibodies can be collected and used for other purposes such as research or diagnostic purposes or for administering to other subjects to produce passive immunity therein, etc.
Subjects include males and/or females of any age, including neonates, juvenile, mature and geriatric subjects. With respect to human subjects, in representative embodiments, the subject can be an infant (e.g., less than about 12 months, 10 months, 9 months, 8 months, 7 months, 6 months, or younger), a toddler (e.g., at least about 12, 18 or 24 months and/or less than about 36, 30 or 24 months), or a child (e.g., at least about 1, 2, 3, 4 or 5 years of age and/or less than about 14, 12, 10, 8, 7, 6, 5, or 4 years of age). In embodiments of the invention, the subject is a human subject that is from about 0 to 3, 4, 5, 6, 9, 12, 15, 18, 24, 30, 36, 48 or 60 months of age, from about 3 to 6, 9, 12, 15, 18, 24, 30, 36, 48 or 60 months of age, from about 6 to 9, 12, 15, 18, 24, 30, 36, 48 or 60 months of age, from about 9 to 12, 15, 18, 24, 30, 36, 48 or 60 months of age, from about 12 to 18, 24, 36, 48 or 60 months of age, from about 18 to 24, 30, 36, 48 or 60 months of age, or from about 24 to 30, 36, 48 or 60 months of age.
In embodiments of the invention, the subject has maternal antibodies to dengue virus.
A “subject in need” of the methods of the invention can be a subject known to be, or suspected of being, infected with, or at risk of being infected with, dengue virus.
Pharmaceutical formulations (e.g., immunogenic formulation) comprising the dengue virus epitopes, polypeptides, chimeric flavivirus VLPs or chimeric flavivirus particles, nucleic acids, vectors, cells or compositions of the invention and a pharmaceutically acceptable carrier are also provided, and can be formulated for administration in a pharmaceutical carrier in accordance with known techniques. See, e.g., Remington, The Science And Practice of Pharmacy (latest edition). In the manufacture of a pharmaceutical composition according to embodiments of the present invention, the composition of the invention is typically admixed with, inter alia, a pharmaceutically acceptable carrier. By “pharmaceutically acceptable carrier” is meant a carrier that is compatible with other ingredients in the pharmaceutical composition and that is not harmful or deleterious to the subject. The carrier may be a solid or a liquid, or both, and is preferably formulated with the composition of the invention as a unit-dose formulation, for example, a tablet, which may contain from about 0.01 or 0.5% to about 95% or 99% by weight of the composition. The pharmaceutical compositions are prepared by any of the well-known techniques of pharmacy including, but not limited to, admixing the components, optionally including one or more accessory ingredients. In certain embodiments, the pharmaceutically acceptable carrier is sterile and would be deemed suitable for administration into human subjects according to regulatory guidelines for pharmaceutical compositions comprising the carrier.
Furthermore, a “pharmaceutically acceptable” component such as a salt, carrier, excipient or diluent of a composition according to the present invention is a component that (i) is compatible with the other ingredients of the composition in that it can be combined with the compositions of the present invention without rendering the composition unsuitable for its intended purpose, and (ii) is suitable for use with subjects as Provided herein without undue adverse side effects (such as toxicity, irritation, and allergic response). Side effects are “undue” when their risk outweighs the benefit provided by the composition. Non-limiting examples of pharmaceutically acceptable components include any of the standard pharmaceutical carriers such as phosphate buffered saline solutions, water, emulsions such as oil/water emulsion, microemulsions and various types of wetting agents.
In some embodiments, the compositions of the invention can further comprise one or more than one adjuvant. The adjuvants of the present invention can be in the form of an amino acid sequence, and/or in the form or a nucleic acid encoding an adjuvant. When in the form of a nucleic acid, the adjuvant can be a component of a nucleic acid encoding the polypeptide(s) or fragment(s) or epitope(s) and/or a separate component of the composition comprising the nucleic acid encoding the polypeptide(s) or fragment(s) or epitope(s) of the invention. According to the present invention, the adjuvant can also be an amino acid sequence that is a peptide, a protein fragment or a whole protein that functions as an adjuvant, and/or the adjuvant can be a nucleic acid encoding a peptide, protein fragment or whole protein that functions as an adjuvant. As used herein, “adjuvant” describes a substance, which can be any immunomodulating substance capable of being combined with a composition of the invention to enhance, improve or otherwise modulate an immune response in a subject.
In further embodiments, the adjuvant can be, but is not limited to, an immunostimulatory cytokine (including, but not limited to, GM/CSF, interleukin-2, interleukin-12, interferon-gamma, interleukin-4, tumor necrosis factor-alpha, interleukin-1, hematopoietic factor flt3L, CD40L, B7.1 co-stimulatory molecules and B7.2 co-stimulatory molecules), SYNTEX adjuvant formulation 1 (SAF-1) composed of 5 percent (wt/vol) squalene (DASF, Parsippany, N.J.), 2.5 percent Pluronic, L121 polymer (Aldrich Chemical, Milwaukee), and 0.2 percent polysorbate (Tween 80, Sigma) in phosphate-buffered saline. Suitable adjuvants also include an aluminum salt such as aluminum hydroxide gel (alum), aluminum phosphate, or algannmulin, but may also be a salt of calcium, iron or zinc, or may be an insoluble suspension of acylated tyrosine, or acylated sugars, cationically or anionically derivatized polysaccharides, or polyphosphazenes.
Other adjuvants are well known in the art and include without limitation MF 59, LT-K63, LT-R72 (Pal et al., Vaccine 24(6):766-75 (2005)), QS-21, Freund's adjuvant (complete and incomplete), aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE) and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trealose dimycolate and cell wall skeleton (MPL+TDM+CWS) in 2% squalene/Tween 80 emulsion.
Additional adjuvants can include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl. lipid A (3D-MPL) together with an aluminum salt. An enhanced adjuvant system involves the combination of a monophosphoryl lipid A and a saponin derivative, particularly the combination of QS21 and 3D-MPL as disclosed in PCT publication number WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol as disclosed in PCT publication number WO 96/33739. A particularly potent adjuvant formulation involving QS21 3D-MPL & tocopherol in an oil in water emulsion is described in PCT publication number WO 95/17210. In addition, the nucleic acid compositions of the invention can include an adjuvant by comprising a nucleotide sequence encoding the antigen and a nucleotide sequence that provides an adjuvant function, such as CpG sequences. Such CpG sequences, or motifs, are well known in the art.
An adjuvant for use with the present invention, such as, for example, an immunostimulatory cytokine, can be administered before, concurrent with, and/or within a few hours, several hours, and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, and/or 10 days before and/or after the administration of a composition of the invention to a subject.
Furthermore, any combination of adjuvants, such as immunostimulatory cytokines, can be co-administered to the subject before, after and/or concurrent with the administration of an immunogenic composition of the invention. For example, combinations of immunostimulatory cytokines, can consist of two or more immunostimulatory cytokines, such as GM/CSF, interleukin-2, interleukin-12, interferon-gamma, interleukin-4, tumor necrosis factor-alpha, interleukin-1, hematopoietic factor flt3L, CD40L, B7.1 co-stimulatory molecules and B7.2 co-stimulatory molecules. The effectiveness of an adjuvant or combination of adjuvants can be determined by measuring the immune response produced in response to administration of a composition of this invention to a subject with and without the adjuvant or combination of adjuvants, using standard procedures, as described herein and as known in the art.
In embodiments of the invention, the adjuvant comprises an alphavirus adjuvant as described, for example in U.S. Pat. No. 7,862,829.
Boosting dosages can further be administered over a time course of days, weeks, months or years. In chronic infection, initial high doses followed by boosting doses may be advantageous.
The pharmaceutical formulations of the invention can optionally comprise other medicinal agents, pharmaceutical agents, stabilizing agents, buffers, carriers, diluents, salts, tonicity adjusting agents, wetting agents, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
