Zika Vaccines and Methods of Use
The present disclosure relates to Zika vaccines. In certain embodiments, this disclosure relates to vaccine compositions for use in methods of protecting a human subject against Zika disease or infection, wherein said composition comprises a vaccinal for Zika such as a live attenuated or inactivated chimeric Zika virus; live attenuated Zika virus; an inactivated Zika virus; a replication-defective pseudo-infectious Zika virus; a Zika virus-like particle (VLP), a Zika protein or combinations thereof. In certain embodiments, the Zika vaccinal comprises or encodes altered polypeptide sequences disclosed herein.
This application is a division of U.S. application Ser. No. 16/770,164 filed Jun. 5, 2020, which is the National Stage of International Application No. PCT/US2018/064201 filed Dec. 6, 2018, which claims the benefit of U.S. Provisional Application No. 62/595,510 filed Dec. 6, 2017. The entirety of each of these applications is hereby incorporated by reference for all purposes.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED AS AN XML FILE VIA THE OFFICE ELECTRONIC FILING SYSTEMThe Sequence Listing associated with this application is provided in XML format and is hereby incorporated by reference into the specification. The name of the XML file containing the Sequence Listing is 16129USDIV.xml. The XML file is 35 KB, was created on Sep. 28, 2022, and is being submitted electronically via the USPTO patent electronic filing system.
BACKGROUNDZika virus belongs to the flavivirus family of viruses, which include West Nile, Japanese encephalitis, yellow fever, dengue, and tick-borne encephalitis viruses. Zika can be passed from a pregnant woman to her fetus. Infection during pregnancy is believed to be the cause certain birth defects, including microcephaly. Furthermore, individuals infected by the Zika virus are at a higher risk of developing Guillain-Barré syndrome. There have been outbreaks of the Zika virus in the United States, Africa, Southeast Asia, Pacific Islands, parts of the Caribbean, and Central and South America. Thus, there is a need to develop a vaccine to prevent Zika infections.
Flaviviruses are icosahedral and contain a ribonucleic acid (RNA) genome encoding a single polypeptide. During maturation, this polypeptide is cleaved by proteases into structural proteins: anchored capsid (anC), precursor-membrane (prM), and glycoprotein (E). The precursor-membrane protein is cleaved providing the M protein for virion assembly (Zhang et al, EMBO J 22(11):2604-2613, 2003).
Vaccines exist for several related viruses in the flavivirus family, such as dengue, yellow fever, and Japanese encephalitis virus (Cohen, Science 351(6273):543-544, 2016). Arroyo et al. report the molecular basis for attenuation of neurovirulence of a yellow fever Virus/Japanese encephalitis virus chimera vaccine (ChimeriVax-JE). J Virol. 2001, 75(2):934-42. U.S. Pat. No. 6,696,281 reports chimeric flavivirus vaccines containing a yellow fever virus. See also WO 2010085358, WO2014016360, and U.S. Patent Application Publication Number 2017/0014502.
References cited herein are not an admission of prior art.
SUMMARYThe present disclosure relates to Zika vaccines. In certain embodiments, this disclosure relates to vaccine compositions for use in methods of protecting a human subject against Zika disease or infection, wherein said composition comprises a vaccinal for Zika such as a live attenuated or inactivated chimeric Zika virus; live attenuated Zika virus; an inactivated Zika virus; a replication-defective pseudo-infectious Zika virus; a Zika virus-like particle (VLP), a Zika protein or combinations thereof. In certain embodiments, the Zika vaccinal comprises or encodes altered polypeptide sequences disclosed herein.
In certain embodiments, the vaccine is a recombinant Yellow Fever virus encoding Zika virus protein(s). In certain embodiments, genes encoding the structural components of the Zika virus, including prM and E, are inserted into the backbone nucleic acid sequence of Yellow Fever virus, generating a chimeric virus. Typically, mutations in the prM, M, and/or E genes are made to reduce the neurotropism of the virus. In certain embodiments, the chimeric viruses as disclosed herein comprise a nucleic acid sequence encoding the Zika E protein comprising SEQ ID NO: 2 or a variant thereof. In certain embodiments, the variant has one, two, three, four, five, or more amino acid substitutions or conserved amino acid substitutions. In certain embodiments, the variant has SEQ ID NO: 1.
In certain embodiments, the variant comprises one, two, three, four, or all of the following substitutions relative to SEQ ID NO: 2: a) a phenylalanine (F) substitution at position 107; b) a lysine (K) substitution at position 138; c) a valine (V) substitution at position 176; d) a histidine (H) substitution at position 267; and/or e) a methionine (M) substitution at position 283.
In certain embodiments, the chimeric virus comprises a nucleic acid sequence having SEQ ID NO: 3 or SEQ ID NO: 4 or variant comprising synonymous substitutions. In other embodiments, the disclosure relates to chimeric viruses comprising a nucleic acid having greater than 60%, 70%, 80%, 90%, or 95% sequence identity to SEQ ID NO: 3 or SEQ ID NO: 4 or variant having synonymous substitutions. In other embodiments, the disclosure relates to the Zika virus, wherein the virus is attenuated by codon deoptimization.
