CHIMPANZEE ADENOVIRAL VECTOR-BASED FILOVIRUS VACCINES
This invention provides vaccines for inducing an immune response and protection against filovirus infection for use as a preventative vaccine in humans. In particular, the invention provides chimpanzee adenoviral vectors expressing filovirus proteins from different strains of Ebolavirus (EBOV) or Marburg virus (MARV).
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This application is a Continuation Application of U.S. application Ser. No. 15/339,225 filed Oct. 31, 2016, which is a Divisonal Application of U.S. application Ser. No. 13/641,655, filed Jan. 2, 2013, which is a U.S. National Phase Application of PCT/US2011/032682, filed Apr. 15, 2011 which claims the benefit of US Provisional Patent Application No. 61/325,166, filed Apr. 16, 2010 each of which are incorporated herein by reference in their entirety.REFERENCE TO SEQUENCE LISTING
This application includes a Sequence Listing as a text file named “77867-591100US-854933_SEQLIST.txt” created Oct. 15, 2012, and containing 387,507 bytes. The material contained in this text file is incorporated by reference in its entirety for all purposes.FIELD OF THE INVENTION
This invention relates generally to viral vaccines and, more particularly, to filovirus vaccines based on chimpanzee adenoviral vectors.BACKGROUND OF THE INVENTION
The Ebola viruses, and the genetically-related Marburg virus, viruses of the Filoviridae family, are associated with outbreaks of highly lethal hemorrhagic fever in humans and primates in North America, Europe, and Africa (Peters, C. J. et al. in: Fields Virology, eds. Fields, B. N. et al. 1161-1176, Philadelphia, Lippincott-Raven, 1996; Peters, C. J. et al. 1994 Semin Virol 5:147-154). Ebola viruses are negative-stranded RNA viruses comprised of five subtypes, including those described in the Zaire, Sudan, Reston, Ivory Coast and Bundibugyo episodes (Sanchez, A. et al. 1996 PNAS USA 93:3602-3607). The Ebola virus, was first recognized during an outbreak in 1976 in the Ebola River valley of Zaire (currently the Democratic Republic of the Congo), Africa. Mortality rates vary between different species, spanning from approximately 35 to 90% for the most virulent ones, Zaire and Sudan. The development of effective vaccines and/or drugs is a high priority. The Ebola (EBOV) and Marburg (MARV) viruses have also been categorized as priority class A pathogens due to their virulence, ease of dissemination, lack of effective countermeasures to prevent or treat them, and their potential to cause public panic and social disruption.
Although several subtypes have been defined, the genetic organization of Ebola viruses is similar, each containing seven linearly arrayed genes. Among the viral proteins, the envelope glycoprotein exists in two alternative forms, a 50-70 kilodalton (kDa) secreted protein of unknown function encoded by the viral genome and a 130 kDa transmembrane glycoprotein generated by RNA editing that mediates viral entry (Peters, C. J. et al. in: Fields Virology, eds. Fields, B. N. et al. 1161-1176, Philadelphia, Lippincott-Raven, 1996; Sanchez, A. et al. 1996 PNAS USA 93:3602-3607). Other structural gene products include the nucleoprotein (NP), matrix proteins VP24 and VP40, presumed nonstructural proteins VP30 and VP35, and the viral polymerase (reviewed in Peters, C. J. et al. in: Fields Virology, eds. Fields, B. N. et al. 1161-1176, Philadelphia, Lippincott-Raven, 1996). Although spontaneous variation of its RNA sequence does occur in nature, there appears to be less nucleotide polymorphism within Ebola subtypes than among other RNA viruses (Sanchez, A. et al. 1996 PNAS USA 93:3602-3607), suggesting that immunization may be useful in protecting against this disease. Previous attempts to elicit protective immune responses against Ebola virus using traditional active and passive immunization approaches have, however, not succeeded in primates (Peters, C. J. et al. in: Fields Virology, eds. Fields, B. N. et al. 1161-1176, Philadelphia, Lippincott-Raven, 1996: Clegg. J. C. S. et al. 1997 New Generation Vaccines, eds.: Levine, M. M. et al. 749-765, New York, N.Y. Marcel Dekker, Inc.; Jahrling, P. B. et al. 1996 Arch Virol Suppl 11:135-140).
Replication-defective adenovirus vectors (rAd) are powerful inducers of cellular immune responses and have therefore come to serve as useful vectors for gene-based vaccines, particularly for lentiviruses and filoviruses, as well as other nonviral pathogens (Shiver, et al., (2002) Nature 415(6869): 331-5; (Hill, et al., Hum Vaccin 6(1): 78-83; Sullivan, et al., (2000) Nature 408(6812): 605-9; Sullivan et al., (2003) Nature 424(6949): 681-4; Sullivan, et al., (2006) PLoS Med 3(6): e177; Radosevic, et al., (2007); Santra, et al., (2009) Vaccine 27(42): 5837-45. Adenovirus-based vaccines have several advantages as human vaccines since they can be produced to high titers under GMP conditions and have proven to be safe and immunogenic in humans (Asmuth, et al., J Infect Dis 201(1): 132-41; Kibuuka, et al., J Infect Dis 201(4): 600-7: Koup, et al., PLoS One 5(2): e9015; Catanzaro, et al., (2006) J Infect Dis 194(12): 1638-49; Harro, et al., (2009) Clin Vaccine Immunol 16(9): 1285-92). While most of the initial vaccine work was conducted using rAd5 due to its significant potency in eliciting broad antibody and CD8+ T cell responses, pre-existing immunity to rAd5 in humans may limit efficacy (Catanzaro, (2006); Cheng, et al., (2007) PLoS Pathog 3(2): e25; McCoy, et al., (2007) J Virol 81(12): 6594-604; Buchbinder, et al., (2008) Lancet 372(9653): 1881-93). This property might restrict the use of rAd5 in clinical applications for many vaccines that are currently in development including Ebola virus (EBOV) and Marburg virus (MARV).
