US20140004149A1 - Immunogenic Influenza Composition - Google Patents

Immunogenic Influenza Composition Download PDF

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US20140004149A1
US20140004149A1 US13/574,779 US201113574779A US2014004149A1 US 20140004149 A1 US20140004149 A1 US 20140004149A1 US 201113574779 A US201113574779 A US 201113574779A US 2014004149 A1 US2014004149 A1 US 2014004149A1
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influenza
virus
vaccine
immune
epitope
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Gregory Tobin
Peter Nara
George Lin
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Biological Mimetics Inc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A61K39/145—Orthomyxoviridae, e.g. influenza virus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/16—Antivirals for RNA viruses for influenza or rhinoviruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1018—Orthomyxoviridae, e.g. influenza virus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/525—Virus
    • A61K2039/5258—Virus-like particles
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55511—Organic adjuvants
    • A61K2039/55566—Emulsions, e.g. Freund's adjuvant, MF59
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/70—Multivalent vaccine
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/16011—Orthomyxoviridae
    • C12N2760/16034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/16011—Orthomyxoviridae
    • C12N2760/16111—Influenzavirus A, i.e. influenza A virus
    • C12N2760/16134—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • Class One pathogens such as measles, mumps and rubella viruses
  • Class One pathogens are those pathogens, which, in general: (1) infect or cause the most serious disease in infant, very young children, children and young adults; (2) carry a relatively stable microbial genome; (3) have a natural history of disease which results in spontaneous recovery; and (4) induce durable memory, associated with polyclonal and multi-epitope antigen recognition.
  • Class Two pathogens such as, influenza virus, HIV-1, malaria parasites, Mycoplasma , such as those that cause tuberculosis, Trypanosomes, Schistosomes, Leishmania, Anaplasma, Enteroviruses, Astroviruses, Rhinoviruses, Norwalk viruses, toxigenic/pathogenic E. coli, Neisseria, Streptomyces , nontypeable Haemophilus influenza viruses, Hepatitis C virus, cancer cells etc. are characterized by quite opposite features.
  • Class Two pathogens (1) tend to infect and are transmitted in a significantly extended host age range, with infections occurring and reoccurring from childhood through the geriatric period; (2) exhibit microbial genetic instability in defined regions of their genome (a hallmark of the successful evolution of such pathogens); (3) in some cases, include spontaneous recovery of disease that frequently still leaves the host vulnerable to multiple repeated annual infections and/or the establishment of either a chronic/active or chronic/latent infectious state; (4) induce oligoclonal, early immune responses that are directed to a very limited set of immunodominant epitopes which provide either narrow strain-specific protection, no protection and/or enhanced infection; and (5) cause immune dysregulation following infection or vaccination, e.g. epitope-blocking antibody, atypical primary immune response Ig subclasses, anamnestic cross-reactive recall and inappropriate T H1 and/or T H2 cytokine metabolism.
  • epitope-blocking antibody atypical primary immune response Ig subclasses, anamnestic cross-reactive recall and inappropriate
  • a suitable new product is an influenza recombinant HA or NA subunit vaccine that induces immune responses capable of cross-neutralizing both intra-subtype antigenic variants and hetero-subtypes of influenza virus.
  • Influenza is a NIAID Category C pathogen and causes 36,000 deaths and 220,000 hospitalizations in the U.S. every year.
  • a respiratory disease, influenza spreads through droplets and/or contaminated fomites from the cough or sneeze of an infected person.
  • Higher risk groups include children and the elderly, and having influenza commonly leads to secondary complications of influenza-related pneumonias, upper respiratory complications (otitis media in children) and other systems diseases (e.g. cardiovascular and so on).
  • Influenza is the source of the worst pandemic in history; the Spanish flu of 1918 caused over 40 million deaths worldwide. In the U.S., the annual direct medical costs (hospitalization, office visits, medication etc.) of influenza are estimated at $4.6 billion.
  • Influenza virus and when attended by secondary bacterial infections, has long been known to be a cause of excess morbidity and mortality. Complications include pneumonia, bronchitis, congestive heart failure, myocarditis, meningitis, encephalitis and myositis. Some groups of people at high risk for complications are those with chronic pulmonary or cardiovascular disorders, residents of chronic care facilities, including nursing homes, and those persons 85 years and older. (Recommendations of the Advisory Committee on Immunization Practices (ACIP) for Prevention and Control of Influenza. MMWR, 1996, Vol 45; and Thompson et al., JAMA 2003; 289:179-186).
  • ACIP Advisory Committee on Immunization Practices
  • the geriatric population in the United Stated has doubled between the years 1976 and 1999, and is expected to rise over the next few years as the post World War II baby boomers age. People in that age bracket are 16 times more likely to die of an influenza-associated disease than are persons aged 65 to 69. Another important contributing factor to the increase of influenza-associated deaths in the 1990's is the predominance of the influenza A (H3N2) virus, a more virulent form of the recently circulating influenza viruses.
  • H3N2 influenza A virus
  • Influenza is a single-stranded ribonucleic acid (RNA) virus which mutates rapidly to form new virulent strains.
  • the strains are classified into three groups, influenza A, B and C.
  • the virus is further classified based on two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), into at least 16 HA and at least 9 NA subtypes.
  • HA hemagglutinin
  • NA neuraminidase
  • Recent whole genome analysis of the human influenza virus sponsored by the NIAID/NIH and collected between 1996-2004 from New York State revealed that despite sharing the same HA, multiple, persistent, phylogenetically distinct lineages co-circulate in the same population resulting in reassortment and the generation of antigenically novel clades.
  • Influenza can be obtained from swine, birds, horses, dogs and other mammals.
  • Antigenic variation is an evolved mechanism to ensure rapid sequence variation of specific pathogen gene(s) encoding homologues of an individual protein antigen, usually involving multiple, related gene copies, resulting in a change in the structure of an antigen on the surface of the pathogen.
  • the host immune system during infection or re-infection is less capable of recognizing the pathogen and must make new antibodies to recognize the changed antigens before the host can continue to combat the disease.
  • the host cannot stay completely immune to the viral disease. That phenomenon stands as one of the more, if not, most daunting problem challenging modern vaccine development today.
  • the immune response generated after infection or vaccination with all currently licensed vaccines is highly subtype and strain specific.
  • antibodies elicited during natural, experimental infection and vaccination are only capable of neutralizing the homologous virus.
  • the subtype/strain-specific humoral immune response appears to be due to the relative immunodominance of various antigenic sites found on the globular head of the hemagglutinin molecule (Wiley et al., Nature, 1981; 289:373-378). More specifically, the antibody response has been mapped to five major antigenic sites within the globular head of the HA.
  • a and B are the most immunodominant and also were associated with the highest amount of amino acid hypervariability, due, in part, to reoccurring point mutations, deletions and occasional introduction of N-linked glycosylation sites, known collectively as the “antigenic drift” of the virus (Cox & Bender, Semin. Virol. 1995; 6:359-70; Busch et al., Sci. 286:1921, 1999; Plotkin & Dushoff, PNAS 100:7152, 2003; and Munoz & Deem, Vaccine 23, 1144, 2005).
  • the immunologic mechanisms for immunodominance behind deceptive imprinting are not fully understood, and no one mechanism yet fully explains how or why certain epitopes have evolved to be immunoregulatory and immunodominant.
  • the range of immune responses observed in the phenomenon include the induction of highly strain/isolate-specific neutralizing antibody capable of inducing passive protection in experimental animal model-viral challenge systems all the way to the induction of a binding non-protective/non-neutralizing, blocking and even pathogen-enhancing antibody that, in some cases, prevents the host immune system from recognizing nearby adjacent epitopes to interfering with CD 4 T cell help.
  • Vaccination is the best way to prevent the disease and the current trivalent killed virus and modified live (attenuated) influenza vaccines are developed every year based on world-wide epidemiological surveillance of active viral strains. Both vaccines contain influenza A and influenza B subtypes.
  • the licensed influenza vaccines consist of inactivated whole or chemically split subunit preparations from two influenza A subtypes (H1N1 and H3N2) and one influenza B subtype. Production of influenza vaccines involves the adaptation of the selected variants for high yield in eggs by serial passage or reassortment with other high-yield strains. Selected influenza viruses are grown in chicken eggs, and the influenza virions purified from allantoic fluid. Whole or split virus preparations are then killed by treatment with an inactivating agent, such as formalin.
  • an inactivating agent such as formalin.
  • the vaccine strains are matched to the influenza virus strains causing disease. Changes can occur in the hemagglutinin of egg-grown influenza virus when compared to primary isolates from infected individuals (Oxford et al., J. Gen. Virol. 72:185-189, 1989; and Rocha et al., J. Gen. Virol. 74:2513-2518, 1993) reducing the potential effectiveness of the vaccine;
  • the current licensed manufacturing system yields one vaccine per chicken egg infected with the influenza virus and the production time is approximately 24 weeks.
  • the current licensed influenza vaccines do not: (1) induce antibodies capable of neutralizing the common annually recurring antigenic variants circulating during an epidemic, as well as the sub-type viruses and reassortment viruses; (2) illicit a strong immune response in the elderly; and (3) find wide applicability due to side effects, for example, some vaccines cannot be administered to children.
  • the disclosure relates, in part, to novel influenza antigens with enhanced or novel immunogenicity.
  • An influenza composition of interest can serve as an improved vaccine, resulting from modifications providing the virus or viral subunit antigen with a different array of and/or newly recognizable epitopes.
  • FIG. 1 depicts Table 1 relating to the results of testing immune refocused HA antigens.
  • FIG. 2 depicts Table 2 relating to particular mutations and the sequences thereof.
  • FIG. 3 depicts the approximate location of a set of examples of immune refocusing mutations on H1N1 HA.