In certain embodiments, this disclosure relates to non-naturally occurring Zika E proteins. In certain embodiments, this disclosure relates to non-naturally occurring virus particles or virus-like particles comprising a Zika E protein disclosed herein In certain embodiments, the Zika E protein comprises one, two, three, four, or all of the following substitutions relative to SEQ ID NO: 2: a) a phenylalanine (F) substitution at position 107; b) a lysine (K) substitution at position 138; c) a valine (V) substitution at position 176; d) a histidine (H) substitution at position 267; and/or e) a methionine (M) substitution at position 283.
In certain embodiments, this disclosure relates to recombinant nucleic acids and vectors comprising recombinant viral or chimeric viral genomes or nucleic acids encoding proteins or polypeptides disclosed herein. In certain embodiments, this disclosure relates to cells or expression systems comprising said recombinant nucleic acids or vectors.
In certain embodiments, the disclosure relates to the use of a vaccine composition of the present disclosure for the manufacture of a medicament for protecting or treating a human subject against Zika disease or infection. In certain embodiments, the disclosure relates to treating a subject diagnosed with a Zika infection by administering a Zika composition disclosed herein in combination with another active agent or antiviral agent. In certain embodiments, a subject is a person who is diagnosed with exhibiting symptoms or at risk of a Zika infection.
In certain embodiment, this disclosure relates to pharmaceutical compositions comprising a Zika composition disclosed herein and a pharmaceutically acceptable excipient. In certain embodiments, this disclosure relates to pharmaceutical compositions comprising Zika E proteins disclosed herein or a non-naturally occurring virus particle or virus-like particle comprising the same and a pharmaceutically acceptable excipient.
In certain embodiment, this disclosure relates to vaccines comprising a chimeric virus disclosed herein and an adjuvant. In certain embodiments, this disclosure relates to vaccine compositions comprising or encoding Zika E proteins disclosed herein or a non-naturally occurring virus particle or virus-like particle comprising the same and an adjuvant.
In certain embodiments, the disclosure relates to kits comprising a composition disclosed herein and instructions for the use of said composition in a method of treating or protecting a human subject against Zika disease or infection.
Before the present disclosure is described in greater detail, it is to be understood that this disclosure is not limited to particular embodiments described, and 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 disclosure will be limited only by the appended claims.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present disclosure, the preferred methods and materials are now described.
All publications and patents cited in this specification are herein incorporated by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference and are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosure. Further, the dates of publication provided could be different from the actual publication dates that may need to be independently confirmed.
As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present disclosure. Any recited method can be carried out in the order of events recited or in any other order that is logically possible.
Embodiments of the present disclosure will employ, unless otherwise indicated, techniques of medicine, organic chemistry, biochemistry, molecular biology, pharmacology, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.
As used herein, the term “combination with” when used to describe administration with an additional treatment means that the agent may be administered prior to, together with, or after the additional treatment, or a combination thereof.
As used herein, the terms “treat” and “treating” are not limited to the case where the subject (e.g., patient) is cured and the condition or disease is eradicated. Rather, embodiments, of the present disclosure also contemplate treatment that merely reduces symptoms, and/or delays conditions or disease progression. As used herein, the terms “prevent” and “preventing” include the prevention of the recurrence, spread or onset. It is not intended that the present disclosure be limited to complete prevention. In some embodiments, the onset is delayed, or the severity is reduced.
As used herein, the term “nucleic acid” is intended to mean a ribonucleic or deoxyribonucleic acid or analog thereof, including a nucleic acid analyte presented in any context; for example, a probe, target or primer. A nucleic acid can include native or non-native bases. In this regard, a native deoxyribonucleic acid can have one or more bases selected from the group consisting of adenine, thymine, cytosine or guanine and a ribonucleic acid can have one or more bases selected from the group consisting of uracil, adenine, cytosine or guanine. It will be understood that a deoxyribonucleic acid used in the methods or compositions set forth herein can include uracil bases and a ribonucleic acid can include a thymine base.
The term “inactivated virus”, as used herein, refers to a virus that has been rendered incapable of replication to any significant degree in host cells which would otherwise permit replication of the wild type virus. Inactivation may be achieved through several methods, including formalin or heat exposure.
The term “live attenuated virus”, as used herein, refers to a virus whose virulence has been reduced by mutation, of at least one nucleotide, or by codon deoptimization (alteration of synonymous codons) or the deletion, or addition of a codon pair, while still keeping the virus viable such that the entire nucleotide sequence of the virus is not naturally occurring. It is understood that the terms provide for a modified virus having at least one mutation (i.e., a change in the nucleotide sequence) of at least one gene or non-coding sequence, which reduces its virulence as compared to naturally occurring virus. A live attenuated virus is contrasted with an inactivated virus.
The term “chimeric virus”, as used herein, refers to a hybrid virus created by joining nucleic acid fragments from two or more different viruses or virus strain, in which the final virus contains essential genes necessary for replication; however, the entire nucleic acid sequence is not found in nature.