To circumvent the issue of pre-existing immunity to rAd5, several alternative vectors are currently under investigation. These include adenoviral vectors derived from rare human serotypes and vectors derived from other animals such as chimpanzees (Vogels, et al., (2003) J Viral 77(15): 8263-71: Abbink, et al., (2007) J Viral 81: 4654-63; Santra, (2009) Vaccine 27(42): 5837-45). Chimpanzee adenoviral vectors are also described in WO 2010/086189, WO 2005/071093 and WO 98/10087.
It would thus be desirable to provide a vaccine to elicit an immune response against a filovirus or disease caused by infection with filovirus using improved adenoviral vectors. It would further be desirable to provide methods of making and using said vaccine. The present invention addresses these and other needs.BRIEF SUMMARY OF THE INVENTION
This invention provides vaccines for inducing an immune response and protection against filovirus infection for use as a preventative vaccine in humans. In particular, the invention provides chimpanzee adenoviral vectors (adenoviral vectors derived from chimpanzees) expressing filovirus proteins. For example, these vaccines include chimpanzee adenovirus serotypes ChAd3, ChAd63. PanAd3, PanAd1, PanAd2, or ChAd83 expressing filovirus envelope glycoprotein (GP), including different strains of Ebolavirus (EBOV) or Marburg (MARV). Exemplary Chimp Adenoviral Ebola and Marburg sequences are provided in SEQ ID NOs:1-9.Definitions
An “adenovirus capsid protein” refers to a protein on the capsid of an adenovirus (e.g., chimpanzee adenovirus) that is involved in determining the serotype and/or tropism of a particular adenovirus. Adenoviral capsid proteins typically include the fiber, penton and/or hexon proteins. As used herein an “adenovirus capsid protein” may be, for example, a chimeric capsid protein that includes capsid protein sequences from two adenoviral iolates.
The terms “adjuvant” and “immune stimulant” are used interchangeably herein, and are defined as one or more substances that cause stimulation of the immune system. In this context, an adjuvant is used to enhance an immune response to the adenovirus vectors of the invention.
The term “corresponding to”, when applied to positions of amino acid residues in sequences, means corresponding positions in a plurality of sequences when the sequences are optimally aligned.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences. (e.g., adenovirus capsid proteins of the invention and polynucleotides that encode them) refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. Percentage of sequence identity is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue 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 and multiplying the result by 100 to yield the percentage of sequence identity.
An “isolated” nucleic acid molecule or adenovirus vector is a nucleic acid molecule (e.g., DNA or RNA) or virus, which has been removed from its native environment. For example, recombinant DNA molecules contained in a vector are considered isolated for the purposes of the present invention. Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the DNA molecules of the present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.
“Operably linked” indicates that two or more DNA segments are joined together such that they function in concert for their intended purposes. For example, coding sequences are operably linked to promoter in the correct reading frame such that transcription initiates in the promoter and proceeds through the coding segment(s) to the terminator.
A “polynucleotide” is a single- or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases typically read from the 5′ to the 3′ end. Polynucleotides include RNA and DNA, and may be isolated from natural sources, synthesized in vitro, or prepared from a combination of natural and synthetic molecules. When the term is applied to double-stranded molecules it is used to denote overall length and will be understood to be equivalent to the term “base pairs”.
A “polypeptide” is a polymer of amino acid residues joined by peptide bonds, whether produced naturally or synthetically. Polypeptides of less than about 50 amino acid residues are commonly referred to as “oligopeptides”.
The term “promoter” is used herein for its art-recognized meaning to denote a portion of a gene containing DNA sequences that provide for the binding of RNA polymerase and initiation of transcription of an operably linked coding sequence. Promoter sequences are typically found in the 5′ non-coding regions of genes.
A “protein” is a macromolecule comprising one or more polypeptide chains. A protein may also comprise non-peptidic components, such as carbohydrate groups. Carbohydrates and other non-peptidic substituents may be added to a protein by the cell in which the protein is produced, and will vary with the type of cell. Proteins are defined herein in terms of their amino acid backbone structures; substituents such as carbohydrate groups are generally not specified, but may be present nonetheless.
The phrase “substantially identical,” in the context of two nucleic acids or polypeptides of the invention (e.g., adenovirus capsid proteins or filovirus antigens), refers to two or more sequences or subsequences that have at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, and 95% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. In some embodiments, the substantial identity exists over a region of the sequences that is at least about 50 residues, at least about 100 residues, or at least about 150 residues in length. In one embodiment, the sequences are substantially identical over the entire length of the coding regions.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally, Current Protocols in Molecular Biology, F. M. Ausubel et al., eds. Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).
Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschuel et al. (1977) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues: always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, less than about 0.01, or less than about 0.001.
A further indication that two nucleic acid sequences or polypeptides of the invention are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions, as described below.
The present invention also relates to chimpanzee adenovirus vectors which include the nucleic acid molecules of the present invention, host cells which are genetically engineered with the recombinant vectors, the production of filovirus polypeptides or fragments thereof by recombinant techniques and these chimpanzee adenovirus vectors for use in inducing an immune response.
The present invention also relates to pharmaceutical compositions (also referred to as immunogenic compositions) comprising the chimpanzee vectors described above, and a pharmaceutically acceptable diluent, carrier, or excipient carrier as well as to such compositions for use in inducing an immune response. Additionally the compositions may also contain an aqueous medium or a water containing suspension, often mixed with other constituents in order to increase the activity and/or the shelf life. These constituents may be salt, pH buffers, stabilizers (such as skimmed milk or casein hydrolysate), emulsifiers, and preservatives. An adjuvant may be included in the pharmaceutical composition to augment the immune response to the viral antigen expressed from the recombinant virus.Filovirus Antigens
The nucleic acid molecules of the invention may encode structural gene products of any filovirus species. There are five species of Ebola viruses, Zaire (type species, also referred to herein as ZEBOV), Sudan (also referred to herein as SEBOV). Reston, Bundibugyo, and Ivory Coast. There is a single species of Marburg virus (also referred to herein as MARV).
The particular antigen expressed in the vectors of the invention is not a critical aspect of the present invention. The adenoviral vectors of the invention can be used to express proteins comprising an antigenic determinant of a wide variety of filovirus antigens. In a typical embodiment, the vectors of the invention include nucleic acid encoding the transmembrane form of the viral glycoprotein (GP). In other embodiments, the vectors of the invention may encode the secreted form of the viral glycoprotein (SGP), or the viral nucleoprotein (NP).
One of skill will recognize that the nucleic acid molecules encoding the filovirus antigenic protein may be modified, e.g., the nucleic acid molecules set forth herein may be mutated, as long as the modified expressed protein elicits an immune response against a pathogen or disease. Thus, as used herein, the term “filovirus antigenic protein” refers to a protein that comprises at least one antigenic determinant of a filovirus protein described above.
The term encompasses filovirus antigens (i.e., gene products of a filovirus), as well as recombinant proteins that comprise one or more filovirus antigenic determinants.
In some embodiments, the protein may be mutated so that it is less toxic to cells (see e.g., WO2006/037038). The present invention also includes vaccines comprising a combination of nucleic acid molecules. For example, and without limitation, nucleic acid molecules encoding GP, SGP and NP of the Zaire, Sudan and Ivory Coast Ebola strains may be combined in any combination, in one vaccine composition.Adenoviral Vectors
As noted above, exposure to certain adenoviruses has resulted in immune responses against certain adenoviral serotypes, which can affect efficacy of adenoviral vaccines. The present invention provides adenoviral vectors comprising capsid proteins from chimpanzee adenoviruses.
Thus, the vectors of the invention comprise a chimpanzee adenovirus capsid protein (e.g., a fiber, penton or hexon protein). One of skill will recognize that it is not necessary that an entire chimpanzee capsid protein be used in the vectors of the invention. Thus, chimeric capsid proteins that include at least a part of a chimpanzee capsid protein can be used in the vectors of the invention. The vectors of the invention may also comprise capsid proteins in which the fiber, penton, and hexon proteins are each derived from a different serotype, so long as at least one capsid protein is derived from a chimpanzee adenovirus. For example, the fiber protein can be derived from PanAd3, the penton from ChAd3, and the hexon from ChAd63. In other embodiments, the fiber, penton and hexon proteins can be those provided in SEQ ID NOS:1-9.
In certain embodiments the recombinant adenovirus vector of the invention is derived mainly or entirely from a chimpanzee adenovirus. Exemplary chimpanzee adenoviruses are known in the art and include, for example, ChAd3 and ChAd63 (described in WO 2005/071093), and PanAd3, PanAd1, PanAd2, and ChAd83 (described in WO 2010/086189). ChAd 3, ChAd63, and ChAd83 were isolated from the common chimpanzee (Pan troglodytes) and PanAd3, PanAd1, PanAd2 were isolated from the bonobo or pygmy chimpanzee (Pan paniscus).
In some embodiments, the adenovirus is replication deficient, e.g. because it contains a deletion in the E1 region of the genome. This allows propagation of such adenoviruses in well known complementing cell lines that express the E1 genes, such as for example 293 cells, PER.C6 cells, and the like. In certain embodiments, the adenovirus is a chimpanzee adenovirus, with a deletion in the E1 and E3 region into which an expression cassette encoding the antigen has been cloned. The construction of chimpanzee adenovirus comprising heterologous sequences encoding antigens is described in WO 2005/071093 and WO 2010/086189.
Typically, a vector of the invention is produced using a nucleic acid comprising the entire recombinant adenoviral genome (e.g., a plasmid, cosmid, or baculovirus vector). Thus, the invention also provides isolated nucleic acid molecules that encode the adenoviral vectors of the invention. The nucleic acid molecules of the invention may be in the form of RNA or in the form of DNA obtained by cloning or produced synthetically. The DNA may be double-stranded or single-stranded.
