WO2018152526A1 - Zika virus vaccines - Google Patents

Abstract

The present invention relates to a vaccine for Zika virus, the vaccine comprising Zika virus membrane and envelope proteins. More specifically, the vaccine comprises nucleic acid molecules encoding modified Zika virus membrane and/or envelope proteins. When introduced into a cell, the encoded proteins are produced, which results in the production of a virus-like particle capable of eliciting an immune response against Zika virus.

Description

ZIKA VIRUS VACCINES

REFERENCE TO SEQUENCE LISTING

This application contains a Sequence Listing submitted as an electronic text file named "6137NIAID-63-PCT2_Sequence_Listing_ST25.txt", having a size in bytes of 2314 KB, and created on February 20, 2018. The information contained in this electronic file is hereby incorporated by reference in its entirety pursuant to 37 CFR § 1.52(e)(5).

FIELD OF TECHNOLOGY

The present invention relates to vaccines for immunizing individuals against Zika virus. More specifically, the present invention relates to the use of Zika virus proteins, nucleic acid molecule encoding such proteins, and VLPs made from such proteins to elicit a protective immune response against Zika virus.

BACKGROUND

Zika virus (ZIKV) is a mosquito-transmitted flavivirus that has emerged from relative obscurity to cause an epidemic of great public health concern. During the half- century that followed its discovery in Uganda in 1947, Zika virus was rarely linked to disease in humans, despite considerable transmission. The emergence of a Zika virus epidemic was first reported in Yap island in 2007, followed by outbreaks in French Polynesia in 2013 and 2014, and regularly thereafter in other islands of the Pacific. The introduction of Zika virus into the Western Hemisphere occurred in 2014-2015 in Haiti and Brazil and spread rapidly to 33 or more countries. Historically, symptomatic Zika virus infection of humans was described as a self-limiting mild febrile illness associated with rash, arthralgia, and conjunctivitis. However, recent Zika virus infection has also been associated with neurological complications, including Guillain-Barre syndrome and meningoencephalitis. Of significant concern, Zika virus infection is now strongly linked to microcephaly and intrauterine growth retardation in the fetuses of women infected with the virus while pregnant. This association has recently been confirmed in murine models of Zika virus.

Flaviviruses are spherical virus particles that incorporate two structural proteins into their lipid envelope, precursor to membrane/membrane (prM/M) and envelope (E). Virions assemble on membranes of the endoplasmic reticulum as non-infectious immature virus particles that incorporate prM and E as heterotrimeric spikes arranged with icosahedral symmetry. In this configuration, E proteins are incapable of low pH-triggered conformational changes required to drive membrane fusion following virus entry (Heinz et al., 1994). During transit through the secretory pathway, prM is cleaved by a cellular furin- like protease, resulting in the formation of an infectious mature virion that retains only the short M peptide. The high-resolution structure of the mature Zika virus virion and the ectodomain of the E protein have been solved. Similar to other flaviviruses, mature Zika virus virions are relatively smooth particles that incorporate 180 copies each of the E and cleaved M proteins. The E protein is arranged on mature virions as antiparallel dimers that lie relatively flat against the lipid envelope in a herringbone pattern. Each E protein is composed of three structural domains connected by flexible linkers and is anchored to the viral membrane by a helical structure and two antiparallel transmembrane domains.

The capsid (C) protein, at the amino terminus of the polyprotein, is separated from the prM protein by a signal sequence directing the translocation of prM. The NS2B-3 protease complex catalyzes cleavage at the carboxy terminus of the C protein on the cytoplasmic side of the ER membrane. This is the only site in the structural polyprotein region which is cleaved by this enzyme. The type I transmembrane protein prM is anchored in the lipid bilayer by a carboxy terminus membrane anchor, which is immediately followed by the signal sequence for translocation of the E protein, also a type I transmembrane protein. Thus the amino terminus of the prM and E proteins are generated by signal peptidase cleavages. However, it has been noted for a number of flaviviruses that when the entire structural polyprotein region is expressed from cDNA, the signal peptidase-mediated cleavage at the amino terminus of prM does not occur efficiently, in contrast to that at the amino terminus of the E protein. This inefficient production of prM is reflected in the deficiency of secretion of the prM-E heterodimer and, in turn, the lack of immunogenicity often observed when such constructs are used for vaccination.

Neutralizing antibodies play a critical role in protection against flavivirus infection and disease. All three E protein domains contain epitopes recognized by neutralizing antibodies. Additionally, potent neutralizing antibodies have been isolated that bind surfaces composed of more than one domain or E protein. These quaternary epitopes have been identified as components of the neutralizing antibody response to dengue (DENV), yellow fever (YFV), West Nile (WNV), and tick-borne encephalitis (TBEV) viruses. Antibodies that bind prM have been isolated from infected humans, but show limited neutralizing capabilities in vitro. Because neutralizing antibody titers correlate with protection by vaccines for Japanese encephalitis virus (JEV), YFV, and TBEV, eliciting neutralizing antibodies is a desired feature of candidate vaccines for related flaviviruses, including Zika virus. Flaviviruses circulate as genetically distinct genotypes or lineages, in part due to the high error rate associated with RNA virus replication. Zika virus strains have been grouped into two lineages, African and Asian, which differ by <5% at the amino acid level. The African lineage includes the historical MR-766 strain originally identified in 1947, whereas virus strains from the Asian lineage have been attributed to the recent outbreaks in Yap, French Polynesia, and the Americas. Understanding how sequence variation among Zika virus strains impacts antibody recognition is of particular importance to vaccine development. DENV, for example, circulates as four distinct serotypes that differ by 25- 40% at the amino acid level. The challenges of eliciting a protective neutralizing antibody response against all four DENV serotypes has hampered delayed vaccine development. Desirable Zika vaccine candidates should provide equivalent protection against both Asian and African lineages. Previous attempts at producing such a vaccine have been made, and suck work is disclosed, for example, in US Pat. Nos. 7,227,011; 7,417, 136; 7,662,394; 8, 109,609; US2014/0335117; and US2015/0246951, all of which are incorporated herein by reference in their entirety. However, there remains a need for a safe and effective vaccine against flaviviruses, and Zika virus in particular. The present disclosure satisfies this need and provides additional benefits as well.

SUMMARY

This disclosure provides nucleic acid molecules encoding a polyprotein, which comprises at least a portion of a Zika virus prM protein joined to at least a portion of a Zika virus E protein, and wherein the at least a portion of a Zika virus prM protein comprises a signal sequence that is heterologous to Zika virus. These nucleic acid molecules may be operatively linked to a control sequence. The control sequence may include a promoter that drives expression of the nucleic acid sequence. The expression of these polyproteins in a cell results in production of a virus-like particle (VLP). These VLP are capable of eliciting an immune response against Zika virus.

In these nucleic acid molecules, the heterologous signal sequence may be, for example, human CD5, mouse IL-2, bovine prolactin, or a flavivirus structural protein. If from a flavivirus protein, the heterologous signal sequence may be from a flavivirus prM protein. These flavivirus proteins may be from yellow fever virus, Dengue virus, Japanese encephalitis virus, or West Nile Virus. The heterologous signal sequence may be encoded by a nucleic acid sequence at least 80%, at least 85%, at least 90%, at least 95%, or at least 97% identical to, or comprises SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO:23, or SEQ ID NO:25. Alternatively or additionally, the heterologous signal sequence may comprise an amino acid sequence at least 80%, at least 85%>, at least 90%, at least 95%, or at least 97% identical to, or comprises SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:24, or SEQ ID NO:26.

In these nucleic acid molecules, the Zika virus prM protein may be encoded by a nucleic acid molecule comprising a nucleic acid sequence at least 80%>, at least 85%>, at least 90%, at least 95%, at least 97%, or 100% identical to SEQ ID NO: l . Alternatively or additionally, the Zika virus prM protein may be encoded by a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO:240- 450, SEQ ID NO:460- 468, SEQ ID NO:475-480, and SEQ ID NO:523-564. Alternatively, or additionally, the Zika virus prM protein may comprise an amino acid sequence at least 80%>, at least 85%>, at least 90%, at least 95%, at least 97%, or 100% identical to SEQ ID NO:2. Alternatively or additionally, the Zika virus prM protein may comprise an amino acid sequence at least 80%>, at least 85%>, at least 90%, at least 95%, at least 97%, or 100% identical to the sequence of a modified protein listed in Table 3 A or Table 3B. Alternatively, or additionally, the Zika virus prM protein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%), at least 95%, at least 97%, or 100% identical to the sequence of a modified protein listed in Table 3 A or Table 3B, and wherein the prM protein comprises at least one mutation from the modified protein listed in Table 3A or Table 3B. Alternatively, or additionally, the Zika virus prM protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%), at least 95%, or at least 97% identical to a protein sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO :481-522, and wherein the prM protein comprises at least one mutation from the protein sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO :481-522. Alternatively, or additionally, the Zika virus prM protein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to SEQ ID NO:4.

In these nucleic acid molecules, the Zika virus envelope (E) protein may be encoded by a nucleic acid molecule comprising a nucleic acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to SEQ ID NO:3. Alternatively or additionally, the Zika virus envelope protein may be encoded by a nucleic acid molecule listed in Table 3 A or Table 3B. Alternatively or additionally, the Zika virus envelope protein may be encoded by a nucleic acid molecule comprising a sequence selected from the group consisting of SEQ ID NO:240- 450, SEQ ID NO:460-468, SEQ ID NO:475-480, and SEQ ID NO:523-564. Alternatively, or additionally, the Zika virus envelope protein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to SEQ ID NO:4. Alternatively or additionally, the Zika virus envelope protein in these nucleic acids may be modified by substituting the stem region and/or the transmembrane region with a corresponding region from the envelope protein of a different flavivirus. Both the stem region and the transmembrane region may be replaced with the corresponding region of an envelope protein from a different flavivirus, such as, for example, yellow fever virus, Dengue virus, Japanese encephalitis virus and West Nile Virus. Alternatively, or additionally, the Zika virus envelope protein comprises at least one mutation that stabilizes a VLP comprising the envelope protein. Alternatively, or additionally, the Zika virus envelope protein may comprise at least one mutation that enhances the immunogenicity of a VLP comprising the envelope protein. Alternatively, or additionally, the envelope protein may comprise at least one mutation in at least one of the fusion peptide, the fusion loop, the M loop, and the be loop region. These mutations may be at any (e.g., one or more) amino acid position corresponding to a location selected from the group consisting of R2, G5, N8, S16, G28, A54, T76, Q77, D87, W101, G106, L107, N134, T160, T170, E177, R193, P222, W225, T231, K251, Q253, V255, V256, V257, Q261, E262, H266, E262, D296, K297, L300, S304, Y305, L307, K316, and E320, of SEQ ID NO:4. Alternatively or additionally, the Zika virus envelope protein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to the sequence of a modified protein listed in Table 3 A or Table 3B, wherein the envelope protein comprises at least one mutation from the modified protein listed in Table 3 A or Table 3B. Alternatively, or additionally, the Zika virus envelope protein may comprise a protein encoded by a nucleic acid molecule listed in Table 3A or Table 3B. Alternatively, or additionally, the Zika virus envelope protein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522, and wherein the Zika virus envelope protein comprises at least one mutation from the sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

This disclosure also provides cells comprising any one of these nucleic acid molecules. This disclosure also provides methods of producing a Zika virus-like particles, by introducing into a cell any one of these nucleic acid molecules such that the encoded fusion protein is expressed. Thus, this disclosure also provides a protein encoded by these nucleic acid molecules. These proteins may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to a polypeptide sequence listed in Table 3A or Table 3B, wherein the protein comprises at least one mutation from the polypeptide sequence listed in Table 3 A or Table 3B. Alternatively, or additionally, these proteins may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%), at least 97%, or 100% identical to a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO: 469-474, and SEQ ID NO:481- 522, wherein the protein comprises at least one mutation from the sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

This disclosure also provides A virus-like particle comprising a protein encoded by these nucleic acid molecules or proteins that is capable of inducing an immune response to Zika virus. Similarly, this disclosure encompasses a composition comprising any one of these nucleic acid molecule or proteins or VLPs, and a pharmaceutically acceptable carrier.

This disclosure also provides methods of eliciting an immune response against Zika virus in an individual, by administering at least one of these nucleic acid molecules, or proteins or VLPs, or compositions to the individual. Similarly, this disclosure provides methods of immunizing an individual against Zika virus, by administering at least one of these nucleic acid molecules, or proteins or VLPs, or compositions to the individual.

An exemplary embodiment of this disclosure is a nucleic acid molecule comprising a nucleotide sequence encoding a polyprotein comprising the Japanese Encephalitis Virus envelope protein signal sequence joined to a protein comprising Zika virus prM protein, which is joined to a modified Zika virus envelope protein. The stem and transmembrane region of this modified Zika virus envelope protein are from the envelope protein of Japanese Encephalitis virus, and the modified envelope protein optionally comprises at least one mutation from a protein sequence listed in Table 3A or Table 3B. In this nucleic acid molecule, the polyprotein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to a polypeptide sequence listed in Table 3A or Table 3B, wherein the protein maintains the at least one mutation from the polypeptide listed in Table 3 A or Table 3B. In these nucleic acid molecules, the polyprotein may comprise an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or 100% identical to a sequence selected from SEQ ID NO:29-239, SEQ ID NO:451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522, wherein the protein maintains the at least one mutation from the sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481- 522. Thus, this disclosure provides a VLP comprising a protein encoded by any one of these nucleic acid molecules.

This disclosure also provides a method of detecting anti-Zika virus antibodies in a sample, by contacting at least a portion of the sample with a VLP of this disclosure under conditions suitable for forming a VLP-antibody complex, and then detecting the presence of the VLP-antibody complex, if present. The presence of the VLP-antibody complex indicates the presence of anti-Zika virus antibodies in the sample.

BRIEF DESCRIPTION OF THE FIGURES

FIGs. 1A-1D describe the ZIKAV DNA vaccine design and characterization. FIG. 1A is a schematic representation of the ZIKAV genome and ZIKAV DNA vaccine constructs VRC5283 and VRC5288. The ZIKV genome encodes the structural proteins capsid (C), premembrane (prM) and envelope (E), and nonstructural proteins NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5 expressed as a single polyprotein that is cleaved by host cell proteases into individual proteins. The codon-modified prM-E gene from ZIKV strain H/PF/2013 (GenBank accession AHZ13508.1) was inserted into a mammalian expression vector (VRC8400) downstream of a signal sequence derived from Japanese encephalitis virus (JEV) (GenBank accession ADZ48450.1), and named VRC5283. VRC5283 was further modified to create VRC5288 by swapping the stem and transmembrane (ST/TM) regions of ZIKV E with the analogous sequence from JEV. FIG. IB shows the expression and secretion of ZIKV E analyzed by Western blot of transfected 293 T cell ly sates and SVP precipitate pelleted from culture supernatants through a 20% sucrose cushion demonstrating that the VRC5288 construct secretes more particles than VRC5283. FIG. 1C shows the results of a particle-capture ELIS A quantifying the secretion of ZIKV SVP from transfected cells and demonstrates roughly 10-fold greater particle release from VRC5288- than VRC5283-transfected cells (endpoint titers of 1 :274 and 1 :24, respectively). FIG. ID shows electron micrographs of ZIKV subviral particles (SVP) purified from the culture supernatant of VRC5288-transfected 293-F cells and subjected to negative staining and electron microscopy. SVP are labeled with arrowheads. The VRC8400 empty backbone plasmid vector was used as a control.

FIGs. 2A-2D demonstrate that ZIKV DNA vaccines elicit robust binding and neutralizing antibodies in nonhuman primates. Rhesus macaques (n=6/group) were either mock immunized with VRC8400 empty backbone expression plasmid or with VRC5283 or VRC5288 vaccine plasmids. The VRC8400 (black lines), VRC5283 (dark blue lines), and VRC5288 (dark red lines) recipients were injected with 4 mg doses at weeks 0 and 4. Other VRC5283 recipients (light blue lines) were injected with 1 mg at weeks 0 and 4, and a group of VRC5288 recipients (light red lines) were injected once with 1 mg. All injections were given intramuscularly. Arrows indicate vaccination time points. FIG. 2A shows macaque sera assayed weekly for ZIKV binding antibodies by ELISA. Each line represents an individual animal and dashed line indicates the limit of detection (reciprocal titer of 64). Any measurement below the limit of detection was assigned a value of half the limit of detection for graphing and statistical purposes. FIG. 2B shows the NAb response elicited by vaccination analyzed using ZIKV reporter virus particles (RVPs). RVPs were produced by complementation of a GFP-expressing WNV replicon with a plasmid encoding the structural genes (C-prM-E) of ZIKV strain H/PF/2013. RVPs were mixed with serial threefold dilutions of serum for 1 h at 37°C prior to being added to Raji-DCSIG R cells. After 48 h, GFP-expressing infected cells were quantitated by flow cytometry. The dilution of sera required for half-maximal inhibition of virus infection (ECso) was estimated by nonlinear regression analysis. Lines connect the average ECso values of 2-5 independent experiments, each performed with duplicate technical replicates, for the individual monkeys in each group, at each timepoint. Error bars denote the standard error of mean. The dotted line denotes the limit of confidence for the RVP assay (reciprocal titer of 60). Measurements below the limit of detection were assigned a value of 30. The average binding antibody (FIG. 2C) and NAb (FIG. 2D) responses for each vaccine group are shown. Error bars denote the standard error of the mean.

FIGs. 3A and 3B demonstrate that ZIKV DNA vaccines reduce viremia in ZIKV- challenged rhesus macaques. Eight weeks after the first vaccination, macaques were challenged with 1000 FFU of ZIKV PRVABC59. FIG. 3 A shows the results of qPCR of the capsid gene as used to determine the genome copies/ml on days 1-5 and 7 post-challenge. Each line represents an individual animal. FIG. 3B shows the mean viral load after challenge in each group. Error bars represent the standard error of the mean. Viral load in recipients of one dose of 1 mg VRC5288 was significantly reduced compared to viremia in mock- immunized VRC8400 recipients when comparing area under the curve (AUC) of viral load trajectories by Wilcoxon Exact Test (two-sided p=0.041). Dashed line indicates the limit of detection (100 copies/ml). Any value below the limit of detection was assigned a value half the limit of detection for graphing and AUC calculation. FIGs. 4A-4C show that the protection from ZIKV challenge correlates with NAb titers present at challenge. Animals that had detectable viremia post-challenge were analyzed with respect to pre-challenge NAb activity. FIG. 4A is the reciprocal EC50 NAb titer of each animal individually plotted to reflect whether infection occurred or not. Lines indicate individual animals. Protected (no detectable viremia) and infected (viremia detectable on two successive days) animals are represented by gray and red lines, respectively. The sole animal that received two 4 mg doses of VRC5288 and was found to have a low level of viremia on days 3 and 7 after challenge is denoted as "breakthrough" (black outlined dots). That animal had the lowest prechallenge NAb titer of any recipient of two vaccine doses. The two animals in the one dose group that did not have detectable viremia until day 3 had the 2 highest NAb activities within that group. FIG. 4B is the probability of infection (Logit) based on the reciprocal EC50 NAb titer indicating that prevention of viremia would be expected in approximately 70% of animals with NAb titers >1000. FIG. 4C shows that the level of peak viremia on day 3 is inversely related to the prechallenge serum NAb titer. Viremic animals are shown in red, completely protected animals in grey and the breakthrough animal from the group that received 2x 4mg of VRC5288 is outlined in black. Grey box indicates a NAb titer <1000 reciprocal EC50 serum dilution.

FIGs. 5A-5D demonstrate the immunogenicity of VRC5283 and VRC5288 DNA vaccine candidates in mice. The binding and neutralizing antibody response in mice elicited by vaccination with ZIKV DNA vaccine candidates was analyzed using an ELISA (FIG. 5 A) and ZIKV RVPs (FIGs. 5B-5D), respectively. Groups of ten BALB/c and C57BL/6 mice were immunized with one 50 μg dose of VRC5283 or VRC5288 vaccine and bled weekly for serological studies. FIG. 5A shows the binding antibodies assayed using a particle-based ELISA. To assess NAb responses, ZIKV strain H/PF/2013 RVPs were mixed with serial fourfold dilutions of serum for 1 h at 37°C prior to being added to Raji-DCSIGNR cells. After 48 h, GFP-positive infected cells were quantitated by flow cytometry. The dilution of sera required for half-maximal inhibition of virus infection (EC50) was estimated by non-linear regression analysis. Representative dose-response neutralization profiles are shown for individual mice immunized with VRC5288 (FIG. 5B) or VRC5283 (FIG. 5C) DNA vaccine candidates. The neutralizing activity of sera collected 56 days post-vaccination (closed circles) is shown relative to sera collected 59 days post-vaccination from a mouse vaccinated with a control construct, VRC4974 (open circles). VRC4974 is identical to VRC5283 with the exception of a three amino acid deletion at the amino terminus of prM that prevents S VP particle release. Error bars reflect the range of two technical replicates, present even when not visible. FIG. 5D shows the EC50 serum neutralization titer determined for each mouse, at each of the indicated time points. Dots denote the titers for individual animals (n=l). Bars and associated error bars denote the group mean neutralization titer and standard error, respectively.