  • Panel A depicts the structure of the HA trimer comprising three HA-1 and HA-2 chains.
  • Panels B, C and D depict HA monomers showing amino acids in approximate locations of selected mutations.
  • the figures were adapted from the structural file, 1RU7.pdb, of the H1N1 HA of influenza, (A/PR8/1934, Gamblin et al., Science, 303:1838-1842, 2004), which also can be found in the RCSB Protein Data Bank
  • FIG. 4 depicts Table 3 which provides combination mutations in 2 and 3 epitopes.
  • FIG. 5 depicts Table 4 which provides combination mutations in 5 epitopes.
  • Influenza is defined herein as virus that includes types A, B and C.
  • the virus can be found in birds and a variety of mammals, such as, cats, dogs, horses, hogs and so on.
  • Type A is the most virulent in humans and can result in either seasonal epidemics or occasionally and more rarely, more fatal pandemic episodes.
  • the types are defined by a number of serotypes, which is a reflection of the host immune response to antigens expressed on the virus particle surface.
  • Two structures on the virus surface that carry the majority of epitopes correlated with vaccine protection are a hemagglutinin (HA or H) and a neuraminidase (NA or N). There are at least 16 known H subtypes and at least 9 known N subtypes.
  • HA mediates virus attachment and fusion.
  • NA possesses sialidase activity.
  • Wild type refers to a naturally occurring organism or portions thereof.
  • the term also relates to nucleic acids and proteins found in a naturally occurring organism of a naturally occurring population arising from natural processes, such as seen in polymorphisms arising from natural mutation and maintained by genetic drift, natural selection and so on, and does not include a nucleic acid or protein with a sequence obtained by, for example, recombinant means.
  • Immunogen and “antigen” are used interchangeably herein as a molecule that elicits a specific immune response of antibody (humoral-mediated) and/or T cell origin (cell-mediated), for example, containing an antibody that binds to that molecule or a CD 4 + or CD 8 + T cell that recognizes a cell expressing that molecule, such as, a virally infected cell. That molecule can contain one or more sites to which a specific antibody or T cell binds. As known in the art, such sites are known as epitopes or determinants.
  • An antigen can be polypeptide, polynucleotide, polysaccharide, a lipid and so on, as well as a combination thereof, such as a glycoprotein or a lipoprotein.
  • An immunogenic compound or product, or an antigenic compound or product is one which elicits a specific immune response, which can be humoral, cellular or both.
  • a vaccine is an immunogen or antigen used to generate an immunoprotective response, that is, the response, such as, antibody, reduces the negative impact of the immunogen or antigen, or entity expressing same, in a host.
  • the dosage is derived, extrapolated and/or determined from preclinical and clinical studies, as known in the art. Multiple doses can be administered as known in the art, and as needed to ensure a prolonged prophylactic or non-reactive state.
  • the successful endpoint of the utility of a vaccine for the purpose of the instant disclosure is the resulting presence of an induced immune response in a host (e.g.
  • the induced antibody in some way combines with a compound, molecule and the like carrying the cognate antigen or immunogen, or directs the host to neutralize, reduce, prevent and/or eliminate a pathogen from infecting and/or causing clinical disease. That immune response can be monitored practicing methods known in the art, such as, an ELISA, Western blot and so on. Immunoprotection for the purposes of the instant disclosure is the presence of such anti-pathogen, anti-immunogen, anti-viral and the like immune response (e.g.
  • a circulating anti-influenza antibody of at least seven days, at least fourteen days, at least seventeen days, at least twenty-one days, at least thirty days or more is evidence of efficacy of a vaccine of interest.
  • a hemagglutination inhibition (HI) titer of approximately 1:40 against the homologous single strain of influenza used to make the vaccine can be an endpoint that signals a candidate vaccine is obtained.
  • any delay in lethality following exposure can be evidence of protection for the purposes of the disclosure.
  • the first mice can succumb at about day 10 following exposure.
  • the first day an exposed mouse succumbs is extended at least one day, at least two days, at least three days or more is considered protection for the purposes of the instant disclosure.
  • the time of immunoprotection can be at least 14 days, at least 21 days, at least 28 days, at least 35 days, at least 45 days, at least 60 days, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years or longer.
  • the immunoprotection is observed in outbred populations, and to different forms, subtypes, strains, variants, alleles and the like of a pathogen.
  • the composition of interest can comprise virus particles, inactivated or attenuated (modified live) or a subunit of the virus, such as, for example, NA or HA.
  • the composition also can comprise a virus-like particle (VLP), which is known in the art as a structure that expresses virus proteins and antigens as found on an intact replicating virion, but in the context of the instant disclosure, expressing an immunodampened immunodominant epitope.
  • VLP virus-like particle
  • an antigen, a determinant or portion thereof can be cloned into the genome of a wild-type virus, replacing the homologous wild type gene(s).
  • the recombinant virus then is the same as a wild type virus save the immunodampened molecule.
  • That virus can be influenza or another virus carrier.
  • a strain of influenza virus which propagates well in eggs can be manipulated to express an immunodampened molecule, and that recombinant virus can be propagated using the existing materials and methods of vaccine production using eggs to yield an immunodampened vaccine.
  • the vaccine can be tailored to generate an immune response to one antigen, two antigens or more; to one virus, to two separate lines, strains, clades and so on of virus or more; to one epitope, two epitopes or more; to one serotype, two serotypes or more; and so on. That can be obtained by including plural components, compositions, viruses, VLP's and so on wherein one of said components, compositions, viruses, VLP's and so on expresses an immunodampened antigen of interest which can generate a response to plural HA types, NA types or both. Alternatively, the plural elements can be joined in a single multifunctional composition.
  • Immunodominant epitope is an epitope that selectively provokes an immune response in a host to the effective or functional exclusion, which may be partial or complete, of other epitopes on and of that antigen.
  • immunodampen an epitope is to modify an epitope to substantially prevent the immune system of the host from producing antibodies, helper or cytotoxic T cells against that epitope. However, immunodampen does not necessarily result in the complete removal of said epitope or reactivity to that epitope.
  • Immune refocusing or immune refocusing technology (IRT) can be used to create effective vaccines against pathogens expressing immunodominant epitopes.
  • the technique is applied most appropriately in organisms that have evolved a strategy known as Deceptive Imprinting to evade the host immune response, for example, by having an immunodominant epitope that displays a high level of antigenic drift.
  • Such an immunodominant epitope ordinarily takes the form of a plurality of amino acids that can be changed without affecting the survivability of the pathogenic organism.
  • Immune refocusing is synonymous of immunodampen.
  • Immunodampening of an immunodominant epitope of an antigen can result in the production in a host organism of high titer antibodies or T cell responses against non-dominant epitopes on that antigen and/or new titers of antibodies or T cell responses to otherwise relatively immune silent epitopes.
  • Such immunodampened antigens can serve as effective vaccines against organisms that have an antigen with a moderately or highly variable and/or conserved immunodominant epitope(s).
  • the antibodies raised to such immunodominant epitopes or antigens can serve as effective vaccines against cognate organisms.
  • An immunodominant epitope can be identified by examining serum or T cell reactivity from a host organism infected with the pathogenic organism. The serum is evaluated for content of antibodies that bind to the identified antigens that are likely to cause an immune response in a host organism. If an immunodominant epitope is present, substantially many antibodies in the serum will bind to the immunodominant epitope, with little or no binding to other epitopes present on or in the antigen.
  • the immunodominant epitope is immunodampened as taught herein using the materials and methods taught herein and as known in the art as a design choice. Such manipulations can be made at the nucleic acid level, at the level of the protein, at the level of a carbohydrate and so on, or combinations thereof, practicing methods taught herein and known in the art.
  • N-linked carbohydrate can be determined by the primary amino acid sequence of the polypeptide.
  • An N-linked glycosylation site can be added or removed from an epitope practicing methods and materials known in the art.
  • a recombinant gp120 of HIV that displays a molecularly introduced N-linked sequon (NXT/S), which resulted in the addition of a supernumerary N-linked glycan in the immunodominant V3 domain, exhibited novel antigenic properties, such as the inability to bind antibodies that recognize wild type V3 epitopes while inducing antibody responses to other previously silent or less immunogenic epitopes. Presence of the supernumerary carbohydrate moiety did not compromise the infectious viability of the HIV-1 recombinant virus. Test animals immunized with the recombinant glycoprotein showed moderate to high titers of antibodies that neutralize infection to both homologous and heterologous wildtype HIV-1 in vitro.
  • a particular amino acid of the immunodominant epitope can be replaced, substituted or deleted to dampen immunogenicity.
  • Immunodampening can occur by replacing, substituting or deleting one amino acid, two amino acids, three amino acids or more of the immunodominant epitope, for example, by site-directed mutagenesis of the nucleic acid encoding the antigen.
  • Immunodampening can be affected by any of a variety of techniques such as, altering, substituting or deleting specific amino acids of the epitope, or adding, for example, a glycosylation site at or near the epitope.
  • the changes can be effected at the level of the polypeptide or at the level of the polynucleotide, practicing methods known in the art.
  • a polypeptide can be altered by adding, deleting or substituting one or more molecules, groups, compounds and the like to a target site on or in an epitope.
  • a particular amino acid can be derivatized chemically or can be modified to carry an extra group, such as a polysaccharide, such as, polyethylene glycol.
  • a screening analysis of binding of the mutein that is, the manipulated antigen of interest, that is, the immunodampened antigen of interest
  • known antibody that binds to one or more immunodominant epitopes of influenza
  • a polypeptide can be synthesized to contain one or more changes to the primary amino acid sequence of the immunodominant epitope.