The adenovirus vectors of the invention are typically replication defective. In these embodiments, the virus is rendered replication-defective by deletion or inactivation of regions critical to replication of the virus, such as the E1 region. The regions can be substantially deleted or inactivated by, for example, inserting the gene of interest (usually linked to a promoter). In some embodiments, the vectors of the invention may contain deletions in other regions, such as the E2, E3 or E4 regions or insertions of heterologous genes linked to a promoter. For E2- and/or E4-mutated adenoviruses, generally E2- and/or E4-complementing cell lines are used to generate recombinant adenoviruses. Mutations in the E3 region of the adenovirus need not be complemented by the cell line, since E3 is not required for replication.
A packaging cell line is typically used to produce sufficient amount of adenovirus vectors of the invention. A packaging cell is a cell that comprises those genes that have been deleted or inactivated in a replication-defective vector, thus allowing the virus to replicate in the cell. Suitable cell lines include, for example, PER.C6. 911, 293, and E1 A549.
As noted above, a wide variety of filovirus antigenic proteins can be expressed in the vectors of the invention. If required, the heterologous gene encoding the filovirus antigenic protein can be codon-optimized to ensure proper expression in the treated host (e.g., human). Thus, codon-optimized antigens are also referred to as humanized antigens. In some embodiments, the viral GP, SGP or NP protein is codon-optimized. For example, codon-optimized antigens include those of SEQ ID NOS: 11, 12, and 14. Codon-optimization is a technology widely applied in the art. Typically, the heterologous gene is cloned into the E1 and/or the E3 region of the adenoviral genome.
The heterologous filovirus gene may be under the control of (i.e., operably linked to) an adenovirus-derived promoter (e.g., the Major Late Promoter) or may be under the control of a heterologous promoter. Examples of suitable heterologous promoters include the CMV promoter and the RSV promoter. In some embodiments, the promoter is located upstream of the heterologous gene of interest within an expression cassette.
As noted above, the adenovirus vectors of the invention can comprise a wide variety of filovirus antigens known to those of skill in the art.Immunogenic Compositions
Purified or partially purified adenovirus vectors of the invention may be formulated as a vaccine (also referred to as an “immunogenic composition”) according to methods well known in the art. Such compositions may include adjuvants to enhance immune responses. The optimal ratios of each component in the formulation may be determined by techniques well known to those skilled in the art.
The preparation and use of immunogenic compositions are well known to those of skill in the art. Liquid pharmaceutical compositions generally include a liquid carrier such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil. Physiological saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may be included.
The compositions are suitable for single administrations or a series of administrations. When given as a series, inoculations subsequent to the initial (priming) administration are given to boost the immune response and are typically referred to as booster inoculations. The compositions of the invention can be used as a boosting composition primed by antigen using any of a variety of different priming compositions, or as the priming composition. Thus, one aspect of the present invention provides a method of priming and/or boosting an immune response to an antigen in an individual. For example, in some embodiments, a priming administration of one adenoviral vector of the invention is followed by a booster inoculation of the second adenoviral vector.
The timing of the administration of boosting compositions is well within the skill in the art. Boosting compositions are generally administered weeks or months after administration of the priming composition, for example, 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 or one to two years. Methods of accelerated vaccination by administering a single dose of a recombinant adenovirus are described for example in U.S. Pat. No. 7,635,485.
The compositions of the invention may comprise other filovirus antigens or the priming or boosting inoculations may comprise other antigens. The other antigens used in combination with the adenovirus vectors of the invention are not critical to the invention and may be, for example, filovirus antigens, nucleic acids expressing them, virus like particles (VLPs), or prior art viral vectors. Such viral vectors include, for example, other adenoviral vectors, vaccinia virus vectors, avipox vectors such as fowlpox or canarypox, herpes virus vectors, vesicular stomatitis virus vectors, or alphavirus vectors. One of skill will recognize that the immunogenic compositions of the invention may comprise multiple antigens and vectors.
The antigens in the respective priming and boosting compositions (however many boosting compositions are employed) need not be identical, but should share antigenic determinants.
In some embodiments, heterologous prime-boost approaches can be used, for example, priming with Pan3-EBOV and boosting with ChAd3EBOV, priming with ChAd3EBOV and boosting with rLCMV (recombinant lymphocytic choriomeningitis virus), or priming with ChAd63EBOV and boosting with rLCMV. The rLCMV can be constructed as described in Flatz, L. et al., Nature Medicine, 16:339-345, 2010, except that the sequence encoding the antigenic protein is a sequence encoding a filovirus GP protein of the invention. In other embodiments, the boost can be rMVA (modified vaccinia virus Ankara) encoding an Ebola GP protein. Preparation and use of rMVA vectors is known and described for example in Ourmanov et al. J. Virol. 83:5388-5400, 2009 and Martinon et al. Vaccine 26:532-545, 2008. The vaccines of the invention can be used to generate protection against all human EBOV threats including Bundibugyo and Ivory Coast in a single vaccine. Finally, the vaccines against EBOV and MARV may also be mixed into a single inoculation in order to provide protection against both filoviruses simultaneously. In “prime and boost” immunization regimes, the immune response induced by administration of a priming composition is boosted by administration of a boosting composition. Effective boosting can be achieved using replication-defective adenovirus vectors, following priming with any of a variety of different types of priming compositions, as described for example in U.S. Pat. No. 7,094,598, which is incorporated herein by reference.
