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US20090022735A1 - Receptor Binding Polypeptides - Google Patents

Receptor Binding Polypeptides Download PDF

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US20090022735A1
US20090022735A1 US12/180,806 US18080608A US2009022735A1 US 20090022735 A1 US20090022735 A1 US 20090022735A1 US 18080608 A US18080608 A US 18080608A US 2009022735 A1 US2009022735 A1 US 2009022735A1
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polypeptide
seq
protein
nucleic acid
cells
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Pele Choi Sing Chong
Shie-Liang Hsieh
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National Health Research Institutes
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National Health Research Institutes
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Publication of US20090022735A1 publication Critical patent/US20090022735A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • 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
    • A61K39/02—Bacterial antigens
    • A61K39/09—Lactobacillales, e.g. aerococcus, enterococcus, lactobacillus, lactococcus, streptococcus
    • A61K39/092—Streptococcus
    • 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
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A61K39/215—Coronaviridae, e.g. avian infectious bronchitis 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
    • A61K39/385—Haptens or antigens, bound to carriers
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • 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
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • 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
    • A61K2039/55505—Inorganic adjuvants
    • 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
    • A61K2039/55561—CpG containing adjuvants; Oligonucleotide containing adjuvants
    • 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
    • A61K2039/60—Medicinal preparations containing antigens or antibodies characteristics by the carrier linked to the antigen
    • A61K2039/6031—Proteins
    • A61K2039/6075—Viral proteins
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
    • 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
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • 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
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • Virus is the cause of various disorders. For example, members of the coronavirus family cause hepatitis in mice, gastroenteritis in pigs, and respiratory infections in birds and humans. Among the more than 30 strains isolated so far, three or four infect humans.
  • SARS severe acute respiratory syndrome
  • This life-threatening respiratory coronavirus touched off worldwide outbreaks in 2003.
  • Vaccines and drugs against SARS coronavirus (CoV) are being vigorously sought. Nevertheless, the progress has been rather slow due to safety concerns.
  • This invention is based, at least in part, on the discovery of receptor binding domains of the SARS CoV Spike (S) protein.
  • GenBank Accession No. AY278741 (SEQ ID NO: 1) represents the genomic sequence of the SARS CoV Urbani strain, which contains an open reading frame encoding a polypeptide that is 7,073 amino acid residues (aa.) in length (SEQ ID NO: 2).
  • the nucleic acid encoding the S protein of this strain corresponds to nucleotides (nt) 21,492-25,259 of GenBank Accession No. AY278741. Listed below are the nucleic acid and amino acid sequences of the S protein:
  • One aspect of the invention features an isolated polypeptide containing SEQ ID NO: 4 or an immunogenic fragment derived from SEQ ID NO: 4.
  • the immunogenic fragment is at least 10 amino acid residues in length, i.e., any number between 10 and 1255 (the length of SEQ ID NO: 4), inclusive. Examples of such an immunogenic fragment include the domains listed below:
  • the polypeptide of this invention contains SEQ ID NO: 24 or 26.
  • the polypeptide is a glycoprotein containing a polysaccharide, e.g., a polysaccharide from S. pneumococcal.
  • the polypeptide is a fusion protein including a heterologous polypeptide that contains an Fc portion of an immunoglobin, e.g., an IgG.
  • the immunoglobin is IgG1, and more preferably, a human IgG1.
  • the fusion protein can also include a heterologous polypeptide that contains a surface portion of a protein of a pathogen, such as the HA or NA of an influenza virus.
  • isolated polypeptide refers to a polypeptide substantially free from naturally associated molecules, i.e., it is at least 75% (i.e., any number between 75% and 100%, inclusive) pure by dry weight. Purity can be measured by any appropriate standard method, for example, by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. An isolated polypeptide of the invention can be purified from a natural source, produced by recombinant DNA techniques, or by chemical methods.
  • a “heterologous” protein or nucleic acid is one that originates from a foreign species, or, if from the same species, is substantially modified from its original form.