The term “Zika virus”, as used herein, refers to the virus of the family Flaviviridae causing Zeka fever or Zika virus disease. Zika virus disease is often asymptomatic or with only mild symptoms. Zika virus infection increase the risk of developing the peripheral nerve disorder, Guillain-Barré syndrome. Similar to other Flaviviruses, Zika virus is icosahedral and contains a ribonucleic acid (RNA) genome of about 10.7 kB, encoding a single polypeptide. During maturation, this polypeptide is cleaved by proteases into structural and non-strutural proteins. Structural proteins include an anchored capsid (anC), precursor-membrane glycoprotein (prM), and glycoprotein (E). In the final step of virion assembly, prM is cleaved into an N-terminal precursor-peptide and an M protein (Zhang et al, EMBO J 22(11):2604-2613, 2003).
Zika virus polyprotein is provides for in NCBI Reference Sequence: YP_002790881.1. The membrane glycoprotein precursor M has the following sequence:
Cleavage of the prM provides protein M with the sequence:
Envelope protein E has the sequence:
The term “virus-like particles or VLPs”, as used herein, refers to virus particles that do not contain replicative genetic material but present at their surface a E protein in a repetitive ordered array similar to the virion structure. Typically, VLPs also contain prM and/or M, and E proteins. VLPs may be produced in vitro (Zhang et al, J. Virol. (2011) 30 (8):333). VLPs may also be produced in vivo. To that end, nucleic acid constructs (e.g. DNA or RNA constructs) encoding prM and E proteins may be introduced into a cell of a subject, e.g. a human subject, via methods known in the art, e.g. via use of a viral vector. Any viral vector may be used provided it is able to contain and express both prM and E Zika virus sequences.
The term “replication-defective pseudo-infectious virus”, as used herein, refers to a virion particle that is replication-defective in vivo, owing to the absence in their genome of an essential sequence of the replicative cycle, for example the sequence encoding a capsid protein. However, the virion particles can propagate in a culture of helper cells that provide for the essential sequence(s) in trans. Replication-deficient pseudoinfectious viruses for use in the present disclosure include any virus according to the above definition which is capable of expressing the prM and E proteins of a Zika virus of any serotype or mutant disclosed herein. Examples include replication defective flavivirus/Zika chimeras such as replication defective YF/Zika, West Nile virus/Zika, and Japanese Encephalitis virus/Zika chimeras.
The term “CCID50” refers to the quantity of virus (e.g. vaccinal virus) infecting 50% of the cell culture. The CCID50 assay is a limit dilution assay with statistical titer calculation (Morrison D et al J Infect Dis. 2010; 201(3):370-7)).
In certain embodiments, term “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
In certain embodiments, sequence “identity” refers to the number of exactly matching amino acids (expressed as a percentage) in a sequence alignment between two sequences of the alignment calculated using the number of identical positions divided by the greater of the shortest sequence or the number of equivalent positions excluding overhangs wherein internal gaps are counted as an equivalent position. For example, the polypeptides GGGGGG (SEQ ID NO: 8) and GGGGT (SEQ ID NO: 9) have a sequence identity of 4 out of 5 or 80%. For example, the polypeptides GGGPPP (SEQ ID NO: 10) and GGGAPPP (SEQ ID NO: 11) have a sequence identity of 6 out of 7 or 85%. In certain embodiments, any recitation of sequence identity expressed herein may be substituted for sequence similarity. Percent “similarity” is used to quantify the similarity between two sequences of the alignment. This method is identical to determining the identity except that certain amino acids do not have to be identical to have a match. Amino acids are classified as matches if they are among a group with similar properties according to the following amino acid groups: Aromatic—F Y W; hydrophobic—A V I L; Charged positive: R K H; Charged negative—D E; Polar—S T N Q. The amino acid groups are also considered conserved substitutions.
The term “recombinant” when made in reference to a nucleic acid molecule refers to a nucleic acid molecule which is comprised of segments of nucleic acid joined together by means of molecular biological techniques. The term “recombinant” when made in reference to a protein or a polypeptide refers to a protein molecule which is expressed using a recombinant nucleic acid molecule.
The terms “vector” or “expression vector” refer to a recombinant nucleic acid containing a desired coding sequence and appropriate nucleic acid sequences necessary for the expression of the operably linked coding sequence in a particular host organism or expression system, e.g., cellular or cell-free. Nucleic acid sequences necessary for expression in prokaryotes usually include a promoter, an operator (optional), and a ribosome binding site, often along with other sequences. Eukaryotic cells are known to utilize promoters, enhancers, and termination and polyadenylation signals.
Protein “expression systems” refer to in vivo and in vitro (cell free) systems. Systems for recombinant protein expression typically utilize cells transfecting with a DNA expression vector that contains the template. The cells are cultured under conditions such that they translate the desired protein. Expressed proteins are extracted for subsequent purification. In vivo protein expression systems using prokaryotic and eukaryotic cells are well known. Also, some proteins are recovered using denaturants and protein-refolding procedures. In vitro (cell-free) protein expression systems typically use translation-compatible extracts of whole cells or compositions that contain components sufficient for transcription, translation and optionally post-translational modifications such as RNA polymerase, regulatory protein factors, transcription factors, ribosomes, tRNA cofactors, amino acids and nucleotides. In the presence of an expression vectors, these extracts and components can synthesize proteins of interest. Cell-free systems typically do not contain proteases and enable labeling of the protein with modified amino acids. Some cell free systems incorporated encoded components for translation into the expression vector. See, e.g., Shimizu et al., Cell-free translation reconstituted with purified components, 2001, Nat. Biotechnol., 19, 751-755 and Asahara & Chong, Nucleic Acids Research, 2010, 38(13): e141, both hereby incorporated by reference in their entirety.