FIG. 6 shows the immunogenicity of increasing doses of VRC5283 and VRC5288 vaccine candidates in mice. ZIKV H/PF/2013 RVPs were mixed with four-fold serial dilutions of sera collected and pooled from four mice 21 days post-vaccination with 2, 10, or 50 μg of VRC5283 or VRC5288, and from sera collected 59 days post-vaccination with a control construct, VRC4974. VRC4974 is identical to VRC5283 with the exception of a three amino acid deletion at the amino terminus of prM that prevents SVP release. Immune complexes were incubated for 1 h at 37°C prior to being added to Raji-DCSIG R cells. After 48 h, GFP-positive infected cells were quantitated by flow cytometry and the results analyzed by non-linear regression. Error bars denote the range of technical duplicates, present even when not visible.

FIGs. 7A and 7B show neutralization of WNV and ZIKV RVPs by DNA vaccine- immune sera. WNV NY99 (FIG. 7 A) and ZIKV H/PF/2013 (FIG. 7B) RVPs were mixed with four-fold serial dilutions of sera pooled from four mice 14 days post-vaccination with a single 50 μg dose of WNV (VRC8111), ZIKV (VRC5283 and VRC5288) or MERS (VRC3593) DNA constructs. Immune complexes were incubated for 1 h at 37°C prior to being added to Raji-DCSIGNR cells. After 48 h, GFP-positive infected cells were quantitated by flow cytometry and the results analyzed by non-linear regression. Dose- response neutralization curves from a representative experiment of two independent assays are shown. Error bars denote the range of technical duplicates.

FIGs. 8A-8C shows the immunogenicity of VRC5283 and VRC5288 vaccine candidates in nonhuman primates. The NAb response in macaques elicited by vaccination with ZIKV DNA vaccine candidates was analyzed using ZIKV RVPs as described in FIG. 2. Representative dose- response neutralization profiles are shown for individual animals immunized with VRC5283 (FIG. 8A) or VRC5288 (FIG. 8B) DNA vaccine candidates. The neutralizing activity of sera collected 7 weeks post-vaccination (W7, closed circles) is shown relative to pre-immune sera from the same animal (PRE, open circles). Error bars reflect the range of two technical replicates, present even when not visible. FIG. 8C shows the EC50 serum neutralization titer determined for each animal, at each of the indicated timepoints. Dots denote the average titers for individual animals, calculated from 2-5 independent experiments. Bars and associated error bars denote the group mean neutralization titer and standard deviation, respectively. The dotted line denotes the limit of confidence for the RVP assay (defined by the highest concentration of sera used in the assay); samples with titers <60 are reported at half the limit of detection (1 :30).

FIG. 9 shows the magnitude of the neutralizing antibody response elicited in vaccinated nonhuman primates as a function of pre-immune titers. The NAb response in macaques elicited by vaccination with ZIKV DNA vaccine candidates (FIG.9A-Control: VRC8400; FIG.9B-4mg VRC5283; FIG.9C-lmg VRC5283; FIG.9D-4mg VRC5288; FIG.9E-lmg VRC5288) was analyzed using ZIKV RVPs as described in FIG. 2. The data presented represents the fold-change in the ECso titer of sera collected at the indicated time post-vaccination as compared to the pre-immune titer of that same animal (Post-vaccination EC50/ Pre-immune EC50). Lines represent individual animals and connect the fold-change values calculated from average EC50 NAb titers at each timepoint that are representative of 2-5 independent experiments, each performed with duplicate technical replicates. In each panel, the area under the curve for the line connecting group mean fold-change values is shaded gray. The dotted line denotes four standard deviations from pre-immune EC50 NAb titers. Note that the scales of the left-most and right-most panels have a smaller range than the middle three panels.

FIGs. 1 OA- IOC show a comparison of serum neutralization titers determined by three distinct assays. The neutralizing potency of nonhuman primate sera collected 6 weeks after vaccination was determined by three ZIKV neutralization assays: reporter virus particles (RVP), microneutralization (MN), or focus reduction neutralization test (FRNT). Sera from all 30 animals comprising all five vaccination groups were tested in the RVP and MN assays. A subset of monkeys, the 12 animals that received two doses of 4 mg VRC5283 or VRC5288, was assessed via FRNT. Neutralization titers for individual serum samples tested using the indicated assays are plotted on the x- and y-axis. Shown are comparisons of RVP ECso versus MN ECso (FIG. 10A), RVP EC90 versus MN ECso (FIG. 10B), and RVP EC50 versus FRNT EC50 (FIG. IOC). RVP EC50 and EC90 values represent the average of 2- 4 independent experiments performed with duplicate technical replicates, FRNT EC50 values represent the average of 1-4 independent experiments performed with duplicate technical replicates, and MN EC50 values represent a single experiment. Error bars reflect the standard deviation. The correlation between independent measurements was evaluated by Spearman's correlation.

FIGs. 11A-11D. demonstrate that prior WNV infection does not protect against or enhance ZIKV infection. Sera from one of six control animals (macaque A8V016) that received two doses of 4 mg VRC8400 displayed detectable ZIKV antibody binding by ELISA but no neutralizing activity. To investigate whether this animal had pre-existing immunity to the related flavivirus WNV, WNV NY99 RVPs were mixed with serial dilutions of a potently neutralizing WNV mAb E16 (FIGs. 11 A and 11B), week 0 and 8 sera from macaque A8V016 (FIGs. l lC and 11D), and week 0 and 8 sera from a second control group animal, macaque A13V091 (FIGs. HE and 1 IF). Immune complexes were incubated for 1 h at 37°C prior to being added to Raji-DCSIGNR cells (FIGs. 11 A, 11C 11, and E) or FcyR+ K562 cells (FIGs. 1 IB, 1 ID, and 1 IF) to detect neutralizing and enhancing activity, respectively. After 48 h, GFP- positive infected cells were quantitated by flow cytometry and the Raji-DCSIGNR results analyzed by non-linear regression. Error bars denote the range of duplicate technical replicates from a single assay. The ability to both neutralize and enhance infection of WNV RVPs indicates prior WNV exposure in macaque A8 V016. (FIG. 11 G) Viral loads of animals vaccinated with two 4 mg doses of VRC8400 on day 1-7 after challenge. Macaque A8V016 is shown in purple demonstrating no protection from or enhancement of ZIKV infection.

FIGs. 12A-12C show that DNA vaccines are immunogenic in mice. Mice were vaccinated with 5C^g of DNA by intramuscular injection, followed by electroporation at week 0 and 4. Binding antibodies were assessed at week 2 (FIG. 12A) and 8 (FIG. 12B) post-vaccination by ELISA. All vaccines elicited binding antibodies after a single dose of DNA that were boosted by second dose at week 4. FIG. 12C. Neutralizing antibodies were assessed at week 8 post-vaccination by reporter virus particle (RVP) neutralization assay. All vaccines elicited robust neutralizing antibody responses.

FIGs. 13 A and 13B show the profile for the clinical trials. VRC5288=VRC5288 plasmid backbone with Zika virus and Japanese encephalitis virus chimeric envelope protein E. VRC5283=VRC5283 plasmid backbone with wild-type Zika virus protein E.

FIG. 14 lists the baseline characteristics pf participants in the study.

FIG. 15 shows the local and systemic reactogenicity of groups in the study.

FIG. 16 lists neutralizing antibody titers, and T-cell responses 4 weeks after the final vaccination in the VRC319 and VRC320 studies.

FIGs. 17A and 17B show neutralizing activity 4 weeks after the final vaccination. IIN the VCR319 study (Fig. 17A), samples were collected in week 12 for groups 1 and 3, week 16 for group 1, and week 24 for group 24. In the VRC 320 study (Fig. 17B), all samples ere collected at week 12. The charts show geometric means titers derived from two to four independent assays per sample. The dotted line shows the limit of detection of the assay (dilution 1 :30). ECso = dilution of sera required to neutralize half of infection events. N/S=needle and syringe. FIGs. 18 A- 18G show neutralizing activity 4 weeks after each vaccination. Each line represents the ECso of an individual participant over time. Arrows indicate the timing of vaccination. Values shown are the means of two to four independent assays per sample.

FIGs. 19A-19D show immunogenicity at baseline and 4 weeks after the final vaccination. Results were measured by intracellular cytokine staining showing T-cell responses. Figs. A and B show the results of the VRC319 study. Figs. C and D show the results of the VRC320 study. Data are group arithmetic mean proportions and SDs of total T cells producing interleukin-2, interferon-gamma, tumor necrosis factor-alpha, or a combination of these cytokines against pooled envelope protein E, small envelope protein M, and peptide pr.

DETAILED DECRIPTION

This disclosure provides novel Zika virus vaccines, and the use of nucleic acid molecules encoding Zika virus structural proteins, proteins encoded by such nucleic acid molecules, and virus-like particles formed from such proteins, as vaccines for immunizing individuals against infection with Zika virus. Embodiments of the invention comprise a nucleic acid molecule encoding a polyprotein comprising a Zika virus prM protein having a heterologous signal sequence, joined to a Zika virus envelope (E) protein, such that expression of the encoded polyprotein results in the production of virus-like particles capable of inducing an immune response against Zika virus.

It is to be understood that this invention is not limited to the specific embodiments described herein, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the claims.

Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. The publications and applications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in art to which the subject matter herein belongs. As used herein, the following definitions are supplied in order to facilitate the understanding of the present invention.

As used herein, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. For example, a nucleic acid molecule refers to one or more nucleic acid molecules. As such, the terms "a", "an", "one or more" and "at least one" can be used interchangeably. The terms "comprising," "including," and "having" can also be used interchangeably. Furthermore, the phrase "selected from the group consisting of refers to one or more members of the group in the list that follows, including mixtures (i.e. combinations) of two or more members. As used herein, "at least one" means one or more. The term "comprise" is generally used in the sense of "including", that is to say "permitting the presence of one or more features or components." Where descriptions of various embodiments use the term comprising, those skilled in the art will understand that in some specific instances, an embodiment can be alternatively described using the transitional phrase "consisting essentially of."

The claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as "solely," "only" and the like in connection with the recitation of claim elements, or use of a "negative" limitation. Further, while various embodiments and technical aspects of the invention may appear in separate locations in the specification, it should be clear that combinations of such embodiments and technical aspects are also encompassed by the invention.

The term "nucleic acid" refers to deoxyribonucleic acid or ribonucleic acid, and polymers thereof, in either single-stranded or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides which have binding properties similar to the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al. (1991) Nucleic Acid Res 19:5081; Ohtsuka et al. (1985) J Biol Chem 260:2605-2608; Cassol et al. (1992); Rossolini et al. (1994) Mol Cell Probes 8:91-98).

As used herein, a polyprotein is a protein that, after synthesis, is cleaved by enzymes to produce two or more functionally distinct proteins. For example, the entire genome of Zika virus is translated into a polyprotein, which is then processed co- and post- translationally into the individual structural and non- structural proteins.

As used herein, a "fusion protein" is a recombinant protein containing amino acid sequences from at least two unrelated proteins that have been joined together, via a peptide bond, to make a single protein. The unrelated amino acid sequences can be joined directly to each other or they can be joined using a linker sequence. As used herein, proteins are unrelated, if their amino acid sequences are not normally found joined together via a peptide bond in their natural environment(s) (e.g., inside a cell). For example, heterologous sequences are not normally found in nature joined together via a peptide bond. As a more specific example, the signal sequence from a Japanese Encephalitis Virus prM protein is not normally found in the prM protein from Zika virus. However, such a construct can be recombinantly produced by the hand of man.

The term "heterologous" is a relative term and is used when comparing the origin of at least two individual molecules (i.e., DNA, RNA, protein, etc.). As used herein, the term heterologous is used to describe at least two different molecules as being from different organisms of different species. For example, the envelope protein of Dengue virus would be considered heterologous to the envelope protein of Japanese Encephalitis Virus or Zika virus. Likewise, the signal sequence of the Japanese Encephalitis Virus prM protein would be considered heterologous to the signal sequence of the Zika Virus prM protein.

As used herein, a signal sequence, signal peptide, and the like, refers to an amino acid sequence that directs translocation of a protein comprising the signal sequence through a membrane. Signal peptides have a low degree of sequence conservation but often have common structural motifs (Lee et al., Virology, 2000, Jan; 74(1) :24-32). For example, amino acids in the amino terminus region of the signal peptide often contain basic side chains, whereas the central core region is usually rich in apolar amino acids. Moreover, the carboxy terminus region frequently contains amino acids with polar side chains and residues with alpha-helix-breaking properties (proline, glycine, or serine). However, such motifs may vary as evidenced by the flavivirus prM signal sequences, which are nonpolar in their carboxy terminus cleavage regions. Signal peptides also vary in size, but are typically between 5 to 30 contiguous amino acids in length. Any signal sequence can be used to practice the present invention, as long as the chosen signal sequence is capable of directing translocation of a protein comprising the signal sequence through a membrane. Examples of such membranes include, but are not limited to, nuclear membranes, cell membranes, membranes of the endoplasmic reticulum, and the like. Preferred signal sequences are those from viral structural proteins, and more preferably flavivirus structural proteins. As used herein, a flavivirus structural protein refers to a flavivirus capsid (C) protein, a premembrane (prM), a membrane (M) protein, an envelope (E) protein, or portions of such proteins that are capable of forming virus-like particles (VLPs).

As used herein, the term "modified" refers to a protein or nucleic acid molecule, the properties of which have been altered by the hand of man so that it differs in sequence and/or structure from the same protein or nucleic acid molecule found in nature. For example, a nucleic acid molecule in which the nucleotide sequence has been altered using recombinant techniques would be considered a modified nucleic acid molecule. Such alterations include, but are not limited to, substitution of one or more nucleotide, deletion of one or more nucleotide, insertion of one or more nucleotide, and incorporation of nucleotide analogues. Likewise, a protein, the sequence of which has been altered by the hand of man, is a modified protein. Such modifications include, but are not limited to, substitution of one or more amino acid, deletion of one or more amino acid, insertion of one or more amino acid, and the like. It should be understood that modified proteins include those proteins in which an entire region has been substituted using a corresponding region from a corresponding protein in another organism. For example, membrane proteins are known to contain sequences that anchor the protein in a membrane. A membrane anchor region of a first protein can be substituted with a membrane anchor region from a second protein. In such a scenario, the resulting hybrid protein would be considered a modified protein.

The terms "corresponding," "corresponds to," and the like, refer to a structural and/or functional similarity between regions in two or more different proteins. Regions in different proteins are considered to correspond when they perform the same function and/or have nearly identical amino acid sequences and/or three-dimensional structures. For example, the membrane anchor regions of envelope proteins from Zika virus and Dengue virus would be considered to be corresponding regions since they both serve to anchor the envelope protein in the membrane. Corresponding regions of proteins may, but need not, have similar sequences. Moreover, due to sequence variability in corresponding proteins between different species, which may include insertions and deletions of amino acids, corresponding regions may not be present in identical linear locations in the proteins. For example, while the stem region of the Zika virus envelope protein may span amino acids 402 through 445 of the Zika virus envelope protein, it may span amino acids 400 through 443 in the Dengue envelope protein. Similarly, the corresponding region of the West Nile Virus envelope protein might span amino acids 405 through 448. Methods of identifying and comparing corresponding regions of proteins are known to those skilled in the art.

As used herein, the "stem region" of a flavivirus envelope protein refers to the sequence of amino acids between the ectodomain and the C-terminal transmembrane anchor region of the envelope protein. In Zika virus, this region spans amino acids 402-445 and has the sequence IGKAFEATVRGAKRMAVLGDTAWDFGSVGGVFNSLGKGIHQIF, represented by SEQ ID NO: 6, and encoded by SEQ ID NO: 5. The corresponding region in the envelope protein of Japanese Encephalitis Virus also spans amino acids 402-445, and has the sequence LGKAFSTTLKGAQRLAALGDTAWDFGSIGGVFNSIGKAVHQVF, represented by SEQ ID NO:8, and encoded by SEQ ID NO:7. Using such sequences, one skilled in the art can determine the corresponding region in the envelope protein of any other flavivirus.

As used herein, the transmembrane region of a flavivirus envelope protein refers to the sequence of amino acids starting at the carboxy terminus of the stem region and going until the carboxy terminus of the envelope protein. In Zika virus, this region spans amino acids 446-501 and has the sequence:

GAAFKSLFGGMSWFSQILIGTLLVWLGLNTKNGSIASLTCLALG GVMTFLSTAVSA (SEQ ID NO: 10), encoded by SEQ ID NO:9. The corresponding region in the envelope protein of Japanese Encephalitis Virus also spans amino acids 446-500 and has the sequence GGAFRTLFGGMSWITQGLMGALLLWMGVNARDRSIALAFLATGGVLV FLATN VHA, (SEQ ID NO: 12), encoded by SEQ ID NO: 11. Using such sequences, one skilled in the art can determine the corresponding region in the envelope protein of any other flavivirus.

As used herein, the term "immunogenic" refers to the ability of a specific protein, or a specific region thereof, to elicit an immune response to the specific protein, or to proteins comprising an amino acid sequence having a high degree of identity with the specific protein. According to the present invention, two proteins having a high degree of identity have amino acid sequences at least 85% identical, at least 87% identical, at least 90% identical, at least 92% identical, at least 94% identical, at least 96% identical, at least 98% identical or at least 99% identical.

As used herein, an immune response refers to the development in a subject of a humoral and/or a cellular immune response to a Zika virus structural protein. As used herein, a "humoral immune response" refers to an immune response mediated by antibody molecules, including secretory (IgA) or IgG molecules, while a "cellular immune response" is one mediated by T-lymphocytes and/or other white blood cells. One important aspect of cellular immunity involves an antigen-specific response by cytolytic T-cells ("CTL"s). CTLs have specificity for peptide antigens that are presented in association with proteins encoded by the major histocompatibility complex (MHC) and expressed on the surfaces of cells. CTLs help induce and promote the destruction of intracellular microbes, or the lysis of cells infected with such microbes. Another aspect of cellular immunity involves an antigen-specific response by helper T-cells. Helper T-cells act to help stimulate the function, and focus the activity of, nonspecific effector cells against cells displaying peptide antigens in association with MHC molecules on their surface. A cellular immune response also refers to the production of cytokines, chemokines and other such molecules produced by activated T-cells and/or other white blood cells, including those derived from CD4+ and CD8+T- cells.

An immunological response may be one that stimulates CTLs, and/or the production or activation of helper T-cells. The production of chemokines and/or cytokines may also be stimulated. The vaccine may also elicit an antibody -mediated immune response. Hence, an immunological response may include one or more of the following effects: the production of antibodies (e.g., IgA or IgG) by B-cells; and/or the activation of suppressor, cytotoxic, or helper T-cells and/or T-cells directed specifically to a structural protein present in, or encoded by, the vaccine. These responses may serve to neutralize infectivity, and/or mediate antibody-complement, or antibody dependent cell cytotoxicity (ADCC) to provide protection to an immunized individual. Such responses can be determined using standard immunoassays and neutralization assays, well known in the art.

As used herein, "neutralizing antibodies" are antibodies that prevent Zika virus from completing one round of replication. As defined herein, one round of replication refers to the life cycle of the virus, starting with attachment of the virus to a host cell and ending with budding of newly formed virus from the host cell. This life cycle includes, but is not limited to, the steps of attaching to a cell, entering a cell, cleavage of the polyprotein, fusion of the viral membrane with endosomal membrane, release of viral proteins into the cytoplasm, formation of new viral particles and budding of viral particles from the host cell membrane.

As used herein, "broadly neutralizing antibodies" are antibodies that neutralize more than one strain of Zika virus. For example, broadly neutralizing antibodies elicited against an Asian strain of Zika virus may neutralize an African strain of Zika virus. As a further example, broadly neutralizing antibodies elicited against the EC Yap Micronesia (2007) stain of Zika virus may neutralize the FSS 13025 Cambodian (2010) strain of Zika virus. Nucleic Acid Molecules

One embodiment provides a nucleic acid molecule encoding a polyprotein comprising a signal sequence joined to at least a portion of a Zika virus prM protein, which is joined to at least a portion of a Zika virus envelope (E) protein, wherein the signal sequence is heterologous to Zika virus. Any signal sequence may be joined to the at least a portion of a Zika virus prM protein, as long as it is heterologous to Zika virus, and as long as it is able to direct translocation of the polyprotein. The signal sequence may be from a viral protein, a bacterial protein, or a mammalian protein. Examples of signal sequences useful for practicing the invention are provided in the following Table.

Table 1. Exemplary sequences useful for practicing the invention

SEQ

ID Molecule Comments

NO:

15 NAM Nucleic acid sequence encoding Japanese Encephalitis virus

stem/transmembrane region

16 Protein Amino acid sequence of Japanese Encephalitis virus

stem/transmembrane region

17 NAM Nucleic acid sequence encoding signal sequence from Japanese

encephalitis virus prM

18 Protein Amino acid sequence encoded by SEQ ID NO: 17

19 NAM Nucleic acid sequence encoding signal sequence human CD5 protein

20 Protein Amino acid sequence encoded by SEQ ID NO: 19

21 NAM Nucleic acid sequence encoding signal sequence from Zika virus prM

22 Protein Amino acid sequence encoded by SEQ ID NO: 19 (Zika prM signal sequence)

23 NAM Nucleic acid molecule encoding signal sequence from mouse IL-2

24 Protein Signal sequence from IL-2

25 NAM Nucleic acid molecule encoding signal sequence from bovine prolactin

26 Protein Signal sequence from bovine prolactin

27 Protein Precursor peptide from Zika virus prM protein

28 Protein Zika virus membrane protein after removal of precursor peptide

The signal sequence may be from a flavivirus protein, which may be a protein from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the signal sequence is from a flavivirus prM protein, which may be the prM protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the signal sequence is from the prM protein of a Japanese Encephalitis Virus. In one embodiment, the signal sequence is from a mammalian CD5 protein. In one embodiment, the signal sequence is from a CD5 protein from a mouse or human. In one embodiment, the signal sequence is from interleukin-2 (IL-2). In one embodiment, the signal sequence is from bovine prolactin.