  • the invention also features an isolated nucleic acid that contains a sequence encoding one of the above-mentioned polypeptides.
  • the sequence include (1) those encoding S, RBD1, RBD2, S1, S2, S3, RBD-2C, RBD-55, and TM, which, respectively, correspond to nt. 21492-25259, 21729-22172, — 22341-23696, 21492-22490, 22491-23489, 23490-24491, 22791-22892, 23181-23330, and 24873-25256 of GenBank Accession No. AY278741 (SEQ ID NOs: 3, 5, 7, 17, 19, 21, 23, 25, and 27, respectively)
  • fusion proteins RBD1-(Gly) 8 -TM, RBD2-(Gly) 8 -TM, RBD1-(Gly) 8 -RBD2, and RBD1-(Gly) 8 -RBD2-(Gly) 8 -TM (SEQ ID NOs: 9, 11, 13, and 15, respectively; linkers shown in the upper case):
  • nucleic acid of this invention examples include nucleic acids encoding the peptides listed in Table 2.
  • nucleic acid contains SEQ ID NO: 23 or 25.
  • nucleic acid refers to a DNA molecule (e.g., a cDNA or genomic DNA), an RNA molecule (e.g., an mRNA), or a DNA or RNA analog.
  • a DNA or RNA analog can be synthesized from nucleotide analogs.
  • the nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
  • isolated nucleic acid is a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid or to that of any fragment of a naturally occurring genomic nucleic acid.
  • the term therefore covers, for example, (a) a DNA which has the sequence of part of a naturally occurring genomic DNA molecule but is not flanked by both of the coding sequences that flank that part of the molecule in the genome of the organism in which it naturally occurs; (b) a nucleic acid incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion protein.
  • the nucleic acid described above can be used to express the polypeptide of this invention. For this purpose, one can operatively linked the nucleic acid to suitable regulatory sequences to generate an expression vector
  • a “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • the vector can be capable of autonomous replication or integrate into a host DNA. Examples of the vector include a plasmid, cosmid, or viral vector.
  • the vector of this invention includes a nucleic acid in a form suitable for expression of the nucleic acid in a host cell.
  • the vector includes one or more regulatory sequences operatively linked to the nucleic acid sequence to be expressed.
  • a “regulatory sequence” includes promoters, enhancers, and other expression control elements (e.g., polyadenylation signals).
  • Regulatory sequences include those that direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and/or inducible sequences.
  • the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like.
  • the expression vector can be introduced into host cells to produce the polypeptide of this invention.
  • a host cell that contains the above-described nucleic acid. Examples include E. coli cells, insect cells (e.g., using baculovirus expression vectors), yeast “effective amount” is an amount of the composition that is capable of producing a medically desirable result, e.g., as described above, in a treated subject.
  • This invention relates to receptor binding domains or immunogenic fragments of the S protein of a coronavirus, such as SARS. Since these domains mediate target cell binding and entry of the coronavirus or induce immune response, they can be targeted for diagnosing or treating an infection with the coronavirus.
  • a polypeptide of this invention contains the sequence of the S protein, such as SEQ ID NO: 4 or an immunogenic fragment thereof. It can also contain the sequence of the S protein of SARS CoV TW1, Tor-2, SIN2500, SIN2774, SIN2748, SIN2677, SIN2679, CUHK-W1, HKU39849, GZO1, BJO1, BJO2, BJO3 BJO4, and other strains.
  • the polypeptide contains a receptor-binding domain of the S protein or a functional equivalent.
  • a functional equivalent of the a protein receptor binding domain refers to a polypeptide derived from the coronavirus S protein, e.g., a fusion polypeptide or a polypeptide having one or more point mutations, insertions, deletions, truncations, or a combination thereof.
  • such functional equivalents include polypeptides, whose sequences differ from the S protein by one or more conservative amino acid substitutions or by one or more non-conservative amino acid substitutions, deletions, or insertions.
  • Such a functional equivalent can be encoded by a nucleic acid that hybridizes under high stringency conditions to a probe the sequence of which consists of SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, or 25.