A “selectable marker” is a nucleic acid introduced into a recombinant vector that encodes a polypeptide that confers a trait suitable for artificial selection or identification (report gene), e.g., beta-lactamase confers antibiotic resistance, which allows an organism expressing beta-lactamase to survive in the presence antibiotic in a growth medium. Another example is thymidine kinase, which makes the host sensitive to ganciclovir selection. It may be a screenable marker that allows one to distinguish between wanted and unwanted cells based on the presence or absence of an expected color. For example, the lac-z-gene produces a beta-galactosidase enzyme which confers a blue color in the presence of X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactoside). If recombinant insertion inactivates the lac-z-gene, then the resulting colonies are colorless. There may be one or more selectable markers, e.g., an enzyme that can complement to the inability of an expression organism to synthesize a particular compound required for its growth (auxotrophic) and one able to convert a compound to another that is toxic for growth. URA3, an orotidine-5′ phosphate decarboxylase, is necessary for uracil biosynthesis and can complement ura3 mutants that are auxotrophic for uracil. URA3 also converts 5-fluoroorotic acid into the toxic compound 5-fluorouracil. Additional contemplated selectable markers include any genes that impart antibacterial resistance or express a fluorescent protein. Examples include, but are not limited to, the following genes: ampr, camr, tetr, blasticidinr, neor, hygr, abxr, neomycin phosphotransferase type II gene (nptll), p-glucuronidase (gus), green fluorescent protein (gfp), egfp, yfp, mCherry, p-galactosidase (lacZ), lacZa, lacZAM15, chloramphenicol acetyltransferase (cat), alkaline phosphatase (phoA), bacterial luciferase (luxAB), bialaphos resistance gene (bar), phosphomannose isomerase (pmi), xylose isomerase (xylA), arabitol dehydrogenase (at1D), UDP-glucose:galactose-1-phosphate uridyltransferasel (galT), feedback-insensitive a subunit of anthranilate synthase (OASA1D), 2-deoxyglucose (2-DOGR), benzyladenine-N-3-glucuronide, E. coli threonine deaminase, glutamate 1-semialdehyde aminotransferase (GSA-AT), D-amino acidoxidase (DAAO), salt-tolerance gene (rstB), ferredoxin-like protein (pflp), trehalose-6-P synthase gene (AtTPS1), lysine racemase (lyr), dihydrodipicolinate synthase (dapA), tryptophan synthase beta 1 (AtTSB1), dehalogenase (dhlA), mannose-6-phosphate reductase gene (M6PR), hygromycin phosphotransferase (HPT), and D-serine ammonialyase (dsdA).
A “label” refers to a detectable compound or composition that is conjugated directly or indirectly to another molecule, such as an antibody or a protein, to facilitate detection of that molecule. Specific, non-limiting examples of labels include fluorescent tags, enzymatic linkages, and radioactive isotopes. In one example, a “label receptor” refers to incorporation of a heterologous polypeptide in the receptor. A label includes the incorporation of a radiolabeled amino acid or the covalent attachment of biotinyl moieties to a polypeptide that can be detected by marked avidin (for example, streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods). Various methods of labeling polypeptides and glycoproteins are known in the art and may be used. Examples of labels for polypeptides include, but are not limited to, the following: radioisotopes or radionucleotides (such as 35S or 131I) fluorescent labels (such as fluorescein isothiocyanate (FITC), rhodamine, lanthanide phosphors), enzymatic labels (such as horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase), chemiluminescent markers, biotinyl groups, predetermined polypeptide epitopes recognized by a secondary reporter (such as a leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags), or magnetic agents, such as gadolinium chelates. In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
In certain embodiments, the disclosure relates to recombinant polypeptides comprising sequences disclosed herein or variants or fusions thereof wherein the amino terminal end or the carbon terminal end of the amino acid sequence are optionally attached to a heterologous amino acid sequence, label, or reporter molecule.
In certain embodiments, the disclosure relates to the recombinant vectors comprising a nucleic acid encoding a polypeptide disclosed herein or fusion protein thereof.
In certain embodiments, the recombinant vector optionally comprises a mammalian, human, insect, viral, bacterial, bacterial plasmid, yeast associated origin of replication or gene such as a gene or retroviral gene or lentiviral LTR, TAR, RRE, PE, SLIP, CRS, and INS nucleotide segment or gene selected from tat, rev, nef, vif, vpr, vpu, and vpx or structural genes selected from gag, pol, and env.
In certain embodiments, the recombinant vector optionally comprises a gene vector element (nucleic acid) such as a selectable marker region, lac operon, a CMV promoter, a hybrid chicken B-actin/CMV enhancer (CAG) promoter, tac promoter, T7 RNA polymerase promoter, SP6 RNA polymerase promoter, SV40 promoter, internal ribosome entry site (IRES) sequence, cis-acting woodchuck post regulatory regulatory element (WPRE), scaffold-attachment region (SAR), inverted terminal repeats (ITR), FLAG tag coding region, c-myc tag coding region, metal affinity tag coding region, streptavidin binding peptide tag coding region, polyHis tag coding region, HA tag coding region, MBP tag coding region, GST tag coding region, polyadenylation coding region, SV40 polyadenylation signal, SV40 origin of replication, Col E1 origin of replication, f1 origin, pBR322 origin, or pUC origin, TEV protease recognition site, loxP site, Cre recombinase coding region, or a multiple cloning site such as having 5, 6, or 7 or more restriction sites within a continuous segment of less than 50 or 60 nucleotides or having 3 or 4 or more restriction sites with a continuous segment of less than 20 or 30 nucleotides.