  • the nucleic acid sequence of the immunodominant epitope can be modified to express an immunodampened epitope.
  • the nucleic acid sequence can be modified by, for example, site-directed mutagenesis to express amino acid substitutions, insertions, deletions and the like, some of which may introduce further modification at or near the immunodominant epitope, such as, introducing a glycosylation site, such as, mutations which cause N-glycosylation or O-glycosylation at or near the immunodominant epitope and so on.
  • a nucleic acid of interest encoding one or more immunodampened epitopes in a polypeptide of interest can be placed in a cloning and/or expression vector practicing materials and methods as known in the art and generally commercially available as a design choice.
  • plasmids, cosmids, viruses, replicons and so on can be used, again, many are commercially available.
  • Viral vectors include those obtained from adenovirus, AAV, alpha viruses, phage and so on. Influenza also can be used.
  • Suitable host cells for propagating the vector of interest are known and include prokaryotic cells, eukaryotic cells, bacteria, insect cells, mammal cells and so on. The cells can be configured to secrete the recombinant protein of interest. That polypeptide can be purified and used as an immunogen.
  • the polypeptide can be inserted into a vector comprising an influenza genome or an influenza virus, generally replacing the homologous encoding sequence from which the polypeptide was derived to enable expression of the immune refocused polypeptide on said influenza virus, virus-like particle or structure, virus surface structure component, subunit and so on.
  • the immune refocusing technology is independent of vector technology and can be applied to multiple expression systems. Accordingly, the immune refocused antigens can be incorporated into a number of currently utilized and novel vaccine vectors including, but not restricted to: 1) recombinant influenza viruses to be produced using currently acceptable technologies such as in cultured mammalian cells or chicken embryos; 2) recombinant temperature-sensitive influenza viruses such as Flu-Mist; 3) split vaccines; 4) subunit vaccines expressed in insect, mammalian, yeast, bacterial, or other cells; 5) DNA expression plasmids; and 6) heterologous viral expression systems, such as, recombinant vaccinia virus, adenovirus, lentivirus, and the like.
  • Subunit vaccines produced in insect, mammalian or other in vitro expression system can be purified using conventional chromatographies, separations and purifications such as ion exchange, lectin-binding resins, size fractionations, antibody affinity and the like.
  • the immunogens can be expressed with fusion domains designed to facilitate purification.
  • HA antigens can be expressed as, for example, polyhistidine fusions to permit rapid and simplified purification on metal-activated resins.
  • Such fusion partners can be removed by specific proteolytic cleavage using methods known to the art, if so desired.
  • epitope muteins a mutant epitope that varies from wild type
  • alanine scanning mutagenesis Cunningham & Wells, Science 244:1081-1085 (1989); and Cunningham & Wells, Proc. Natl. Acad. Sci. USA 84:6434-6437 (1991)).
  • One or more residues are replaced by alanine (Ala) or polyalanine residue(s).
  • Those residues demonstrating functional sensitivity to the substitutions then can be refined by introducing further or other mutations at or for the sites of substitution.
  • the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined.
  • a substituted amino acid may be selected based on, for example, size, shape or other parameter of the replaced amino acid.
  • glutamine may be substituted for glutamic acid to reduce the charge of an epitope with minimal change in size and shape.
  • a more systematic method for identifying amino acid residues to modify comprises identifying residues involved in immune system stimulation or immunodominant antibody recognition and those residues with little or no involvement with immune system stimulation or immunodominant antibody recognition.
  • An alanine scan of the involved residues is performed, with each Ala mutant tested for reducing immune system stimulation to an immunodominant epitope or immunodominant antibody recognition.
  • those residues with little or no involvement in immune system stimulation are selected to be modified.
  • Modification can involve deletion of one or more residues, substitution of a residue or insertion of one or more residues adjacent to a residue of interest.
  • the modification involves substitution of the residue by another amino acid.
  • a conservative substitution can be a first substitution. If such a substitution results in inducing immune system stimulation or increased reactivity with known immunodominant antibody, then another conservative substitution can be made to determine if more substantial changes are obtained.
  • Even more substantial modification in the ability to alter the immune system response away from the immunodominant epitope can be accomplished by selecting an amino acid that differs more substantially in properties from that normally resident at a site.
  • a substitution can be made while maintaining: (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation; (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • the naturally occurring amino acids can be divided into groups based on common side chain properties:
  • hydrophobic methionine (M or Met), alanine (A or Ala), valine (V or Val), leucine (L or Leu) and isoleucine (I or Ile);
  • cysteine C or Cys
  • S or Ser serine
  • T or Thr threonine
  • asparagine N or Asn
  • glutamine Q or Gln
  • H or H histidine
  • K or Lys lysine
  • R or Arg arginine
  • Non-conservative substitutions can entail exchanging an amino acid with an amino acid from another group.
  • Conservative substitutions can entail exchange of one amino acid for another from within a group.
  • Preferred amino acid substitutions are those which dampen an immunodominant epitope, but can also include those which, for example: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter immune system stimulating activity and/or (4) confer or modify other physico-chemical or functional properties of such analogs.
  • Analogs can include various muteins of a sequence other than the naturally occurring peptide sequence. For example, single or multiple amino acid substitutions (such as, conservative amino acid substitutions) may be made in the naturally occurring or mutein sequence.
  • a conservative amino acid substitution generally should not substantially change the structural characteristics of the parent sequence (e.g., a replacement amino acid should not tend to break a helix that occurs in the parent or mutein sequence, or disrupt other types of secondary structure that characterizes the parent sequence) unless for a change in the bulk or conformation of the R group or side chain (Proteins, Structures and Molecular Principles (Creighton, ed., W. H. Freeman and Company, New York (1984); Introduction to Protein Structure, Branden & Tooze, eds., Garland Publishing, New York, N.Y. (1991)); and Thornton et al. Nature 354:105 (1991)).
  • the epitope mutant with altered biological properties will have an amino acid sequence having at least 75% amino acid sequence identity or similarity with the amino acid sequence of the parent molecule, at least 80%, at least 85%, at least 90% and often at least 95% identity.
  • Identity or similarity with respect to parent amino acid sequence is defined herein as the percentage of amino acid residues in the candidate sequence that are identical (i.e., same residue) or similar (i.e., amino acid residue from the same group based on common side-chain properties, supra) with the parent molecule residues, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.
  • Covalent modifications of the molecules of interest are included within the scope of the disclosure, for example, to immunodampen a molecule or to obtain a functional equivalent that may or may not carry enhanced, additional or different features or properties, exclusive of immunodampening. Such may be made by chemical synthesis or by enzymatic or chemical cleavage of the molecule, if applicable.
  • Other types of covalent modifications of the molecule can be introduced into the molecule by reacting targeted amino acid residues of the molecule with an organic derivatizing agent that is capable of reacting with selected side chains or with the N-terminal or C-terminal residue.
  • WO05/35726 teaches various methods for introducing, modifying, changing, replacing and so on substituents found on biomolecules.
  • cysteinyl residues can be reacted with ⁇ -haloacetates (and corresponding amines), such as chloroacetic acid or chloroacetamide, to yield carboxylmethyl or carboxyamidomethyl derivatives.
  • Cysteinyl residues also can be derivatized by reaction with bromotrifluoroacetone, ⁇ -bromo- ⁇ -(5-imidozoyl)propionic acid, chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyl disulfide, p-chloromercuribenzoate, 2-chloromercura-4-nitrophenol or chloro-7-nitrobenzo-2-oxa-1,3-diazole, for example.
  • Histidyl residues can be derivatized by reaction with diethylpyrocarbonate at pH 5.5-7.0.
  • p-bromophenacyl bromide also can be used, the reaction is preferably performed in 0.1 M sodium cacodylate at pH 6.0.
  • Lysinyl and a amino terminal residues can be reacted with succinic or other carboxylic acid anhydrides to reverse the charge of the residues.
  • suitable reagents for derivatizing ⁇ -amino-containing residues include imidoesters, such as, methyl picolinimidate, pyridoxal phosphate, pyridoxal, chloroborohydride, trinitrobenzenesulfonic acid, O-methylisourea and 2,4-pentanedione, and the amino acid can be transaminase-catalyzed with glyoxylate.
  • Arginyl residues can be modified by reaction with one or several conventional reagents, such as, phenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione and ninhydrin. Derivatization of arginine residues often requires alkaline reaction conditions. Furthermore, the reagents may react with lysine as well as the arginine E amino group.
  • tyrosyl residues can be made with aromatic diazonium compounds or tetranitromethane.
  • aromatic diazonium compounds or tetranitromethane For example, N-acetylimidizole and tetranitromethane can be used to form O-acetyl tyrosyl species and 3-nitro derivatives, respectively.
  • Carboxyl side groups (aspartyl or glutamyl) can be modified by reaction with carbodiimides (R—N ⁇ C ⁇ C—R′), where R and R′ can be different alkyl groups, such as 1-cyclohexyl-3-(2-morpholinyl-4-ethyl)carbodiimide or 1-ethyl-3-(4-azonia-4,4-dimethylpentyl)carbodiimide.
  • aspartyl and glutamyl residues can be converted to asparaginyl and glutaminyl residues by reaction with ammonium ions.
  • Glutaminyl and asparaginyl residues are frequently deamidated to the corresponding glutamyl and aspartyl residues, respectively, under neutral or basic conditions.
  • the deamidated form of those residues falls within the scope of the disclosure.
  • sugar(s) may be attached to: (a) arginine and histidine; (b) free carboxyl groups; (c) free sulfhydryl groups, such as those of cysteine; (d) free hydroxyl groups, such as those of serine, threonine or hydroxyproline; (e) aromatic residues such as those of phenylalanine, tyrosine or tryptophan; or (f) the amide group of glutamine.