  • hybridizes under stringent conditions refers to conditions for hybridization in 6 ⁇ sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2 ⁇ SSC, 0.1% SDS at 50-65° C. All of the above-described functional equivalents retain substantially the receptor binding activity of coronavirus, e.g., SRAS CoV S protein, i.e., binding to target cells including VERO E6, NIH3T3. This activity can be determined by the assays described in the examples presented below.
  • SSC sodium chloride/sodium citrate
  • a polypeptide of the invention can be obtained as a synthetic polypeptide or a recombinant polypeptide.
  • a nucleic acid encoding it can be linked to another nucleic acid encoding a fusion partner, e.g., Glutathione-S-Transferase (GST), 6 ⁇ -His epitope tag, or M13 Gene 3 protein.
  • GST Glutathione-S-Transferase
  • 6 ⁇ -His epitope tag e.g., 6 ⁇ -His epitope tag
  • M13 Gene 3 protein e.g., M13 Gene 3 protein.
  • the resultant fusion nucleic acid expresses in suitable host cells a fusion protein that can be isolated by methods known in the art.
  • the isolated fusion protein can be further treated, e.g., by enzymatic digestion, to remove the fusion partner and obtain the recombinant polypeptide of this invention.
  • a polypeptide of the invention can be used to generate antibodies in animals (for production of antibodies) or humans (for treatment of diseases).
  • Methods of making monoclonal and polyclonal antibodies and fragments thereof in animals are known in the art. See, for example, Harlow and Lane, (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York.
  • the term “antibody” includes intact molecules as well as fragments thereof, such as Fab, F(ab′) 2 , Fv, scFv (single chain antibody), and dAb (domain antibody; Ward, et. al. (1989) Nature, 341, 544).
  • These antibodies can be used for detecting the S polypeptide, e.g., in determining whether a test sample from a subject contains coronavirus or in identifying a compound that binds to the polypeptide. As these antibodies interfere with the cell binding and entry of the coronavirus, they are also useful for treating a coronavirus infection.
  • the polypeptide is coupled to a carrier protein, such as KLH, mixed with an adjuvant, and injected into a host animal.
  • a carrier protein such as KLH
  • Antibodies produced in the animal can then be purified by peptide affinity chromatography.
  • Commonly employed host animals include rabbits, mice, guinea pigs, and rats.
  • Various adjuvants that can be used to increase the immunological response depend on the host species and include Freund's adjuvant (complete and incomplete), mineral gels such as aluminum hydroxide, CpG, surface-active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol.
  • Useful human adjuvants include BCG (bacille Calmette-Guerin) and Corynebacterium parvum.
  • Monoclonal antibodies, homogeneous populations of antibodies to a polypeptide of this invention can be prepared using standard hybridoma technology (see, for example, Kohler et al. (1975) Nature 256, 495; Kohler et al. (1976) Eur. J. Immunol. 6, 511; Kohler et al. (1976) Eur J Immunol 6, 292; and Hammerling et al. (1981) Monoclonal Antibodies and T Cell Hybridomas, Elsevier, N.Y.).
  • monoclonal antibodies can be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture such as described in Kohler et al. (1975) Nature 256, 495 and U.S. Pat. No. 4,376,110; the human B-cell hybridoma technique (Kosbor et al. (1983) Immunol Today 4, 72; Cole et al. (1983) Proc. Natl. Acad. Sci. USA 80, 2026, and the EBV-hybridoma technique (Cole et al. (1983) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).
  • Such antibodies can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD, and any subclass thereof.
  • the hybridoma producing the monoclonal antibodies of the invention may be cultivated in vitro or in vivo. The ability to produce high titers of monoclonal antibodies in vivo makes it a particularly useful method of production.
  • chimeric antibodies can be used. See, e.g., Morrison et al. (1984) Proc. Natl. Acad. Sci. USA 81, 6851; Neuberger et al. (1984) Nature 312, 604; and Takeda et al. (1984) Nature 314:452.