VaccinesIn certain embodiments, this disclosure relates to vaccine compositions for use in methods of protecting a human subject against Zika disease or infection, wherein said composition comprises: a live attenuated or inactivated chimeric Zika virus; live attenuated Zika virus; an inactivated Zika virus; replication-defective pseudo-infectious Zika virus; a Zika virus-like particle (VLP) or combinations thereof. In certain embodiments, the chimeric or attenuated virus comprises mutations disclosed herein.
In certain embodiments, a vaccine of the instant disclosure is a recombinant Yellow Fever virus encoding Zika virus proteins. In certain embodiments, the vaccine has been attenuated or inactivated. In certain embodiments, genes encoding the structural components of the Zika virus, including prM, M, and E are inserted into the backbone nucleic acid sequence of Yellow Fever virus, generating a chimeric virus. Typically, mutations in the prM, M, and E genes are made to reduce the neurotropism of the virus.
In certain embodiments, this disclosure relates to an attenuated, live, chimeric virus comprising a yellow fever virus in which nucleotide sequences encoding structural components of the yellow fever virus are replaced with nucleotide sequences encoding structural components of a Zika virus. In other embodiments, this disclosure relates to chimeric viruses wherein the replaced nucleotide sequences encode for the precursor membrane protein (prM), membrane protein (M), and envelope (E) proteins of a Zika virus.
In certain embodiments, the disclosure contemplates a vaccinal Zika or uses disclosed herein that contains a polypeptide or a nucleic acid that encodes SEQ ID NO: 5, 6, and/or 7 or a polypeptide with 80, 90, 95, 96, 97, 98, or 99% or greater sequence identity or similarity thereto.
In certain embodiments, this disclosure relates to chimeric viruses wherein the nucleotide sequences of a Zika virus are derived from either the Asian or African strains or serotypes of Zika virus. In other embodiments, this disclosure relates to chimeric viruses wherein attenuation of the is accomplished through a series of mutations in the nucleotides encoding the precursor membrane protein, membrane protein, and envelope proteins are introduced, reducing the neurotropism of the virus.
In certain embodiments, the nucleic acid based vaccinal Zika as disclosed herein are capable of replication in a host cell or human subject. In certain embodiments, the nucleic acid based vaccinal Zika as disclosed herein are killed or inactivated, e.g., after replication that generates virus particles.
In certain embodiments, the chimeric viruses as disclosed herein comprises a nucleic acid sequence encoding the Zika E protein comprising SEQ ID NO: 2 or a variant thereof. In certain embodiments, the variant has one, two, three, or more amino acid substitutions or conserved amino acid substitutions. In certain embodiments, the variant has SEQ ID NO: 1.
In certain embodiments, the variant has the variant comprises one, two, three, four, or all of the following substitutions relative to SEQ ID NO: 2: a) a phenylalanine (F) substitution at position 107; b) a lysine (K) substitution at position 138; c) a valine (V) substitution at position 176; d) a histidine (H) substitution at position 267; and/or e) a methionine (M) substitution at position 283.
In certain embodiments, the chimeric virus comprises a nucleic acid sequence having SEQ ID NO: 3 or SEQ ID NO: 4 optionally comprising synonymous substitutions. In other embodiments, the disclosure relates to chimeric viruses comprising a nucleic acid having greater than 60%, 70%, 80%, 90%, or 95% sequence identity to SEQ ID NO: 3 or SEQ ID NO: 4 or variant having synonymous substitutions. In other embodiments, the disclosure relates to the chimeric virus, wherein the virus is further attenuated by codon deoptimization.
The ability of a vaccine composition of the present disclosure to provoke an immune response in a subject (i.e. induce the production of neutralizing antibodies) can be assessed, for example, by measuring the neutralizing antibody titre raised against the Zika virus serotype(s) comprised within the composition. The neutralizing antibody titre may be measured by the Plaque Reduction Neutralization Test (PRNT50) test. Briefly, neutralizing antibody titre is measured in sera collected from vaccinated subjects at least 28 days following administration of a vaccine composition of the present disclosure. Serial, two-fold dilutions of sera (previously heat-inactivated) are mixed with a constant challenge-dose of Zika virus as appropriate (expressed as PFU/mL). The mixtures are inoculated into wells of a microplate with confluent Vero cell monolayers. After adsorption, cell monolayers are incubated for a few days. The presence of Zika virus infected cells is indicated by the formation of infected foci and a reduction in virus infectivity due to the presence of neutralizing antibodies in the serum samples can thus be detected. The reported value (end point neutralization titre) represents the highest dilution of serum at which >50% of Zika challenge virus (in foci counts) is neutralized when compared to the mean viral focus count in the negative control wells (which represents the 100% virus load). The end point neutralization titres are presented as continuous values. As PRNT tests may slightly vary from a laboratory to another the LLOQ may also slightly vary. Accordingly, in a general manner, it is considered that seroconversion occurs when the titre is superior or equal to the LLOQ of the test.