  • arginine and histidine the sugar(s) may be attached to: (a) arginine and histidine; (b) free carboxyl groups; (c) free sulfhydryl groups, such as those of cysteine; (d) free hydroxyl groups, such as those of serine, threonine or hydroxyproline; (e) aromatic residues such as those of phenylalanine, tyrosine or tryptophan; or (f) the amide group of glutamine.
  • Sugar residues also can be added enzymatically using, for example, a glucosyl transferase, a sialyl transferase, a galactosyl transferase and so on.
  • Chemical deglycosylation for example, can require exposure of the molecule to the compound, trifluoromethanesulfonic acid, or an equivalent compound, resulting in cleavage of most or all sugars except the linking sugar (N-acetylglucosamine or N-acetylgalactosamine), while leaving the remainder of the molecule intact.
  • Chemical deglycosylation is described, for example, in Hakimuddin et al., Arch. Biochem. Biophys. 259:52 (1987) and in Edge et al., Anal. Biochem. 118:131 (1981).
  • Enzymatic cleavage of carbohydrate moieties on molecules can be achieved by any of a variety of endoglycosidases and exoglycosidases as described, for example, in Thotakura et al., Meth. Enzymol. 138:350 (1987).
  • a mannosidase, a fucosidase, glucosaminosidase, a galactosidase and so on can be used.
  • RNA or DNA encoding the HA, NA and the like of influenza is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to the relevant genes, Innis et al. in PCR Protocols. A Guide to Methods and Applications, Academic (1990) and Sanger et al., Proc. Natl. Acad. Sci. 74:5463 (1977)).
  • the DNA may be placed into expression vectors, which then are placed into host cells, such as, E. coli cells, NS0 cells, COS cells, Chinese hamster ovary (CHO) cells or myeloma cells, to obtain synthesis of the protein of interest in the recombinant host cells.
  • the RNA or DNA also may be modified, for example, by substituting bases to optimize for codon usage in a particular host cell or by covalently joining to the coding sequence of a heterologous polypeptide.
  • a polynucleotide of interest encoding and expressing one or more immunodampened epitopes can be expressed practicing molecular biology and recombinant materials and methods as known in the art to obtain a source of recombinant polypeptide of interest.
  • a polynucleotide of interest encoding one or more immunodampened epitopes can replace the homologous wild type sequence in an influenza genome to yield a virus, a virus-like structure or subunit thereof that expresses the one or more immunodampened epitopes.
  • that virus strain can be propagated using standard techniques, such as the currently used egg-based technology, to generate an immunogen, which can be used alone as a vaccine or can be combined with other active agents, such as, an unmodified virus or a plurality of viruses, for example, to simulate the current bivalent and trivalent vaccines.
  • phrases and terms, as well as combinations thereof, “functional fragment, portion, variant, derivative or analog” and the like, as well as forms thereof, of an influenza virus, antigen, component, subunit, HA, NA and the like thereof relate to an element having qualitative biological activity in common with the wild type or parental element or the original non-immunodampened antigen from which the variant, derivative, analog and the like was derived.
  • a functional portion, fragment or analog of HA is one which stimulates an immune response as does native HA, although the response may be to a different epitope on the HA.
  • functional equivalents of a virus, or portion or derivative thereof, of interest.
  • the term “functional equivalents” includes the virus and portions thereof with the ability to stimulate an immune response to influenza.
  • the encoding nucleic acid can be modified to encode amino acid insertions, deletions or substitutions that do no adversely impact the two goals referred to herein.
  • the amino acids are modified, derivatized, substituted and so on practicing materials and methods known in the art so long as the two goals referred to herein are not adversely impacted. As taught herein, such changes and modifications from the original immunodampened polypeptide are considered functional equivalents thereof.
  • the degree of immunodampening can be quantified in an in vitro or animal assay as taught herein or as known in the art.
  • the degree of enabling a response to previously silent epitopes can be quantified in an in vitro or animal assay as taught herein or as known in the art.
  • the degree of acceptable reduction in the degree of one of the two goals taught herein is a design choice. Generally, a reduction of no more than 25% of reactivity is tolerated because normally, the desire is to have as little reaction to the immunodominant epitopes as possible.
  • a modification to the original immunodampened sequence reveals, for example, a return of 25% of reactivity thereto as determined, for example, in an ELISA using an antibody to that immunodominant epitope as compared to no reactivity in the original immunodampened epitope, that could be considered an acceptable reduction in reactivity for a functional equivalent. It may be that no more than a 20% reduction, no more than a 15% reduction, no more than a 10% reduction, no more than a 5% reduction or no reduction is considered acceptable for a functional equivalent of an immunodampened antigen.
  • a reduction of no more than 25% is tolerated because normally, the desire is to have as much reaction to the previously silent epitopes as possible.
  • a modification to the original immunodampened sequence reveals, for example, a loss of 25% of reactivity to the previously silent epitope as determined, for example, in an ELISA using an antibody that was raised to the previously silent epitope as compared to maximal reactivity in the original immunodampened epitope, that could be considered an acceptable reduction in reactivity for a functional equivalent. It may be that no more than a 20% reduction, no more than a 15% reduction, no more than a 10% reduction, no more than a 5% reduction or no reduction is considered acceptable for a functional equivalent of an antigen expressing previously silent epitopes.
  • IDNPEs immunodominant non-protective epitopes
  • intramolecular modifications e.g. deletions, charge changes, adding one or more N-linked sequons and so on
  • the changes to the IDNPE can induce a new hierarchy of immune responses at either or both the B and T cell levels (Garrity et al., J. Immunol. (1997) 159(1):279-89) against subdominant or previously silent epitopes. That technology as described herein is known as, “Immune Refocusing.”
  • a mouse is immunized to the dampened antigen as known in the art, serum obtained and tested in an in vitro assay for reactivity therewith. That antiserum then can be tested on wild type virus to determine if the antibody still recognizes the wild type epitope or the wild type antigen. That can be done, for example, in an ELISA or a Western blot. The latter can be informative, revealing whether the particular immunodominant epitope is bound, and if the antiserum remains reactive with influenza, the size and possibly, the identity of the molecule carrying the epitope reactive with the mouse antiserum.
  • Immune refocused vaccine candidates are designed to fold correctly and to adopt native-like conformational epitopes for stimulation of appropriate immune responses. Prior to antigenic testing, it is customary to assess the ability of purified HA antigens to bind conformationally-dependent antibodies and virus receptors on cell surfaces. Methods to assess such interactions are well known in the art and are widely available.
  • mice Prior to development of immune refocused antigens as commercial vaccines, non-clinical studies are frequently required.
  • animals such as mice, guinea pigs, rabbits, chickens, rats, ferrets, etc. are injected or otherwise immunized with the immune refocused vaccine candidates.
  • the panel of immune sera is assessed for multiple activities including reactivity to purified antigen or virus (binding activity), hemagglutination inhibition (inhibition of virus-receptor interactions, HI) and virus neutralization (inhibition of infection of cultured cells and/or inhibition of replication in cultured cells, VN).
  • a comparison of heterologous HI and VN activities of sera from animals immunized with immune refocused antigen with sera from animals immunized with unmutated antigen is used to assess broadening of and improvements to protective immunity.
  • HI and VN assays are conducted against heterologous strains of H1N1 or other serotypes of influenza virus with the various immune sera raised in the antigenicity study.
  • An increase in the HI or VN titer of a test serum relative to sera from unmodified antigen immunization indicates that the antigen used to raise said test sera stimulates broadened and improved immunity.
  • a hypothetic data set is provided in Table 1 of FIG. 1 .
  • Immune refocused HA antigens (Mut H1, Mut H2, Mut H3 and Mut H4) were derived from the A/California/04/2009 strain and are tested for antiviral activities against homologous and heterologous virus.
  • Heterologous viruses (strains 2-4) are presented in order of increasing antigenic divergence from the parental California/04/2009 (Cal/04/09) strain. All immunogens stimulated HI and VN titers equivalent to those induced by unmodified antigen (WT-HA).
  • Sera from Mut-H1 contain statistically higher levels of antiviral activities against strains 2-4 compared to the titers from the WT-HA as determined by both assays.
  • Sera from Mut-H2 and Mut-H3 have 2-fold higher titers of HI and VN activity against strain 2, but that may not be statistically significant if the serum dilution series are done in 2-fold dilutions.
  • sera from Mut-H2 and Mut-H3 do have significantly higher HI and VN titers against more highly divergent strains 3 and 4. Analysis of the data shown in Table 1 suggests that Mut-H1 or Mut-H2 stimulate the highest levels of antiviral activities normally measured as correlates in influenza pre-clinical trials.
  • Additional animal model studies can be performed to further assess protective immunity of immune refocused antigen candidates.
  • groups of ferrets are immunized with unmodified antigen or a leading immune refocused candidate (e.g., Mut-H2 presented in Table 1).
  • a leading immune refocused candidate e.g., Mut-H2 presented in Table 1.
  • the two groups of ferrets are divided into subgroups and each subgroup is inoculated (challenged) with virus from either homologous or heterologous strains of influenza such as those referred to in Table 1.
  • Measurements of disease, pathogenesis and virus replication are collected during the two weeks following challenge.
  • Candidates may also stimulate enhanced reactivity to the parental immunodominant antigen, while targeting immune refocused epitopes for immune recognition.
  • the mouse antiserum thereto can be tested for reactivity with a number of influenza strains in standardized anti-viral-based assays to determine how generic the reactivity of that antibody is, that is, whether the newly recognized epitopes on the dampened antigen are generic to a wider range of influenza strains and if the antibody has broad antiviral activity.
  • a recombinant HA (rHA) subunit protein vaccine can be sufficient to protect against challenge from homologous strains of influenza virus.