  • a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region.
  • single chain antibodies U.S. Pat. Nos.
  • Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge.
  • antibody fragments can be generated by known techniques. For example, such fragments include, but are not limited to, F(ab′) 2 fragments that can be produced by pepsin digestion of an antibody molecule, and Fab fragments that can be generated by reducing the disulfide bridges of F(ab′) 2 fragments.
  • Antibodies can also be humanized by methods known in the art.
  • monoclonal antibodies with a desired binding specificity can be commercially humanized (Scotgene, Scotland; and Oxford Molecular, Palo Alto, Calif.). Fully human antibodies, such as those expressed in transgenic animals are also features of the invention (see, e.g., Green et al. (1994) Nature Genetics 7, 13; and U.S. Pat. Nos. 5,545,806 and 5,569,825).
  • a polypeptide of the invention can also be used to prepare an immunogenic composition (e.g., a vaccine) for generating antibodies against coronavirus (e.g., SRAS CoV) in a subject susceptible to the coronavirus.
  • an immunogenic composition e.g., a vaccine
  • coronavirus e.g., SRAS CoV
  • Such compositions can be prepared, e.g., according to the method described in the examples below, or by any other equivalent methods known in the art.
  • the composition contains an effective amount of a polypeptide of the invention, and a pharmaceutically acceptable carrier such as phosphate buffered saline or a bicarbonate solution.
  • the carrier is selected on the basis of the mode and route of administration, and standard pharmaceutical practice. Suitable pharmaceutical carriers and diluents, as well as pharmaceutical necessities for their use, are described in Remington's Pharmaceutical Sciences.
  • An adjuvant e.g., a cholera toxin, Escherichia coli heat-labile enterotoxin (LT), liposome, immune-stimulating complex (ISCOM), or immunostimulatory sequences oligodeoxynucleotides (ISS-ODN), can also be included in a composition of the invention, if necessary.
  • the S protein, fragments or analogs thereof or peptides may be components of a multivalent composition of vaccine against respiratory diseases.
  • This multivalent composition contains at least one immunogenic fragment of S protein described above, along with at least one protective antigen isolated from influenza virus, para-influenza virus 3 , Strentococcus pneumoniae, Branhamella ( Moroxella ) gatarhalis, Staphylococcus aureus , or respiratory syncytial virus, in the presence or absence of adjuvant.
  • Vaccines may be prepared as injectables, as liquid solutions or emulsions.
  • the S protein, fragments or analogs thereof or peptides corresponding to portions of S protein may be mixed with physiologically acceptable and excipients compatible. Excipients may include, water, saline, dextrose, glycerol, ethanol, and combinations thereof.
  • the vaccine may further contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or adjuvants to enhance the effectiveness of the vaccines.
  • Methods of achieving adjuvant effect for the vaccine includes use of agents, such as aluminum hydroxide or phosphate (alum), commonly used as 0.05 to 0.1 percent solutions in phosphate buffered saline.
  • Vaccines may be administered parenterally, by injection subcutaneously or intramuscularly.
  • other modes of administration including suppositories and oral formulations may be desirable.
  • binders and carriers may include, for example, polyalkalene glycols or triglycerides.
  • Oral formulations may include normally employed incipients such as, for example, pharmaceutical grades of saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10-95% of the S protein, fragment analogs, or peptides.
  • the vaccines are administered in a manner compatible with the dosage formulation, and in an amount that is therapeutically effective, protective and immunogenic.
  • the quantity to be administered depends on the subject to be treated, including, for example, the capacity of the individual's immune system to synthesize antibodies, and if needed, to produce a cell-mediated immune response. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner. However, suitable dosage ranges are readily determinable by one skilled in the art and may be of the order of micrograms of the polypeptide of this invention. Suitable regimes for initial administration and booster doses are also variable, but may include an initial administration followed by subsequent administrations. The dosage of the vaccine may also depend on the route of administration and varies according to the size of the host.