A vaccine composition according to the present disclosure may be administered in a single dose. A vaccine composition according to the present disclosure may be administered in multiple doses. Doses of a vaccine composition according to the present disclosure may be administered in an initial vaccination regimen followed by booster vaccinations. For example, a vaccine composition according to the present disclosure may be administered in one, two or three doses or more than three doses, e.g. four doses. Preferably, the first dose and the third dose are to be administered approximately twelve months apart. For example, an initial vaccination regimen according to the present disclosure is administered in three doses, wherein the first and third doses of said vaccination regimen are to be administered approximately twelve months apart. Advantageously, a vaccine composition according to the present disclosure is to be administered in a first dose, a second dose and a third dose. In such an embodiment, said first dose and said third dose may be administered approximately twelve months apart. For instance, a vaccine composition of the present disclosure may be administered in a first dose, a second dose and a third dose, wherein said second dose is to be administered about six months after said first dose and wherein said third dose is to be administered about twelve months after said first dose. Alternatively, the three doses may be administered at zero months, at about three to four months (e.g. at about three-and-a-half months) and at about twelve months (i.e. a regimen wherein the second dose of the composition is administered at about three-and-a-half months after the first dose, and wherein the third dose of the composition is administered at about twelve months after the first dose).
A vaccine composition for use the present disclosure, e.g. for use in a method according to the present disclosure preferably comprises a Zika vaccinal. Such Zika vaccinal includes, for example, inactivated viruses, live attenuated viruses, and live attenuated chimeric Zika viruses. Preferably, the Zika vaccinal are live attenuated chimeric Zika viruses. Preferably, a live attenuated chimeric Zika virus according to the present disclosure comprises one or more proteins from a Zika virus and one or more proteins from a different flavivirus. Advantageously, said different flavivirus is a yellow fever virus, for example a yellow fever virus of strain YF 17D. Preferably, a chimeric Zika virus according to the present disclosure comprises the prM-E amino acid sequences of a Zika virus, for example, a chimeric Zika virus according to the present disclosure comprises a yellow fever virus genome whose prM-E whose prM-E sequence has been substituted with the prM-E sequence of a Zika virus.
The exact quantity of a Zika vaccinal of the present disclosure to be administered may vary according to the age and the weight of the patient being vaccinated, the frequency of administration as well as the other ingredients (e.g. adjuvants) in the composition. The quantity of a live attenuated Zika virus comprised in a vaccine composition of the present disclosure lies within a range of from about 103 to about 107 CCID50. Generally, the quantity of a live attenuated Zika virus comprised in a vaccine composition of the present disclosure lies within a range of from about 103 to about 106 CCID50 or of from about 103 to about 107 CCID50, for example within a range of from about 5×103 to about 5×105 CCID50, for example within a range of from about 1×104 to about 1×105 CCID50, for example about 105 CCID50. The quantity of a live attenuated Zika virus comprised in a vaccine composition of the present disclosure may also lie within a range of from about 104 to about 107 CCID50, for example about 106 CCID50. Generally, the quantity of a VLP comprised in the composition lies within a range of from about 100 ng to about 100 μg of VLP, preferably within a range of from about 100 ng to about 50 μg, preferably within a range of from about 100 ng to about 20 μg, preferably about 1 μg to 10 μg. The amount of VLP can be determined by ELISA. Advantageously, a vaccine composition according to the present disclosure comprises an effective amount of a Zika antigen as defined herein.
A vaccine composition for use in a method reported herein may optionally contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, human serum albumin, essential amino acids, nonessential amino acids, L-arginine hydrochlorate, saccharose, D-trehalose dehydrate, sorbitol, tris (hydroxymethyl) aminomethane and/or urea. In addition, the vaccine composition may optionally comprise pharmaceutically acceptable additives including, for example, diluents, binders, stabilizers, and preservatives.
A vaccine composition of the present disclosure may comprise a Zika antigen which is a Zika immunoprotein. A Zika immunoprotein, as used herein, is a Zika envelope (E) protein, or derivative or fragment thereof, that when administered to an immunocompetent subject induces neutralizing antibodies against a Zika virus. Zika immunoproteins include native and derivatized forms of Zika E proteins, including chemical conjugates, immunological fragments, and fusion proteins thereof.
Zika immunoproteins, or derivatives or fragments thereof may be conjugated to carrier molecules. Such conjugation may be achieved by chemical conjugation techniques or through the recombinant expression of fusion proteins comprising the Zika immunoproteins or derivatives or fragments thereof and the carrier molecule. Examples of carrier molecules which may be used for preparing conjugates include diphtheria toxoid, tetanus toxoid, fragment C of tetanus toxin, mutants of diphtheria toxin including CRM 197, CRM 176, CRM228, CRM 45, CRM 9, CRM 45, CRM 102, CRM 103 and CRM 107, pneumococcal pneumolysin, OMPC, heat shock proteins, pertussis proteins, pneumococcal surface protein PspA or the toxin A or B of Clostridium difficile.