  • An rHA also can be used as an immunogen in older adults.
  • a second generation, immune refocused HA subunit vaccine as taught herein could induce protective immunity against heterologous strains as well (Treanor et al., J. Infectious Diseases 2006; 193:1223-8).
  • a candidate vaccine of interest can protect not only to the cognate antigen, such as H1, but also to different lines or isolates of HI, as well as to H2, H3, H4 and so on.
  • the HA and NA of influenza were selected as targets for refocusing the host immune response to other non-dominant sites on HA and NA as novel targets for an immunoprotective response, preferably one of broad scope and spectrum, active on a wide variety of strains and so on.
  • HA has five immunodominant sites or epitopes, known as A-E.
  • Site A includes amino acids 140-146 of HA type strains and has the sequence, KRRSNKS (SEQ ID NO:1).
  • KRRSNKS SEQ ID NO:1
  • GG GG
  • Site B includes amino acids 189-197 of HA with the sequence SDQISLYAQ (SEQ ID NO:2). That forms a helix which interacts with amino acids 158-161 having the sequence, KYKY (SEQ ID NO:3).
  • a number of possible changes can be made to the B site, such as substitute NAS for QIS; substitute NIT for SLY; substitute NST for KYK at 158; and substitute NTS for YKY at 159, all of those changes introducing an N-glycosylation sequence at those four sites.
  • Site C includes amino acids 276-278 having the sequence KCN. NCT can substitute for KCN.
  • Site D includes a large antiparallel loop at amino acids 201-220. The entire loop can be deleted. Also, the glycosylation site, NIT, can substitute for RIT at sites 201-203.
  • Site E includes amino acids 79-82, FQNK (SEQ ID NO:4).
  • the glycosylation site, NET can substitute for QNK.
  • the A site change above can be obtained by site-directed mutagenesis using the primers, ATop: GGAACAAGCTCTGCTTGCggcggtTTCTTTAGTAGATTGAATTGG (SEQ ID NO:5) and ABottom: CCAATTCAATCTACTAAAGAAaccgccGCAAGCAGAGCTTGTTCC (SEQ ID NO:6) to obtain the sequence, GTSSACGGFFSRLN (SEQ ID NO:7) containing the deletion described above and insertion of the GG dipeptide at that deletion site.
  • the B site changes can be obtained by using primers, B1Top: CAAATCAGCCTATATGCTaatGCATCAGGAAGAATCAC (SEQ ID NO:8) and B1bottom: GTGATTCTTCCTGATGCattAGCATATAGGCTGATTTG (SEQ ID NO:9) to yield the sequence QISLYANASGR1 (SEQ ID NO:10); the primers B2Top: CACCACCCGGTTACGGACaatGACacAATCAGCCTATATGCTCAAGC (SEQ ID NO:11) and B2bottom GCTTGAGCATATAGGCTGATTgtGTCattGTCCGTAACCGGGTGGTG (SEQ ID NO:12) to yield the sequence HHPVTDNDTISLYAQ (SEQ ID NO:13); the primers B3Top: CGGACAGTGACCAAATCAatCTAtcTGCTCAAGCATCAGGAAG (SEQ ID NO:14) and B3Bottom: CTTCCTGATGCTTGAGCAgaTAGatTGATTTGGTCACT
  • the C site change can be obtained using the primers C1top: GATCAGATGCACCCATTGGCAAtTGCAgTTCTGAATGCATCACTCC (SEQ ID NO:23) and C1bottom: GGAGTGATGCATTCAGAAcTGCAaTTGCCAATGGGTGCATCTGATC (SEQ ID NO:24) to yield the sequence SDAPIGNCSSECIT (SEQ ID NO:25).
  • the D site change can be obtained using the primers D1Top: CTATATGCTCAAGCATCAGGAAatATCACAGTCTCTACCAAAAG (SEQ ID NO:26) and D1Bottom: CTTTTGGTAGAGACTGTGATatTTCCTGATGCTTGAGCATATAG (SEQ ID NO:27) to obtain the sequence LYAQASGNITVSTKRS (SEQ ID NO:28).
  • the E site change can be obtained using the primers E1Top: GATGGCTTCCAAAATAAGAcATGGGACCTTTTTGTTGAAC (SEQ ID NO:29) and E1bottom: GTTCAACAAAAAGGTCCCATgTCTTATTTTGGAAGCCATC (SEQ ID NO:30) to yield the sequence DGFQNKTWDLFVE (SEQ ID NO:31).
  • HAS1 CAGTCCTCATCAGATCCTTG (SEQ ID NO:32)
  • HAS2 GGTAAGGGATATCTCCAGCAG (SEQ ID NO:33) primers can be used for sequencing, with HAS3: cgcgattgcgccaaatatgcc (SEQ ID NO:34) as a negative.
  • T cell epitopes also can be immunodampened.
  • a major CD 4 epitope in the region of residues 177 to 199 comprises an MHC Class II binding epitope outside of the already targeted B site.
  • Mutations in the residues LYIWGVHHP (SEQ ID NO:37) to dampen the T cell response include replacing LYIW with VYIW (SEQ ID NO:38) or VTIW (SEQ ID NO:39); and replacing VHHP with IHAG (SEQ ID NO:40).
  • a recombinant polypeptide of interest comprising one or more immunodampened epitopes, or a vehicle comprising same, such as, a virus-like particle, a subunit composition of a virus
  • a vehicle comprising same such as, a virus-like particle, a subunit composition of a virus
  • the antibody can be made using materials and methods known in the art, and thus, can be polyclonal, by immunizing animals and collecting serum or could be obtained from humans exposed to same, similar to the current practice of administering immune globulin, or can be monoclonal practicing known materials and methods.
  • the antibody can be collected and administered as a passive vaccine.
  • the immunogen of interest is administered to a nonhuman mammal for the purpose of obtaining preclinical data, for example.
  • nonhuman mammals include nonhuman primates, dogs, cats, rodents and other mammals.
  • Such mammals may be established animal models for a disease to be treated with the formulation, or may be used to study toxicity of the immunogen of interest.
  • dose escalation studies may be performed in the mammal.
  • TSE transmissible spongiform encephalopathies
  • plasmids harboring the vaccine-encoding sequence can carry a non-antibiotic selection marker, since it is not always ideal to use antibiotic resistance markers for selection and maintenance of plasmids in bacteria that are designed for use in humans, although a preferred embodiment relates to use of a recombinant subunit vaccine.
  • the present disclosure provides a selection strategy in which, for example, a catabolic enzyme is utilized as a selection marker by enabling the growth of bacteria in medium containing a substrate of said catabolic enzyme as a carbon source.
  • a catabolic enzyme includes, but is not restricted to, lacYZ encoding lactose uptake and ⁇ -galactosidase (GenBank Nos.
  • selection markers that provide a metabolic advantage in defined media include, but are not restricted to, galTK (GenBank No. X02306) for galactose utilization, sacPA (GenBank No. J03006) for sucrose utilization, trePAR (GenBank No. Z54245) for trehalose utilization, xylAB (GenBank No. CAB13644 and AAB41094) for xylose utilization etc.
  • the selection can involve the use of antisense mRNA to inhibit a toxic allele, such as the sacB allele (GenBank No. NP — 391325).
  • the specific method used to formulate the novel vaccines and formulations described herein is not critical to the present disclosure and can be selected from or can include a physiological buffer (Felgner et al., U.S. Pat. No. 5,589,466 (1996)); aluminum phosphate or aluminum hydroxyphosphate (e.g. Ulmer et al., Vaccine, 18:18 (2000)), monophosphoryl-lipid A (also referred to as MPL or MPLA; Schneerson et al. J. Immunol., 147:2136-2140 (1991); e.g. Sasaki et al. Inf. Immunol., 65:3520-3528 (1997); and Lodmell et al.
  • a physiological buffer (Felgner et al., U.S. Pat. No. 5,589,466 (1996)); aluminum phosphate or aluminum hydroxyphosphate (e.g. Ulmer et al., Vaccine, 18:18 (2000)), monophosphoryl-lipid A (also
  • the antigens generated practicing the methods taught herein or antibodies reactive therewith are compatible with adjuvants, such as, Alhydrogel and novel compositions developed by companies such as Novartis and GlaxoSmithKline (e.g., MF59 and AS03) and with modulators and enhancers such as CpG and cytokines
  • the formulation herein also may contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely impact each other.
  • Such molecules suitably are present in combination in amounts that are effective for the purpose intended.
  • the adjuvant can be administered sequentially, before or after antigen administration.
  • the immunogen of interest can be used with a second component, such as a therapeutic moiety conjugated to or mixed with same, administered as a conjugate, separately in combination, mixed prior to use and so on as a therapeutic, see, for example, Levine et al., eds., New Generation Vaccines. 2 nd Marcel Dekker, Inc., New York, N.Y., 1997).
  • the other therapeutic agent(s) can be any drug, vaccine and the like used for an intended purpose.
  • the therapeutic agent can be a biological, a small molecule and so on.
  • the immunogen of interest can be administered concurrently or sequentially with a second influenza immunogenic composition, a third second influenza immunogenic composition and so on, immunodampened or not, for example.
  • an immunodampened antigen of interest can be combined with an existing vaccine to form a bivalent vaccine, a trivalent vaccine and so on, although that approach would minimize the use thereof if the existing vaccine is made in eggs.
  • an immunodampened antigen of interest can be combined with more than one other antigen, subunit, component, VLP and so on to form a polyvalent vaccine.