As noted above, the immunogenic compositions of the invention may comprise adjuvants. Adjuvants suitable for co-administration in accordance with the present invention should be ones that are potentially safe, well tolerated and effective in people including QS-21, Detox-PC, MPL-SE, MoGM-CSF, TiterMax-G, CRL-1005, GERBU, TERamide, PSC97B, Adjumer, PG-026, GSK-I, GcMAF, B-alethine, MPC-026, Adjuvax, CpG ODN, Betafectin, Alum, and MF59.
Other adjuvants that may be administered include lectins, growth factors, cytokines and lymphokines such as alpha-interferon, gamma interferon, platelet derived growth factor (PDGF), granulocyte-colony stimulating factor (gCSF), granulocyte macrophage colony stimulating factor (gMCSF), tumor necrosis factor (TNF), epidermal growth factor (EGF), IL-I, IL-2, IL-4, IL-6, IL-8, IL-10, and IL-12 or encoding nucleic acids therefore.
As noted above, the compositions of the invention may comprise a pharmaceutically acceptable excipient, carrier, buffer, stabilizer or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material may depend on the route of administration, e.g., oral, intravenous, cutaneous or subcutaneous, intramucosal (e.g., gut), intranasal, intramuscular, or intraperitoneal routes. Adiminstration is typically intramuscular.
Intramuscular administration of the immunogenic compositions may be achieved by using a needle to inject a suspension of the adenovirus vector. An alternative is the use of a needless injection device to administer the composition (using, e.g., Biojector™) or a freeze-dried powder containing the vaccine.
For intravenous, cutaneous or subcutaneous injection, or injection at the site of affliction, the adenovirus vector will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, or Lactated Ringer's Injection. Preservatives, stabilizers, buffers, antioxidants and/or other additives may be included, as required. A slow-release formulation may also be employed.
Typically, administration will have a prophylactic aim to generate an immune response against a filovirus antigen before infection or development of symptoms. Diseases and disorders that may be treated or prevented in accordance with the present invention include those in which an immune response may play a protective or therapeutic role. In other embodiments, the adenovirus vectors can be administered for post-exposure prophylactics.
The immunogenic compositions containing the adenovirus vectors are administered to a subject, giving rise to an anti-filovirus immune response in the subject. An amount of a composition sufficient to induce a detectable immune response is defined to be an “immunologically effective dose.” As shown below, the immunogenic compositions of the invention induce a humoral as well as a cell-mediated immune response. In a typical embodiment the immune response is a protective immune response.
The actual amount administered, and rate and time-course of administration, will depend on the nature and severity of what is being treated. Prescription of treatment, e.g., decisions on dosage etc., is within the responsibility of general practitioners and other medical doctors, or in a veterinary context a veterinarian, and typically takes account of the disorder to be treated, the condition of the individual patient, the site of delivery, the method of administration and other factors known to practitioners. Examples of the techniques and protocols mentioned above can be found in Remington's Pharmaceutical Sciences, 16th edition, Osol, A. ed., 1980.
Following production of adenovirus vectors and optional formulation of such particles into compositions, the adenovirus vectors may be administered to an individual, particularly human or other primate. Administration may be to humans, or another mammal, e.g., mouse, rat, hamster, guinea pig, rabbit, sheep, goat, pig, horse, cow, donkey, monkey, dog or cat. Delivery to a non-human mammal need not be for a therapeutic purpose, but may be for use in an experimental context, for instance in investigation of mechanisms of immune responses to the adenovirus vector.
In one exemplary regimen, the adenovirus vector is administered (e.g., intramuscularly) in the range of from about 100 μl to about 10 ml of saline solution containing concentrations of from about 104 to 1012 virus particles/mi. Typically, the adenovirus vector is administered in an amount of about 109 to about 1012 viral particles (vp) to a human subject during one administration. For example, the adenovirus vector can be administered in an amount of about 109, 1010, 1011, or 1012 vp per administration. In some embodiments, the dose administered is from about 1010 to about 1012 vp. An initial vaccination can be followed by a boost as described above. The composition may, if desired, be presented in a kit, pack or dispenser, which may contain one or more unit dosage forms containing the active ingredient. The kit, for example, may comprise metal or plastic foil, such as a blister pack. The kit, pack, or dispenser may be accompanied by instructions for administration.
The present invention also provides kits for enhancing the immunity of a host to a pathogen. These kits may include any one ore more vaccines according to the present invention in combination with a composition for delivering the vaccine to a host and/or a device, such as a syringe, for delivering the vaccine to a host.
The vaccine according to the invention is administered as a pre-exposure (or post-exposure) single dose in a manner compatible with the dosage formulation, and in such amount as will be prophylactively effective. Immunity is defined as the induction of a significant level of protection after vaccination compared to an unvaccinated human or other host.
The vaccine of the present invention, i.e., the recombinant virus, may be administered to a host, such as a human subject, via any pharmaceutically acceptable routes of administration. The routes of administration include, but are not limited to, intramuscular, intratracheal, subcutaneous, intranasal, intradermal, rectal, oral and parental route of administration. Routes of administration may be combined, if desired, or adjusted depending upon the type of the pathogenic virus to be immunized against and the desired body site of protection.