For injection, the carrier will typically be a liquid. For other methods of administration, the carrier may be either solid or liquid. For inhalation administration, the carrier will be respirable, and is typically in a solid or liquid particulate form.
The compositions of the invention can be formulated for administration in a pharmaceutical carrier in accordance with known techniques. See, e.g., Remington, The Science And Practice of Pharmacy (9^thEd. 1995). In the manufacture of a pharmaceutical composition according to the invention, the VLPs are typically admixed with, inter alia, an acceptable carrier. The carrier can be a solid or a liquid, or both, and is optionally formulated with the compound as a unit-dose formulation, for example, a tablet. A variety of pharmaceutically acceptable aqueous carriers can be used, e.g., water, buffered water, 0.9% saline, 0.3% glycine, hyaluronic acid, pyrogen-free water, pyrogen-free phosphate-buffered saline solution, bacteriostatic water, or Cremophor EL[R] (BASF, Parsippany, N.J.), and the like. These compositions can be sterilized by conventional techniques. The formulations of the invention can be prepared by any of the well-known techniques of pharmacy.
The pharmaceutical formulations can be packaged for use as is, or lyophilized, the lyophilized preparation generally being combined with a sterile aqueous solution prior to administration. The compositions can further be packaged in unit/dose or multi-dose containers, for example, in sealed ampoules and vials.
The pharmaceutical formulations can be formulated for administration by any method known in the art according to conventional techniques of pharmacy. For example, the compositions can be formulated to be administered intranasally, by inhalation (e.g., oral inhalation), orally, buccally (e.g., sublingually), rectally, vaginally, topically, intrathecally, intraocularly, transdermally, by parenteral administration (e.g., intramuscular [e.g., skeletal muscle], intravenous, subcutaneous, intradermal, intrapleural, intracerebral and intra-arterial, intrathecal), or topically (e.g., to both skin and mucosal surfaces, including airway surfaces).
For intranasal or inhalation administration, the pharmaceutical formulation can be formulated as an aerosol (this term including both liquid and dry powder aerosols). For example, the pharmaceutical formulation can be provided in a finely divided form along with a surfactant and propellant. Typical percentages of the composition are 0.01-20% by weight, preferably 1-10%. The surfactant is generally nontoxic and soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, if desired, as with lecithin for intranasal delivery. Aerosols of liquid particles can be produced by any suitable means, such as with a pressure-driven aerosol nebulizer or an ultrasonic nebulizer, as is known to those of skill in the art. See, e.g., U.S. Pat. No. 4,501,729. Aerosols of solid particles can likewise be produced with any solid particulate medicament aerosol generator, by techniques known in the pharmaceutical art. Intranasal administration can also be by droplet administration to a nasal surface.
Injectable formulations can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Alternatively, one can administer the pharmaceutical formulations in a local rather than systemic manner, for example, in a depot or sustained-release formulation.
Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules and tablets of the kind previously described. For example, an injectable, stable, sterile formulation of the invention in a unit dosage form in a sealed container can be provided. The formulation can be provided in the form of a lyophilizate, which can be reconstituted with a suitable pharmaceutically acceptable carrier to form a liquid composition suitable for injection into a subject. The unit dosage form can be from about 1 μg to about 10 grams of the formulation. When the formulation is substantially water-insoluble, a sufficient amount of emulsifying agent, which is pharmaceutically acceptable, can be included in sufficient quantity to emulsify the formulation in an aqueous carrier. One such useful emulsifying agent is phosphatidyl choline.
Pharmaceutical formulations suitable for oral administration can be presented in discrete units, such as capsules, cachets, lozenges, or tables, as a powder or granules; as a solution or a suspension in an aqueous or non-aqueous liquid; or as an oil-in-water or water-in-oil emulsion. Oral delivery can be performed by complexing a compound(s) of the present invention to a carrier capable of withstanding degradation by digestive enzymes in the gut of an animal. Examples of such carriers include plastic capsules or tablets, as known in the art. Such formulations are prepared by any suitable method of pharmacy, which includes the step of bringing into association the protein(s) and a suitable carrier (which may contain one or more accessory ingredients as noted above). In general, the pharmaceutical formulations are prepared by uniformly and intimately admixing the compound(s) with a liquid or finely divided solid carrier, or both, and then, if necessary, shaping the resulting mixture. For example, a tablet can be prepared by compressing or molding a powder or granules, optionally with one or more accessory ingredients. Compressed tablets are prepared by compressing, in a suitable machine, the formulation in a free-flowing form, such as a powder or granules optionally mixed with a binder, lubricant, inert diluent, and/or surface active/dispersing agent(s). Molded tablets are made by molding, in a suitable machine, the powdered protein moistened with an inert liquid binder.
Pharmaceutical formulations suitable for buccal (sub-lingual) administration include lozenges comprising the compound(s) in a flavored base, usually sucrose and acacia or tragacanth; and pastilles in an inert base such as gelatin and glycerin or sucrose and acacia.
Pharmaceutical formulations suitable for parenteral administration can comprise sterile aqueous and non-aqueous injection solutions, which preparations are preferably isotonic with the blood of the intended recipient. These preparations can contain anti-oxidants, buffers, bacteriostats and solutes, which render the composition isotonic with the blood of the intended recipient. Aqueous and non-aqueous sterile suspensions, solutions and emulsions can include suspending agents and thickening agents. Examples of nonaqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
Pharmaceutical formulations suitable for rectal administration are optionally presented as unit dose suppositories. These can be prepared by admixing the active agent with one or more conventional solid carriers, such as for example, cocoa butter and then shaping the resulting mixture.
Pharmaceutical formulations suitable for topical application to the skin preferably take the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. Carriers that can be used include, but are not limited to, petroleum jelly, lanoline, polyethylene glycols, alcohols, transdermal enhancers, and combinations of two or more thereof. In some embodiments, for example, topical delivery can be performed by mixing a pharmaceutical formulation of the present invention with a lipophilic reagent (e.g., DMSO) that is capable of passing into the skin.
Pharmaceutical formulations suitable for transdermal administration can be in the form of discrete patches adapted to remain in intimate contact with the epidermis of the subject for a prolonged period of time. Formulations suitable for transdermal administration can also be delivered by iontophoresis (see, for example, Pharmaceutical Research 3:318 (1986)) and typically take the form of a buffered aqueous solution of the compound(s). Suitable formulations can comprise citrate or bis\tris buffer (pH 6) or ethanol/water and can contain from 0.1 to 0.2M active ingredient.
In embodiments of the invention, the dosage of a virus particle of this invention can be in a range of about 10⁴to about 10⁷plaque forming units (PFUs). In embodiments of this invention, the dosage of a VLP of this invention can be in a range of about 500 micrograms to about 5 milligrams. In embodiments of this invention, the dosage of a protein of this invention can be in a range of about 10° to about 10⁴micrograms+/−adjuvant.
Further, the composition can be formulated as a liposomal formulation. The lipid layer employed can be of any conventional composition and can either contain cholesterol or can be cholesterol-free. The liposomes that are produced can be reduced in size, for example, through the use of standard sonication and homogenization techniques.
The liposomal formulations can be lyophilized to produce a lyophilizate which can be reconstituted with a pharmaceutically acceptable carrier, such as water, to regenerate a liposomal suspension.
The immunogenic formulations of the invention can optionally be sterile, and can further be provided in a closed pathogen-impermeable container.