  • a chemically modified peptide or a peptide analog includes any functional chemical equivalent of the peptide characterized by its increased stability and/or efficacy in vivo or in vitro in respect of the practice of the invention.
  • the term peptide analog also refers to any amino acid derivative of a peptide as described herein.
  • a peptide analog can be produced by procedures that include, but are not limited to, modifications to side chains, incorporation of unnatural amino acids and/or their derivatives during peptide synthesis and the use of cross-linkers and other methods that impose conformational constraint on the peptides or their analogs.
  • side chain modifications include modification of amino groups, such as by reductive alkylation by reaction with an aldehyde followed by reduction with NaBH 4 ; amidation with methylacetimidate; acetylation with acetic anhydride; carbamylation of amino groups with cyanate; trinitrobenzylation of amino groups with 2, 4, 6, trinitrobenzene sulfonic acid (TNBS); alkylation of amino groups with succinic anhydride and tetrahydrophthalic anhydride; and pyridoxylation of lysine with pyridoxa-5′-phosphate followed by reduction with NABH 4 .
  • modification of amino groups such as by reductive alkylation by reaction with an aldehyde followed by reduction with NaBH 4 ; amidation with methylacetimidate; acetylation with acetic anhydride; carbamylation of amino groups with cyanate; trinitrobenzylation of amino groups with 2, 4, 6, trinitrobenzene sulfonic acid (TNBS); alkylation
  • the guanidino group of arginine residues may be modified by the formation of heterocyclic condensation products with reagents such as 2,3-butanedione, phenylglyoxal and glyoxal.
  • the carboxyl group may be modified by carbodiimide activation via o-acylisourea formation followed by subsequent derivatization, for example, to a corresponding amide.
  • Sulfhydryl groups may be modified by methods, such as carboxymethylation with iodoacetic acid or iodoacetamide; performic acid oxidation to cysteic acid; formation of mixed disulphides with other thiol compounds; reaction with maleimide; maleic anhydride or other substituted maleimide; formation of mercurial derivatives using 4-chloromercuribenzoate, 4-chloromercuriphenylsulfonic acid, phenylmercury chloride, 2-chloromercuric-4-nitrophenol and other mercurials; carbamylation with cyanate at alkaline pH.
  • Tryptophan residues may be modified by, for example, oxidation with N-bromosuccinimide or alkylation of the indole ring with 2-hydroxy-5-nitrobenzyl bromide or sulphonyl halides. Tryosine residues may be altered by nitration with tetranitromethane to form a 3-nitrotyrosine derivative. Modification of the imidazole ring of a histidine residue may be accomplished by alkylation with iodoacetic acid derivatives or N-carbethoxylation with diethylpyrocarbonate.
  • Examples of incorporating unnatural amino acids and derivatives during peptide synthesis include, but are not limited to, use of norleucine, 4-amino butyric acid, 4-amino-3-hydroxy-5-phenylpentanoic acid, 6-aminohexanoic acid, t-butylglycine, norvaline, phenylglycine, ornithine, sarcosine, 4-amino-3-hydroxy-6-methylheptanoic acid, 2-thienyl alanine and/or D-isomers of amino acids.
  • a nucleic acid molecule of this invention may also be used directly for immunization by administration of the nucleic acid directly to a subject via a live vector, such as Salmonella , BCG, adenovirus, poxvirus or vaccinia. Immunization methods based on nucleic acids are well known in the art.
  • a subject susceptible to coronavirus infection can be identified and administered a polypeptide-containing composition of the invention.
  • the dose of the composition depends, for example, on the particular polypeptide, whether an adjuvant is co-administered with the polypeptide, the type of adjuvant co-administered, the mode and frequency of administration, as can be determined by one skilled in the art. Administration is repeated as necessary, as can be determined by one skilled in the art.
  • a priming dose can be followed by three booster doses at weekly intervals.
  • a booster shot can be given at 4 to 8 weeks after the first immunization, and a second booster can be given at 8 to 12 weeks, using the same formulation.