Doses or effective amounts of the recombinant virus may depend on factors such as the condition, the selected viral antigen, the age, weight and health of the host, and may vary among hosts. The appropriate titer of the recombinant virus of the present invention to be administered to an individual is the titer that can modulate an immune response against the viral antigen and elicits antibodies against the pathogenic virus from which the antigen is derived. An effective titer can be determined using an assay for determining the activity of immunoeffector cells following administration of the vaccine to the individual or by monitoring the effectiveness of the therapy using well known in vivo diagnostic assays.
The chimp Ad vectors of the invention can be used as single inoculations to provide either immediate (e.g., 2-4 weeks) or long-term (e.g., one year) immune protection.Nucleic Acid Molecules
As indicated herein, nucleic acid molecules of the present invention may be in the form of RNA or in the form of DNA obtained by cloning or produced synthetically. The DNA may be double-stranded or single-stranded. Single-stranded DNA or RNA may be the coding strand, also known as the sense strand, or it may be the non-coding strand, also referred to as the anti-sense strand. By “isolated” nucleic acid molecule(s) is intended a nucleic acid molecule, DNA or RNA, which has been removed from its native environment. For example, recombinant DNA molecules contained in a vector are considered isolated for the purposes of the present invention. Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the DNA molecules of the present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.
Nucleic acid molecules of the present invention include DNA molecules comprising an open reading frame (ORF) encoding a modified or wild-type filovirus or adenovirus structural gene product; and DNA molecules which comprise a sequence substantially different from those described above but which, due to the degeneracy of the genetic code, still encode an ORF of a filovirus structural gene product. Of course, the genetic code is well known in the art.
The present invention is further directed to fragments of the nucleic acid molecules described herein. By a fragment of a nucleic acid molecule having the nucleotide sequence of an ORF encoding a wild-type filovirus or adenovirus structural gene product is intended fragments at least about 15 nt., at least about 20 nt., at least about 30 nt., or at least about 40 nt. in length. Of course, larger fragments 50, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nt. in length are also intended according to the present invention as are fragments corresponding to most, if not all, of the nucleotide sequence of the ORF encoding a wild-type filovirus or adenovirus structural gene product. By a fragment at least 20 nt. in length, for example, is intended fragments which include 20 or more contiguous bases from the nucleotide sequence of the ORF of a wild-type filovirus or adenovirus structural gene product.
In another aspect, the invention provides a nucleic acid molecule comprising a polynucleotide which hybridizes under stringent hybridization conditions to a portion of the polynucleotide in a nucleic acid molecule of the invention described above. By “stringent hybridization conditions” is intended overnight incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1×SSC at about 65° C.
By a polynucleotide which hybridizes to a “portion” of a polynucleotide is intended a polynucleotide (either DNA or RNA) hybridizing to at least about 15 nucleotides (nt.), at least about 20 nt., at least about 30 nt., or about 30-70 nt. of the reference polynucleotide.
By a portion of a polynucleotide of “at least 20 nt. in length,” for example, is intended 20 or more contiguous nucleotides from the nucleotide sequence of the reference polynucleotide. Of course, a polynucleotide which hybridizes only to a poly A sequence or a complementary stretch of T (or U) residues, would not be included in a polynucleotide of the invention used to hybridize to a portion of a nucleic acid of the invention, since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly A stretch or the complement thereof (e.g., practically any double-stranded cDNA clone).
As indicated herein, nucleic acid molecules of the present invention which encode a filovirus structural gene product may include, but are not limited to those encoding the amino acid sequence of the full-length polypeptide, by itself, the coding sequence for the full-length polypeptide and additional sequences, such as those encoding a leader or secretory sequence, such as a pre-, or pro- or prepro-protein sequence, the coding sequence of the full-length polypeptide, with or without the aforementioned additional coding sequences, together with additional, non-coding sequences, including for example, but not limited to introns and non-coding 5′ and 3′ sequences, such as the transcribed, non-translated sequences that play a role in transcription, mRNA processing, including splicing and polyadenylation signals, for example, ribosome binding and stability of mRNA; and additional coding sequence which codes for additional amino acids, such as those which provide additional functionalities.
The present invention further relates to variants of the nucleic acid molecules of the present invention, which encode portions, analogs or derivatives of the filovirus or adenovirus structural gene product. Variants may occur naturally, such as a natural allelic variant. By an “allelic variant” is intended one of several alternate forms of a gene occupying a given locus on a genome of an organism. (Genes II, Lewin, B., ed., John Wiley & Sons, 1985 New York). Non-naturally occurring variants may be produced using art-known mutagenesis techniques.
Such variants include those produced by nucleotide substitutions, deletions or additions, which may involve one or more nucleotides. The variants may be altered in coding regions, non-coding regions, or both. Alterations in the coding regions may produce conservative or non-conservative amino acid substitutions, deletions or additions. In some embodiments, the variations are silent substitutions, additions and deletions, which do not alter the properties and activities of the filovirus or adenovirus structural gene product or portions thereof. In some embodiments the variants are conservative substitutions.