  • small molecule and analogous terms include, but are not limited to, peptides, peptidomimetics, amino acids, amino acid analogues, polynucleotides, polynucleotide analogues, carbohydrates, lipids, nucleotides, nucleotide analogues, organic or inorganic compounds (i.e., including heterorganic and/organometallic compounds) having a molecular weight less than about 10,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 5,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 1,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 500 grams per mole, and salts, esters, combinations thereof and other pharmaceutically acceptable forms of such compounds which stimulate an immune response or are immunogenic, or have a desired pharmacologic activity.
  • organic or inorganic compounds i.e., including heterorganic and/organometallic compounds
  • the immunogen of the disclosure may be administered alone or in combination with other types of treatments, including a second immunogen or a treatment for the disease being treated.
  • the second component can be an immunostimulant.
  • the immunogen of the instant disclosure may be conjugated to various effector molecules such as heterologous polypeptides, drugs and so on, see, e.g., WO 92/08495; WO 91/14438; WO 89/12624; U.S. Pat. No. 5,314,995; and EPO 396,387.
  • An immunogen may be conjugated to a therapeutic moiety such as an antibiotic (e.g., a therapeutic agent) or an adjuvant.
  • Therapeutic compounds of the disclosure alleviate at least one symptom associated with influenza.
  • the products of the disclosure may be provided in pharmaceutically acceptable compositions as known in the art or as described herein.
  • physiologically acceptable means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in humans.
  • the products of interest can be administered to a mammal in any acceptable manner.
  • Methods of introduction include, but are not limited to, parenteral, subcutaneous, transdermal, intraperitoneal, intrapulmonary, intranasal, epidural, inhalation and oral routes, and if desired for immunosuppressive treatment, intralesional administration.
  • Parenteral infusions include intramuscular, intradermal, intravenous, intraarterial or intraperitoneal administration.
  • the products or compositions may be administered by any convenient route, for example, by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa etc.) and may be administered together with other biologically active agents.
  • Administration can be systemic or local.
  • the product can be suitably administered by pulse infusion, particularly with declining doses of the products of interest.
  • the dosing is given by injection, preferably intravenous or subcutaneous injections, depending, in part, on whether the administration is brief or chronic.
  • Various other delivery systems are known and can be used to administer a product of the present disclosure, including, e.g., encapsulation in liposomes, microparticles or microcapsules (see Langer, Science 249:1527 (1990); Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein et al., eds., (1989)).
  • the active ingredients may be entrapped in a microcapsule prepared, for example, by coascervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nanoparticles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nanoparticles and nanocapsules
  • Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
  • the composition of interest may also be administered into the lungs of a patient in the form of a dry powder composition, see e.g., U.S. Pat. No. 6,514,496.
  • the therapeutic products or compositions of the disclosure may be administered locally to the area in need of treatment; that may be achieved by, for example, and not by way of limitation, local infusion, topical application, by injection, by means of a catheter, by means of a suppository or by means of an implant, said implant being of a porous, non-porous or gelatinous material, including hydrogels or membranes, such as silastic membranes or fibers.
  • care is taken to use materials to which the protein does not absorb or adsorb.
  • the product can be delivered in a controlled release system.
  • a pump may be used (see Langer, Science 249:1527 (1990); Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); and Saudek et al., NEJM 321:574 (1989)).
  • polymeric materials can be used (see Medical Applications of Controlled Release, Langer et al., eds., CRC Press (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen et al., eds., Wiley (1984); Ranger et al., J. Macromol.
  • a controlled release system can be placed in proximity of the therapeutic target.
  • Sustained release preparations may be prepared for use with the products of interest.
  • Suitable examples of sustained release preparations include semi-permeable matrices of solid hydrophobic polymers containing the immunogen, which matrices are in the form of shaped articles, e.g., films or matrices.
  • Suitable examples of such sustained release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethylmethacrylate), poly(vinylalcohol)), polylactides (U.S. Pat. No.
  • copolymers of L-glutamic acid and ethyl-L-glutamate non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers (such as injectable microspheres composed of lactic acid-glycolic acid copolymer) and poly-D-( ⁇ )-3-hydroxybutyric acid.
  • polymers such as, ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days
  • certain hydrogels release cells, proteins and products for and during shorter time periods. Rational strategies can be devised for stabilization depending on the mechanism involved.
  • compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations, depots and the like.
  • the composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides.
  • Oral formulations can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate etc. Examples of suitable carriers are described in “Remington's Pharmaceutical Sciences,” Martin.
  • Such compositions will contain an effective amount of the immunogen preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient.
  • the formulation will be constructed to suit the mode of administration.
  • Therapeutic formulations of the product may be prepared for storage as lyophilized formulations or aqueous solutions by mixing the product having the desired degree of purity with optional pharmaceutically acceptable carriers, diluents, excipients or stabilizers typically employed in the art, i.e., buffering agents, stabilizing agents, preservatives, isotonifiers, non-ionic detergents, antioxidants and other miscellaneous additives, see Remington's Pharmaceutical Sciences, 16th ed., Osol, ed. (1980).
  • Such additives are generally nontoxic to the recipients at the dosages and concentrations employed, hence, the excipients, diluents, carriers and so on are pharmaceutically acceptable or are generally regarded as safe.
  • An immune refocused polypeptide (which includes an antigen, a portion thereof, an epitope, a determinant and so on, which can be produced as a subunit substantially free of contaminating proteins, including other influenza proteins, in combination with other viral or non-viral polypeptides; as an IR polypeptide of interest which can be expressed or produced in recombinant viruses, VLP's or in combination with one or more proteins of virus or cell origin; as an IR polypeptide which can be expressed or produced as an isolated molecule and then combined with one or more proteins of virus or cell origin; and so on, or an antibody thereto) can be obtained or made in substantially pure form.
  • an “isolated” or “purified” immunogen or vaccine is substantially free of contaminating proteins from the medium from which the immunogen or vaccine is obtained, or substantially free of chemical precursors or other chemicals in the medium used which contains components that are chemically synthesized.
  • the language “substantially free of subcellular material” includes preparations of a cell in which the cell is disrupted to form components which can be separated from subcellular components of the cells, including dead cells, and portions of cells, such as cell membranes, ghosts and the like, from which the immunogen or vaccine is isolated or recombinantly produced.
  • an immunogen or vaccine that is substantially free of subcellular material includes preparations of the immunogen or vaccine having less than about 30%, 25%, 20%, 15%, 10%, 5%, 2.5% or 1%, (by dry weight) of subcellular contaminants, or any other element that differs from the product of interest.
  • the terms “stability” and “stable” in the context of a liquid formulation comprising an immunogen or vaccine refer to the resistance of the immunogen or vaccine in a formulation to thermal and chemical aggregation, degradation or fragmentation under given manufacture, preparation, transportation and storage conditions, such as, for one month, for two months, for three months, for four months, for five months, for six months or more.
  • the “stable” formulations of the disclosure retain biological activity equal to or more than 80%, 85%, 90%, 95%, 98%, 99% or 99.5% under given manufacture, preparation, transportation and storage conditions.
  • the stability of said immunogen or vaccine preparation can be assessed by degrees of aggregation, degradation or fragmentation by methods known to those skilled in the art, including, but not limited to, physical observation, such as, with a microscope, particle size and count determination and so on, compared to a reference.
  • carrier refers to a diluent, adjuvant, excipient or vehicle with which the therapeutic is administered.
  • physiological carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a suitable carrier when the pharmaceutical composition is administered intravenously.
  • Saline solutions and aqueous dextrose and glycerol solutions also can be employed as liquid carriers, particularly for injectable solutions.
  • Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, ethanol and the like.
  • the composition if desired, can also contain minor amounts of wetting or emulsifying agents, or pH or buffering agents.
  • the carrier can include a salt and/or buffer.
  • Buffering agents help to maintain the pH in the range which approximates physiological conditions. Buffers are preferably present at a concentration ranging from about 2 mM to about 50 mM.
  • Suitable buffering agents for use with the instant disclosure include both organic and inorganic acids, and salts thereof, such as citrate buffers (e.g., monosodium citrate-disodium citrate mixture, citric acid-trisodium citrate mixture, citric acid-monosodium citrate mixture etc.), succinate buffers (e.g., succinic acid-monosodium succinate mixture, succinic acid-sodium hydroxide mixture, succinic acid-disodium succinate mixture etc.), tartrate buffers (e.g., tartaric acid-sodium tartrate mixture, tartaric acid-potassium tartrate mixture, tartaric acid-sodium hydroxide mixture etc.), fumarate buffers (e.g., fumaric acid-monosodium fumarate mixture, fuma
  • Preservatives may be added to retard microbial growth, and may be added in amounts ranging from 0.2%-1% (w/v).
  • Suitable preservatives for use with the present disclosure include phenol, benzyl alcohol, m-cresol, octadecyldimethylbenzyl ammonium chloride, benzyaconium halides (e.g., chloride, bromide and iodide), hexamethonium chloride, alkyl parabens, such as, methyl or propyl paraben, catechol, resorcinol, cyclohexanol and 3-pentanol.
  • phenol benzyl alcohol, m-cresol, octadecyldimethylbenzyl ammonium chloride, benzyaconium halides (e.g., chloride, bromide and iodide), hexamethonium chloride, alkyl parabens, such
  • Isotonicifiers may be present to ensure physiological isotonicity of liquid compositions of the instant disclosure and include polhydric sugar alcohols, preferably trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol.
  • Polyhydric alcohols can be present in an amount of between about 0.1% to about 25%, by weight, preferably about 1% to about 5% taking into account the relative amounts of the other ingredients.
  • Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the therapeutic agent or helps to prevent denaturation or adherence to the container wall.