Example 1: Identification of Human Neutralizing Antibodies that Bind to Complex Epitopes of Dengue Virions

Serum Samples.
Human serum samples were collected from individuals who had experienced a DENV infection during travel to an endemic region. Rhesus macaque (Macaca mulatta) sera were taken from animals vaccinated with a VEEV replicon particle (VRP-rE) expressing 80% of DENV3 E protein. More information is provided in SI Methods.
Virus and rE Proteins.
The DENV1 (West Pac 74), DENV2 (S-16803), DENV3 (CH-53489 and Thailand 95), and DENV4 (TVP-360) strains were used in the present study. All viruses used in the neutralization assays were grown in C6/36 Aedes albopictus mosquito cells at 28° C. and titered on Vero-81 cells as previously described (15). DENV was purified as previously described (42). The rE proteins from each of the four DENV serotypes were purchased from Hawaii Biotech, Inc.
Depletion of DENV-Specific Abs from Human Immune Sera.
Purified DENVs were adsorbed onto 4.0 μm Polybead polystyrene microspheres following the manufacturer's instructions (Polysciences, Inc.). Control beads were adsorbed with BSA instead. Human immune sera were depleted of virus-specific Abs by incubating sera with virus-adsorbed beads at 37° C. Detailed information is given in SI Methods.
Depletion of DENV rE-Specific Abs from Human and Monkey Immune Sera.
DENV rE proteins were covalently conjugated to cyanogen bromide (CNBr)-activated beads following the manufacturer's protocol (Sigma). Control beads were conjugated with the blocking reagent instead of rE protein. DENV rE-specific Abs were depleted by incubating human and rhesus macaque immune sera with rE-conjugated beads at 37° C. Detailed information is given in SI Methods.
Detection of DENV or rE-Binding Abs by ELISA.
ELISAs were conducted as previously described (5). Sera were used at dilutions of 1:40 and 1:25 for the depletion confirmation ELISAs in the virus and rE depletion experiments, respectively. More information is provided in SI Methods.
Detection of rE-Binding by Western Blot.
Detailed information is provided in SI Methods.