Nucleic acid molecules of the invention may encode proteins comprising variants of signal sequences or variants of Zika virus structural proteins. As used herein, a "variant" refers to a protein or nucleic acid molecule, the sequence of which is similar, but not identical to, a reference sequence, wherein the activity of the variant protein (or the protein encoded by the variant nucleic acid molecule) is not significantly altered. These variations in sequence can be naturally occurring variations or they can be engineered through the use of genetic engineering techniques known to those skilled in the art. Examples of such techniques are found in Sambrook, Fritsch, Maniatis, et al., in Molecular Cloning—A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, 1989, pp. 9.31- 9.57), or in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1- 6.3.6, both of which are incorporated herein by reference in their entirety.

With regard to variants, any type of alteration in the amino acid, or nucleic acid, sequence is permissible so long as the resulting variant protein retains the desired activity (e.g., the ability to direct translocation or to elicit an immune response). Examples of such variations include, but are not limited to, deletions, insertions, substitutions, and combinations thereof. For example, with regard to proteins, it is well understood by those skilled in the art that one or more amino acids can often be removed from the amino and/or carboxy terminus of a protein without significantly affecting the activity of that protein. Similarly, one or more amino acids can be inserted into a protein without significantly affecting the activity of the protein.

As noted, variant proteins encoded by nucleic acid molecules of the present invention can contain amino acid substitutions relative to the proteins disclosed herein. Any amino acid substitution is permissible as long as the desired activity of the protein is not significantly affected. In this regard, amino acids can be classified into groups based on their physical properties. Examples of such groups include, but are not limited to, charged amino acids, uncharged amino acids, polar uncharged amino acids, and hydrophobic amino acids. Preferred variants that contain substitutions are those in which an amino acid is substituted with an amino acid from the same group. Such substitutions are referred to as conservative substitutions.

Naturally occurring residues may be divided into classes based on common side chain properties:

1) hydrophobic: Met, Ala, Val, Leu, lie;

2) neutral hydrophilic: Cys, Ser, Thr;

3) acidic: Asp, Glu;

4) basic: Asn, Gin, His, Lys, Arg;

5) residues that influence chain orientation: Gly, Pro; and

6) aromatic: Trp, Tyr, Phe.

For example, non-conservative substitutions may involve the exchange of a member of one of these classes for a member from another class.

In making amino acid changes, the hydropathic index of amino acids may be considered. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics. The hydropathic indices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5). The importance of the hydropathic amino acid index in conferring interactive biological function on a protein is generally understood in the art (Kyte et al., 1982, J. Mol. Biol. 157: 105-31). It is known that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. In making changes based upon the hydropathic index, the substitution of amino acids whose hydropathic indices are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

The substitution of like amino acids may also be made effectively on the basis of hydrophilicity, particularly where the biologically functionally equivalent protein or peptide thereby created is intended for use in immunological inventions, as in the present case. The greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e., with a biological property of the protein. The following hydrophilicity values have been assigned to these amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0+1); glutamate (+3.0+1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5+1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (- 1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); and tryptophan (-3.4). In making changes based upon similar hydrophilicity values, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred. One may also identify epitopes from primary amino acid sequences on the basis of hydrophilicity.

Desired amino acid substitutions (whether conservative or non-conservative) can be determined by those skilled in the art at the time such substitutions are desired. For example, amino acid substitutions can be used to identify important residues of the structural protein, or to increase or decrease the immunogenicity, solubility or stability of the Zika virus structural proteins described herein. Exemplary amino acid substitutions are shown below in Table 2.

Table 2. Exemplary Amino Acid Substitutions Amino Acid Substitutions

Original Amino Acid Exemplary Substitutions

Ala Val, Leu, He

Arg Lys, Gin, Asn

Asn Gin

Asp Glu

Cys Ser, Ala

Gin Asn

Glu Asp

Gly Pro, Ala

His Asn, Gin, Lys, Arg

lie Leu, Val, Met, Ala

Leu He, Val, Met, Ala

Lys Arg, Gin, Asn

Met Leu, Phe, He

Phe Leu, Val, He, Ala, Tyr

Pro Ala

Ser Thr, Ala, Cys

Thr Ser

Tip Tyr, Phe

Tyr Tip, Phe, Thr, Ser

Val He, Met, Leu, Phe, Ala

As used herein, the phrase "significantly affect a proteins' activity" refers to a decrease in the activity of a protein by at least 10%, at least 20%, at least 30%, at least 40% or at least 50%. Such an activity may be measured, for example, as the ability of a protein to direct translocation, form VLPs and/or to elicit an immune response (e.g., antibodies) against Zika virus. Such activity may be measured by determining the titer of such antibodies against Zika virus, or by measuring the breadth of Zika virus strains neutralized by the elicited antibodies. Methods of determining the above-recited activities are known to those skilled in the relevant arts.

In one embodiment, the signal sequence comprises an amino acid sequence at least 90%) identical, at least 95% identical, or at least 97% identical to the signal sequence of a flavivirus protein. In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to the signal sequence of a protein from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97%) identical to the signal sequence of a flavivirus prM protein. In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to the signal sequence of prM protein from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the signal sequence is at least 90% identical, at least 95% identical, or at least 97% identical to the signal sequence of the prM protein of Japanese Encephalitis Virus. In one embodiment, the signal sequence comprises the amino acid sequence of the signal sequence of the prM protein of Japanese Encephalitis Virus.

In one embodiment, the signal sequence is at least 90% identical, at least 95% identical, or at least 97% identical to the signal sequence of a CD5 protein. In one embodiment, the signal sequence is at least 90% identical, at least 95% identical, or at least 97% identical to the signal sequence of a human CD5 protein. In one embodiment, the signal sequence is at least 90% identical, at least 95% identical, or at least 97% identical to the signal sequence of a murine CD5 protein.

In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO: 18. In one embodiment, the signal sequence comprises SEQ ID NO: 18. In one embodiment, the signal sequence is encoded by a nucleic acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO: 17. In one embodiment, the signal sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 17. In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO:20. In one embodiment, the signal sequence comprises SEQ ID NO:20. In one embodiment, the signal sequence is encoded by a nucleic acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO: 19. In one embodiment, the signal sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 19. In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97%) identical to SEQ ID NO:24. In one embodiment, the signal sequence comprises SEQ ID NO:24. In one embodiment, the signal sequence is encoded by a nucleic acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO:23. In one embodiment, the signal sequence is encoded by a nucleic acid sequence comprising SEQ ID NO:23. In one embodiment, the signal sequence comprises an amino acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO:26. In one embodiment, the signal sequence comprises SEQ ID NO:26. In one embodiment, the signal sequence is encoded by a nucleic acid sequence at least 90% identical, at least 95% identical, or at least 97% identical to SEQ ID NO:25. In one embodiment, the signal sequence is encoded by a nucleic acid sequence comprising SEQ ID NO:25.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99% identical, or 100% identical, to SEQ ID NO: 18. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99%, or 100% identical, to SEQ ID NO: 17. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99% identical, or 100% identical, to SEQ ID NO:20. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99%, or 100% identical, to SEQ ID NO: 19. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99%) identical, or 100% identical, to SEQ ID NO:24. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99%, or 100% identical, to SEQ ID NO:23. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99%) identical, or 100% identical, to SEQ ID NO:26. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97% identical, at least 99%, or 100% identical, to SEQ ID NO:25.

As noted, the polyprotein comprises at least a portion of a Zika virus prM protein joined to at least a portion of a Zika virus envelope protein. As used herein, a portion refers to at least 20 amino acids that are contiguous in the referenced Zika virus protein. It will be understood that portions greater than 20 contiguous amino acids can be used in embodiments of the invention, as long as the resulting construct encodes a protein capable of inducing an immune response against Zika virus, and/or capable of forming virus-like particles (VLPs) that induce an immune response against Zika virus. Preferred portions are those capable of forming virus-like particles (VLPs). As used herein, a virus-like particle (VLP) is a particle that is formed from the self-assembly of one or more viral structural proteins, but which lacks a sufficient portion of the viral genome so that, upon entry into a cell, the VLP cannot produce progeny virus particles. While VLPs may contain some genetic material, preferred particles are those lacking genetic material. VLPs of the invention may, but need not, have a three-dimensional structure similar to a native Zika virus particle. Preferred VLPs of the invention are those in which the VLPs display the Zika virus proteins comprised therein in such a manner that administration of the VLPs to an individual result in elucidation of an immune response against Zika virus.

In one embodiment, the at least a portion of a Zika virus prM protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a Zika virus prM protein. In one embodiment, the at least a portion of a Zika virus prM protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from SEQ ID NO:2. In one embodiment, the at least a portion of a Zika virus prM protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a protein encoded by a nucleic acid sequence comprising SEQ ID NO: l . In one embodiment, the at least a portion of a Zika virus prM protein comprises a Zika virus prM protein. In one embodiment, the at least a portion of a Zika virus prM protein comprises SEQ ID NO:2. In one embodiment, the at least a portion of a Zika virus prM protein consists of SEQ ID NO:2.

In one embodiment, the at least a portion of a Zika virus prM protein is encoded by a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, or at least 450 contiguous nucleotides from a polynucleotide sequence encoding a Zika virus prM protein. In one embodiment, the at least a portion of a Zika virus prM protein is encoded by a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, or at least 450 contiguous nucleotides from a polynucleotide sequence encoding a protein comprising SEQ ID NO:2. In one embodiment, the at least a portion of a Zika virus prM protein is encoded by a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, or at least 450 contiguous nucleotides from SEQ ID NO: l . In one embodiment, the at least a portion of a Zika virus prM protein is encoded by SEQ ID NO: 1.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein comprising at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a Zika virus prM protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein comprising at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from SEQ ID NO:2. In one embodiment, the nucleic acid molecule comprises at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, or at least 450 contiguous nucleotides from a polynucleotide sequence encoding a Zika virus prM protein. In one embodiment, the nucleic acid molecule comprises at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, or at least 450 contiguous nucleotides from a polynucleotide sequence encoding a protein comprising SEQ ID NO:2. In one embodiment, the nucleic acid molecule comprises at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, or at least 450 contiguous nucleotides from SEQ ID NO: 1. In one embodiment, the nucleic acid molecule comprises SEQ ID NO: 1.

In one embodiment, the at least a portion of a Zika virus envelope protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a Zika virus envelope protein. In one embodiment, the at least a portion of a Zika virus envelope protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from SEQ ID NO:4. In one embodiment, the polyprotein comprises a Zika virus envelope protein. In one embodiment, the at least a portion of a Zika virus envelope protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a protein encoded by SEQ ID NO:3. In one embodiment, the at least a portion of a Zika virus envelope protein comprises a full-length Zika virus envelope protein. In one embodiment, the at least a portion of the Zika virus envelope protein comprises SEQ ID NO:4.

In one embodiment, the at least a portion of a Zika virus envelope protein is encoded by a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, at least 450 contiguous nucleotides, at least 600 contiguous nucleotides, at least 750 contiguous nucleotides, at least 900 contiguous nucleotides, at least 1050 contiguous nucleotides, at least 1200 contiguous nucleotides, at least 1350 contiguous nucleotides, or at least 1500 contiguous nucleotides, from a polynucleotide sequence encoding a Zika virus envelope protein. In one embodiment, the at least a portion of a Zika virus envelope protein is encoded by a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, at least 450 contiguous nucleotides, at least 600 contiguous nucleotides, at least 750 contiguous nucleotides, at least 900 contiguous nucleotides, at least 1050 contiguous nucleotides, at least 1200 contiguous nucleotides, at least 1350 contiguous nucleotides, or at least 1500 contiguous nucleotides, from a polynucleotide sequence encoding a protein comprising SEQ ID NO:4. In one embodiment, the at least a portion of a Zika virus envelope protein is encoded by a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, at least 450 contiguous nucleotides, at least 600 contiguous nucleotides, at least 750 contiguous nucleotides, at least 900 contiguous nucleotides, at least 1050 contiguous nucleotides, at least 1200 contiguous nucleotides, at least 1350 contiguous nucleotides, or at least 1500 contiguous nucleotides from SEQ ID NO:3. In one embodiment, the at least a portion of a Zika virus envelope protein is encoded by SEQ ID N0 3.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein comprising at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a Zika virus envelope protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein comprising at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from SEQ ID NO:4. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein comprising at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a protein encoded by SEQ ID NO:3.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, at least 450 contiguous nucleotides, at least 600 contiguous nucleotides, at least 750 contiguous nucleotides, at least 900 contiguous nucleotides, at least 1050 contiguous nucleotides, at least 1200 contiguous nucleotides, at least 1350 contiguous nucleotides, or at least 1500 contiguous nucleotides from a polynucleotide sequence encoding a Zika virus envelope protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, at least 450 contiguous nucleotides, at least 600 contiguous nucleotides, at least 750 contiguous nucleotides, at least 900 contiguous nucleotides, at least 1050 contiguous nucleotides, at least 1200 contiguous nucleotides, at least 1350 contiguous nucleotides, or at least 1500 contiguous nucleotides from a polynucleotide sequence encoding a protein comprising SEQ ID NO:4. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence comprising at least 75 contiguous nucleotides, at least 150 contiguous nucleotides, at least 300 contiguous nucleotides, at least 375 contiguous nucleotides, at least 450 contiguous nucleotides, at least 600 contiguous nucleotides, at least 750 contiguous nucleotides, at least 900 contiguous nucleotides, at least 1050 contiguous nucleotides, at least 1200 contiguous nucleotides, at least 1350 contiguous nucleotides, or at least 1500 contiguous nucleotides from SEQ ID NO:3.

In one embodiment, the at least a portion of a Zika virus prM is a variant of a Zika virus wild-type Zika virus prM protein. In preferred embodiments, such variants are capable of forming VLPs and/or eliciting an immune response against Zika virus. In one embodiment, the at least a portion of a Zika virus prM protein comprises at least at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, having a sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97% identical, or at least 99% identical to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a Zika virus prM protein. In one embodiment, the at least a portion of a Zika virus prM protein comprises at least at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, having a sequence at least 80%, at least 85%), at least 90%, at least 95%, at least 97% identical, or at least 99% identical to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a protein encoded by SEQ ID NO: l . In one embodiment, the at least a portion of a Zika virus prM protein comprises at least at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, having a sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97% identical, or at least 99% identical to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a protein comprising SEQ ID NO:2.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding the at least a portion of a variant Zika virus prM. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding at least at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, having a sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 97% identical, or at least 99% identical to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a Zika virus prM protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding at least at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, having a sequence at least 80%, at least 85%), at least 90%, at least 95%, at least 97% identical, or at least 99% identical to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a protein encoded by SEQ ID NO: l . In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding at least at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, having a sequence at least 80%, at least 85%), at least 90%, at least 95%, at least 97% identical, or at least 99% identical to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, or at least 150 contiguous amino acids, from a protein comprising SEQ ID NO:2.

In one embodiment, the at least a portion of a Zika virus envelope is a variant of a Zika virus wild-type envelope protein. In preferred embodiments, such variants are capable of forming VLPs and/or eliciting an immune response against Zika virus. In one embodiment, the at least a portion of a Zika virus envelope protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, having a sequence at least 80%) identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a Zika virus envelope protein. In one embodiment, the at least a portion of a Zika virus envelope protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, having a sequence at least 80% identical, at least 85%o identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from SEQ ID NO:4. In one embodiment, the at least a portion of a Zika virus envelope protein comprises at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, having a sequence at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a protein encoded by SEQ ID NO:3.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, having a sequence at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a Zika virus envelope protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, having a sequence at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from a protein encoded by SEQ ID NO:3. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, having a sequence at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to at least 25 contiguous amino acids, at least 50 contiguous amino acids, at least 100 contiguous amino acids, at least 125 contiguous amino acids, at least 150 contiguous amino acids, at least 200 contiguous amino acids, at least 250 contiguous amino acids, at least 300 contiguous amino acids at least 350 contiguous amino acids, at least 400 contiguous amino acids, at least 450 contiguous amino acids, or at least 500 contiguous amino acids, from SEQ ID NO:4.

As has been described, polypeptides encoded by nucleic acid molecules of the invention can comprise modified proteins. Such modifications can include replacement, deletion, or insertion of individual amino acids, as well as entire regions or domains with corresponding regions or domains from other proteins. Thus, in one embodiment, the polyprotein comprises a Zika virus envelope protein of the invention that has been modified relative to a wild-type Zika virus envelope protein. In one embodiment, a nucleic acid molecule of the invention encodes a polyprotein comprising a modified Zika virus envelope protein. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing the stem region, the transmembrane region, or both (the stem/transmembrane region) with the corresponding region from the envelope protein of another flavivirus. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14 with the corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region encoded by SEQ ID NO:5, SEQ ID NO:9 or SEQ ID NO: 13 with the corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14 with the corresponding region from Japanese Encephalitis Virus. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region encoded by SEQ ID NO:5, SEQ ID NO:9 or SEQ ID NO: 13 with the corresponding region from Japanese Encephalitis Virus.

In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 6 (stem region) with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97%, identical or at least 99% identical to SEQ ID NO: 8. In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO:6 (stem region) with an amino acid sequence comprising SEQ ID NO:8. In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO:6 (stem region) with an amino acid sequence consisting of SEQ ID NO:8.

In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 10 (transmembrane region) with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97%, identical or at least 99% identical to SEQ ID NO: 12. In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 10 (transmembrane region) with an amino acid sequence comprising SEQ ID NO: 12. In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 10 (transmembrane region) with an amino acid sequence consisting of SEQ ID NO: 12.

In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 14 (stem/transmembrane region) with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97%, identical or at least 99% identical to SEQ ID NO: 16. In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 14 (stem/transmembrane region) with an amino acid sequence comprising SEQ ID NO: 16. In one embodiment, modification of the Zika virus envelop protein comprises replacing the region of the envelope protein corresponding to SEQ ID NO: 14 (stem/transmembrane region) with an amino acid sequence consisting of SEQ ID NO: 16.

In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region encoded by SEQ ID NO:5, SEQ ID NO:9 or SEQ ID NO: 13 with the corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14 with the corresponding region from Japanese Encephalitis Virus. In one embodiment, modification of a Zika virus envelope protein of the invention comprises replacing a region encoded by SEQ ID NO:5, SEQ ID NO:9 or SEQ ID NO: 13 with the corresponding region from Japanese Encephalitis Virus.

In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region), has been replaced with the corresponding region from the envelope protein of another flavivirus. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region), has been replaced with the corresponding region from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from Japanese Encephalitis Virus.

In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which a region corresponding to SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which a region corresponding to SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the stem region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO:6 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO:8. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region of the protein comprising SEQ ID NO:6 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO:8. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 6 has been replaced with SEQ ID NO: 8. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region comprising SEQ ID NO:6 has been replaced with SEQ ID NO:8.

In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85%> identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 12. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region of the protein comprising SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 12. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 10 has been replaced with SEQ ID NO: 12. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region comprising SEQ ID NO: 10 has been replaced with SEQ ID NO: 12.

In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the stem/transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region of the protein comprising SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 14 has been replaced with SEQ ID NO: 16. In one embodiment, the polyprotein comprises a modified Zika virus envelope protein in which the region comprising SEQ ID NO: 14 has been replaced with SEQ ID NO: 16. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from the envelope protein of another flavivirus. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from Japanese Encephalitis Virus.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which a region corresponding to SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which a region corresponding to SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the stem region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 6 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 8. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region of the protein comprising SEQ ID NO:6 has been replaced with an amino acid sequence at least85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO:8. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 6 has been replaced with SEQ ID NO: 8. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region comprising SEQ ID NO:6 has been replaced with SEQ ID NO:8.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 12. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region of the protein comprising SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 12. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 10 has been replaced with SEQ ID NO: 12. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region comprising SEQ ID NO: 10 has been replaced with SEQ ID NO: 12. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika vims envelope protein in which the stem/transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85% identical, at least 90%) identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region of the protein comprising SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85%> identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to SEQ ID NO: 16. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region corresponding to SEQ ID NO: 14 has been replaced with SEQ ID NO: 16. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a modified Zika virus envelope protein in which the region comprising SEQ ID NO: 14 has been replaced with SEQ ID NO: 16.

As noted above, nucleic acid molecules of the invention encode proteins capable of forming virus-like particles (VLPs) that elicit an immune response to Zika virus. The inventors have found that certain mutations in Zika virus structural proteins can alter the characteristics (e.g., yield, stability, immunogenicity, etc.) of VLPs comprising such proteins. Such mutations can be at locations that increase interactions between amino acids within or between proteins (e.g., hydrophobic interactions, ionic interactions, etc.). Such mutations can also affect glycosylation of the viral structural proteins. Examples of such mutations can be found in the modified proteins listed in Table 3A or Table 3B.

One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence that encodes a protein comprising an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to the prM protein portion of a modified polyprotein listed in Table 3A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding the prM protein portion of a modified polyprotein listed in Table 3A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence that encodes a protein comprising an amino acid sequence at least 90% identical, at least 95%) identical, at least 97% identical, or at least 99% identical, to the prM protein portion of a modified polyprotein comprising a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding the prM protein portion of a modified polyprotein comprising a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469- 474, and SEQ ID NO:481-522.