In certain embodiments, the disclosure relates to a nucleic acid construct or viral vector which is able to express in a human cell a VLP comprising a Zika protein disclosed herein.
A vaccine composition of the present disclosure may comprise one or more adjuvants to enhance the immunogenicity of the Zika vaccinal. Those skilled in the art will be able to select an adjuvant which is appropriate in the context of this disclosure. An adjuvant is preferably used in a vaccine composition of the disclosure comprising an inactivated virus or a VLP or a Zika structural protein. An adjuvant may be used in a vaccine composition of the disclosure comprising a live attenuated virus, as long as said adjuvant does not influence replication.
Suitable adjuvants include an aluminum salt such as aluminum hydroxide gel, aluminum phosphate or alum, but may also be a salt of calcium, magnesium, iron or zinc. Further suitable adjuvants include an insoluble suspension of acylated tyrosine or acylated sugars, cationically or anionically derivatized saccharides, or polyphosphazenes. Alternatively, the adjuvant may be an oil-in-water emulsion adjuvant as well as combinations of oil-in-water emulsions and other active agents. Other oil emulsion adjuvants have been described, such as water-in-oil emulsions. Examples of such adjuvants include MF59, AF03 (WO 2007/006939), AF04 (WO 2007/080308), AF05, AF06 and derivatives thereof. The adjuvant may also be a saponin, lipid A or a derivative thereof, an immunostimulatory oligonucleotide, an alkyl glucosamide phosphate, an oil in water emulsion or combinations thereof. Examples of saponins include Quil A and purified fragments thereof such as QS7 and QS21.
As appreciated by skilled artisans, a vaccine composition of the present disclosure is suitably formulated to be compatible with the intended route of administration. Examples of suitable routes of administration include for instance intramuscular, transcutaneous, subcutaneous, intranasal, oral or intradermal. Advantageously, the route of administration is subcutaneous.
The vaccine compositions of the present disclosure may be administered using conventional hypodermic syringes or safety syringes or jet injectors. For intradermal administration, conventional hypodermic syringes may be employed using the Mantoux technique or specialized intradermal delivery devices and microinjection system.
The volume of a vaccine composition of the present disclosure administered will depend on the method of administration. In the case of subcutaneous injections, the volume is generally between 0.1 and 1.0 ml, preferably approximately 0.5 ml.
Optionally, booster administrations of a vaccine composition according to the present disclosure may be used, for example between six months and ten years, for example six months, one year, three years, five years or ten years after initial immunization (i.e. after administration of the last dose scheduled in the initial immunization regimen).
According to one embodiment, the disclosure also provides a kit comprising a vaccine composition of the disclosure and instructions for the use of said vaccine composition in a method of protecting a human subject against Zika disease. The kit can comprise at least one dose (typically in a syringe) of any vaccine composition contemplated herein. According to one embodiment the kit may comprises a multi-dose formulation (typically in a vial) of any vaccine composition as described herein. The kit further comprises a leaflet mentioning the use of the said vaccine composition for the prevention of Zika disease or the use of the said vaccine for the prophylaxis of Zika disease. The leaflet may further mention the vaccination regimen and the human subject population to be vaccinated.
Methods of UseIn certain embodiments, the disclosure relates to the use of a vaccine composition of the present disclosure for the manufacture of a medicament for protecting or treating a human subject against Zika disease or infection. In certain embodiments, a composition according to the present disclosure, e.g., a composition for use in a method according to the present disclosure reduces the incidence or likelihood of symptomatic virologically confirmed Zika infections.
In accordance with the present disclosure, a method of treating or protecting may results in a reduction in the severity or in the likelihood of developing Zika disease in a human subject exposed to a Zika virus. Advantageously, said reduction is statistically significant. For example, a method of protecting, according to the present disclosure, may result in a reduction in at least one symptom of Zika disease as defined herein or a reduction in a combination of any two or more of those symptoms. The protection may result in a statistically significant reduction in the incidence or likelihood of, e.g. the prevention of, symptomatic virologically-confirmed Zika disease caused by Zika virus of any serotype; a statistically significant reduction in the incidence or likelihood of, e.g. the prevention of Zika infection during pregnancy that can cause a birth defect, microcephaly or incomplete brain development caused by Zika virus of any serotype; a statistically significant reduction in the incidence or likelihood of, e.g. the prevention of fever, rash, headache, joint pain, conjunctivitis (red eyes), and/or muscle pain caused by Zika virus of any serotype; a statistically significant reduction in the incidence or likelihood of, e.g. the prevention of, fever or a reduction in the mean duration and/or intensity of fever; a statistically significant reduction in the incidence or likelihood of, e.g. the prevention of spreading the virus through mosquito bites and sex; and/or a statistically significant reduction in the incidence or likelihood of, e.g. the prevention passing Zika virus from a pregnant woman to her fetus. The duration and intensity of fever are monitored and recorded according to standard hospital procedures. In a human subject, a fever (i.e. a febrile episode) is defined as the observance of two temperature readings of at least 37.5° C. measured twice over an interval of at least 4 hours.