SI Methods

Serum Samples.
Human blood donor recruitment and sample collection were in compliance with the Institutional Review Board of the University of North Carolina at Chapel Hill. All individuals were informed, and written consent was obtained before blood donation. The rhesus macaques (˜7 y of age) were vaccinated with a VEEV replicon particle (VRP-rE) expressing amino acids 1-424 of DENV3 E ectodomain (85% of full-length E protein, also designated as E85), boosted at 7 wk. The serum used for the present experiments was collected at 3 wk after the boost.
Depletion of DENV-Specific Abs from Human Immune Sera.
Beads were washed three times with 0.1 M borate buffer (pH 8.5) and incubated with the relevant purified DENV in borate buffer overnight at room temperature (RT). Control beads were incubated overnight with an equivalent amount of BSA. The control and virus-adsorbed beads were blocked with BSA (10 mg/mL) in borate buffer for 30 min at RT three times and washed six times with PBS. Human immune sera were depleted of virus-specific Abs by incubating sera with virus-adsorbed beads for 2 h at 37° C. with end-over-end mixing. Each immune serum was subjected to at least three sequential rounds of depletions before confirming successful removal of the respective Abs by coated (antigen directly coated on plate) and capture (antigen captured by the mouse MAb 4G2) ELISA.
Depletion of DENV rE-Specific Abs from Human and Monkey Immune Sera.
Cyanogen bromide (CNBr)-activated beads were covalently conjugated with rE protein following the manufacturer's protocol (Sigma). CNBr beads were washed four times with distilled water, followed by three additional washes with coupling buffer [0.1M NaHCO₃, 0.5 M NaCl (pH 8.5)]. The relevant DENV rEprotein diluted in coupling buffer was incubated with CNBr-activated beads for 2 h at RT. Control beads were incubated longer with the blocking reagent instead of rE protein. The unreacted groups on the rE-conjugated beads and control beads were blocked and incubated with 0.2 M glycine (pH 8.0), washed three times with coupling buffer, and then washed four times with PBS. Human and rhesus macaque immune sera were incubated with rE conjugated beads for 2 h at 37° C. Each serum sample was subjected to at least three sequential rounds of Ab depletion before confirming successful removal of the respective Abs detectable by coated or capture ELISA.
Detection of DENV or rE-Binding Abs by ELISA.
ELISA plates were coated with either 50 ng per well of intact purified virus or 100 ng per well of rE protein in carbonate buffer (pH 9.6) for 2 h at RT. Plates were blocked with 3% (vol/vol) normal goat sera in Trisbuffered saline (TBS) containing 0.05% (vol/vol) Tween 20 (blocking buffer). Undepleted, control-depleted, and antigen depleted immune serum were diluted in blocking buffer and incubated on plates for 1 h at 37° C. Sera were used at dilutions of 1:40 and 1:25 for the depletion confirmation ELISAs in the virus and rE depletion experiments, respectively. DENV or rE reactive Abs were detected using an alkaline phosphatase-conjugated goat anti-human IgG secondary Ab and paranitrophenyl phosphate substrate as previously described (5).
Detection of rE-Binding Abs by Western Blot.
Purified DENV (700 ng per well) and DENV rE protein (500 ng per well) were diluted with nonreducing SDS sample buffer, loaded onto a 12% polyacrylamide SDS/PAGE gel, and electrophoresed. Viral proteins were transferred onto polyvinylidene fluoride membranes and blocked overnight at 4° C. with 5% (wt/vol) dried nonfat milk. Membrane was then probed with immune sera (diluted 1:1,000) for 1 h at 37° C., washed three times with TBS containing 0.2% (vol/vol) Tween-20, incubated with a goat anti-human IgG-HRP secondary for 1 h at 37° C., washed three times, and developed using ECL substrate.
Measuring DENV Neutralization by Immune Sera and Monoclonal Antibodies.
Neutralizing activity of both immune sera and monoclonal antibodies were measured using a flow cytometry based neutralization assay with U937 monocytic cells stably transfected with dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) as previously described (15). Briefly, virus and antibody mixtures were pre-incubated for 1 hr at 37° C., prior to the addition of DC-SIGN expressing U937 cells (U937+DC-SIGN). After 2 hrs of incubation at 37° C. with virus-antibody immune complexes, cells were washed twice with infection media. Cells were fixed and permeabilized 24 hrs after infection, probed with 2H2 (anti-prM antibody) conjugated to 488 and infected cells quantified using a Guava flow-cytometer (Milipore).
Focus reduction neutralization assays (FRNT) were conducted using Vero-81 cells as described previously (15). Briefly, virus and serially diluted serum were pre-incubated for 1 hr at 37° C., incubated with Vero-81 cells (grown to 80% confluency) for 2 hrs at 37° C. and then overlaid with methylcellulose containing nutrient media. The cells were fixed at either day 3 (for DENV2 and DENV4) or day 4 (for DENV1 and DENV3) and stained for foci using the anti-E MAb, 4G2, and goat anti-mouse HRP and True blue substrate.
Generation of Anti-DENV hMAbs.
Supernatants from EBV-transformed lymphoblastoid cell lines were screened for binding to DENV by ELISA and, in some cases, tested for neutralization of DENV using a flow cytometry-based assay. Positive wells were fused with HMMA2.5 myeloma cells to generate hybridoma lines as previously described (33, 43). Hybridoma lines then were biologically cloned and grown in serum-free medium (no. 12045084, Gibco Hybridoma-SFM; Invitrogen), and hMAbs were purified using protein G chromatography.
Generation and Characterization of hMAb Neutralization Escape Mutant Viruses.
Virus-Ab mixtures were added to Vero cells and passaged every 3-5 d in the presence of Ab to enrich for escape mutant viruses. Virus growth in the presence of Ab was monitored by quantitative RT-PCR and by immunofluorescent detection of DENV antigens in cell monolayers. Following four to six passages under Ab selection, the capsid, prM, and E genes of the escape variants were amplified by RT-PCR and sequenced to identify mutations associated with the Ab escape phenotype.
Statistical Analysis.
Sigmoidal binding and neutralization curves were compared between undepleted, control-depleted, and virus-depleted or rE-depleted groups using a one-way ANOVA analysis, followed by a Tukey multiple comparison test at P<0.05. The one-dilution binding data (represented in bar charts) for control-depleted and virus-depleted or rE-depleted samples were compared using an unpaired Student t test of means. All statistical analyses were conducted using GraphPad Prism4.
Depletion of Homologous DENV-Specific Abs from Immune Sera.
Studies were undertaken to characterize Abs in human immune sera responsible for potent and long-term neutralization of the homologous virus serotype. We assembled a panel of eight immune sera from healthy volunteers who had been exposed to primary DENV2 or DENV3 infections ˜2-9 yrs before blood collection (Table 4). Human serum from individuals lacking a past history of DENV infections (confirmed by ELISA and neutralization assays) was used as a negative control.
To define the Ab subpopulation in immune sera responsible for DENV neutralization, we developed a bead-based technique to fractionate DENV-specific Abs in immune sera. Polystyrene beads coated with virions of the homologous serotype were incubated with immune sera at 37° C. to deplete DENV-binding Abs. Untreated and control-depleted serum samples bound to whole virus from each of the four DENV serotypes by ELISA and efficiently neutralized DENV (FIG. 1, Panel A and FIG. 1, Panel B). Serum samples depleted using beads coated with the homologous DENV displayed greatly reduced binding and neutralization of DENV (FIG. 1, Panel A and FIG. 1, Panel B), indicating that beads coated with the homologous serotype successfully removed most DENV-specific Abs from immune sera.