Further embodiments of the invention include nucleic acid molecules comprising a polynucleotide having a nucleotide sequence at least 95% identical, or at least 96%, 97%, 98% or 99% identical to a nucleotide sequence encoding a polypeptide having the amino acid sequence of a wild-type filovirus or adenovirus structural gene product or fragment thereof or a nucleotide sequence complementary thereto.
By a polynucleotide having a nucleotide sequence at least, for example, 95% “identical” to a reference nucleotide sequence encoding a filovirus or adenovirus structural gene product is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the virus structural gene product. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5′ or 3′ terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular nucleic acid molecule is at least 95%, 96%, 97%, 98% or 99% identical to the reference nucleotide sequence can be determined conventionally using known computer programs such as the Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix. Genetics Computer Group, University Research Park, 575 Science Drive, Madison. Wis. 53711). Bestfit uses the local homology algorithm of Smith and Waterman, 1981 Advances in Applied Mathematics 2:482-489, to find the best segment of homology between two sequences. When using Bestfit or any other sequence alignment program to determine whether a particular sequence is, for instance, 95% identical to a reference sequence according to the present invention, the parameters are set, of course, such that the percentage of identity is calculated over the full length of the reference nucleotide sequence and that gaps in homology of up to 5% of the total number of nucleotides in the reference sequence are allowed.
Of course, due to the degeneracy of the genetic code, one of ordinary skill in the art will immediately recognize that a large number of the nucleic acid molecules having a sequence at least 95%, 96%, 97%, 98%, or 99% identical to a nucleic acid sequence shown herein in the Sequence Listing will encode a polypeptide of the invention. In fact, since degenerate variants of these nucleotide sequences all encode the same polypeptide, this will be clear to the skilled artisan even without performing the above described comparison assay. It will be further recognized in the art that, for such nucleic acid molecules that are not degenerate variants, a reasonable number will also encode a polypeptide having the desired activity. This is because the skilled artisan is fully aware of amino acid substitutions that are either less likely or not likely to significantly affect protein function (e.g., replacing one aliphatic amino acid with a second aliphatic amino acid).
For example, guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie, J. U. et al. 1990 Science 247:1306-1310, wherein the authors indicate that proteins are surprisingly tolerant of amino acid substitutions.Polypeptides and Fragments
The invention further provides filovirus and adenovirus polypeptides having the amino acid sequence encoded by an open reading frame (ORF) of a wild-type or modified filovirus or adenovirus structural gene, or a peptide or polypeptide comprising a portion thereof.
It will be recognized in the art that some amino acid sequences of the filovirus polypeptides can be varied without significant effect on the structure or function of the protein. If such differences in sequence are contemplated, it should be remembered that there will be critical areas on the protein which determine activity.
Thus, the invention further includes variations of the filovirus or adenovirus polypeptides which show substantial antigenic or other relevant biological activity. Such mutants include deletions, insertions, inversions, repeats, and type substitutions. As indicated, guidance concerning which amino acid changes are likely to be phenotypically silent can be found in Bowie, J. U. et al. 1990 Science 247:1306-1310.
Thus, the fragment, derivative or analog of the polypeptide of the invention may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue and such substituted amino acid residue may or may not be one encoded by the genetic code, or (ii) one in which one or more of the amino acid residues include a substituent group, or (iii) one in which additional amino acids are fused to the mature polypeptide. Such fragments, derivatives and analogs are deemed to be within the scope of those skilled in the art from the teachings herein.
Of course, the number of amino acid substitutions a skilled artisan would make depends on many factors, including those described above. Generally speaking, the number of amino acid substitutions for any given filovirus or adenovirus polypeptide will not be more than 50, 40, 30, 20, 10, 5 or 3.
Amino acids in the filovirus or adenovirus polypeptides of the present invention that are essential for the desired function can be identified by methods known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham & Wells 1989 Science 244:1081-1085). The latter procedure introduces single alanine mutations at every residue in the molecule. The resulting mutant molecules are then tested for biological activity such as changes in immunological character.
The polypeptides of the present invention are conveniently provided in an isolated form. By “isolated polypeptide” is intended a polypeptide removed from its native environment. Thus, a polypeptide produced and/or contained within a recombinant host cell is considered isolated for purposes of the present invention. Also intended as an “isolated polypeptide” are polypeptides that have been purified, partially or substantially, from a recombinant host cell or a native source. For example, a recombinantly produced version of the filovirus or adenovirus polypeptide can be substantially purified by the one-step method described in Smith and Johnson 1988 Gene 67:31-40.
The polypeptides of the present invention include a polypeptide comprising a polypeptide having the amino acid sequence of a wild-type filovirus structural gene product or portion thereof or encoded by a nucleic acid sequence shown herein in the Sequence Listing; as well as polypeptides which are at least 95% identical, or at least 96%, 97%, 98%, or 99% identical to those described above.