In certain embodiment, this disclosure relates to methods of vaccinating a subject against Zika virus comprising administering a Zika vaccinal as disclosed herein to a subject optionally in combination with an adjuvant under conditions such that antibodies that bind a Zika protein are generated in response to the vaccine. In certain embodiments, the antibodies are IgG antibodies in serum, or IgG or IgA antibodies in mucosal secretions or surfaces. In certain embodiments, one detects the presence of a given marker such as an antibody titer or a number of antigen-specific cells above a given threshold, e.g., an amount associated with a normal person in the absence of the vaccine.
In certain embodiment, this disclosure relates to methods of vaccinating a subject against Zika virus comprising administering a Zika vaccinal as disclosed herein to a subject optionally in combination with an adjuvant under conditions such that cells that produce antibodies that bind a Zika protein are generated in response to the vaccine.
In certain embodiments, the cells or antibodies are long live, e.g., cells or antibodies that detectably persist in the subject for longer than 6 months, 1 year, 2 years, 3 year, 5 years or more. In certain embodiments, the cells express CD3, CD4, and/or CD8. In certain embodiments, the cells are long-lived plasma cells secreting specific antibodies of adapted avidity and function, and isotype, even in the absence of virus. In certain embodiments, the cells are specific B and T memory cells of reactive memory or CD8+ cytotoxic T cells.
In certain embodiment, this disclosure relates to methods of treating or preventing a viral infection comprising administering a Zika vaccinal as disclosed herein to a subject optionally in combination with an adjuvant under conditions such that reduced titers of the Zika virus are generated after an infection. In certain embodiments, this disclosure relates to methods of treating or preventing a Zika viral infection comprising administering compositions disclosed herein to a subject optionally in combination with an adjuvant under conditions such that antibodies that bind a Zika protein are generated in response to the vaccine. In another embodiment, this disclosure relates to a method of vaccinating a patient against Zika virus infection by administering the above pharmaceutical composition along with a pharmaceutically acceptable adjuvant.
In certain embodiments, the disclosure relates to the use of a vaccine composition of the present disclosure for the manufacture of a medicament for protecting or treating a human subject against Zika disease or infection. In certain embodiments, the disclosure relates to treating a subject diagnosed with a Zika infection by administering a Zika antigen disclosed herein in combination with another active agent or antiviral agent. In certain embodiments, the agent is selected from a Zika neutralizing antibody, sofosbuvir, finasteride, ivermectin, brequinar, gemcitabine, epigallocatechin gallate, chloroquine, obatoclax, bortezomib, daptomycin, sertraline, pyrimethamine, cyclosporine A, azathioprine, emricasan, niclosamide, mefloquine, palonosetron, 25-hydroxycholesterol, 7-deaza-2-C-methyladenosine (7-deaza-2′-CMA), 2′-C72, methyladenosine (2′-CMA), 2′-C-methylcytidine (2′-CMC), 2′-C-methylguanosine (2′-73 CMG), and 2′-C-methyluridine (2′-CMU).
A subject to which a vaccine composition of the disclousre is to be administered is preferably a person at risk of infection, for instance a person travelling in an area where Zika fever is present, i.e. a Zika endemic area, or a resident of such an area.
EXAMPLESOne can constructe YFV based live attenuated Zika virus (ZKV) vaccine, called “ZKV-YFV chimera vaccines” by introducing two types of genetic modifications into the 17D YFV genome. First, the prM, M and E genes of 17D YFV are replaced with the same genes of ZIKV, generating ZKV-YFV chimera viruses (
One can synthesize chimera virus RNAs in vitro. One can transfect Vero cells to produce the live chimera viruses. Chimera viruses can be investigated for their replication kinetics compared with parental YFV17D and ZKV strains in Vero cells (i.e. MR766 and PR strain). One can determined neurotropism of both wild type and mutant chimera viruses by using various human neuronal cells and a newly tested mouse model as reported Lazear et al, Cell Host Microbe 19(5):720-730, 2016).
Nucleic acid sequences of wild type and mutant YF-ZK chimera viruses are attached, and examples of the E mutations to reduce viral neurotropism are marked in the mutant virus sequence.
Claims
1. A method of vaccinating a subject for Zika virus comprising administering an effective amount of a chimeric virus comprising a nucleic acid encoding a Zika envelope (E) protein having the amino acid sequence of SEQ ID NO: 1.
2. The method of claim 1, wherein the nucleic acid sequence encodes a Zika precursor membrane (prM) protein.
3. The method of claim 1, wherein the chimeric virus is capable of replication in a host cell or human subject.
4. The method of claim 1, wherein the nucleic acid sequence has SEQ ID NO: 4 optionally comprising substitutions that provide synonymous codons.
5. A method of vaccinating a subject for Zika virus comprising administering an effective amount of a chimeric yellow fever virus comprising a nucleic acid encoding a Zika envelope (E) protein having the amino acid sequence of SEQ ID NO: 1.
6. The method of claim 5, wherein the nucleic acid sequence encodes a Zika precursor membrane (prM) protein.
7. The method of claim 5, wherein the chimeric yellow fever virus is capable of replication in a host cell or human subject.
8. The method of claim 5, wherein the nucleic acid sequence has SEQ ID NO: 4 optionally comprising substitutions that provide synonymous codons.
Type: Application
Filed: Oct 10, 2022
Publication Date: Jun 22, 2023
Inventor: Baek Kim (Atlanta, GA)
Application Number: 18/045,330