Depletion of Heterologous DENV-Specific Abs from Immune Sera.
Next, we assessed the contribution of DENV cross-reactive Abs in immune sera to virus binding and neutralization. We used polystyrene beads coated with virus of a heterologous serotype (a serotype that has not infected the DENV-immune subject) to deplete cross-reactive Abs from primary immune sera (FIG. 1 and Table 1). Depletion of primary DENV2-immune sera with DENV3-coated beads led to the removal of all cross-reactive Abs, with the remaining Abs binding to DENV2 in a type-specific manner (FIG. 1, Panel C). Reciprocal depletion of primary DENV3-immune sera with DENV2-coated beads removed all binding to DENV2 and DENV4 but not to DENV3 and, to a lesser extent, DENV1 (FIG. 1, Panel E). This residual DENV1-binding signal may be attributable to Abs targeting sub-complex epitopes that are preferentially shared between DENV1 and DENV3 (11, 18, 36). Removal of cross-reactive Abs from primary immune sera did not change the capacity of the sera to neutralize the virus responsible for infection (FIG. 1, Panel D and FIG. 1, Panel F, FIG. 4, and Table 1). These results demonstrate that the DENV-specific human Ab response consists of both cross-reactive and type-specific Abs. Although the serotype cross-reactive Abs were abundant, in the samples we analyzed, their contribution to neutralization was negligible. Thus, type-specific Abs appear to be primarily responsible for neutralizing the homologous serotype.
Depletion of DENV Recombinant E Protein-Binding Abs from Immune Sera.
The organization of DENV E protein dimers on the surface of the infectious virus has been modeled using crystal structures of DENV recombinant E (rE) and cryo-EM reconstructions of the virion (16, 17, 22, 44). Furthermore, neutralizing mouse MAbs have been mapped extensively to the rE protein, and DENV subunit vaccines using the rE protein are currently being developed (3, 4, 10, 11, 35-37, 39). We next assessed whether epitopes targeted by neutralizing Abs in human immune sera were preserved on the rE protein. DENV rE protein that was covalently coupled to agarose beads was used to deplete Abs in immune sera. Sera were incubated with either control beads or homologous rE-conjugated beads at 37° C. The structure of DENV rE on the beads was confirmed to be conformationally preserved, and rE dimers were confirmed to be intact by successfully depleting mouse MAbs previously mapped to the fusion loop (MAb 4G2), EDIII (MAb 9F16) (36), and E dimer interface (MAbs DV2-10, DV2-46, and DV2-58) (35) (FIG. 5). We also titrated the amount of rE protein on the beads required to deplete rE-binding Abs efficiently from immune sera (FIG. 6). Both untreated and control-depleted immune sera bound to rE from all four serotypes, but the binding was greatest for the homologous serotype (FIG. 2, Panel A and FIG. 2, Panel B). Depletion of primary immune sera using homologous rE ablated binding to rE from each of the four serotypes (FIG. 2, Panel A and FIG. 2, Panel B). Successful depletion of rE-binding Abs was also confirmed by Western blot, where rE and solubilized virions were used as the antigen on the blot (FIG. 2, Panel C). By Western blot, we could not detect binding to rE protein (which is missing 20% of the native protein at the C terminus) or to full-length E protein from the virus (FIG. 2, Panel C). These results established that beads coated with the rE from the homologous serotype efficiently removed all Abs recognizing purified rE protein. We also measured the relative proportion of virion-binding Abs in human immune sera that bound to rE by comparing the binding of untreated, control-depleted, and rE-depleted sera with the homologous virus by ELISA. Results demonstrated an approximate 45±7% reduction in DENV binding following the removal of rE-binding Abs (FIG. 7 and Table 5), indicating that approximately half of the DENV-specific Abs in primary immune sera recognized the intact virus but not rE protein.
Next, we assessed the neutralizing activity of six immune sera depleted of rE-binding Abs. Unexpectedly, four of the six immune sera displayed no loss of neutralization potency after removal of rE-binding Abs (FIG. 2, Panel D and FIG. 2, Panel E and Table 2). One of the three primary DENV2-immune sera and all three of the primary DENV3-immune sera tested displayed no significant loss of neutralization against the homotypic virus after removal of rE-specific Abs. In contrast, two of the three primary DENV2-immune sera displayed a statistically significant two- to threefold drop (P<0.05) in the 50% neutralization (Neut₅₀) titer when rE-specific Abs were removed (Table 2). Sera from rhesus macaques (Macaca mulatta) immunized with Venezuelan equine encephalitis virus (VEEV) replicons expressing DENV3 E85 protein were used as a positive control in these experiments. These animals should develop neutralizing Abs that bind to rE protein; accordingly, rE-coated beads removed >98% of the neutralizing Abs from these vaccine sera (FIG. 2, Panel F). We conclude that although there was some variation among human immune sera in the contribution of rE-reactive Abs to homotypic DENV neutralization, a large fraction of DENV neutralizing Abs in humans consists of neutralizing Abs that bind to intact virions but not the rE protein.
Characterization of hMAbs That Strongly Neutralize DENV. As an alternate approach to identify neutralizing viral epitopes targeted by DENV-immune individuals, we generated a panel of hMAbs that strongly neutralized DENV. These Abs were generated by transforming memory B cells from DENV-immune subjects with EBV and generating hMAbs by electro-fusion as previously described (33). Because strongly neutralizing hMAbs comprise a minor fraction of the total hMAbs isolated from immune subjects (2, 6, 7), we used a two-step screen to isolate strongly inhibitory Abs: We first identified Abs that bound to DENV virions and then tested them for neutralizing activity. We isolated three strongly neutralizing type-specific hMAbs (Neut₅₀value <0.2 μg/mL), designated 1F4, 2D22, and 5J7, that inhibited infection of DENV1, DENV2, and DENV3, respectively. Two of these hMAbs bound to the intact virus but not to rE (Table 3).
Generation of DENV Mutants That Escape Neutralization by hMAbs.
To map the epitopes engaged by neutralizing hMAbs, we subjected the appropriate DENV serotype to Ab pressure and selected for neutralization escape mutant viruses in vitro. DENV1, DENV2, or DENV3 was passaged several times under varying concentrations (0.2-10 μg/mL) of the neutralizing hMAb 1F4, 2D22, or 5J7, respectively. The original WT virus was passaged in parallel in the absence of hMAb treatment. Structural genes of the mutant and WT viruses were sequenced and compared to identify the mutation(s) responsible for neutralization escape. We successfully isolated two escape mutants against DENV1 type-specific MAb 1F4, with two independent single-nucleotide mutations resulting in amino acid changes at position 274 (G→E) in the DI-DII hinge and 47 (K→E) in DI of the E protein (FIG. 3, Panel A and FIG. 3, Panel D) that conferred loss of neutralization. K47 and G274 are located 13.2 Å apart and likely comprise part of the same 1F4 epitope. For the DENV2-specific neutralizing hMAb 2D22, we isolated one mutant with an EDIII mutation at residue 323 (R→G) that resulted in neutralization escape (FIG. 3, Panel B and FIG. 3, Panel E). Selection with the neutralizing DENV3 specific hMAb 5J7 resulted in an escape mutant with a lysine insertion in the E DI-DII hinge region between the amino acid residues Q269 and N270 (FIG. 3, Panel C and FIG. 3, Panel F). All the mutated residues are surface exposed on the structure of the E protein dimer and within the footprint of a complex epitope described for an hMAb (CR4354) that strongly neutralized West Nile virus (WNV) (14, 34) (FIG. 3, Panel G and FIG. 3, Panel H and Table 3).