By a polypeptide having an amino acid sequence at least, for example, 95% “identical” to a reference amino acid sequence of an filovirus or adenovirus polypeptide is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid of the filovirus or adenovirus polypeptide. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular polypeptide is at least 95%, 96%, 97%, 98%, or 99% identical to a reference amino acid sequence can be determined conventionally using known computer programs such as the Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711). When using Bestfit or any other sequence alignment program to determine whether a particular sequence is, for instance, 95% identical to a reference sequence according to the present invention, the parameters are set, of course, such that the percentage of identity is calculated over the full length of the reference amino acid sequence and that gaps in homology of up to 5% of the total number of amino acid residues in the reference sequence are allowed.EXAMPLES
The following examples are offered to illustrate, but not to limit the claimed invention.Example 1
This example shows that humoral and cellular responses generated by ChAdC3 Ebola (S/G) and ChAdC3 Ebola (Zaire) were comparable to those generated by rAd5 Ebola (S/G) and rAd5 Ebola (Zaire) respectively.
Immunization of cynomologous macaques with ChAdC3 Ebola (Zaire) produced antigen-specific antibody and Cd4+ and Cd8+ T cell responses. Protection against infection with a lethal dose of EBOV-Zaire was also demonstrated, as 4 macaques survived the challenge after immunization with ChAdC3 Ebola (Zaire) (see
This example shows that a single immunization with rChAdC3 Ebola (Zaire) elicited humoral and cellular immune responses comparable to those generated by rAd5 Ebola (Zaire).
Immunization of cynomologous macaques with rChAdC3 Ebola (Zaire) produced antigen-specific antibody and Cd4+ and Cd8+ T cell responses. Protection against infection with a lethal dose of EBOV-Zaire was also demonstrated, as 4 out of 4 macaques survived the challenge after immunization with rChAdC3 Ebola (Zaire) (see
This example shows that a single immunization with adenoviral vectors encoding humanized Ebola glycoprotein (EBOV-GP) induced stronger cellular and humoral responses in mice than adenoviral vectors encoding non-humanized EBOV-GP.
Groups of female Balb/C mice were immunized with rAd EBOV-GP (Z) at a dose of 107, 108, and 109 viral particles via intramuscular injection. Cellular immune responses (Cd4+ and Cd8+ T cell responses) in PBMC and humoral responses (IgG) to EBOV-GP were measured at three weeks post immunization by ICS (intracellular cytokine staining) and ELISA, respectively. As shown in
Immunization with rChAd3 encoding humanized EBOV-GP produced significantly higher percentages of CD8+ T cells that express cytokines IFN-γ and TNF-α than the same vector encoding non-humanized EBOV-GP, and the percentage of cytokine positive cells was comparable, although not significantly different, to the percentage of cytokine positive CD8+ T cells produced by rAd5 at 109 viral particles (see
Immunization with rChAd63 encoding humanized EBOV-GP produced significantly higher IgG when compared to the same vector encoding non-humanized EBOV-GP at 108 viral particles. There was no significant difference in the IgG response by rChAd3 encoding humanized and non-humanized EBOV-GP. Further, the IgG response by rChAd3 and rChAd63 encoding humanized and non-humanized EBOV-GP was significantly lower than response generated by Ad5 (see
This example shows that a prime/boost regimen using adenoviral vectors encoding EBOV-GP generated potent immune responses in mice.
Groups of female Balb/C mice were immunized with 108 and 109 rAd EBOV-GP (Z) viral particles via intramuscular injection at week 0 and boosted at week 3. Cellular and humoral immune responses were measured as described above at week 5.
As shown in
Prime with 109 particles of rChAd3 and boost with 109 particles of rChAd63 generated a significantly higher IgG response than a single rAd5 immunization at 3 weeks. Similarly, prime with 109 particles of rChAd63 and boost with 109 particles of rChAd3 generated a significantly higher IgG response than a single rAd5 immunization at 3 weeks.
As shown in
In summary, the above examples demonstrate that rChAd3 consistently generated comparable immune responses as rAd5 for single administration. Further, prime and boost with rChAd3/rChAd63, ChAd63/ChAd3, and ChAd3/LCMV are useful candidates for a combination regimen.
It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.
1. A method of inducing a protective immune response against an Ebola virus infection in a subject, the method comprising intramuscularly administering to the subject an effective amount of viral particles of a recombinant chimpanzee adenovirus type 3 (ChAd3) vector comprising a nucleic acid encoding an Ebola virus glycoprotein, followed by administering to the subject a prophylactically effective amount of a modified vaccinia virus Ankara (MVA) vector comprising a nucleic acid encoding the Ebola virus glycoprotein.
2. The method of claim 1, wherein the Ebola virus is of species Zaire.
3. The method of claim 2, wherein the Ebola virus glycoprotein is encoded by a polynucleotide sequence as shown in SEQ ID NO:10 (Z GP wild-type).
4. The method of claim 1, wherein the Ebola virus is of species Sudan/Gulu.
5. The method of claim 4, wherein the Ebola virus glycoprotein is encoded by a polynucleotide sequence as shown in SEQ ID NO: 11 or 13 (S/G GP codon-optimized or wild-type).
Filed: Jan 24, 2020
Publication Date: May 14, 2020
Applicants: The Government of the United States of America as Represented by the Secretary of the Department of (Rockville, MD), GlaxoSmithKline Biologicals SA (Rixensart)
Inventors: Nancy J. Sullivan (Kensington, MD), Gary J. Nabel (Washington, DC), Clement Asiedu (Olney, MD), Cheng Cheng (Rockville, MD), Alfredo Nicosia (Rome), Riccardo Cortese (Rome), Virginia Ammendola (Napoli), Stefano Colloca (Rome)
Application Number: 16/751,470