  • Typical stabilizers can be polyhydric sugar alcohols; amino acids, such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, threonine etc.; organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, arabitol, erythritol, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol and the like, including cyclitols such as inositol; polyethylene glycol; amino acid polymers; sulfur containing
  • Additional miscellaneous excipients include bulking agents, (e.g., starch), chelating agents (e.g., EDTA), antioxidants (e.g., ascorbic acid, methionine or vitamin E) and cosolvents.
  • bulking agents e.g., starch
  • chelating agents e.g., EDTA
  • antioxidants e.g., ascorbic acid, methionine or vitamin E
  • cosolvents e.g., ascorbic acid, methionine or vitamin E
  • surfactant refers to organic substances having amphipathic structures, namely, are composed of groups of opposing solubility tendencies, typically an oil-soluble hydrocarbon chain and a water-soluble ionic group. Surfactants can be classified, depending on the charge of the surface-active moiety, into anionic, cationic and nonionic surfactants. Surfactants often are used as wetting, emulsifying, solubilizing and dispersing agents for various pharmaceutical compositions and preparations of biological materials.
  • Non-ionic surfactants or detergents may be added to help solubilize the therapeutic agent, as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stresses without causing denaturation of the protein.
  • Suitable non-ionic surfactants include polysorbates (20, 80 etc.), polyoxamers (184, 188 etc.), Pluronic® polyols and polyoxyethylene sorbitan monoethers (TWEEN-20®, TWEEN-80° etc.).
  • Non-ionic surfactants may be present in a range of about 0.05 mg/ml to about 1.0 mg/ml, preferably about 0.07 mg/ml to about 0.2 mg/ml.
  • inorganic salt refers to any compound, containing no carbon, that results from replacement of part or all of the acid hydrogen or an acid by a metal or a group acting like a metal, and often is used as a tonicity adjusting compound in pharmaceutical compositions and preparations of biological materials.
  • the most common inorganic salts are NaCl, KCl, NaH 2 PO 4 etc.
  • the present disclosure can provide liquid formulations of an immunogen or vaccine having a pH ranging from about 5.0 to about 7.0, or about 5.5 to about 6.5, or about 5.8 to about 6.2, or about 6.0, or about 6.0 to about 7.5, or about 6.5 to about 7.0.
  • the instant disclosure encompasses formulations, such as, liquid formulations having stability at temperatures found in a commercial refrigerator and freezer found in the office of a physician or laboratory, such as from about ⁇ 20° C. to about 5° C., said stability assessed, for example, by microscopic analysis, for storage purposes, such as for about 60 days, for about 120 days, for about 180 days, for about a year, for about 2 years or more.
  • the liquid formulations of the present disclosure also exhibit stability, as assessed, for example, by particle analysis, at room temperatures, for at least a few hours, such as one hour, two hours or about three hours prior to use.
  • diluents include a phosphate buffered saline, buffer for buffering against gastric acid in the bladder, such as citrate buffer (pH 7.4) containing sucrose, bicarbonate buffer (pH 7.4) alone, or bicarbonate buffer (pH 7.4) containing ascorbic acid, lactose, or aspartame.
  • carriers include proteins, e.g., as found in skim milk, sugars, e.g., sucrose, or polyvinylpyrrolidone. Typically these carriers would be used at a concentration of about 0.1-90% (w/v) but preferably at a range of 1-10% (w/v).
  • the formulations to be used for in vivo administration must be sterile. That can be accomplished, for example, by filtration through sterile filtration membranes.
  • the subcellular formulations of the present disclosure may be sterilized by filtration.
  • a formulation of interest can include one or more of a flavorant, odorant, scent, colorant, surfactant, binder and so on to provide a more palatable form for ingestion.
  • the immunogen or vaccine composition will be formulated, dosed and administered in a manner consistent with good medical practice. Factors for consideration include severity of the disease, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners.
  • the “therapeutically effective amount” of the immunogen or vaccine thereof to be administered will be governed by such considerations, and can be the minimum amount necessary to prevent, ameliorate or treat a targeted disease, condition or disorder.
  • the amount of antigen or vaccine is an amount sufficient to induce the desired humoral and/or cell mediated immune response or protective in the target host.
  • the amount of immunogen or vaccine of the present disclosure to be administered will vary depending on the species of the subject, physical characteristics of the host, such as age, weight and so on, preferred mode of delivery and so on. Generally, the dosage employed can be about 10 to about 1500 ⁇ g/dose. In comparison, the current subunit preparations contain elements from three subtypes of virus.
  • the trivalent vaccines generally contain about 7 to about 25 ⁇ g of HA from each of the three contributing strain. That can serve as a starting point for titrating a vaccine composition of interest.
  • the term “effective amount” refers to the amount of a therapy (e.g., a prophylactic or therapeutic agent), which is sufficient to reduce the severity and/or duration of a targeted disease, ameliorate one or more symptoms thereof, prevent the advancement of a targeted disease or cause regression of a targeted disease, or which is sufficient to result in the prevention of the development, recurrence, onset, or progression of a targeted disease or one or more symptoms thereof.
  • a therapy e.g., a prophylactic or therapeutic agent
  • a treatment of interest can increase survivability of the host or reduce the severity of disease, based on baseline or a normal level, by at least 5%, preferably at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 100%.
  • an effective amount of a therapeutic or a prophylactic agent reduces the symptoms of a targeted disease, such as a symptom of influenza or duration of illness by at least 5%, preferably at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 100%. Also used herein as an equivalent is the term, “therapeutically effective amount.”
  • composition may also include a solubilizing agent and a local anesthetic such as lidocaine or other “caine” anesthetic to ease pain at the site of the injection.
  • a solubilizing agent such as lidocaine or other “caine” anesthetic to ease pain at the site of the injection.
  • the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water-free concentrate in a sealed container, such as an ampule or sachet indicating the quantity of active agent.
  • a dry lyophilized powder or water-free concentrate in a sealed container, such as an ampule or sachet indicating the quantity of active agent.
  • the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
  • an ampule of sterile water for injection or saline can be provided, for example, in a kit, so that the ingredients may be mixed prior to administration.
  • the ampoule can comprise a fluid containing the active agent of interest, for example, as a concentrate for dilution prior to use or in a form ready for administration.
  • a formulation of interest is provided in a dose and volume suitable for a single, ready to use presentation.
  • the article of manufacture can comprise a container and a label.
  • Suitable containers include, for example, bottles, vials, syringes and test tubes.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition of interest and may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the label on or associated with the container indicates that the composition is used for treating influenza.
  • the article of manufacture may further comprise a second container comprising a pharmaceutically acceptable buffer, such as phosphate-buffered saline, Ringer's solution or dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes and package inserts with instructions for use.
  • a pharmaceutically acceptable buffer such as phosphate-buffered saline, Ringer's solution or dextrose solution.
  • buffers such as phosphate-buffered saline, Ringer's solution or dextrose solution.
  • kits e.g., comprising an immunogenic or vaccine composition of interest, homolog, derivative thereof and so on, for use, for example, as a vaccine, active or passive, and instructions for the use of same and so on.
  • the instructions may include directions for preparing the composition, derivative and so on.
  • the composition can be in liquid form or presented as a solid form, generally, desiccated or lyophilized.
  • the kit can contain suitable other reagents, such as a buffer, a reconstituting solution and other necessary ingredients for the intended use.
  • a packaged combination of reagents in predetermined amounts with instructions for use thereof, such as for a therapeutic use is contemplated.
  • other additives may be included, such as, stabilizers, buffers and the like.
  • the relative amounts of the various reagents may be varied to provide for concentrates of a solution of a reagent, which provides user flexibility, economy of space, economy of reagents and so on.
  • the kit can comprise a delivery means, such as a device containing a needle, such as a syringe, which, optionally can be preloaded with the composition of interest for delivery when needed.
  • H3N2 Eight immune dampened and refocused hemagglutinin genes derived from the Wyoming strain (H3N2) were designed and engineered as described above. For example, nucleotides were substituted by site-directed mutagenesis to introduce N-linked sequons leading to complex carbohydrate modifications, and/or deletions and/or charge changes of the amino acids into the five major immunogenic and highly variable sites containing the strain-specific epitopes.
  • Antigenic Site B (187-196) targets both the B cell and CD4 helper T cell IDNPEs.
  • both DNA and protein subunit vaccines were engineered.
  • full-length hemagglutinin genes were cloned into the pTriEx vector (Invitrogen) behind the cytomegalovirus (CMV) promoter.
  • CMV cytomegalovirus
  • Transient transfection of mammalian cells with the pTriEx-HA constructs demonstrated that full-length hemagglutinin genes resembling native viral proteins were expressed as trimers and could be solubilized from plasma membrane extracts.
  • mice Nine groups of outbred mice were immunized with the DNA constructs containing the eight mutated and one unmodified full length wild type HA glycoproteins. A tenth group was immunized with the empty pTriEx vector for a negative control.
  • recombinant protein was produced for immunization.
  • the HA ectodomain contains the domains for the assembly of the trimeric glycoprotein spike and binding the host cell receptor.
  • removal of the membrane spanning and cytoplasmic domains causes recombinant HA trimers to be released into the culture supernatant. Therefore, each of the mutated HA genes was truncated at the end of the ectodomain and cloned into a vector having the phage T7 promoter.
  • ectodomain vectors Transfection of the ectodomain vectors into cells infected with a recombinant vaccinia virus that expressed the phage T7 RNA polymerase resulted in the production of HA trimers which were secreted into the culture media.
  • the ectodomain trimers were purified for use as protein immunogens.
  • mice were pre-bled. One group of mice was used as a negative control and the other was immunized with unmodified (wild type) antigens.