TABLE 1

Homologous DENV serotype neutralization titers of immune sera
depleted of cross-reactive Abs from subjects following primary injection

	Reciprocal of 50% neutralization titer against the
	homologous virus (SEM)^a,b

Infection	Sample		Control	Cross-reactive
Serotype	ID	Undepleted	depleted	Ab depleted

Primary	001	2600	1650	1412
DENV2		(2040-2700)	(1100-1650)	(1060-1600)
	013	350	320	420
		(260-470)	(260-380)	(370-550)
	019	1202	1047	1000
		(1000-1550)	(930-1580)	(800-1420)
	031	1150	790	640
		(1000-1310)	(650-950)	(540-740)
Primary	003	250	210	300
DENV3		(230-350)	(160-260)	(250-360)
	011	320	300	252
		(265-390)	(260-380)	(211-300)
	118	628	720	618
		(510-770)	(610-860)	(500-750)

^aData is representative of experiments repeated at least thrice for each serum sample. The flow-based neutralization assay using U937 cells stably expressing DC-SIGN (U937 + DC-SIGN) was used to generate the reciprocal Neut₅₀values. The Neut₅₀values of undepleted, control depleted and cross-reactive antibody depleted sera were compared for each serum by one-way ANOVA analysis. No statistical significance was found between control depleted and cross-reactive depleted groups for any of the tested sera.
^bStandard error of mean (SEM) for reciprocal Neut₅₀values were calculated from the sigmoidal neutralization curves using GraphPad Prism4 and given in parenthesis.

TABLE 2

Homologous DENV serotype neutralization titers of primary immune sera
depleted of rE-binding Abs

	Reciprocal of 50% Neutralization titer against the
	homologous virus (SEM)^a

Infection	Sample		Control
Serotype	ID	Undepleted	depleted	rE depleted

Primary	001^b	660	850	260
DENV2		(510-840)	(690-950)	(210-310)
	019^c	1250	1120	500
		(1010-1500)	(950-1350)	(400-600)
	031	1020	860	900
		(790-1300)	(670-1150)	(690-1190)
Primary	003	180	225	215
DENV3		(155-250)	(210-310)	(150-220)
	105	180	200	160
		(140-235)	(160-275)	(130-185)
	118	1580	1480	1120
		(1180-2020)	(1200-1790)	(900-1400)

^aData is representative of experiments repeated at least thrice for each serum sample. Standard errors of mean (SEM) for reciprocal Neut₅₀values were calculated from the sigmoidal neutralization curves using GraphPad Prism4 and are given in parenthesis.
^bThere was a statistically significant difference between the undepleted/control depleted and rE depleted groups for sample by a one-way ANOVA analysis followed by a Tukey's multiple comparison test at P < 0.01.
^cThere was a statistically significant difference between the undepleted and rE depleted groups when analyzed by a one-way ANOVA at P < 0.05.

TABLE 3

Binding and neutralization properties of strongly neutralizing hmAbs

	Analogous
	residue in WNV

Binding (2 μg/ml)^a

Neut₅₀titer (μg/ml)^d

Mutation

(Comparison to

MAbs

Virus

rE

EDIII

prM^c

DENV1

DENV2

DENV3

DENV4

Escape mutant

Escape Mutation

Location

CR4354 epitope)^e

1F4

Type-Specific

−

0.11

>10

1

G274E

DI-DII

276

(DENV1)

hinge

(Contact site)

2

K47E

DI

49

(Contact site)

2D22^b

Type-Specific

−

>10

0.08

>10

3

R323G

DIII

326

(DENV2)

(Near contact

site 328)

5J7^b

Type-Specific

+

−

>10

0.10

>10

4

Q269_N270insK

DI-DII

Before 274

(DENV3)

hinge

(near contact

site 276)

^aBinding of Human MAbs (at 2 μg/ml) to DENV antigens were measured by ELISA.