One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence that encodes a protein comprising an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to the envelope protein portion of a modified polyprotein listed in Table 3A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding the envelope protein portion of a modified polyprotein listed in Table 3 A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence that encodes a protein comprising an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to the envelope protein portion of a modified polyprotein comprising a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO :481-522. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding the envelope protein portion of a modified polyprotein comprising a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence that encodes a protein comprising an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical to a modified polyprotein listed in Table 3 A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding a modified polyprotein listed in Table 3 A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence that encodes a protein comprising an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to a modified polyprotein comprising a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO :481-522. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding a modified polyprotein comprising a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to a sequence encoding the prM protein portion of a polyprotein listed in Table 3 A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97%) identical, or at least 99% identical, to a sequence encoding the envelope protein portion of a polyprotein listed in Table 3 A or Table 3B. One embodiment of the invention is a nucleic acid molecule comprising a nucleic acid sequence at least 90% identical, at least 95%) identical, at least 97% identical, or at least 99% identical, to a sequence encoding an amino acid sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NO:240- 450, SEQ ID NO:460-468, SEQ ID NO:475-480, and SEQ ID NO:523-564. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:240- 450, SEQ ID NO:460-468, SEQ ID NO:475-480, and SEQ ID NO:523- 564.

Expression of the proteins encoded by nucleic acid molecules of the invention results in formation of virus-like particles capable of inducing an immune response in an individual. Thus, in certain embodiments of the invention the nucleic acid sequences encoding the signal sequence joined to the polyprotein, are functionally linked to a control element. Nucleic acid molecules of the invention comprising such control elements can be referred to as expression vectors. As used herein, the term functionally linked means that interaction cellular and/or viral proteins with control elements, affects transcription of the linked nucleotide sequences. As used herein, control elements are nucleotide sequences in the nucleotide molecule at which cellular and or viral proteins bind, such binding affecting transcription of linked nucleotide sequences. Examples of control elements include, but are not limited to, promoter sequences, enhancer sequences, repressor sequences and terminator sequences. Thus, in one embodiment, nucleic acid sequences encoding the signal sequence joined to the polyprotein, are functionally linked to a promoter sequence. A preferred promoter sequence is any promoter sequence that functions (i.e., directs transcription of linked nucleotide sequences) in a mammalian cell. Such promoters can be of mammalian, viral or bacterial origin. Examples of useful promoter sequences include, but are not limited to, mammalian elongation factor -1 (EF-1) promoter and cytomegalovirus (CMV) promoter. Promoters useful for constructing nucleic acid molecules of the invention are known to those skilled in the art. Exemplary expression vectors include polynucleotide molecules, preferably DNA molecules that are derived, for example, from a plasmid, bacteriophage, yeast or virus (e.g., adenovirus, adeno-associated virus, lentivirus, retrovirus, etc.), into which a polynucleotide can be inserted or cloned. Suitable expression vectors are known to those skilled in the art.

Proteins

Nucleic acid molecules of the invention are useful for producing proteins of the invention. Thus, one embodiment of the invention is a protein encoded by a nucleic acid molecule of the invention. One embodiment of the invention is a fusion protein comprising the signal sequence of a Japanese Encephalitis Virus prM protein, joined to a Zika virus membrane protein. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the Zika prM protein has been modified by replacing the signal sequence with the signal sequence from a Japanese Encephalitis Virus prM protein signal sequence. Such a construct is exemplified in Figure 1A. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the region corresponding to SEQ ID NO:22 has been replaced with the signal sequence from a Japanese Encephalitis Virus prM protein signal sequence. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the region comprising SEQ ID NO:22 has been replaced with the signal sequence from a Japanese Encephalitis Virus prM protein signal sequence. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the region corresponding to SEQ ID NO:22 has been replaced with an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 18. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the region corresponding to SEQ ID NO:22 has been replaced with SEQ ID NO: 18. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the region comprising SEQ ID NO:22 has been replaced with an amino acid sequence at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 18. In one embodiment, the fusion protein comprises a modified Zika virus prM protein, wherein the region comprising SEQ ID NO:22 has been replaced with SEQ ID NO: 18. In one embodiment, the fusion protein comprises an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to the sequence of a modified protein listed in Table 3A or Table 3B.

Table 3 A. Exemplary amino acid and nucleic acid sequences of modified polyproteins.

SEQ

ID Molecule Comments

NO:

63 Protein VRC5127-JEVss-E DENV4 Stem/TM

64 Protein VRC 5131-DENV1 16007 JEVss-prM-E80-V5His

65 Protein VRC5132-DENV2_New_Guinea_C_JEVss-prM-E80-V5His

66 Protein VRC5133-WNV_NY99_JEVss-prM-E80-V5His

67 Protein VRC 5134-Zika_H_PF_2013_JEVss-prM-E80-V5His

68 Protein VRC 5135-DENV1 16007 JEVss-prM-E80W101R-V5His

69 Protein VRC 5136-DENV2 New Guinea C JEVss-prM-E80W101R- V5His

70 Protein VRC 5137-WNV_NY99_JEVss-prM-E80Wl 0 lR-V5His

71 Protein VRC 5138-Zika_H_PF_2013_JEVss-prM-E80Wl 0 lR-V5His

72 Protein VRC5220-CMVR-(JEV-ss)Zika-PF2013-(+3AA)prM-E

73 Protein VRC5221 -pcDNA3.1— ZIKV_ArB770 l CprME

74 Protein VRC5222-pcDNA3.1— ZIKV_ArB7701_prME

75 Protein VRC 5223 -pcDNA3.1— ZIK V_ArD7117_CprME

76 Protein VRC5224-pcDNA3.1— ZIKV_ArD7117_prME

77 Protein VRC5225-pcDNA3.1— ZIKV_MR766-CHO_CprME

78 Protein VRC5226-pcDNA3.1— ZIKV_MR766-CHO_prME

79 Protein VRC5227-pcDNA3.1— ZIKV_MR766+CHO_CprME

80 Protein VRC5228-pcDNA3.1— ZIKV_MR766+CHO_prME

81 Protein VRC5229-pcDNA3.1— ZIKV_PHL2012_CprME

82 Protein VRC 5230-pcDNA3.1— ZIK V PHL2012_prME

83 Protein VRC523 l-pcDNA3.1— Zn V_THA2014_CprME

84 Protein VRC5232-pcDNA3.1— ZIKV_THA2014_prME

85 Protein VRC5233-pcDNA3.1-Zika_HPF2013 CprME + CHO mut

86 Protein VRC5234-pcDNA3.1-Zika_HPF2013 CprME + WNV loop + CHO mut

87 Protein VRC5235-pcDNA3.1-Zika_HPF2013 CprME + DV1 loop + CHO mut

88 Protein VRC5236-pcDNA3.1-Zika_HPF2013 CprME + DV2 loop + CHO mut

89 Protein VRC5237-pcDNA3.1-WNV NY99 CprME + Zika HPF2013 loop

+ CHO mut

90 Protein VRC5238-pcDNA3.1-DVl 16007 CprME + Zika HPF2013 1oop +

CHO mut

91 Protein VRC5239-pcDNA3.1-DV2 16681 CprME + Zika HPF2013 loop +

CHO mut

92 Protein VRC5240-pcDNA3. l-Zika_HPF2013 CprME + WNV loop

93 Protein VRC5241-pcDNA3.1-Zika_HPF2013 CprME + DV1 loop

94 Protein VRC5242-pcDNA3.1-Zika_HPF2013 CprME + DV2 loop

95 Protein VRC5243-pcDNA3.1-WNV NY99 CprME + Zika_HPF2013 loop

96 Protein VRC5244-pcDNA3.1-DVl 16007 CprME + Zika_HPF2013 loop

97 Protein VRC5245-pcDNA3.1-DV2 16681 CprME + Zika_HPF2013 loop

98 Protein VRC5271 -CMV/R— ZIKV_ArB770 l CprME

99 Protein VRC5272-CMV/R— ZIKV_ArB770 l_prME SEQ

ID Molecule Comments

NO:

100 Protein VRC5273 -CMV/R— ZIKV_ArD7117_CprME

101 Protein VRC5274-CMV/R— ZIKV_ArD7117_prME

102 Protein VRC5275-CMV/R— ZIKV_MR766-CHO_CprME

103 Protein VRC5276-CMV/R— ZIKV_MR766-CHO_prME

104 Protein VRC5277-CMV/R— Zn V_MR766+CHO_CprME

105 Protein VRC5278-CMV/R— ZIKV_MR766+CHO_prME

106 Protein VRC5279-CMV/R— ZIKV PHL2012_CprME

107 Protein VRC5280-CMV/R— ZIKV PHL2012_prME

108 Protein VRC5281 -CMV/R— ZIKV THA2014_CprME

109 Protein VRC5282-CMV/R— ZIKV THA2014_prME

110 Protein VRC5283-CMVR-(JEV-SA)Zika-PF2013-prM-wl2Gat vector

111 Protein VRC5284-CMVR-(JEV-SA)Zika-PF2013-EA275V-DTM

112 Protein VRC5285-JEVss-prM-EA275V_JEV_Stem/TM

113 Protein VRC5286-CMVR-(JEV-ss)Zika-PF2013-(+3AA)prM-EA275V

114 Protein VRC5288-pCMV/R- JEVss- AEV-ZIKV.PF2013 prME80- JEV.SA14.E20

115 Protein VRC5289-pCMV/R-JEVss-ZIKV.PF2013.prME80.A275V- JEV.SA14.E20

116 Protein VRC5290-pCMV/R-JEVss-AEV-ZIKV.PF2013.prME80.A275V- JEV.SA14.E20

117 Protein VRC5291 -pCMV/R-KZ gc- JEVss- AEV-ZIKV.PF2013 prME80- JEV.SA14.E20

118 Protein VRC5292-pCMV/R- JEVSS-ZIKV.PF2013 prME80- ZIKV.MR766.E20

119 Protein VRC5293-pCMV/R-JEVss-ZIKV.PF2013.prM50E80- ZIKV.MR766.M50E20

120 Protein VRC5294-pCMV/R- JEVss-ZIKV.PF2013.prM30E80- ZIKV.MR766.M70E20

121 Protein VRC5295-pCMV/R-hCD5ss-AEV-ZIKV.PF2013.prME80- JEV.SA14.E20

122 Protein VRC5296-pCMV/R-hCD5 SS-ZIKV.PF2013 prME

123 Protein VRC5296-pCMV/R-hCD5 SS-ZIKV.PF2013 prME. A275 V

124 Protein VRC5299-pCMV/R-hCD5 SS-ZIKV.PF2013 prME

125 Protein VRC5450_KZ-gc-JEVss-AEV- PFwt VRCZIKA BR wt optimized

126 Protein VRC545 l_KZ-gc-JEVss-AEV-PF-pr22- pr72 VRCZIKA BR 1 optimized

127 Protein VRC5452_KZ-gc-JEVss-AEV-PF- furinA VRCZIKA BR 2 optimized

128 Protein VRC5453_KZ-gc-JEVss-AEV-PF- furinB VRCZIKA BR 3 optimized

129 Protein VRC5454_KZ-gc-JEVss-AEV-PF- furinC VRCZIKA BR 4 optimized

130 Protein VRC5455_KZ-gc- JEVss- AEV-PF- furinD VRCZIKA BR 5 optimized SEQ

ID Molecule Comments

NO:

131 Protein VRC5456_KZ-gc-JEVss-AEV-PF- furinE VRCZIKA BR 6 optimized

132 Protein VRC5457_KZ-gc-JEVss-AEV-PF- furinF VRCZIKA BR 7 optimized

133 Protein VRC5458_KZ-gc-JEVss-AEV-PF- furinG VRCZIKA BR 8 optimized

134 Protein VRC5459_KZ-gc-JEVss-AEV-PF- furinH VRCZIKA BR 9 optimized

135 Protein VRC5460_KZ-gc-JEVss-AEV-PF- fusionA VRCZIKA BR 10 optimized

136 Protein VRC546 l KZ-gc-JEVss-AEV-PF- fusionB VRCZIKA BR 11 optimized

137 Protein VRC5462_KZ-gc-JEVss-AEV-PF- fusionC VRCZIKA BR 12 optimized

138 Protein VRC5463_KZ-gc-JEVss-AEV-PF- fusionD VRCZIKA BR 13 optimized

139 Protein VRC5464_KZ-gc-JEVss-AEV-PF- fusionE VRCZIKA BR 14 optimized

140 Protein VRC5465 KZ-gc-JEVss-AEV-PF- E275 VRCZIKA BR 15 optimized

141 Protein VRC5466 KZ-gc-JEVss-AEV-PF- linkWNV VRCZIKA BR 16 optimized

142 Protein VRC5467 KZ-gc-JEVss-AEV-PF- stemWNV VRCZIKA BR 17 optimized

143 Protein VRC5468 KZ-gc-JEVss-AEV-PF- E20WNV VRCZIKA BR 18 optimized

144 Protein VRC5469 KZ-gc-JEVss-AEV-PF- E20JEV VRCZIKA BR 19 optimized

145 Protein VRC5470_KZ-gc-JEVss-AEV-PF- stem+WNV VRCZIKA BR 20 optimized

146 Protein VRC547 l KZ-gc-JEVss-AEV-PF- stem+JEV VRCZIKA BR 21 optimized

147 Protein VRC5472_KZ-gc-JEVss-AEV-PF- ptstemWNV VRCZIKA BR 22 optimized

148 Protein VRC5473_KZ-gc-JEVss-AEV-PF- ptstemJEV VRCZIKA BR 23 optimized

149 Protein VRC5474_KZ-gc-JEVss-AEV-PF- 2Eaas VRCZIKA BR 24 optimized

150 Protein VRC5475_KZ-gc-JEVss-AEV-PF- glycE64 VRCZIKA BR 25 optimized

151 Protein VRC5476_KZ-gc-JEVss-AEV-PF- glycE68 VRCZIKA BR 26 optimized

152 Protein VRC5477 KZ-gc-JEVss-AEV-PF-comb 1-4-10-15-16-19- 26 VRCZIKA BR 27 optimized

153 Protein VRC5478 KZ-gc-JEVss-AEV-PF-comb 1-8-10-15-16-19- 26 VRCZIKA BR 28 optimized SEQ

ID Molecule Comments

NO:

154 Protein VRC5479 KZ-gc-JEVss-AEV-PF-comb 1-4-13-15-16-19- 26 VRCZIKA BR 29 optimized

155 Protein VRC5480 KZ-gc-JEVss-AEV-PF-comb 1-4-10-15-16-18- 26 VRCZIKA BR 30 optimized

156 Protein VRC5481 KZ-gc-JEVss-AEV-PF-comb 1 -4- 10-14-16-19- 26 VRCZIKA BR 31 optimized

157 Protein VRC5482 KZ-gc-JEVss-AEV-PF-comb 1-4-10-15-16-22- 26 VRCZIKA BR 32 optimized

158 Protein VRC5483 KZ-gc-JEVss-AEV-PF-comb4- 10 VRCZIKA BR 33 optimized

159 Protein VRC5484 KZ-gc-JEVss-AEV-PF-comb4- 19 VRCZIKA BR 34 optimized

160 Protein VRC5485 KZ-gc-JEVss-AEV-PF-comb4- 26 VRCZIKA BR 35 optimized

161 Protein VRC5486 KZ-gc-JEVss-AEV-PF-comb 10- 16 VRCZIKA BR 36 optimized

162 Protein VRC5487 KZ-gc-JEVss-AEV-PF-comb 10- 19 VRCZIKA BR 37 optimized

163 Protein VRC5488 KZ-gc-JEVss-AEV-PF-comb 19- 26 VRCZIKA BR 38 optimized

164 Protein VRC5489 KZ-gc-JEVss-AEV-PF-comb 16- 19 VRCZIKA BR 39 optimized

165 Protein VRC5490 KZ-gc-JEVss-AEV-PF-comb 15- 19 VRCZIKA BR 40 optimized

166 Protein VRC549 l KZ-gc-JEVss-AEV-PF- UgandaA VRCZIKA BR 41 optimized

167 Protein VRC5492_KZ-gc-JEVss-AEV-PF- UgandaB VRCZIKA BR 42 optimized

168 Protein VRC5493 diffKZ-gc-JEVss-AEV-PF- E20JEV VRCZIKA BR 43 optimized

169 Protein VRC6101 -ZnCV-prME-Gl 06R

170 Protein VRC6102-ZnCV-prME-L 107D

171 Protein VRC6103-ZIKV-prME-G106R, L107D

172 Protein VRC6104-ZIKV-prME-T76A, Q77G, W101R

173 Protein VRC6105-ZIKV-prME-T76A, Q77G

174 Protein VRC6106-ZIKV-prME-T76A, Q77G, G106R, L107D, W101R

175 Protein VRC6107-ZnCV-prME-G106R, L107D, W101R

176 Protein VRC6108-ZnCV-prME-T76 A

177 Protein VRC6109-ZIKV-prME-Q77G

178 Protein VRC61 10-Zn V-prME-WlOlR

179 Protein VRC61 1 1 -ZnCV-prME-K251 A

180 Protein VRC61 12-ZIKV-prME-Q253A

181 Protein VRC61 13 -ZJK V-prME-H266 A

182 Protein VRC61 14-ZIKV-prME-E262A

183 Protein VRC61 15-ZIKV-prME-V255A SEQ

ID Molecule Comments NO:

184 Protein VRC61 16-Zn V-prME-V256A

185 Protein VRC61 17-Zn V-prME-V257A

186 Protein VRC61 18-ZIKV-prME-Q261 A

187 Protein VRC61 19-Zn V-prME-D296A

188 Protein VRC6120-ZIK V-prME-K297 A

189 Protein VRC6121 -ZJK V-prME-L300 A

190 Protein VRC6122-ZIKV-prME-S304 A

191 Protein VRC6123 -ZIKV-prME-Y305 A

192 Protein VRC6124-ZIK V-prME-L307 A

193 Protein VRC6125-ZIKV-prME-R2A

194 Protein VRC6126-ZIKV-prME-G5 A

195 Protein VRC6127-ZIK V-prME-N8 A

196 Protein VRC6128-Zn V-prME-S 16 A

197 Protein VRC6129-ZIKV-prME-G28 A

198 Protein VRC6130-ZIKV-prME-A54G

199 Protein VRC6131 -ZIKV-prME-D87 A

200 Protein VRC6132-Zn V-prME-Nl 34A

201 Protein VRC6133 -ZJK V-prME-T 170 A

202 Protein VRC6134-Zn V-prME-E 177 A

203 Protein VRC6135-Zn V-prME-T 160 A

204 Protein VRC6136-Zn V-prME-Rl 93 A

205 Protein VRC6137-ZIK V-prME-P222 A

206 Protein VRC6138-ZIKV-prME-W225 A

207 Protein VRC6139-ZIK V-prME-T231 A

208 Protein VRC6140-ZIK V-prME-K316 A

209 Protein VRC6141 -ZIKV-prME-E320 A

210 Protein VRC6142-ZIKV-prME-K251R

21 1 Protein VRC6143 -ZIKV-prME-Q253E

212 Protein VRC6144-ZIK V-prME-E262Q

213 Protein VRC6145-ZIKV-prME-V2551

214 Protein VRC6146-ZIKV-prME-V256I

215 Protein VRC6147-ZIKV-prME-V257I

216 Protein VRC6148-ZIKV-prME-Q26 IE

217 Protein VRC6149-ZIK V-prME-D296N

218 Protein VRC6150-ZIKV-prME-K297R

219 Protein VRC6151 -ZJK V-prME-L3001

220 Protein VRC6152-ZIKV-prME-S304T

221 Protein VRC6153 -ZJK V-prME- Y305F

222 Protein VRC6154-ZIKV-prME-L307I

223 Protein VRC6155-ZIKV-prME-R2K

224 Protein VRC6156-ZIKV-prME-G5 S

225 Protein VRC6157-ZIKV-prME-N8D

226 Protein VRC6158-Zn V-prME-S 16T SEQ

ID Molecule Comments

NO:

227 Protein VRC6159-ZIKV-prME-G28S

228 Protein VRC6160-ZIKV-prME-A54S

229 Protein VRC6161 -ZIKV-prME-D87N

230 Protein VRC6162-Zn V-prME-Nl 34D

231 Protein VRC6163 -Zn V-prME-T 170S

232 Protein VRC6164-ZIK V-prME-E 177Q

233 Protein VRC6165 -ZIK V-prME-T 160 S

234 Protein VRC6166-Zn V-prME-Rl 93K

235 Protein VRC6167-ZIKV-prME-P222G

236 Protein VRC6168-ZIKV-prME-W225F

237 Protein VRC6169-ZIKV-prME-T231 S

238 Protein VRC6170-ZIKV-prME-K316R

239 Protein VRC6171 -ZIKV-prME-E320Q

Nucleic Acid Sequences

240 Nucleic Acid VRC4974-CMVR-(JEV-S A)Zika-PF2013 -prM-E

241 Nucleic Acid VRC4975-CMVR-(mIg-S A)Zika-PF2013-prM-E

242 Nucleic Acid VRC4976-CMVR-Zika-PF2013 -prM-E

243 Nucleic Acid VRC4977-CMVR-(JEV-S A)Zika-PF2013 -E

244 Nucleic Acid VRC4978-CMVR-(mIg-S A)Zika-PF2013 -E

245 Nucleic Acid VRC4979-CMVR- Zika-PF2013-E

246 Nucleic Acid VRC4980-CMVR- Zika-PF2013-E-DTM-Avi3chis

247 Nucleic Acid VRC4983-CMVR- Zika-PF2013-E-DTM

248 Nucleic Acid VRC4984-CMVR- Zika-PF2013-E-DTM-Avi3chis

249 Nucleic Acid VRC5102-CMVR-(JEV-S A)Zika-PF2013 -E-DTM

250 Nucleic Acid VRC5103 -CMVR-(mIg- S A)Zika-PF2013 -E-DTM

251 Nucleic Acid VRC5104-CMVR-(JEV-S A)Zika-PF2013 -E-DFP 1

252 Nucleic Acid VRC5105-CMVR-(JEV-S A)Zika-PF2013-E-DFP2

253 Nucleic Acid VRC5106-CMVR-(JEV-S A)Zika-PF2013 -E-DFP 1 -DTM

254 Nucleic Acid VRC5107-CMVR-(JEV-S A)Zika-PF2013 -E-DFP2-DTM

255 Nucleic Acid VRC5108-CMVR-(JEV-S A)Zika-PF2013 -E-DFP 1 -DTM- Avi3 chis

256 Nucleic Acid VRC5109-CMVR-(JEV-SA)Zika-PF2013-E-DFP2-DTM-Avi3chis

257 Nucleic Acid VRC5110-CMVR-(JEV-S A)Zika-PF2013-prM-CS 1 -E

258 Nucleic Acid VRC511 l-CMVR-(JEV-SA)Zika-PF2013-prM-CS2-E

259 Nucleic Acid VRC5112-CMVR-(JEV-SA)Zika-PF2013-prM-E-DFPl

260 Nucleic Acid VRC5113-CMVR-(JEV-SA)Zika-PF2013-prM-E-DFP2

261 Nucleic Acid VRC5114-CMVR-(JEV-S A)Zika-PF2013 -prM-CS 1 -E-DFP 1

262 Nucleic Acid VRC5115-CMVR-(JEV-S A)Zika-PF2013-prM-CS2-E-DFP 1

263 Nucleic Acid VRC5116-CMVR-(JEV-S A)Zika-PF2013-prM-CS 1 -E-DFP2

264 Nucleic Acid VRC5117-CMVR-(JEV-SA)Zika-PF2013-prM-CS2-E-DFP2

265 Nucleic Acid VRC5118-CMVR-(JEV-S A)Zika-PF2013-prM-CS 1 -E-DFP 1 - DTM

266 Nucleic Acid VRC5119-CMVR-(JEV-S A)Zika-PF2013-prM-CS2-E-DFP 1 - DTM

267 Nucleic Acid VRC5120-CMVR-(JEV-S A)Zika-PF2013 -prM-CS 1 -E-DFP2-DTM SEQ

ID Molecule Comments

NO:

268 Nucleic Acid VRC5121 -CMVR-(JEV-S A)Zika-PF2013 -prM-CS2-E-DFP2-DTM

269 Nucleic Acid VRC5122-JEVss-prM-E_WNV_Stem/TM

270 Nucleic Acid VRC5123-pCMV/R-JEVss-ZIKV.PF2013.prME80-JEV.SA14.E20

271 Nucleic Acid VRC5124-JEVss-E WNV Stem/TM

272 Nucleic Acid VRC5125-JEVss-E JEV Stem/TM

273 Nucleic Acid VRC5126-JEVss-prM-E_ DENV4_Stem/TM

274 Nucleic Acid VRC5127-JEVss-E DENV4 Stem/TM

275 Nucleic Acid VRC 5131-DENV1 16007 JEVss-prM-E80-V5His

276 Nucleic Acid VRC5132-DENV2_New_Guinea_C_JEVss-prM-E80-V5His

277 Nucleic Acid VRC5133-WNV_NY99_JEVss-prM-E80-V5His

278 Nucleic Acid VRC 5134-Zika_H_PF_2013_JEVss-prM-E80-V5His

279 Nucleic Acid VRC 5135-DENV1 16007 JEVss-prM-E80W101R-V5His

280 Nucleic Acid VRC5136-DENV2 New Guinea C JEVss-prM-E80W101R- V5His

281 Nucleic Acid VRC 5137-WNV_NY99_JEVss-prM-E80Wl 0 lR-V5His

282 Nucleic Acid VRC 5138-Zika_H_PF_2013_JEVss-prM-E80Wl 0 lR-V5His

283 Nucleic Acid VRC5220-CMVR-(JEV-ss)Zika-PF2013-(+3AA)prM-E

284 Nucleic Acid VRC5221 -pcDNA3.1— ZIKV_ArB770 l CprME

285 Nucleic Acid VRC5222-pcDNA3.1— ZIKV_ArB7701_prME

286 Nucleic Acid VRC 5223 -pcDNA3.1— ZIK V_ArD7117_CprME

287 Nucleic Acid VRC5224-pcDNA3.1— ZIKV_ArD7117_prME

288 Nucleic Acid VRC5225-pcDNA3.1— ZIKV_MR766-CHO_CprME

289 Nucleic Acid VRC5226-pcDNA3.1— ZIKV_MR766-CHO_prME

290 Nucleic Acid VRC5227-pcDNA3.1— ZIKV_MR766+CHO_CprME

291 Nucleic Acid VRC5228-pcDNA3.1— ZIKV_MR766+CHO_prME

292 Nucleic Acid VRC5229-pcDNA3.1— ZIKV_PHL2012_CprME

293 Nucleic Acid VRC5230-pcDNA3.1— Zn V_PHL2012_prME

294 Nucleic Acid VRC523 l-pcDNA3.1— Zn V_THA2014_CprME

295 Nucleic Acid VRC5232-pcDNA3.1— ZIKV_THA2014_prME

296 Nucleic Acid VRC5233-pcDNA3.1-Zika_HPF2013 CprME + CHO mut

297 Nucleic Acid VRC5234-pcDNA3.1-Zika_HPF2013 CprME + WNV loop + CHO mut

298 Nucleic Acid VRC5235-pcDNA3.1-Zika_HPF2013 CprME + DV1 loop + CHO mut

299 Nucleic Acid VRC5236-pcDNA3.1-Zika_HPF2013 CprME + DV2 loop + CHO mut

300 Nucleic Acid VRC5237-pcDNA3.1-WNV NY99 CprME + Zika HPF2013 loop

+ CHO mut

301 Nucleic Acid VRC5238-pcDNA3.1-DVl 16007 CprME + Zika HPF2013 1oop +

CHO mut

302 Nucleic Acid VRC5239-pcDNA3.1-DV2 16681 CprME + Zika HPF2013 loop +

CHO mut

303 Nucleic Acid VRC5240-pcDNA3. l-Zika_HPF2013 CprME + WNV loop

304 Nucleic Acid VRC5241-pcDNA3.1-Zika_HPF2013 CprME + D VI loop SEQ

ID Molecule Comments

NO:

305 Nucleic Acid VRC5242-pcDNA3.1-Zika_HPF2013 CprME + DV2 loop

306 Nucleic Acid VRC5243-pcDNA3.1-WNV NY99 CprME + Zika_HPF2013 loop

307 Nucleic Acid VRC5244-pcDNA3.1-DVl 16007 CprME + Zika_HPF2013 loop

308 Nucleic Acid VRC5245-pcDNA3.1-DV2 16681 CprME + Zika_HPF2013 loop

309 Nucleic Acid VRC5271 -CMV/R— ZIKV_ArB770 l CprME

310 Nucleic Acid VRC5272-CMV/R— ZIKV_ArB770 l_prME

311 Nucleic Acid VRC5273 -CMV/R— ZIKV_ArD7117_CprME

312 Nucleic Acid VRC5274-CMV/R— ZIKV_ArD7117_prME

313 Nucleic Acid VRC5275-CMV/R— Zn V_MR766-CHO_CprME

314 Nucleic Acid VRC5276-CMV/R— Zn V_MR766-CHO_prME

315 Nucleic Acid VRC5277-CMV/R— ZIKV_MR766+CHO_CprME

316 Nucleic Acid VRC5278-CMV/R— Zn V_MR766+CHO_prME

317 Nucleic Acid VRC5279-CMV/R— ZIK V PHL2012_CprME

318 Nucleic Acid VRC5280-CMV/R— ZIK V PHL2012_prME

319 Nucleic Acid VRC5281 -CMV/R— ZIKV THA2014_CprME

320 Nucleic Acid VRC5282-CMV/R— ZIKV_THA2014_prME

321 Nucleic Acid VRC5283 -CMVR-(JEV-SA)Zika-PF2013 -prM-wl2Gat vector

322 Nucleic Acid VRC5284-CMVR-(JEV-SA)Zika-PF2013-EA275V-DTM

323 Nucleic Acid VRC5285-JEVss-prM-EA275V_JEV_Stem/TM

324 Nucleic Acid VRC5286-CMVR-(JEV-ss)Zika-PF2013-(+3AA)prM-EA275V

325 Nucleic Acid VRC5288-pCMV/R-JEVss-AEV-ZIKV.PF2013.prME80- JEV.SA14.E20

326 Nucleic Acid VRC5289-pCMV/R-JEVss-ZIKV.PF2013.prME80.A275V- JEV.SA14.E20

327 Nucleic Acid VRC5290-pCMV/R-JEVss-AEV-ZIKV.PF2013.prME80.A275V- JEV.SA14.E20

328 Nucleic Acid VRC5291 -pCMV/R-KZ gc- JEVss- AEV-ZIKV.PF2013 prME80- JEV.SA14.E20

329 Nucleic Acid VRC5292-pCMV/R-JEVss-ZIKV.PF2013 prME80- ZIKV.MR766.E20

330 Nucleic Acid VRC5293-pCMV/R-JEVss-ZIKV.PF2013.prM50E80- ZIKV.MR766.M50E20

331 Nucleic Acid VRC5294-pCMV/R-JEVss-ZIKV.PF2013.prM30E80- ZIKV.MR766.M70E20

332 Nucleic Acid VRC5295-pCMV/R-hCD5 ss- AEV-ZIKV.PF2013 prME80- JEV.SA14.E20

333 Nucleic Acid VRC5296-pCMV/R-hCD5 SS-ZIKV.PF2013 prME

334 Nucleic Acid VRC5296-pCMV/R-hCD5 SS-ZIKV.PF2013 prME. A275 V

335 Nucleic Acid VRC5299-pCMV/R-hCD5 SS-ZIKV.PF2013 prME

336 Nucleic Acid VRC5450_KZ-gc-JEVss-AEV- PFwt VRCZIKA BR wt optimized

337 Nucleic Acid VRC5451 KZ-gc-JEVss-AEV-PF-pr22- pr72 VRCZIKA BR 1 optimized

338 Nucleic Acid VRC5452_KZ-gc-JEVss-AEV-PF- furinA VRCZIKA BR 2 optimized SEQ

ID Molecule Comments NO:

339 Nucleic Acid VRC5453_KZ-gc-JEVss-AEV-PF- furinB VRCZIKA BR 3 optimized

340 Nucleic Acid VRC5454_KZ-gc-JEVss-AEV-PF- furinC VRCZIKA BR 4 optimized

341 Nucleic Acid VRC5455_KZ-gc-JEVss-AEV-PF- furinD VRCZIKA BR 5 optimized

342 Nucleic Acid VRC5456_KZ-gc-JEVss-AEV-PF- furinE VRCZIKA BR 6 optimized

343 Nucleic Acid VRC5457_KZ-gc-JEVss-AEV-PF- furinF VRCZIKA BR 7 optimized

344 Nucleic Acid VRC5458_KZ-gc-JEVss-AEV-PF- furinG VRCZIKA BR 8 optimized

345 Nucleic Acid VRC5459_KZ-gc-JEVss-AEV-PF- furinH VRCZIKA BR 9 optimized

346 Nucleic Acid VRC5460_KZ-gc-JEVss-AEV-PF- fusionA VRCZIKA BR 10 optimized

347 Nucleic Acid VRC546 l_KZ-gc-JEVss-AEV-PF- fusionB VRCZIKA BR 11 optimized

348 Nucleic Acid VRC5462 KZ-gc-JEVss-AEV-PF- fusionC VRCZIKA BR 12 optimized

349 Nucleic Acid VRC5463_KZ-gc-JEVss-AEV-PF- fusionD VRCZIKA BR 13 optimized

350 Nucleic Acid VRC5464_KZ-gc-JEVss-AEV-PF- fusionE VRCZIKA BR 14 optimized

351 Nucleic Acid VRC5465 KZ-gc-JEVss-AEV-PF- E275 VRCZIKA BR 15 optimized

352 Nucleic Acid VRC5466 KZ-gc-JEVss-AEV-PF- linkWNV VRCZIKA BR 16 optimized

353 Nucleic Acid VRC5467_KZ-gc-JEVss-AEV-PF- stemWNV VRCZIKA BR 17 optimized

354 Nucleic Acid VRC5468 KZ-gc-JEVss-AEV-PF- E20WNV VRCZIKA BR 18 optimized

355 Nucleic Acid VRC5469 KZ-gc-JEVss-AEV-PF- E20JEV VRCZIKA BR 19 optimized

356 Nucleic Acid VRC5470_KZ-gc-JEVss-AEV-PF- stem+WNV VRCZIKA BR 20 optimized

357 Nucleic Acid VRC547 l_KZ-gc-JEVss-AEV-PF- stem+JEV VRCZIKA BR 21 optimized

358 Nucleic Acid VRC5472_KZ-gc-JEVss-AEV-PF- ptstemWNV VRCZIKA BR 22 optimized

359 Nucleic Acid VRC5473_KZ-gc-JEVss-AEV-PF- ptstemJEV VRCZIKA BR 23 optimized

360 Nucleic Acid VRC5474_KZ-gc-JEVss-AEV-PF- 2Eaas VRCZIKA BR 24 optimized

361 Nucleic Acid VRC5475 KZ-gc-JEVss-AEV-PF- glycE64 VRCZIKA BR 25 optimized SEQ

ID Molecule Comments

NO:

362 Nucleic Acid VRC5476_KZ-gc-JEVss-AEV-PF- glycE68 VRCZIKA BR 26 optimized

363 Nucleic Acid VRC5477 KZ-gc-JEVss-AEV-PF-comb 1-4-10-15-16-19- 26 VRCZIKA BR 27 optimized

364 Nucleic Acid VRC5478_KZ-gc-JEVss-AEV-PF-comb 1-8-10-15-16-19- 26 VRCZIKA BR 28 optimized

365 Nucleic Acid VRC5479 KZ-gc-JEVss-AEV-PF-comb 1-4-13-15-16-19- 26 VRCZIKA BR 29 optimized

366 Nucleic Acid VRC5480 KZ-gc-JEVss-AEV-PF-comb 1-4-10-15-16-18- 26 VRCZIKA BR 30 optimized

367 Nucleic Acid VRC5481 KZ-gc-JEVss-AEV-PF-comb 1-4-10-14-16-19- 26 VRCZIKA BR 31 optimized

368 Nucleic Acid VRC5482 KZ-gc-JEVss-AEV-PF-comb 1-4-10-15-16-22- 26 VRCZIKA BR 32 optimized

369 Nucleic Acid VRC5483 KZ-gc-JEVss-AEV-PF-comb4- 10 VRCZIKA BR 33 optimized

370 Nucleic Acid VRC5484 KZ-gc-JEVss-AEV-PF-comb4- 19 VRCZIKA BR 34 optimized

371 Nucleic Acid VRC5485 KZ-gc-JEVss-AEV-PF-comb4- 26 VRCZIKA BR 35 optimized

372 Nucleic Acid VRC5486 KZ-gc-JEVss-AEV-PF-comb 10- 16 VRCZIKA BR 36 optimized

373 Nucleic Acid VRC5487 KZ-gc-JEVss-AEV-PF-comb 10- 19 VRCZIKA BR 37 optimized

374 Nucleic Acid VRC5488 KZ-gc-JEVss-AEV-PF-comb 19- 26 VRCZIKA BR 38 optimized

375 Nucleic Acid VRC5489 KZ-gc-JEVss-AEV-PF-comb 16- 19 VRCZIKA BR 39 optimized

376 Nucleic Acid VRC5490 KZ-gc-JEVss-AEV-PF-comb 15- 19 VRCZIKA BR 40 optimized

377 Nucleic Acid VRC549 l_KZ-gc-JEVss-AEV-PF- UgandaA VRCZIKA BR 41 optimized

378 Nucleic Acid VRC5492_KZ-gc-JEVss-AEV-PF- UgandaB VRCZIKA BR 42 optimized

379 Nucleic Acid VRC5493 diffKZ-gc-JEVss-AEV-PF- E20JEV VRCZIKA BR 43 optimized

380 Nucleic Acid VRC6101 -ZnCV-prME-Gl 06R

381 Nucleic Acid VRC6102-ZnCV-prME-L 107D

382 Nucleic Acid VRC6103-ZnCV-prME-G106R, L107D

383 Nucleic Acid VRC6104-ZIKV-prME-T76A, Q77G, W101R

384 Nucleic Acid VRC6105-ZnCV-prME-T76A, Q77G

385 Nucleic Acid VRC6106-ZnCV-prME-T76A, Q77G, G106R, L107D, W101R

386 Nucleic Acid VRC6107-ZnCV-prME-G106R, L107D, W101R

387 Nucleic Acid VRC6108-ZIKV-prME-T76 A

388 Nucleic Acid VRC6109-ZnCV-prME-Q77G

389 Nucleic Acid VRC6110-ZnCV-prME-W 101R SEQ

ID Molecule Comments NO:

390 Nucleic Acid VRC61 1 1 -ZIKV-prME-K251 A

391 Nucleic Acid VRC61 12-ZIKV-prME-Q253A

392 Nucleic Acid VRC61 13 -ZJK V-prME-H266 A

393 Nucleic Acid VRC61 14-ZIKV-prME-E262A

394 Nucleic Acid VRC61 15-ZIKV-prME-V255A

395 Nucleic Acid VRC61 16-ZIKV-prME-V256A

396 Nucleic Acid VRC61 17-ZIKV-prME-V257A

397 Nucleic Acid VRC61 18-ZIKV-prME-Q261 A

398 Nucleic Acid VRC61 19-ZIKV-prME-D296A

399 Nucleic Acid VRC6120-ZIK V-prME-K297 A

400 Nucleic Acid VRC6121 -ZJK V-prME-L300 A

401 Nucleic Acid VRC6122-ZIKV-prME-S304 A

402 Nucleic Acid VRC6123 -ZIKV-prME-Y305 A

403 Nucleic Acid VRC6124-ZIK V-prME-L307 A

404 Nucleic Acid VRC6125-ZIKV-prME-R2A

405 Nucleic Acid VRC6126-ZIKV-prME-G5A

406 Nucleic Acid VRC6127-ZIK V-prME-N8 A

407 Nucleic Acid VRC6128-Zn V-prME-S 16 A

408 Nucleic Acid VRC6129-ZIKV-prME-G28A

409 Nucleic Acid VRC6130-ZIKV-prME-A54G

410 Nucleic Acid VRC6131 -ZIKV-prME-D87 A

41 1 Nucleic Acid VRC6132-Zn V-prME-Nl 34A

412 Nucleic Acid VRC6133 -ZJK V-prME-T 170 A

413 Nucleic Acid VRC6134-Zn V-prME-E 177 A

414 Nucleic Acid VRC6135-Zn V-prME-T 160 A

415 Nucleic Acid VRC6136-Zn V-prME-Rl 93 A

416 Nucleic Acid VRC6137-ZIK V-prME-P222 A

417 Nucleic Acid VRC6138-ZIKV-prME-W225 A

418 Nucleic Acid VRC6139-ZIK V-prME-T231 A

419 Nucleic Acid VRC6140-ZIK V-prME-K316 A

420 Nucleic Acid VRC6141 -ZIKV-prME-E320 A

421 Nucleic Acid VRC6142-ZIKV-prME-K251R

422 Nucleic Acid VRC6143 -ZIKV-prME-Q253E

423 Nucleic Acid VRC6144-ZIK V-prME-E262Q

424 Nucleic Acid VRC6145-ZIKV-prME-V2551

425 Nucleic Acid VRC6146-ZIKV-prME-V256I

426 Nucleic Acid VRC6147-ZIKV-prME-V257I

427 Nucleic Acid VRC6148-ZIKV-prME-Q26 IE

428 Nucleic Acid VRC6149-ZIK V-prME-D296N

429 Nucleic Acid VRC6150-ZIKV-prME-K297R

430 Nucleic Acid VRC6151 -ZJK V-prME-L3001

431 Nucleic Acid VRC6152-ZIKV-prME-S304T

432 Nucleic Acid VRC6153 -ZJK V-prME- Y305F SEQ

ID Molecule Comments NO:

433 Nucleic Acid VRC6154-ZIKV-prME-L307I

434 Nucleic Acid VRC6155-ZIKV-prME-R2K

435 Nucleic Acid VRC6156-ZIKV-prME-G5 S

436 Nucleic Acid VRC6157-ZIKV-prME-N8D

437 Nucleic Acid VRC6158-Zn V-prME-S 16T

438 Nucleic Acid VRC6159-ZIKV-prME-G28S

439 Nucleic Acid VRC6160-ZIKV-prME-A54S

440 Nucleic Acid VRC6161 -ZIKV-prME-D87N

441 Nucleic Acid VRC6162-ZIKV-prME-N 134D

442 Nucleic Acid VRC6163 -Zn V-prME-T 170S

443 Nucleic Acid VRC6164-ZIK V-prME-E 177Q

444 Nucleic Acid VRC6165 -ZIK V-prME-T 160 S

445 Nucleic Acid VRC6166-ZIKV-prME-Rl 93K

446 Nucleic Acid VRC6167-ZIKV-prME-P222G

447 Nucleic Acid VRC6168-ZIKV-prME-W225F

448 Nucleic Acid VRC6169-ZIKV-prME-T231 S

449 Nucleic Acid VRC6170-ZIKV-prME-K316R

450 Nucleic Acid VRC6171 -ZIKV-prME-E320Q

451 Protein VRC6906 WlOlR in 5288

452 Protein VRC6907 G106R in 5288

453 Protein VRC6908 L107D in 5288

454 Protein VRC6909 101 106 in 5288

455 Protein VRC6910 101 107 in 5288

456 Protein VRC6911 106 107 in 5288

457 Protein VRC6912 101 106 107 in 5288

458 Protein VRC6913 101 106 in 5283

459 Protein VRC6914 101 107 in 5283

460 Nucleic Acid VRC6906 WlOlR in 5288

461 Nucleic Acid VRC6907 G106R in 5288

462 Nucleic Acid VRC6908 L107D in 5288

463 Nucleic Acid VRC6909 101 106 in 5288

464 Nucleic Acid VRC6910 101 107 in 5288

465 Nucleic Acid VRC6911 106 107 in 5288

466 Nucleic Acid VRC6912 101 106 107 in 5288

467 Nucleic Acid VRC6913 101 106 in 5283

468 Nucleic Acid VRC6914 101 107 in 5283

469 Protein VRC5653 VPL#4 in 5288

470 Protein VRC5654 VPL#5 in 5288

471 Protein VRC5655 VPL#14 in 5288

472 Protein VRC5656 VPL#4 in 5283

473 Protein VRC5657 VPL#5 in 5283

474 Protein VRC5658 VPL#14 in 5283

475 Nucleic Acid VRC5653 VPL#4 in 5288 SEQ

ID Molecule Comments NO:

476 Nucleic Acid VRC5654 VPL#5 in 5288

477 Nucleic Acid VRC5655 VPL#14 in 5288

478 Nucleic Acid VRC5656 VPL#4 in 5283

479 Nucleic Acid VRC5657 VPL#5 in 5283

480 Nucleic Acid VRC5658 VPL#14 in 5283

Table 3B

515 Protein VRC6855 FusL2.3 in 5288

516 Protein VRC6856 FusL3.1 in 5288

517 Protein VRC6857 FusL3.2 in 5288

518 Protein VRC6858 FusL3.3 in 5288

519 Protein VRC6859 FusL9.1 in 5288

520 Protein VRC6860 FusL9.2 in 5288

521 Protein VRC6861 FusL9.3 in 5288

522 Protein VRC6862 FusL9.4 in 5288

523 Nucleic acid VRC6821 VP1 in 5283

524 Nucleic acid VRC6822 VP2 in 5283

525 Nucleic acid VRC6823 VHB1 in 5283

526 Nucleic acid VRC6824 VHB2 in 5283

527 Nucleic acid VRC6825 VHB3 in 5283

528 Nucleic acid VRC6826 Vpmutl in 5283

529 Nucleic acid VRC6827 SSI in 5283

530 Nucleic acid VRC6828 SS2 in 5283

531 Nucleic acid VRC6829 SS3 in 5283

532 Nucleic acid VRC6830 SS4 in 5283

533 Nucleic acid VRC6831 SS5 in 5283

534 Nucleic acid VRC6832 FusL2.1 in 5283

535 Nucleic acid VRC6833 FusL2.2 in 5283

536 Nucleic acid VRC6834 FusL2.3 in 5283

537 Nucleic acid VRC6835 FusL3.1 in 5283

538 Nucleic acid VRC6836 FusL3.2 in 5283

539 Nucleic acid VRC6837 FusL3.3 in 5283

540 Nucleic acid VRC6838 FusL9.1 in 5283

541 Nucleic acid VRC6839 FusL9.2 in 5283

542 Nucleic acid VRC6840 FusL9.3 in 5283

543 Nucleic acid VRC6841 FusL9.4 in 5283

544 Nucleic acid VRC6842 VP1 in 5288

545 Nucleic acid VRC6843 VP2 in 5288

546 Nucleic acid VRC6844 VHB1 in 5288

547 Nucleic acid VRC6845 VHB2 in 5288

548 Nucleic acid VRC6846 VHB3 in 5288

549 Nucleic acid VRC6847 Vpmutl in 5288

550 Nucleic acid VRC6848 SSI in 5288

551 Nucleic acid VRC6849 SS2 in 5288

552 Nucleic acid VRC6850 SS3 in 5288

553 Nucleic acid VRC6851 SS4 in 5288

554 Nucleic acid VRC6852 SS5 in 5288

555 Nucleic acid VRC6853 FusL2.1 in 5288

556 Nucleic acid VRC6854 FusL2.2 in 5288

557 Nucleic acid VRC6855 FusL2.3 in 5288

558 Nucleic acid VRC6856 FusL3.1 in 5288

559 Nucleic acid VRC6857 FusL3.2 in 5288

560 Nucleic acid VRC6858 FusL3.3 in 5288 561 Nucleic acid VRC6859 FusL9.1 in 5288

562 Nucleic acid VRC6860 FusL9.2 in 5288

563 Nucleic acid VRC6861 FusL9.3 in 5288

564 Nucleic acid VRC6862 FusL9.4 in 5288 embodiment, the fusion protein comprises an amino acid sequence of a modified protein Listed in Table 3A or Table 3B. In one embodiment, the fusion protein comprises an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO :481-522. In one embodiment, the fusion protein comprises an amino acid sequence comprising an amino acid sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

One embodiment of the invention is a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from the envelope protein of another flavivirus. In one embodiment, the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from Japanese Encephalitis Virus.

One embodiment of the invention is a modified Zika virus envelope protein in which a region of the envelope protein corresponding to SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the region corresponding to SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

One embodiment of the invention is a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, a region of the envelope protein comprising SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

One embodiment of the invention is a modified Zika virus envelope protein in which the stem region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the region of the envelope protein corresponding to SEQ ID NO:6 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to SEQ ID NO: 8. In one embodiment, the region of the envelope protein comprising SEQ ID NO:6 has been replaced with an amino acid sequence at least 85%> identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to SEQ ID NO: 8. In one embodiment, the region of the envelope protein corresponding to SEQ ID NO: 6 has been replaced with SEQ ID NO: 8. In one embodiment, a region of the envelope protein comprising SEQ ID NO:6 has been replaced with SEQ ID NO:8.

One embodiment of the invention is a modified Zika virus envelope protein in which the transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the region of the envelope protein corresponding to SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to SEQ ID NO: 12. In one embodiment, the region of the envelope protein comprising SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to SEQ ID NO: 12. In one embodiment, the region of the envelope protein corresponding to SEQ ID NO: 10 has been replaced with SEQ ID NO: 12. In one embodiment, the region of the envelope protein comprising SEQ ID NO: 10 has been replaced with SEQ ID NO: 12.

One embodiment of the invention is a modified Zika virus envelope protein in which the stem/transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the region of the envelope protein corresponding to SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the region of the envelope protein comprising SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the region of the envelope protein corresponding to SEQ ID NO: 14 has been replaced with SEQ ID NO: 16. In one embodiment, the region of the envelope protein comprising SEQ ID NO: 14 has been replaced with SEQ ID NO: 16.

The inventors have discovered that certain mutations in Zika virus structural proteins can alter the characteristics (e.g., yield, stability, immunogenicity, etc.) of VLPs comprising such proteins. Thus, in one embodiment, a fusion protein of the invention comprises one or more mutations that increase the yield, stability of immunogenicity of VLPs comprising the mutated structural protein. In one embodiment, a fusion protein of the invention comprises a Zika virus structural protein comprising one or more mutations from a modified protein listed in Tablel .

One embodiment of the invention is protein comprising an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to the amino acid sequence of a modified protein listed in Table 1. Table 1 lists the sequences of modified polyproteins, some of which contain site specific mutations such as substitution mutations meant to alter the stability or immunogenicity, for example, of VLPs made from such proteins. Thus, those skilled in the art will understand that proteins having some percent identity with the sequences listed in Table 3A or Table 3B, will contain the mutations of the sequence to which they are being compared. For example, a protein having some identity with SEQ ID NO: 192, will still contain a leucine to alanine substitution at the amino acid position corresponding to position 305. Thus, one embodiment of the invention is protein comprising an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to the amino acid sequence of a modified protein listed in Table 1, wherein the protein comprises the one or more mutations present in the modified protein having a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522. One embodiment of the invention is protein comprising an amino acid sequence of a modified protein listed in Table 3A or Table 3B. One embodiment of the invention is protein comprising an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99%) identical, to the amino acid sequence of a modified protein having a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522, wherein the protein comprises the one or more mutations present in the modified protein having a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522. In one embodiment, a protein of the invention comprises an amino acid sequence of a modified protein having a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481- 522.

VLPS

As has been discussed, proteins of the invention are capable of forming virus-like particles (VLPs) that elicit an immune response to Zika virus. Preferred VLPs are those that display on their surface epitopes that elicit an immune response to Zika virus. Thus, one embodiment of the invention is a virus-like particle (VLP) comprising a protein encoded by one or more nucleic acid molecules of the invention. One embodiment of the invention is a VLP comprising one or more proteins of the invention. One embodiment of the invention is a VLP comprising a membrane and/or envelope protein of the invention.

One embodiment of the invention is VLP comprising a modified Zika virus envelope protein in which the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from the envelope protein of another flavivirus. In one embodiment, the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the stem region, the transmembrane region, or both (the stem/transmembrane region) has been replaced with the corresponding region from Japanese Encephalitis Virus. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which a region of the envelope protein corresponding to SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which a corresponding to SEQ ID NO: 6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

In one embodiment, the VLP comprises a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of a flavivirus selected from the group consisting of Dengue virus, Japanese Encephalitis Virus, Murray Valley Encephalitis Virus, St. Louis Encephalitis Virus, West Nile Virus, and Yellow Fever Virus. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which a region of the envelope protein comprising SEQ ID NO:6, SEQ ID NO: 10 or SEQ ID NO: 14, has been replaced with a corresponding region from the envelope protein of Japanese Encephalitis Virus.

In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the stem region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein corresponding to SEQ ID NO:6 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO:8. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein comprising SEQ ID NO:6 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 8. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein corresponding to SEQ ID NO: 6 has been replaced with SEQ ID NO:8. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which portion of the envelope protein comprising SEQ ID NO:6 has been replaced with SEQ ID NO:8.

One embodiment of the invention is a VLP comprising a modified Zika virus envelope protein in which the transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein corresponding to SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 12. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the portion of the envelope protein comprising SEQ ID NO: 10 has been replaced with an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 12. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein corresponding to SEQ ID NO: 10 has been replaced with SEQ ID NO: 12. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the portion of the envelope protein comprising SEQ ID NO: 10 has been replaced with SEQ ID NO: 12.

One embodiment of the invention is a VLP comprising a modified Zika virus envelope protein in which the stem/transmembrane region has been replaced with the corresponding region from Japanese Encephalitis Virus envelope protein. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein corresponding to SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the portion of the envelope protein comprising SEQ ID NO: 14 has been replaced with an amino acid sequence at least 85%) identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to SEQ ID NO: 16. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the region of the envelope protein corresponding to SEQ ID NO: 14 has been replaced with SEQ ID NO: 16. In one embodiment, the VLP comprises a modified Zika virus envelope protein in which the portion of the envelope protein comprising SEQ ID NO: 14 has been replaced with SEQ ID NO: 16.

As previously discussed, mutations (e.g., substitution mutations) in specific locations in Zika virus structural proteins can alter the characteristics (e.g., yield, stability, immunogenicity, etc.) of VLPs comprising such proteins. Thus, in one embodiment, the VLP comprises a modified protein of the invention, wherein the protein comprises at least one mutation from a modified protein listed in Table 3A or Table 3B. In one embodiment, the VLP comprises a protein comprising an amino acid sequence at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, or at least 99% identical, to the amino acid sequence of a modified protein listed in Table 3A or Table 3B, wherein the protein comprises the mutation of the modified protein listed in Table 3A or Table 3B. In one embodiment, the VLP comprises a protein comprising the amino acid sequence of a modified protein listed in Table 3A or Table 3B. In one embodiment, the VLP comprises a protein comprising an amino acid sequence at least 85% identical, at least 90% identical, at least 95%) identical, at least 97% identical, or at least 99% identical, to the amino acid sequence of a modified protein having a sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481- 522. In one embodiment, the VLP comprises a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO:29-239, SEQ ID NO: 451-459, SEQ ID NO:469-474, and SEQ ID NO:481-522.

In one embodiment, the VLP comprises a modified Zika virus membrane protein. In one embodiment, the modified Zika virus membrane protein comprises a mutation from modified membrane protein listed in Table 3 A or Table 3B. In one embodiment, the modified Zika virus membrane protein comprise a mutation at a position corresponding to amino acid position H7 in SEQ ID NO:2.

In one embodiment, the VLP comprises a modified Zika virus envelope protein. In one embodiment, the modified Zika virus envelope protein comprises a mutation in the fusion peptide. In one embodiment, the modified Zika virus envelope protein comprises a mutation in the fusion loop. In one embodiment, the modified Zika virus envelope protein comprises a mutation in the M loop. In one embodiment, the modified Zika virus envelope protein comprises a mutation at a location involved in glycosylation. In one embodiment, the modified Zika virus envelope protein comprises a mutation at a location corresponding to one or more locations selected from the group consisting of R2, G5, N8, SI 6, G28, A54, T76, Q77, D87, W101, G106, L107, N134, T160, T170, E177, R193, P222, W225, T231, K251, Q253, V255, V256, V257, Q261, E262, H266, E262, D296, K297, L300, S304, Y305, L307, K316, and E320, of SEQ ID NO:4.

It will be understood by those skilled in the art that VLPs of the invention can comprise membrane proteins of the invention, and/or envelope proteins of the invention. Thus in one embodiment, a VLP of the invention comprises a modified Zika virus membrane protein and a wild-type Zika virus envelope protein. In one embodiment, a VLP of the invention comprises a wild-type Zika virus membrane protein and a modified Zika virus envelope protein of the invention. In one embodiment, a VLP of the invention comprises a modified Zika virus membrane protein of the invention and a modified Zika virus envelope protein of the invention.

One embodiment of the invention is a virus-like particle produced from introduction of a nucleic acid molecule of the invention into a cell, wherein the virus-like particle comprises a Zika virus envelope protein of the invention and/or a Zika virus membrane protein of the invention.

One embodiment of the invention is a method for producing Zika VLPs, comprising introducing into a cell, a nucleic acid molecule of the invention. In certain embodiment, isolation of VLPs may be desired. In such embodiments, the method further comprises isolating or purifying the VLPs. As used herein, the terms isolate, purify, and the like, do not infer any particular level of percentage or purity. Instead, such terms refer to removing the desired component (e.g., VLPs) from surrounding material (e.g., cell matter) to a degree sufficient for the intended purpose (e.g., laboratory analysis, introduction to tissue culture cells, injection into a person, etc.). Purification methods suitable for an intended purpose are known to those skilled in the art.

One embodiment of the invention is a pharmaceutical composition comprising a nucleic acid molecule, a protein, or a VLP of the invention. Such compositions are suitable for the therapeutic delivery of nucleic acid molecules, including expression vectors described herein, proteins, or VLPs, of the invention. Hence, the invention provides pharmaceutical compositions that comprise a therapeutically-effective amount of one or more nucleic acid molecules, proteins, or VLPs, described herein, formulated together with one or more pharmaceutically-acceptable carriers (additives) and/or diluents. As used herein, a therapeutically-effective amount means the amount of a compound (e.g., a nucleic acid molecule) required to achieve a desired result (e.g., induce an immune response against Zika virus). While it is possible for a nucleic acid molecule, proteins, or VLP, of the invention to be administered alone, it is preferable they be administered as a pharmaceutical composition.

Pharmaceutical compositions of the invention may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; (8) inhaled into the lungs, for example, by nebulizer or aerosol inhaler; or (9) nasally. Examples of suitable carriers, additives and diluents are described in U.S. Patent Publication No. 2015/0361428, which is incorporated herein by reference in its entirety.

One embodiment of the present invention is a method to induce an immune response to Zika virus in individual, the method comprising administering to the individual a nucleic acid molecule of the invention, a protein of the invention, a VLP of the invention, or a therapeutic composition comprising a nucleic acid molecule, a protein, or a VLP, of the invention. One embodiment of the present invention is a method to induce an immune response to Zika virus in an individual, the method comprising:

a) obtaining a nucleic acid molecule of the invention, a protein of the invention, a VLP of the invention, or a therapeutic composition comprising a nucleic acid molecule, a protein, or a VLP, of the invention; and,

b) administering to the individual the nucleic acid molecule of the invention, the protein of the invention, the VLP of the invention, or the therapeutic composition comprising the nucleic acid molecule, the protein, or the VLP, of the invention, such that an immune response against Zika virus is produced.

One embodiment of the present invention is a method to vaccinate an individual against Zika virus, the method comprising administering to the individual a nucleic acid molecule of the invention, a protein of the invention, a VLP of the invention, or a therapeutic composition comprising a nucleic acid molecule, a protein, or a VLP, of the invention. One embodiment of the present invention is a method to vaccinate an individual against infection with Zika virus, the method comprising:

a) obtaining a nucleic acid molecule of the invention, a protein of the invention, a VLP of the invention, or a therapeutic composition comprising a nucleic acid molecule, a protein, or a VLP, of the invention; and,

b) administering to the individual the nucleic acid molecule of the invention, the protein of the invention, the VLP of the invention, or the therapeutic composition comprising the nucleic acid molecule, the protein, or the VLP, of the invention, such that an immune response against Zika virus is produced.

One embodiment of the present invention is a method to protect an individual against infection by Zika virus, the method comprising administering to the individual a nucleic acid molecule of the invention, a protein of the invention, a VLP of the invention, or a therapeutic composition comprising a nucleic acid molecule, a protein, or a VLP, of the invention. One embodiment of the present invention is a method to protect an individual against infection by Zika virus, the method comprising:

a) obtaining a nucleic acid molecule of the invention, a protein of the invention, a VLP of the invention, or a therapeutic composition comprising a nucleic acid molecule, a protein, or a VLP, of the invention; and,

b) administering to the individual the nucleic acid molecule of the invention, the protein of the invention, the VLP of the invention, or the therapeutic composition comprising the nucleic acid molecule, the protein, or the VLP, of the invention, such that a protective immune response against Zika virus is produced.

Vaccines of the present invention can be used to vaccinate individuals using a prime/boost protocol. Such a protocol is described in U.S. Patent Publication No. 20110177122, which is incorporated herein by reference in its entirety. In such a protocol, a first vaccine composition may be administered to the individual (prime) and then after a period of time, a second vaccine composition may be administered to the individual (boost). Administration of the boosting composition is generally weeks or months after administration of the priming composition, preferably about 2-3 weeks or 4 weeks, or 8 weeks, or 16 weeks, or 20 weeks, or 24 weeks, or 28 weeks, or 32 weeks. In one embodiment, the boosting composition is formulated for administration about 1 week, or 2 weeks, or 3 weeks, or 4 weeks, or 5 weeks, or 6 weeks, or 7 weeks, or 8 weeks, or 9 weeks, or 16 weeks, or 20 weeks, or 24 weeks, or 28 weeks, or 32 weeks after administration of the priming composition

The first and second vaccine compositions can be, but need not be, the same composition. Thus, in one embodiment of the present invention, the step of administering the vaccine comprises administering a first vaccine composition, and then at a later time, administering a second vaccine composition. In one embodiment, the first vaccine composition comprises a nucleic acid molecule or a VLP of the present invention. In one embodiment, the second vaccine composition can comprise a nucleic acid molecule or a VLP of the invention.

Current diagnostic tests for infection with Zika virus use specific Zika virus proteins or inactivated virus to detect anti-Zika virus antibodies in an individual's blood. However, because VLPs of the invention have a three-dimensional structure resembling Zika virus, and because these VLPs are non-infectious, they provide a safer and more accurate reagent for detecting anti-Zika virus antibodies. Thus, one embodiment of the invention is a method of detecting anti-Zika virus antibodies in a sample, comprising:

a. contacting at least a portion of the sample with a VLP of the invention, under conditions suitable for forming a VLP:antibody complex; and, b. detecting the presence of the VLP: antibody complex, if present;

wherein the presence of the VLP: antibody complex indicates the presence of anti-Zika virus antibodies in the sample.

Because assays of the present invention can detect anti-Zika virus antibodies in a sample, including a blood sample, such assays can be used to identify individuals having anti-Zika antibodies. Thus, one embodiment of the present invention is a method to identify an individual having anti-Zika virus antibodies, the method comprising:

a. contacting a sample from an individual being tested for anti-Zika antibodies with a VLP of the present invention; and,

b. analyzing the contacted sample for the presence of a VLP:antibody complex wherein the presence of a VLP:antibody complex indicates the individual has anti- influenza antibodies.

Any assay format can be used to conduct the disclosed method. Examples of useful assay formats include, but are not limited to, a radial diffusion assay, an enzyme-linked immunoassay, a competitive enzyme-linked immunoassay, a radioimmunoassay, a fluorescence immunoassay, a chemiluminescent assay, a lateral flow assay, a flow-through assay, a parti culate-based assay (e.g., using particulates such as, but not limited to, magnetic particles or plastic polymers, such as latex or polystyrene beads), an immunoprecipitation assay, a BioCoreJ assay (e.g., using colloidal gold), an immunodot assay (e.g., CMG Immunodot System, Fribourg, Switzerland), and an immunoblot assay (e.g., a western blot), an phosphorescence assay, a flow-through assay, a chromatography assay, a PAGe-based assay, a surface plasmon resonance assay, a spectrophotometric assay, and an electronic sensory assay.