  • mice in the principal groups were immunized by injection of 10 micrograms of DNA (in 0.1 mL sterile water) of mutated HA glycoproteins into each quadriceps muscle. After a rest of 5 weeks, the mice were boosted with a second DNA immunization. After another 4-5 weeks, the mice were again boosted by two subcutaneous immunizations of 10 micrograms each of purified ectodomain glycoprotein. The first protein immunization was formulated in Complete Freund's Adjuvant and the second in Incomplete Freund's Adjuvant. Two weeks following the final immunization, the mice were euthanized and bled out for serum.
  • the sera were tested for 1) reactivity to mutant and wild type HA proteins in Western blot and ELISA formats, 2) recognition of linear epitopes by peptide ELISA, 3) protection of conformational epitopes from degradation by proteases, and 4) functional testing by hemagglutination inhibition and virus neutralization of homologous and heterologous influenza strains.
  • mice immunized with the panel of immune refocused HA subunit engineered antigens resulted in the generation of high titer antisera as measured by an HA-specific ELISA. All groups of mice exhibited titers to wild type HA in the range of 1:100-300,000. Down selection of the various mutated HA glycoproteins were made based on the ability of the antisera to exhibit cross subtype HI antibody in a standard HI assay.
  • Mutants A2, B1, B2, B3, CE, CEB4, CEB5, and D1 of H3N2 A/Wyoming/03/2003 gave equal to or higher cross subtype HI and/or virus neutralization titers against a panel of heterologous virus subtypes used in the assay.
  • immune dampening and refocusing resulted in the production of HA glycoprotein subunit vaccine candidates capable of inducing significantly improved cross-subtype anti-viral protection as measured in vitro by standardized and accepted surrogate HI and virus neutralization assays.
  • Mutant A2 is the mutation in the A epitope of HA wherein KRRSNKS (SEQ ID NO:1) is replaced by GG.
  • B1 is the mutation in the B epitope of HA wherein a glycosylation site is introduced at amino acid 197 (QIS to NAS).
  • B2 is the mutation in the B epitope of HA wherein a glycosylation site is introduced at amino acid 189 (SDQ to NVT).
  • B3 is the mutation in the B epitope of HA wherein a glycosylation site is introduced at amino acid 193 (SLY to NIT).
  • CE contains two mutations, a glycosylation site is introduced into the C epitope at position 276 (KCN ⁇ NCT) and a glycosylation site is added into the E epitope at position 83 (NKK ⁇ NKT).
  • CEB4 is CE with an additional mutation in the B epitope, a glycosylation site is added at position 158 (KYK ⁇ NST).
  • CEB5 is the CE with an additional mutation in the B epitope, a glycosylation site was added at position 159.
  • D1 is the mutation in the D epitope of HA wherein a glycosylation site is introduced at amino acid 201 (RIT to NIT).
  • refocused polypeptide antigens were tested for hemagglutinin inhibition titer and serum neutralization titer when compared to different strains of H3N2 virus.
  • the mutants were derived from the A/Wyoming/2003 strain.
  • M3 has the B2 epitope;
  • M5 has the CE epitopes;
  • M6 has the B4CE epitopes as described above.
  • Mice were exposed to the various muteins, A/Wyoming/2003 strain virus as the wild type positive control and carrier alone as the negative control.
  • Mouse serum was then tested for hemagglutinin inhibition titers against three strains, the cognate Wyoming strain, Panama/1999 and Wellington/2004 strains.
  • mice serum was tested for serum neutralization titers against the cognate Wyoming strain, Korea/2003, Korea/2002, Fujian/2002, Brisbane/03/2006 and Brisbane/10/2007 strains.
  • mice exposed to carrier produced no specific antibody.
  • composition of interest stimulated protective immunity against viruses that exist in the future relative to the parental strain, as well as against viruses that were more commonly found in the past.
  • an immune refocused H3N2 vaccine based on Brisbane/07 will stimulate protective responses against viruses not yet evolved and, thereby, avoid the necessity of reformulating over the next several years.
  • An immune refocused Wyoming-based or Brisbane-based vaccine can be developed to protect against all H3N2 strains, both past and future.
  • the design of immune refocused hemagglutinin antigens of the swine-like H1N1v A/California/04/2009 strain is based on multiple considerations, including analyses of immunodominant epitopes, evolution and sequence diversity and structural data.
  • the following mutations are designed to refocus immune responses away from immunodominant, highly variable sites and toward more broadly protective epitopes.
  • immune refocusing mutations can take several forms including deletions, addition or subtraction of glycosylation sites as well as substitutions that affect charge, hydropathy, or some other chemical property of an epitope.
  • Glycosylation additions have the advantage of masking epitopes with a relatively large moiety while charge changes focus on particular sites where antibody interacts with antigen. Because of the high degree of structural similarity among HA proteins of various influenza strains and serotypes, analysis of 3-D structures of the related A/PR8/34 was used to identify putative loops and other flexible sites of the HA sequence. The HA of A/California/04/2009 was aligned with A/PR8/34 HA to transpose the identified residues of PR8 to Cal/04/09.
  • FIG. 2 provides Table 2 which presents single-site mutations intended to refocus immunity toward more broadly protective responses.
  • the initial proposed mutations are comprised largely of amino acid substitutions that affect glycosylation patterns and/or local charge elements.
  • the mutations were selected based on available sequence and structural data used to identify immunodominant epitopes that contribute to strain-specific responses.
  • sequences and mutations are arranged in Table 2 to correlate to epitope sites along the HA glycoprotein starting at the N-terminus. Residues comprising the C-terminal portion of the D site (starting at 214) and the fusion domain (starting at 314) have been offset to conserve space in the table.
  • Mutations M1 and M3 of Epitope C and M6 and M7 of Epitope E were selected as being in or closely near sites implicated as binding monoclonal antibodies. Because they are in highly flexible loops and in regions of high sequence variability, we predict that they contribute to strain-specific immunity; (ii) Mutations M1, M2, M5, M6, M8, M9, M10, M14, M16, M18, M20, M22, M23, and M25 serve the dual purposes of introducing a glycosylation site into an immunodominant, strain-specific site while simultaneously altering the charges associated with amino acids in the epitopes;
  • Mutation M5 serves the specific purpose of adding a glycosylation to the E epitope to refocusing immunity towards conserved elements in the fusion domain or the HA-1 HA-2 fusion site (as do other C and E mutations);
  • FIG. 3 identifies a subset of the single-site mutations superimposed on the structure of the A/PR8/34 HA structure.
  • FIG. 1 demonstrates that the mutations have largely been inserted into highly flexible loops to mask epitopes without disrupting the native-like folding of the recombinant proteins. Insertion of mutations into the variable loops ensures that most conformational epitope can be formed
  • HA mutations can be engineered using, for example, known methods such as, site-specific mutagenesis (quick-change) or, for example, gene synthesis.
  • site-specific mutagenesis quick-change
  • gene synthesis can be used for more complex combinations.
  • Single-site mutations are most helpful in assessing immune refocusing techniques directed to specific residues of each epitope.
  • improved immune refocused antigens can incorporate mutations to multiple antigenic sites. Examples of immune refocused HA antigens containing mutations in 2 or 3 epitopes are provided in FIG. 4 which presents Table 3. Examples of immune refocused HA antigens containing mutations in all five epitopes are provided in FIG. 5 which presents Table 4.
  • the mutations are comprised of combinations of the single-site mutations presented in FIG. 2 which presents Table 2. Analysis of structural models, as shown in FIG. 3 , is useful in the design of combination mutations so that the mutations selected will have reduced probability of interfering with each other in terms of charge, steric inhibition, or other negative consequence.
  • Antigens based on the H1N1 HA sequences that are described in Example 3 may be used as a vaccine to stimulate broadened immunity against all H1N1 variants. Additional mutations can be made as taught herein such that the H1N1-based antigen can stimulate protective immunity against influenza strains from other serotypes, such as, H2, H5 and so forth.
  • the antigen design method taught herein can be used to produce vaccines or antibodies based on other serotypes of influenza, such as, H2N2, H5N1, H7, H9 and others.
  • Such mutations can be designed to stimulate immunity for the purpose of producing a broadly reactive antibody that can be used for therapeutics, diagnostics or other applications.
  • the safety, toxicity and potency of recombinant immunogens are evaluated according to the guidelines in 21 CFR 610, which include: (i) general safety tests, as well as acute and chronic toxicity tests.
  • Immunogenicity data are derived from an accepted animal model that responds well to human influenza vaccine (e.g. guinea pigs, mice, ferrets or cotton rats).
  • the investigations include an evaluation of immune responses according to dose and dose intervals using vaccine that contains the strain intended for the final product.
  • Immunogenicity studies in relevant animal models are used to document consistency of production, in particular during the validation phase of a vaccine for novel influenza viruses manufacturing process. Suitable non-clinical endpoints selected for the animal studies include death, weight loss, virus excretion rates, clinical signs such as fever, oculo-nasal secretions and so on.
  • Groups of ferrets or other suitable animals are inoculated intraperitoneally with 100 ⁇ l of immunogen containing 300 ⁇ g of the immunogen of interest. Suitable negative and positive controls are used.
  • the animals are monitored for general health and body weight for 14 days post infection. Similar to animals that receive placebo, animals that receive the immunogen remain healthy, and do not lose weight or display overt signs of disease during the observation period.
  • the immunogen is deemed safe if no adverse health effects are observed and the animals gain weight at the normal rate compared to animals inoculated with placebo as an internal control.
  • groups of ferrets are inoculated intradermally with 300 ⁇ g of the immunogen at graded doses or saline.
  • mice are given a total of 3 doses of vaccine at 0, 14 and 60 days and the immune response to hemagglutinin is measured by ELISA using sera collected from the animals at 10 day intervals.
  • the neutralization of influenza virus is measured in the collected sera, for example, 80 days after the first vaccination.

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