^bBinding and neutralization properties of 2D22 and 5J7 were taken from previous study (32).

^cBinding to prM was determined by western blot analysis.

^dNeut₅₀values were generated using the flow-based neutralization assay with U937-DC-SIGN cells. Values in bold indicate the lowest Neut₅₀concentration and the most neutralization sensitive serotype for each MAb.

^eComparison of the escape mutations generated against 1F4, 2D22 and 5J7 to the CR4354 epitope in WNV (14, 38)

TABLE 4

Panel of late convalescent DENV-immune sera from individuals
with past primary DENV2 or DENV3 infection

				DENV Neutralization^b
			Interval between	(FRNT₅₀reciprocal titer)
Sample	Location of	Year of	infection and	DENV serotype	Infecting

ID	Infection	Infection	sample collection		1	2	3	4	Serotype

001^a	Sri Lanka	1996	9 years	<20	271	<20	42	Primary
013^a	South Pacific	1997	8 years	178	>1280	65	140	DENV2
019	Thailand	1997	8 years	95	>1280	120	105
031	South Pacific	1997	8 years	28	>320	88	167
003^a	Thailand	2001	4 years	30	87	338	<20	Primary
011^a	El Salvador	1998	7 years	84	124	1032	169	DENV3
105	Thailand	2002	8 years	<20	<20	210	<20
118	Nicaragua	2009	1.5 years	60	32	980	76

^aThe FRNT₅₀values for these serum samples were reported in a previous study (42).
^bFRNT₅₀values in bold signify the highest 50% neutralization reciprocal titers for each serum sample.

TABLE 5

Binding properties of DENV-immune sera with and without
rE-binding Abs to the homologous virus serotype

	50% Reciprocal binding titers to the
	homologous virus (SEM)^a

Infection	Sample		Control	Homotypic rE
Serotype	ID	Undepleted	depleted	Depleted^d

Primary	001^b	280 (260-290)	310 (290-335)	133	(130-140)
DENV2	031^b	445 (415-475)	455 (435-475)	260	(240-275)^b
Primary	003^b	216 (205-225)	190 (180-200)	108	(105-115)^b
DENV3	105^b	60 (53-66)	63 (60-68)	37^b	(34-42)
	118^c	440 (400-490)	350 (325-375)	265^c	(250-280)

^aData representative of experiments repeated at least twice for each serum sample. Standard error of mean for each reciprocal 50% reciprocal binding titer (EC₅₀) given in parentheses.
^bThere is a statistically significant difference between the control depleted and rE depleted groups by a one way ANOVA analysis followed by a Tukey's multiple comparison test at P < 0.001.
^cThere is a statistically significant difference between the control depleted and rE depleted group when analyzed by a one way ANOVA at P < 0.05.
^dThe rE-reactive antibodies account for about 45 ± 7% of the total homotypic virus binding antibodies.

TABLE 6

Amino acid residues of the DI-
DII hinge region and DIII region of dengue
virus E glycoproteins of DENV1, DENV2,
DENV3, DENV4 and corresponding regions
of YFV and JEV. Amino acid numbering is
based on amino acid sequences shown in the
sequence alignment in FIG. 11.

	Epitope	Amino acid residues

	DI-DII hinge of E	DENV1, 2, 3, 4: AA 47-59
	protein	YFV: AA 47-59
		JEV: AA 47-59
		DENV1, 2, 3, 4: AA 124-133
		YFV: AA 124-133
		JEV: AA124-133
		DENV3: AA 199-222
		DENV1, 2, 4: AA 201-224
		YFV: AA 198-220
		JEV: AA 206-228
		DENV3: AA 269-278
		DENV1, 2, 4: AA 271-280
		YFV: AA 265-278
		JEV: AA 273-282
	DIII of E protein	DENV3: AA 305-308
		DENV1, 2, 4: AA 307-310
		YFV: AA305-308
		JEV: AA 309-312
		DENV3: AA 323-325
		DENV1, 2, 4: AA 325-327
		YFV: AA 323-325
		JEV: AA327-329
		DENV3: AA 359-362
		DENV1, 2, 4: AA 361-364
		YFV: AA 359-362
		JEV: AA 364-369
		DENV3: AA 382-383
		DENV1, 2, 4: AA 384-385
		YFV: AA 382-383
		JEV: AA 389-390

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35. Sukupolvi-Petty, S., S. K. Austin, M. Engle, J. D. Brien, K. A. Dowd, K. L. Williams, S. Johnson, R. Rico-Hesse, E. Harris, T. C. Pierson, D. H. Fremont, and M. S. Diamond. 2010. Structure and function analysis of therapeutic monoclonal antibodies against dengue virus type 2. J Virol 84:9227-39.
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Example 2: Escape Mutant Studies

Infection with one DENV serotype elicits protective antibodies against that serotype, but also cross-reactive with other DENV serotypes. These cross-reactive antibodies enhance the risk of severe dengue on second infection in that individual with another DENV serotype. The envelope protein (E) is the major antigenic determinant of dengue virus, and the epitopes that exclusively provide neutralization, but are not cross reactive, have not been previously identified. This represents a major challenge in dengue virus vaccine design.
A set of discontinuous strands have been identified that make up the EDI-II hinge region of the DENV E glycoprotein, as the key epitope region targeted by neutralizing human antibodies. This epitope is conserved in the E protein of all four DENV serotypes. This region was identified through a multi-step process. Initially, DENV-3 was serial passaged in the presence of the DENV-3 type specific potentially neutralizing human mAb, 5J7, resulting in the generation of several viral escape mutants. These mutants were sequenced and three key amino acid mutations conferring escape were identified. To generate a model of the putative 5J7 epitope, the escape mutant residues were located on the DENV-3 E crystal structure. Using a strategy initially developed to identify norovirus epitopes, (1-3) modeling software was used to identify all residues within 12 Å of all three mutation sites. The DENV-4 E sequence was then aligned with the DENV-3 structure and each DENV-4 residue that varied from DENV-3 residues within that 12 Å region was identified, 25 residues in total (Table 7). To assess the role of this antigenic region identified by the 5J7 escape mutants, a “chimeric” nucleotide E gene sequence that introduced the variable DENV-4 residues into the DENV-3 E backbone was synthesized by Biobasic. The DENV 3/4 12A (25 residues changed) E genes was then recombined into the existing DENV-3 3001 clone using reverse genetics, see methods (4). The new clone was designated 3001A12. 3001A12 was screened in a 50% Focus Reduction Neutralization Assay (FRNT₅₀), using human sera to dengue virus serotypes 3 and 4 (4). The assay results clearly demonstrated that 3001A12 was completely neutralized by human and monkey immune sera to DENV 4, while the capacity of DENV-3 immune sera to neutralize 3001A12 were significantly diminished (FIGS. 8-10). This is the first “proof-of-concept” for identification and transfer of the epitope region that defines a DENV serotype. Studies are underway to assess the immunogenic potential of these chimeric viruses in mice to stimulate the generation of neutralizing antibodies, and in DENV-3 and -4 immune nonhuman primates to assess whether or not the gain and loss of neutralization in vitro is preserved in vivo.