One embodiment of the present invention is method to identify an individual that has been exposed to Zika virus, the method comprising:

a. contacting at least a portion of a sample from an individual being tested for anti-Zika antibodies with a VLP of the present invention;

b. analyzing the contacted sample for the presence or level of a VLP: antibody complex, wherein the presence or level of VLP: antibody complex indicates the presence or level of recent anti-Zika virus antibodies; and, c. comparing the recent anti-Zika virus antibody level with a past anti-Zika virus antibody level;

wherein an increase in the recent anti-Zika virus antibody level over the past anti- Zika virus antibody level indicates the individual has been exposed to Zika virus subsequent to determination of the past anti-Zika virus antibody level.

Methods of the present invention are also useful for determining the response of an individual to a vaccine. Thus, one embodiment is a method for measuring the response of an individual to a Zika virus vaccine, the method comprising:

a. administering to the individual a vaccine for Zika virus; b. contacting at least a portion of a sample from the individual with a VLP of the present invention;

c. analyzing the contacted sample for the presence or level of a VLP:antibody complex, wherein the presence or level of VLP: antibody complex indicates the presence or level of recent anti-Zika virus antibodies

wherein an increase in the level of antibody in the sample over the pre-vaccination level of antibody in the individual indicates the vaccine induced an immune response in the individual.

While not necessary to perform the disclosed method, it may be preferable to wait some period of time between the step of administering the vaccine and the step of determining the level of anti-Zika virus antibody in the individual. In one embodiment, determination of the level of anti-Zika virus antibodies present in the individual is performed at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least one week, at least two weeks, at least three weeks, at least four weeks, at least two months, at least three months or at least six months, following administration of the vaccine.

Also included in this disclosure are kits useful for practicing the disclosed methods. A kit may include nucleic acid molecules, proteins or VLPs of the invention. These kits may also contain at least some of the reagents required to produce such nucleic acid molecules, proteins and/or VLPs. Such reagents may include, but are not limited to, isolated nucleic acid molecules, such as expression vectors, primers, sets of primers, or an array of primers.

The kit may also comprise instructions for using the kit, and various reagents, such as buffers, necessary to practice the methods of the invention. These reagents or buffers may be useful for administering nucleic acid molecules of VLPs of the invention to a cell or an individual. The kit may also comprise any material necessary to practice the methods of the invention, such as syringes, tubes, swabs, and the like.

EXAMPLES

Example 1. Rapid Development of a Zika Virus Vaccine

This example demonstrates that a defined threshold of DNA vaccine-induced Zika virus-neutralizing antibodies protects rhesus macaques from viremia following challenge.

Zika virus (ZIKV) was identified as a cause of congenital disease during an explosive outbreak in the Americas and Caribbean in 2015. Because of the ongoing fetal risk from endemic disease and travel -related exposures, a vaccine to prevent viremia in women of child-bearing age and their partners is imperative. Vaccination experiments conducted with DNA expressing the prM and E proteins of ZIKV was immunogenic in mice and nonhuman primates, and protection against viremia after ZIKV challenge correlated with serum neutralizing activity. These data not only suggest DNA vaccination could be a successful approach to protect against ZIKV infection, but also establish a protective threshold of neutralizing activity that will prevent viremia following acute infection. Application of these approaches to vaccination and serological evaluation have been advanced into clinical studies to establish a similar protective threshold of immunity in humans.

The emergence of Zika virus (ZIKV) in the Americas and the Caribbean follows a series of global threats to public health from mosquito-borne viral diseases over the last three decades. ZIKV was discovered in Africa in 1947 where it circulated widely for decades without causing significant or frequent disease in humans. ZIKV was associated with a relatively mild febrile dengue-like illness with rash and arthralgia (7). Outbreaks characterized by a high attack rate in the Yap islands in 2007 (2), French Polynesia in 2013 (3), then Brazil in 2015 (4) revealed the epidemic potential of ZIKV and an association between infection of pregnant women and neurodevelopmental defects of the infected fetus (5) reminiscent of congenital rubella syndrome. Because of the profound impact on individuals and society as a whole from a disabling congenital disease, WHO declared ZIKV infection a global health emergency in February 2016. Although it is likely that the incidence of ZIKV infection will decline significantly within 1-2 years (6), it is also likely to become endemic in tropical and subtropical regions with sporadic outbreaks and potential for spread into new geographical areas, as observed with other emerging arboviruses like West Nile (WNV) and chikungunya viruses. Therefore, unless immunity is established before child-bearing age, pregnant women will continue to be at risk for an infection that could harm their fetus. Further, because men can harbor ZIKV in semen for several months following a clinically inapparent infection and can sexually transmit virus to a pregnant partner (7), even women in nonendemic regions will have some ongoing risk if exposed to men who have traveled to endemic regions. These unique features of transmission and disease suggest there will be an ongoing need for a ZIKV vaccine to maintain a high level of immunity in the general population and in travelers to endemic regions to reduce the frequency of fetal infection.

Licensed flavivirus vaccines against yellow fever (YF), tick-borne encephalitis (TBE), Japanese encephalitis (JEV), and dengue (DENV) viruses have been developed using multiple platforms including whole-inactivated and live-attenuated viruses (8-11). While these approaches are likely to be effective for ZIKV (72), the development process traditionally takes many years. To rapidly address the critical need for a preventive vaccine to curtail the current Zika outbreak in the Americas, we chose a gene-based vaccine delivery approach that leverages our prior experience with a DNA-based WNV vaccine (13). Advantages of DNA vaccines include the ability to rapidly test multiple candidate antigen designs, rapidly produce GMP material, an established safety profile in humans, and a relatively straightforward regulatory pathway into clinical evaluation. An important aspect of the current ZIKV DNA vaccine development process is that rapid evaluation of intervention approaches provides the opportunity to define efficacy in the setting of natural transmission and to establish a correlation of protection that might be applied to other interventions to facilitate licensure.

Antigen Design. Antigen design was guided by prior knowledge about humoral immunity to flaviviruses. Neutralizing antibodies (NAb) are a critical component of protection from disease, and vaccine elicited-neutralizing activity is associated with protection from most flaviviruses (14). The primary target of NAb s is the envelope (E) protein arrayed on the surface of the virus particle. Because the most potent monoclonal NAbs map to conformational epitopes in domain III (Dili) of the E protein (75), or more complex quaternary epitopes that bridge between antiparallel E dimers or between dimer rafts (16, 17), our goal was to identify constructs that produced antigens that most faithfully capture the antigenic complexity of infectious virions. Expression of the structural proteins premembrane (prM) and E have been shown sufficient for the production and release of virus-like subviral particles (SVPs) with antigenic and functional properties similar to those of infectious virions (75, 19).

To identify promising vaccine candidates, prM-E constructs were synthesized and screened for expression and efficiency of particle release from transfected cells.

DNA vector constructs. ZIKV DNA vaccine plasmid VRC5283 was based on the H/PF/2013 French Polynesian virus isolate (GenBank accession AHZ 13508.1). The plasmid encodes the ZIKV structural proteins prM and E under the control of the CMV immediate early promoter for expression in mammalian cells. The insert was synthesized by GenScript (Piscataway, NJ) using human codon-optimized ZIKV virus sequence and the Japanese encephalitis virus (JEV) signal sequence published previously for a WNV DNA vaccine (23). The JEV signal sequence is derived from JEV-GKP/0944234 (GenBank #ADZ48450.1) and is followed by the ZIKV prM-E genes. Another DNA vaccine, VRC5288, is based on VRC 5283 with the last 98 amino acids (stem and transmembrane regions) of E protein swapped with the last 98 amino acids of E protein of JEV (GenBank# BAA14218.1). The inserts were cloned into the mammalian expression vector VRC8400 (13, 20, 21). VRC4974 is identical to VRC5283 with the exception of a three amino acid deletion at the amino terminus of prM that prevents SVP release. VRC81 1 1 is a previously described WNV DNA vaccine used here as another control, and was described before (13, 34). VRC3593 is a vaccine candidate for the Middle East respiratory syndrome coronavirus (MERS-CoV) (26).

Cell lines and viruses. Mammalian cells were maintained at 37°C in the presence of 7% CO2. HEK-293T and Vero cells were grown in Dulbecco' s Modified Eagle medium (DMEM) containing Glutamax and supplemented with 7% fetal bovine serum (FBS) and 100 U/mL penicillin-streptomycin (PS) (Invitrogen). Raji cells stably expressing DC- SIGNR (Raj i-DC SIGNR) were cultured in RPMI-1640 medium supplemented with 7% FBS and 100 U/ml PS (32). Freestyle 293-F cells (Invitrogen) were grown in Freestyle 293 Expression medium supplemented with 7% FBS and 100 U/ml PS and maintained at 37°C in the presence of 8% CO2 according to the manufacturer' s instructions. ZIKV strain H/PF/2013 collected during the 2013 French Polynesian outbreak (33) was used for FRNT neutralization assays (described in greater detail below). Stocks of ZIKV were produced by infecting pre-plated Vero cells and collecting supernatant on days 2-4. Virus was clarified, passed through a 0.2 μΜ membrane filter, and stored in aliquots at -80°C until use. The Puerto Rican ZIKV strain PRVABC59 (30) was used in MN assays.

prM-E sequences were inserted into a CMV-immediate early promoter containing vector (VRC8400) that has been evaluated clinically in several prior studies (13, 20, 21).

The prM-E sequence in these constructs was selected from a French Polynesian isolate (ZIKV strain H/PF/2013, GenBank: AHZ13508.1) that is identical or highly related to strains circulating in the Americas. Neutralization studies with contemporary sera and multiple ZIKV strains indicate ZIKV exists as a single serotype, suggesting a vaccine antigen is expected to provide protection against all ZIKV strains (22). To improve expression, the ZIKV prM signal sequence was exchanged with the analogous region of JEV, as previously reported (23), to create vector VRC5283 (FIG. 1 A). A second chimeric ZIKV/JEV prM-E construct, VRC5288, also encoding the JEV signal sequence, was designed in which the final 98 amino acids of E, that comprise the stem and transmembrane regions (ST/TM), were swapped with the corresponding JEV sequence, which has previously been shown to improve SVP secretion (24). Western Blotting. HEK-293T cells were transiently transfected with plasmid DNA using Fugene 6 (Promega, WI, USA). Culture supernatant was collected, and cells were rinsed with PBS, pH7.4 and lysed by M-PER Mammalian Protein Extraction Reagent (Therm oFisher, MA, USA) at two to three days post-transfection. SVP precipitate (SVP ppt) was pelleted through a 20% sucrose cushion at 32,000 rpm in a TH-641 rotor (Therm oFisher, MA, USA) for 4 hours at 4 °C and removed from the tube. The pellet was dissolved in T E buffer (50mM Tris, 140 mM NaCl, 5 mM EDTA, pH 7.4). The total protein content of partially purified SVP and cell lysate was quantitated by BCA method. A mass of SVP ppt (0.5 μg) and cell lysate (25 μg) was mixed with NuPAGE LDS sample buffer (ThermoFisher, MA, USA) and run on NuPAGE Novex 4-12% Bis-Tris Protein Gel (ThermoFisher, MA, USA). Protein was transferred to a PVDF membrane by Trans-Blot Turbo Transfer System (Bio-Rad, CA, USA). Membranes were blocked for 1 h at RT in blocking buffer (5% skim milk (BD Difco, NJ, USA) + 2% BSA (Fisher, MD, USA) in PBS, pH7.4 with 0.05% Tween 20 (PBST)) then incubated for 1 h at RT with a 1 : 1000 dilution of VRC5283 -immunized mouse serum in dilution buffer, and washed three times with PBST. Membranes were incubated for 1 h at RT with horseradish peroxidase (HRP) conjugated goat anti-mouse IgG, Fcy-specific (Jackson ImmunoResearch, PA, USA) in dilution buffer and washed three times with PBST. The membrane was developed by SuperSignal West Pico Chemiluminescent Substrate (ThermoFisher, MA, USA), and the images were taken by ChemiDoc MP System (Bio-Rad, NJ, USA).

Antigen-capture ELISA (Ag-ELISA). ZIKV SVPs were captured in a particle capture ELISA format using two previously described fusion loop-specific pan anti- flavivirus monoclonal antibodies (mAbs). 96 well Nunc MaxiSorp plate were coated with 1 μg/mL of 6b6c-l mAb (GeneTex, CA, USA) in carbonate-bicarbonate buffer, pH9.6 (Sigma, MO, USA) was added to 96 well Nunc MaxiSorp plate, and the plates were incubated at 4°C overnight. The plates were then blocked at 37°C for 1 h with PBS, pH7.4 in 5% skim milk with 2% BSA (blocking buffer). Serial dilutions of culture supernatant in dilution buffer (blocking buffer with 0.05 % Tween 20) were added to the plates, and the plates were incubated at 37°C for 1 h. Biotinylated 4G2 mAb (5 μg/mL) (ATCC HB-112, VA, USA) was added to the plates, incubated at 37°C for 1 h and washed with PBST. HRP- conjugated streptavidin (ThermoFisher, MA, USA) was added to the plates, incubated at 37°C for 30 min and washed with PBST. The assay was developed using 3,3',5',5- Tetramethylbenzidine HRP substrate (TMB) (KPL, MD, USA), stopped by the addition of 0.5 M H2SO4 and then measured at 450 nm (SpectraMax Plus384, Molecular Devices, CA, USA).

Particle-based anti-ZIKV antibody ELISA. Partially purified ZIKV SVP (2 μ^πιΐ.) were added to 96 well Nunc MaxiSorp plates and incubated at 4°C overnight. Serial dilutions of sera from ZIKV DNA vaccine-immunized animals in dilution buffer were added to the plates, and incubated at RT for 1 h. HRP conjugated goat anti-mouse IgG, Fcy-specific (Jackson ImmunoRe search Laboratories) or HRP conjugated goat anti-monkey IgG, Fc- specific (Nordic MUbio, Susteren, The Netherlands) was added to the plates, and the plates were incubated at RT for 1 h and washed with PBST. The ELISA was developed and measured as described above.

These transient transfection studies revealed that both vectors resulted in expression by mammalian cells (FIG. IB, right panel), with more efficient SVP release into the supernatant for VRC5288, as measured by Western blots of virus supernatants partially purified through a 20% sucrose cushion (FIG. IB, right panel), and a particle-capture ELISA (FIG. 1C).

Negative-stain electron microscopy. The Electron Microscopy Laboratory at the National Cancer Institute examined the morphology of the SVPs. Freestyle 293-F cells were transiently transfected with plasmid DNA and supernatant was harvested three days later. SVP were purified from the supernatant by Ion Exchange Chromatography and Multimodal Chromatography. Purified SVPs were fixed by mixing with an equal volume of fixative containing 4% formaldehyde in 100 mM Na-cacodylate buffer, pH 7.4. Samples were adsorbed to freshly glow-discharged carbon-film grids, washed with several drops of buffer containing 10 mM HEPES, pH 7.0, and 150 mM NaCl, and stained with 0.75% uranyl formate. Images were collected using an FEI Tecnai T20 electron microscope operated at 200 kV and equipped with a 2k x 2k Eagle CCD camera.

The electron microscopic analysis of negative stained purified VRC5288 SVP preparations revealed roughly spherical particles consistent with the appearance of other flavivirus SVPs (FIG. ID) (18, 25).

The immunogenicity of each DNA candidate was then assessed in BALB/c and C57BL/6 mice.

Vaccination of mice. C57BL/6 and BALB/c mice were obtained from Jackson Laboratories. Animals were chosen and randomized based on age. 8-12 week old C57BL/6 or BALB/c mice were immunized intramuscularly (IM) by electroporation (BTX AgilePulse, Holliston, MA) with 50 μg of plasmid DNA at week 0. Sera was collected weekly and binding antibody responses were analyzed by ELISA and NAb responses were analyzed by RVP neutralization assay.

Reporter virus particle (RVP) production. RVPs are pseudo-infectious virions capable of a single round of infection that are produced by complementation of a GFP- expressing WNV sub-genomic replicon (35) with a plasmid encoding the viral structural proteins (C-prM-E). RVPs incorporating the structural proteins of WNV (35, 36), DENV (37-39), and recently ZIKV (22) have been described. In the current study, WNV NY99 and ZIKV H/PF/2013 RVPs were produced by co-transfection of 293T cells with the replicon and corresponding structural gene plasmid. Transfected cells were incubated at 30°C and virus-containing supernatants were harvested on days 3-6. Stocks were passed through a 0.2 μΜ filter and stored in aliquots at -80°C until use.

RVP neutralization assay. ZIKV RVP neutralization assays were performed as recently described (22). Previously titered RVPs were sufficiently diluted to ensure antibody excess at informative points on the dose-response curves and incubated with serial dilutions of mouse or macaque sera for 1 h at 37°C to allow for steady-state binding. Antibody -RVP complexes were then used to infect Raji-DCSIGNR cells in duplicate technical replicates. Infections were carried out at 37°C and GFP-positive infected cells detected by flow cytometry 24-48 h later. Neutralization results were analyzed by non-linear regression to estimate the dilution of sera required for half-maximal neutralization of infection (ECso titer) (Prism 6 software; GraphPad). The initial dilution of sera (1 :60, based on the final volume of RVPs, cells, and sera) was set as the limit of confidence of the assay. Neutralization titers predicted by non-linear regression as <60 were reported as a titer of 30 (half the limit of confidence).

The mice were immunized intramuscularly once with 50 μg of DNA in the quadriceps using electroporation as previously described (26). Serum was evaluated for binding to ZIKV SVPs (FIG. 5A) and neutralizing activity using ZIKV reporter virus particles (RVP) (FIGs. 5B-5D) (22).

Vaccination with either VRC5283 or VRC5288 elicited ZIKV-specific NAbs after a single immunization with titers up to 10⁵ reciprocal ECso serum dilution in C57BL/6 mice (FIG. 5D). NAb titers were similar in mice vaccinated with 2, 10, or 50 μg DNA (FIG. 6), and were of similar magnitude to the level observed with a previously described WNV DNA vaccine (FIGs.7A and 7B) (73).

Vaccination and Challenge of nonhuman primates. Rhesus macaques (Macaca mulatto.) were used in the nonhuman primate study. Macaques were housed and all experiments performed at Bioqual, Inc. (Rockville, MD). Animals were chosen and randomized based on age and weight. Rhesus macaques (6/group) were randomized by body weight and administered 4 mg or 1 mg of VRC8400, VRC5283 or VRC5288 IM using PharmaJet (Golden, CO) at week 0 and 4 (FIGs. 2A-2D). Blood was collected weekly for analysis of antibody responses by ELISA and RVP neutralization assay. The immunized animals were challenged SC with a dose of 10³ FFU at week 8 and blood samples were collected for determination of viral load.

All data was graphed and statistics performed on logio transformed data. Neutralizing antibody responses from weeks 0-8 were summarized by the area under the curve, on a logarithmic scale. Differences between the groups were determined using a Kruskal-Wallis test to compare all five groups; since this was significant (p<.0001) pairwise comparisons were made using Wilcoxon Rank Sum tests. P-values presented have been adjusted for multiple comparisons using Holm' s procedure. For viral load comparisons, viral loads trajectories were summarized by area under the curve on a logarithmic scale and significance determined by a Wilcoxon Exact Test.

Immunogenicity in rhesus macaques was evaluated after vaccine doses were delivered intramuscularly by a needle-free injection device (PharmaJet) (FIGs. 2A-2D, 8A-C, and 9A- 9E). Six animals per group received two 1 mg (VRC5283) or 4 mg (VRC5283 and VRC5288) doses of vaccine at 0 and 4 weeks, while one group received a single 1 mg dose of VRC5288 at week 0. After a single dose of DNA, binding and neutralizing antibody were detectable by week two and peaked at week three. All ZIKV vaccine groups had significantly higher NAb responses than macaques that received VRC8400 control vector when comparing area under the curve (AUC) using a Kruskal-Wallis test (p=0.022, FIG. 2D).

The macaques that received a single 1 mg dose of VRC5288 had significantly lower

NAb titers than macaques that received two doses of either vaccine at either dose level (p=0.022). There were no significant differences in NAb titer between animals that received two doses of VRC5283 or animals that received two doses of VRC5288 by AUC comparison.

FRNT neutralization assay. Neutralizing activity of macaque sera was assessed using a focus reduction neutralization test (FRNT) as recently described for ZIKV (28). Serial dilutions of sera were incubated with 100 FFU of ZIKV H/PF/2013 for 1 h at 37°C. Antibody -virus complexes were added to pre-plated Vero cell monolayers in 96-well plates. After 4 h, cells were overlaid with 1% (w/v) methylcellulose in Opti-MEM medium (Invitrogen) supplemented with 2% FBS and lx PS. Plates were fixed 40 h later with 1% PFA in PBS. Wells were incubated sequentially with 500 ng/mL of the pan-flavivirus mAb E60 and HRP-conjugated goat anti- mouse IgG in PBS supplemented with 0.1% saponin and 0.1% BSA. ZIKV-infected foci were visualized by TrueBlue peroxidase substrate ( PL) and quantitated on an ImmunoSpot macroanalyzer (Cellular Technologies). Neutralization results were analyzed as described for the RVP neutralization assay to estimate the ECso titer. The initial dilution of sera (1 :60, based on the final volume of virus, cells, and sera) was set as the limit of confidence of the assay. Neutralization titers predicted by non-linear regression as <60 were reported as a titer of 30 (half the limit of confidence).