REFERENCES FOR EXAMPLE 2

1. Debbink et al. “Genetic mapping of a highly variable norovirus GII.4 blockade epitope: Potential role in escape from human herd immunity” J Virol. 86(2):1214-26 (2012)
2. Lindesmith et al. “Monoclonal antibody-based antigenic mapping of norovirus GII.4-2002” J Virol. 86(2):873-83 (2012)
3. Lindesmith et al. “Immunogenetic mechanisms driving norovirus GII.4 antigenic variation. PLoS Pathog. 8(5):e1002705 (2012)
4. Messer et al. “Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization” PLoS Negl Trop Dis. 6(2):e1486 (2012)

The foregoing is illustrative of the present invention, and is not to be construed as limiting thereof. The invention is defined by the following claims, with equivalents of the claims to be included therein.
All publications, patent applications, patents and other references cited herein are incorporated by reference in their entireties for the teachings relevant to the sentence and/or paragraph in which the reference is presented.

TABLE 7

Mutations in 3001A12. The letter to the left of the number indicates
original amino acid, the number indicates amino acid position, and the
letter to the right of the number indicates the amino acid replacing the
original amino acid. Positions are based on the
DENV3 E glycoprotein amino acid sequence.

	T51K	M205L
	Q52E	R208K
	L53V	F212L
	T55L	S220A
	K58T	I268V
	L59Y	Q269D
	P124K	N270S
	E126T	S271G
	K128N	G272D
	V129L	T274N
	T198K	S275H
	N201K	I276M
	A203T

Claims

1. (canceled)

2. A chimeric dengue virus E glycoprotein comprising a dengue virus E glycoprotein backbone from dengue virus serotype 2 that comprises the following amino acid substitutions that introduce an epitope that is recognized by an antibody that is reactive with a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone; wherein the amino acid residue numbering is based on the amino acid sequence of SEQ ID NO:20:

Q52E, P53V, T55L, K58T, N124K, M1251, E126T, K128N, V129L, Q200K, E202K, N203K, A205T, R210K, L221T, P222A, Q271D, M272S, S273G, S274D, L277H, L278M, and T280A.

3. A flavivirus particle or virus like particle (VLP) comprising the E glycoprotein of claim 2.

4. An isolated nucleic acid molecule encoding the E glycoprotein of claim 2.

5. An isolated nucleic acid molecule encoding the flavivirus particle or VLP of claim 3.

6. A method of producing an immune response to a dengue virus in a subject, comprising administering to the subject an effective amount of the chimeric dengue virus E glycoprotein of claim 2 and/or an isolated nucleic acid molecule expressing said chimeric dengue virus E glycoprotein.

7. A method of producing an immune response to a dengue virus in a subject, comprising administering to the subject an effective amount of the flavivirus particle or VLP of claim 3.

8. A method of treating and/or preventing a dengue virus infection in a subject in need thereof, the method comprising administering to the subject an effective amount of the chimeric dengue virus E glycoprotein of claim 2 and/or an isolated nucleic acid molecule expressing said chimeric dengue virus E glycoprotein.

9. A method of protecting a subject from the effects of dengue virus infection, the method comprising administering to the subject an effective amount of the chimeric dengue virus E glycoprotein of claim 2 and/or an isolated nucleic acid molecule expressing said chimeric dengue virus E glycoprotein.

10. A chimeric dengue virus E glycoprotein comprising a dengue virus E glycoprotein backbone from dengue virus serotype 3 that comprises the following amino acid substitutions that introduce an epitope that is recognized by an antibody that is reactive with a dengue virus serotype that is different from the dengue virus serotype of the dengue virus E glycoprotein backbone; wherein the amino acid residue numbering is based on the amino acid sequence of SEQ ID NO:17:

N270T, G273T, and S275T.

11. A flavivirus particle or virus like particle (VLP) comprising the E glycoprotein of claim 10.

12. An isolated nucleic acid molecule encoding the E glycoprotein of claim 10.

13. An isolated nucleic acid molecule encoding the flavivirus particle or VLP of claim 11.

14. A method of producing an immune response to a dengue virus in a subject, comprising administering to the subject an effective amount of the chimeric dengue virus E glycoprotein of claim 10 and/or an isolated nucleic acid molecule expressing said chimeric dengue virus E glycoprotein.

15. A method of producing an immune response to a dengue virus in a subject, comprising administering to the subject an effective amount of the flavivirus particle or VLP of claim 11.

16. A method of treating and/or preventing a dengue virus infection in a subject in need thereof, the method comprising administering to the subject an effective amount of the chimeric dengue virus E glycoprotein of claim 10 and/or an isolated nucleic acid molecule expressing said chimeric dengue virus E glycoprotein.

17. A method of protecting a subject from the effects of dengue virus infection, the method comprising administering to the subject an effective amount of the chimeric dengue virus E glycoprotein of claim 10 and/or an isolated nucleic acid molecule expressing said chimeric dengue virus E glycoprotein.