Microneutralization assay. Neutralizing activity of macaque sera was assessed using a previously described ZIKV microneutralization (MN) assay (12, 30). Serial dilutions of macaque sera were incubated with 100 PFU of ZIKV PRVABC59 at 35°C for 2 h. Antibody- virus complexes were added to pre-plated Vero cell monolayers in 96-well plates and incubated for 4 days. Fixed cells were stained with a flavivirus-reactive antibody conjugated to FIRP and developed by the addition of TMB substrate and measurement of the absorbance at 450nm. Absorbance data was analyzed by linear regression to calculate the MNso titer. Seropositivity was defined as a titer of > 10.

Sera collected at week 6 were also evaluated for NAb activity by the conventional focus-reduction neutralization test (FRNT) (27, 28) and a microneutralization (MN) assay (12, 29, 30).

The results of both assays strongly correlated with the ECso RVP values (FIG. 10, Table 4), although the RVP assay was more sensitive as demonstrated by a capacity to detect neutralization activity in macaques that received only a single 1 mg dose of VRC5288 as compared to the MN results (average week 6 ECso reciprocal serum NAb titers of 322 versus <10 for RVP and MN assays, respectively). Further comparison of these values suggested that the MN values corresponded more closely to the EC90 RVP values (2-fold versus 13.4- fold average difference in RVP EC90/ MN ECso and RVP EC MN ECso NAb titers, respectively, for all animals at week 6). These data indicate that both VRC5283 and VRC5288 elicit substantial ZIKV-specific NAb in macaques. Table 4. Comparison of the ECso neutralization titers of nonhuman primate sera collected

6-weeks post-vaccination determined by three distinct assays.

RVP= reporter virus particle neutralization assay, MN= microneutralization assay, FRNT= focus reduction neutralization test, HP= non-human primate, AVE= average of the indicated number of experiments, STDEV= standard deviation, nd= not determined,— = standard deviation not available because sample not tested or only tested n=l .

Quantitative RT-PCR. RT-PCR was used to determine viral loads as previously described (12). Briefly, RNA was extracted using a QIAcube HT (Qiagen, Germany). Primers were designed to amplify a region the capsid gene from ZIKV BeH815744. Viral load assays were performed at BIDMC and assay sensitivity was 100 copies/ml.

Eight weeks after the first immunization, all animals were challenged subcutaneously with 10³ focus-forming units (FFU) of the Puerto Rican ZIKV strain PRVABC59 (GenBank KU501215.1) and blood was collected daily for quantitative PCR analysis of ZIKV genome copies in plasma (12). This analysis was blinded to group, animal number, and day and deconvoluted by an independent examiner. Control animals showed peak virus load (VL) on day 3 or 4 between 10⁴ and 10⁶ genome copies/ml. Animals that received two doses of 4 mg or 1 mg of VRC5283 or 4 mg of VRC5288 were largely protected from viremia with 17 of 18 animals having no detectable viremia on any day (FIG. 3 A). One animal that received two 4 mg doses of VRC5288 had a low-level positive PCR in one of two assays performed on day 3 plasma and another blip at day 7. All six animals that received only a single dose of 1 mg of VRC5288 were viremic with peak VL on day 3 between 10² and 10⁵ genome copies/ml. This viral load was significantly reduced compared to the animals that received two doses of the VRC8400 control vector when comparing area under the curve (AUC) by a Wilcoxon Exact Test (two-sided p=0.041). The reproducibility and cutoff for low values has been established at < 100 genome copies/ml, so it cannot be ruled out that low level viremia may have occurred in other animals.

Seventeen of eighteen (94%) animals that received 2 doses of vaccine had no detectable viremia post-challenge. The animal with the blips above background at day 3 and 7 in the VRC5288 two-dose 4 mg group had a prechallenge ECso NAb titer of 1218, which was among the lowest titers of all the two-dose vaccine groups (FIG. 4A). These data suggest the threshold for protection from viremia with this challenge dose is a reciprocal EC50 serum NAb titer of approximately 1000 as measured using the RVP assay (FIG. 4B). This corresponds roughly to a reciprocal EC50 MN titer of 100 (FIGs. lOA-lOC) which is similar to the titer of NAb required to prevent viremia in nonhuman primates passively treated with immune serum (12).

The occurrence of breakthrough viremia provided an opportunity to analyze immune correlates of protection. The level of pre-challenge NAb activity in serum on week 8 correlated with the level of viremia (Day 3 : FIG. AC, Spearman Rho= -0.856, pO.0001). This correlation remained significant when the day of viremia was varied, and when restricted to the viremic animals. Animals receiving a single dose of 1 mg VRC5288 had prechallenge reciprocal EC50 NAb titers measured by the RVP assay between 203 and 417. The two animals with the highest NAb activity were the ones with delayed onset of viremia at day 3. The MN assay, as noted above, at the 6 week time point (2 weeks prechallenge) was <10 in the 1 mg single dose group that uniformly had breakthrough infection (Table 4). Therefore, the larger dynamic range of the RVP assay will allow a more precise definition of the protective threshold needed to prevent viremia in a particular model or against a particular challenge inoculum. One concern routinely raised about vaccination against flaviviruses is the possibility of enhanced disease if there is incomplete or waning immunity, as observed in a subset of secondary dengue virus infections (37). In this study, the 1 mg single-dose group that received VRC5288 had low, sub-protective levels of neutralizing antibody that resulted in breakthrough infections. In those animals, there were reduced levels of viremia compared to unvaccinated controls and no visible signs of illness or enhancement of replication. Retrospectively, we also determined that one animal in the mock-immunized control group with a detectable level of ZIKV antibody binding, but no neutralizing activity, had preexisting WNV-specific NAbs (FIGs. 11A-G). The level of virus replication in this animal was the median of the group and there was no evidence of disease enhancement in the setting of prior flavivirus exposure.

Vaccine development for ZIKV must be specific and guided by an expanded understanding of ZIKV virology, pathogenesis, immunity, and transmission. It must also be strategic, matching technical and manufacturing feasibility with the target populations that will benefit most from vaccination. In addition, to achieving both rapid deployment and long-term protection, it should be staged. This means that a rapid response to the global health emergency may require a different vaccine approach than the longer term goal of achieving durable immunity in the general population as ZIKV becomes a sporadic, endemic infection. Both VRC5288 and VRC5283 will be evaluated in humans. A Phase 1 clinical trial (NCT02840487) of VRC5288 was launched to test a variety of regimens and doses for safety and immunogenicity. These trials represent the initial efforts to define the level of vaccine-induced NAbs required for prevention of ZIKV viremia. Establishing a functional serological correlate of sterilizing immunity is key for leveraging the information gained from efficacy trials from one candidate vaccine to the next. These studies and others that may evaluate alternative antigen designs and delivery approaches as well as combination vaccine regimens will provide safety and immunogenicity data in humans that will inform the next steps of vaccine development and provide options for achieving both the short-term goal of identifying an intervention to protect women of child-bearing age in the current ZIKV outbreak, and the long-term goal of vaccinating the general population of endemic regions and travelers to those regions.

Example 2. Clinical trial of Zika DNA vaccine

This example shows the safety, tolerability, and immunogenicity of two Zika virus DNA vaccine candidates in healthy adults. Methods

Study design and participants

VRC 319 and VRC 320 are phase 1, randomised, open-label clinical trials of Zika virus DNA vaccine candidates. Eligible participants were healthy adults, aged 18-35 years in VRC 319 and 18-50 years in VRC 320, without abnormal findings in clinical laboratory tests, medical history, or physical examinations. Volunteers for VRC 319 were recruited at the NIH Clinical Center, Bethesda, MD, and the University of Maryland Center for Vaccine Development, Baltimore, MD, USA, and the Hope Clinic of the Emory Vaccine Center, Decatur, GA, USA, and those for VRC 320 were recruited at the NIH Clinical Center. Research nurses enrolled the participants.

Participants were assigned to vaccination groups using computer-generated randomization schedules prepared using statistical methods. The schedules were provided to the study site pharmacies and the data management centre. In VRC 319, participants were assigned 1 : 1 to four different vaccination schedules. In VRC 320, participants were assigned 1 : 1 to three groups of single-dose or split- dose vaccination.

Vaccines

The vaccines used in this study consisted of phosphate buffered saline, purified plasmid comprising mammalian expression control elements, coding sequences for Zika virus prM and E from a French Polynesia isolate (strain H/PF/2013), and standard bacterial origin of replication and selection elements. In the VRC5288 vaccine, the Zika virus coding sequence was modified by substituting Japanese encephalitis virus sequences for the stem and trans-membrane regions of the E protein, and in both vaccines, the prM signal sequence in the Zika virus coding sequence was exchanged with an analogous Japanese encephalitis virus region to improve secretion of Zika subviral particles from transfected cells. Both vaccines were manufactured by the VRC Pilot Plant, operated under contract by Leidos Biomedical Research (Frederick, MD, USA) according to Good Manufacturing Practices, and supplied in doses of 4 mg/mL.

Study procedures

4 mg vaccine was given in all vaccinations. Volunteers enrolled into VRC 319 received VRC5288 as single intramuscular injections given via needle and syringe. Group 1 received vaccine on weeks 0 and 8, group 2 on weeks 0 and 12, group 3 on weeks 0, 4, and 8, and group 4 on weeks 0, 4, and 20. VRC 319 was originally designed to assess VRC5288 delivered by the needle-free Stratis device (Pharmajet, Golden, CO, USA), but a modification was needed to deliver a DNA vaccine with high viscosity that was not made in time for the trial. The device, therefore, was only used in the VRC 320 trial. Volunteers enrolled into VRC 320 received VRC5283 on weeks 0, 4, and 8. Group 1 received single doses given via needle and syringe into one deltoid; group 2 received split doses (2 mg each), one in each deltoid, given via needle and syringe; and group 3 received split doses (2 mg each), one into each deltoid, given via syringe and needle-free device, in which a spring- powered injector pressurises a narrow stream of vaccine into the tissue without electroporation or other externally applied factors.

Outcomes

The primary endpointwas vaccine safety, which was assessed by local and systemic reactogenicity. Safety and tolerability were monitored by clinical and laboratory assessments using diary cards to record local and systemic reactogenic events occurring in the 7 days after each injection. All adverse events occurring within 28 days after each injection were recorded by clinic staff. Serious adverse events were recorded for the entire duration of the study. These were classified as events or suspected adverse reactions that, in the view of the investigator or study sponsor, led to death, a life-threatening event, admission to hospital or prolongation of a hospital stay, inability to continue normal life functions, or a congenital anomaly or birth defect, or led to a medical or surgical intervention to prevent one of these outcomes. The FDA toxicity grading scale for healthy adults and adolescent volunteers enrolled in preventive vaccine clinical trials was used. Secondary endpoints were immunogenicity assessed by a reporter virus particle neutralisation assay and antigen-specific T-cell response.

Neutralising antibody responses

Vaccine antibody response was assessed by measuring Zika-virus-specific neutralising antibodies with a previously described reporter virus particle assay.⁴⁰ Briefly, Zika virus reporter virus particles were produced in human embryonic kidney 293 T cells by co- transfection with two plasmids, one encoding a green fluorescent protein expression West Nile virus replicon and the other encoding the structural proteins of the Zika virus H/PF/2013 strain. Zika virus reporter virus particles were incubated with serial threefold dilutions of heat-inactivated sera in duplicate technical replicates and added to Raji cells expressing the flavivirus attachment factor DC-SIGNR.⁴¹ Infected cells expressing green fluorescent protein were counted 24 h after infection by flow cytometry. The dilution of sera needed to neutralise half of infection events (ECso) was estimated by non-linear regression with GraphPad Prism version 7. The initial dilution of sera (1 :30) was set as the limit of detection of the assay; ECso values of negative samples were reported as half the limit of detection (1 : 15). Positive antibody response was defined as a EC50 greater than or equal to 30.

T-cell response by intracellular cytokine staining

A previously described intracellular cytokine staining assay was used to assess T- cell responses.⁴² Briefly, cryopreserved peripheral-blood mononuclear cells were stimulated with overlapping peptide pools (length 15 amino acids, overlapping by 11 amino acids) for the Zika virus E protein, small envelope protein M, and the pr peptide. Peripheral-blood mononuclear cells were collected at baseline, at the time of each vaccination, and 4 weeks after each vaccination. Data were analysed with FlowJo software (version 9.9.6, Treestar, Ashland, OR, USA), and the proportions of total CD4 and CD8 T cells producing interleukin 2, interferon γ, tumour necrosis factor a, or a combination of these cytokines, were quantified. Boolean gating was done and all cytokine-positive gates were summed to calculate the total proportion of cytokine-positive cells responding to a peptide pool. For total vaccine responses, the proportions of cytokine-positive T cells responding to pooled peptides were summed. Groups were analysed with background-subtracted data for positive change from baseline.

Statistical analysis

Sample size was calculated primarily on the ability to identify serious adverse events. For VRC 319, it was estimated that 20 participants per group would provide 90% power to detect at least one serious adverse event within a group if the true rate was not less than 0.109. For VRC 320, it was estimated that 15 participants per group would provide 90% power to detect at least one serious adverse event within a group if the true rate was not less than 0.142.

The group-wise magnitudes of antibody response was calculated as geometric mean titres (GMTs) with 95% CIs, and a two-sample t test was used to compare group GMTs within and across trials. The magnitude of mean T-cell responses before and after vaccination was compared by Wilcoxon' s signed-rank test within groups and by Wilcoxon' s rank sum test between groups. In accordance with the trial protocols, we made no adjustments for multiple comparisons in the analyses of immunogenicity because the trials were not powered to detect differences. All statistical analyses were done using R version 3.4.1. These trials are registered with ClinicalTrials.gov, numbers NCT02840487 and NCT02996461. Results

80 participants of 154 screened were enrolled in VRC 319, from Aug 2, 2016, to Sept 29, 2016, and 45 of 105 in VRC 320, from Dec 12, 2016, to April 19, 2017 (Fig 14). One participant from VRC 319 and two from VRC 320 withdrew after one dose of vaccine due to time commitments, precluding further trial participation, but were included in the safety analyses. Follow-up continues, and is expected to close in August 2018, for VRC 319 and in February 2019, for VRC 320. In VRC 319, the groups varied by sex and race, but age, body-mass index, and ethnicity were similar, whereas in VRC 320, only race varied notably (Fig. 14).

Vaccinations were safe and well tolerated in both trials, with local and systemic reactogenic events for VRC5288 and VRC5283 being mild to moderate (appendix). In both studies, pain and tenderness at the injection site was the most frequent local event (37 [46%] of 80 participants in VRC 319 and 36 [80%] of 45 in VRC 320) and malaise and headache were the most frequent systemic events (22 [27%] and 18 [22%], respectively, in VRC 319 and 17 [38%] and 15 [33%], respectively, in VRC 320; Fig. 15) One serious adverse event was reported, which was appendicitis 8 months after vaccination with VRC5288, but was deemed not to be related to vaccination.

The GMTs after vaccination with VRC5288 in VRC 319 were greater after three doses of vaccine than after two doses (Fig. 16, appendix). Positive antibody responses ranged from 60% to 89% 4 weeks after final vaccination (Fig. 17). The highest GMT and the greatest antibody response and antibody titres were seen in group 4 participants after three doses of vaccine with an extended time between the second and third doses (Fig. 15). After the third dose, the GMT was boosted to greater than the GMTs after the second dose in both three-dose groups (p=0 0048 for group 3 and p<0 0001 for group 4, Fig. 18A-18G).

The GMT achieved with VRC5283 in VRC 320 was substantially higher with needle-free injection in group 3 than with needle and syringe administration in groups 1 and 2 (Fig. 16 and Fig. 19). Positive antibody response increased from single-dose needle and syringe administration (77%) to split-dose needle and syringe administration (93%) to split- dose needle-free syringe administration (100%; Fig. 17). The GMT of 304 in VRC 320 group 3 was the greatest across all groups in both studies (p<0 0001 vs groups 1-3 and p=0 0028 vs group 4 in VRC 319; p=0 0015 vs group 1 and p=0 0085 vs group 2 in VRC 320; appendix). Split-dose administration of vaccine with needle and syringe also improved GMT compared with single-dose administration via the same method (appendix). In the two groups receiving VRC5283 by needle and syringe, the antibody levels were higher after splitting the dose (p=0 0015 for group 2). Boosting with the third dose only significantly increased the GMT to greater than that after the second dose in group 1 (p=0 0016). EC80 results are shown in the appendix.

4 weeks after last vaccination with VRC5288 in VRC 319, in group 4, T-cell responses to pooled peptides were significantly increased (CD4 p=0 0108 and CD8 cells p=0 0039) compared with baseline (Figs. 18A-18G). Group 3 showed increased CD8 (p=0 0304) responses to pooled peptides. The greatest T-cell responses overall were seen 4 weeks after needle-free administration of VRC5283 in VRC 320 (Figs. 19A-19D). CD 8 cell counts in participants who received VRC5283 via needle-free injection had increased total cytokine responses compared with baseline for pooled peptides (p=0 0166) and specifically for E-protein peptides (p=0 0004, appendix). CD4 cell counts from this group were also increased with pooled peptides (p=0 0004), again specifically for E-protein peptides (ρ=0·0001, appendix). VRC5283 given in split doses via needle and syringe also produced a significant CD4 response to pooled peptides (p=0 0353), but not a significant CD8 response. There were no significant responses to small envelope protein M or pr peptide.

The results of these studies show that the DNA vaccines assessed were safe, well- tolerate, and immunogenic.

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The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying knowledge within the skill of the art, readily modify and/or adapt for various applications such specific embodiments, without undue experimentation, without departing from the general concept of this disclosure. Therefore, such adaptations and modifications are intended to be within the meaning and range of equivalents of the disclosed embodiments, based on the teaching and guidance presented herein. It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limitation, such that the terminology or phraseology of the present specification is to be interpreted by the skilled artisan in light of the teachings and guidance.

Claims

CLAIMS What is claimed:

1. A nucleic acid molecule comprising a nucleotide sequence encoding a polyprotein, wherein the polyprotein comprises at least a portion of a Zika virus prM protein joined to at least a portion of a Zika virus E protein, and wherein the at least a portion of a Zika virus prM protein comprises a signal sequence that is heterologous to Zika virus.

2. The nucleic acid molecule of claim 1, wherein the heterologous signal sequence is from a protein selected from the group consisting of human CD5, mouse IL-2, bovine prolactin, and a flavivirus structural protein.

3. The nucleic acid molecule of claim 1, wherein the Zika virus prM protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, or at least 97% identical to a sequence selected from the group consisting of SEQ ID NOs:451- 459, SEQ ID NOs:469-474, and SEQ ID NOs:481-522, and wherein the prM protein comprises at least one mutation from a modified protein represented by a sequence selected from the group consisting of SEQ ID NOs:451-459, SEQ ID NOs:469-474, and SEQ ID NOs:481-522.

4. The nucleic acid molecule of claim 1, wherein the Zika virus envelope protein has been modified by substituting the stem region and/or the transmembrane region with a corresponding region from the envelope protein of a different flavivirus.

5. The nucleic acid molecule of claim 1, wherein the Zika virus envelope protein comprises at least one mutation that stabilizes a VLP comprising the envelope protein.

6. The nucleic acid molecule of claim 5, wherein the at least one mutation is in a region selected from the group consisting of the fusion peptide, the fusion loop, the M loop, and the be loop.

7. The nucleic acid molecule of claim 5, wherein the at least one mutation is at an amino acid position corresponding to one or more locations selected from the group consisting of W101, G106, and L107 of SEQ ID NO:4.

8. The nucleic acid molecule of claim 1, wherein the Zika virus envelope protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least

95%), or at least 97% identical to a sequence selected from the group consisting of SEQ ID NOs:451-459, SEQ ID NOs:469-474, and SEQ ID NOs:481-522, and wherein the prM protein comprises at least one mutation from a modified protein represented by a sequence selected from the group consisting of SEQ ID NOs:451-459, SEQ ID NOs:469-474, and SEQ ID NOs:481-522.

9. The nucleic acid molecule of claim 1, wherein the polyprotein comprises a Japanese Encephalitis Virus envelope protein signal sequence joined to a polyprotein comprising Zika virus prM protein, the Zika virus prM protein being joined to a modified Zika virus envelope protein, wherein the stem and transmembrane region of the modified Zika virus envelope protein are from the envelope protein of Japanese Encephalitis virus, and wherein the modified envelope protein optionally comprises at least one mutation from a modified protein represented by a sequence selected from the group consisting of SEQ ID NOs:451-459, SEQ ID NOs:469-474, and SEQ ID NOs:481-522.

10. A method of producing a Zika virus-like particle, comprising introducing into a cell the nucleic acid molecule of any one of claims 1-9 such that the encoded fusion protein is expressed.

11. A protein encoded by the nucleic acid molecule of any one of claims 1-9.

12. A virus-like particle (VLP) comprising a protein encoded by the nucleic acid molecule of any one of claims 1-9, or the protein of claim 11, wherein the VLP is capable of inducing an immune response to Zika virus.

13. Use of the VLP of claim 12 in eliciting an immune response against Zika virus in an individual.

14. A method of detecting anti-Zika virus antibodies in a sample, comprising: a. contacting at least a portion of the sample with a VLP of claim 12, under conditions suitable for forming a VLP:antibody complex; and,

b. detecting the presence of the VLP: antibody complex, if present;

wherein the presence of the VLP: antibody complex indicates the presence of anti- Zika virus antibodies in the sample.