  • Sera or T-cells can be taken from the subject for testing the immune response elicited by the composition against the coronavirus S protein or infection. Methods of assaying antibodies or cytotoxic T cells against a protein or infection are well known in the art. Additional boosters can be given as needed.
  • the immunization protocol can be optimized for eliciting a maximal immune response.
  • efficacy testing is desirable. In an efficacy testing, a non-human subject can be administered via an oral or parenteral route with a composition of the invention.
  • both the test subject and the control subject are challenged with an LD 95 dose of a coronavirus. End points other than lethality can also be used. Efficacy is determined if subjects receiving the composition dies at a rate lower than control subjects. The difference in death rates should be statistically significant.
  • the above-described S protein and its fragment can be used as a carrier and linked to other antigens of interest to generate antibodies against the antigens.
  • the S protein or its fragment can be generally utilized to prepare chimeric molecules and conjugate compositions against pathogenic bacteria, including encapsulated bacteria.
  • the glycoconjugates of the present inventions may be applied to immunize a subject to generate antibodies against the bacteria and confer protection against infection with any bacteria having polysaccharide antigens, e.g., Haemophilus influenzae, Streptococcus pneumoniae, Escherichia coli, Neisseria meningitidis, Salmonella typhi, Streptococcus mutans, Cryptococcus neoformans, Klebsiella, Staphylococcus aureus , and Pseudomonas aeruginosa .
  • the S protein or fragment may be used to induce immunity toward abnormal polysaccharides of tumor cells, thereby to produce anti-tumor antibodies for chemotherapy or diagnosis.
  • a diagnosing method using the above-described polypeptides or antibodies is also within the scope of this invention. Presence of the polypeptides or antibodies in a subject indicates that the subject is infected with a coronavirus.
  • To detect the antibodies or polypeptides one can obtain a test sample from a subject and detect the presence or absence of the antibodies or polypeptides using standard techniques, including ELISAs, immunoprecipitations, immunofluorescence, EIA, RIA, and Western blotting analysis.
  • the nucleic acid of this invention is useful as a hybridization probe for identifying coronavirus, e.g., SARS CoV, in a sample.
  • the sample can be a clinical sample, including exudates, body fluids (e.g., serum, amniotic fluid, middle ear effusion, sputum, bronchoalveolar lavage fluid) and tissues.
  • body fluids e.g., serum, amniotic fluid, middle ear effusion, sputum, bronchoalveolar lavage fluid
  • a variety of hybridization conditions may be employed to achieve varying degrees of selectivity of the probe toward the target sequences. A high degree of selectivity requires stringent conditions, such as that described in the Summary section
  • a hybridization reaction can be performed both in a solution or on a solid phrase.
  • a test sequence from a sample is affixed to a selected matrix or surface.
  • the fixed nucleic acid is then subjected to specific hybridization with selected probes comprising the nucleic acid of the present invention under desired conditions.
  • the selected conditions will depend on the particular circumstances based on the particular criteria required depending on, for example, on the G+C contents, type of target nucleic acid, source of nucleic acid, size of hybridization probe etc.
  • specific hybridization is detected or quantified, by means of the label.
  • the selected probe should be at least 18 bp and may be in the range of 30 bp to 90 bp long.
  • a small interference RNA corresponding to the nucleotide sequences of the present invention comprising the sequence of the S protein receptor binding domains such as RBD1 and RBD2, can be useful to block SARS CoV replication in vivo.
  • a polypeptide of this invention can also be used in a screening method of identifying a compound for treating an infection with a coronavirus, e.g., SARS CoV.
  • the method includes (1) contacting a polypeptide of this invention with a suitable cell, to which the coronavirus binds to; and (2) determining a binding level between the polypeptide and the cell the presence or absence of a test compound.
  • the binding level in the presence of the test compound if lower than that in the absence of the test compound, indicates that the test compound can be used to treat an infection with the coronavirus.
  • the cell include VERO E6 cells, NIH3T3 cells, HeLa cells, BHK-21 cells, and COS-7 cells.
  • the above-described polypeptides and antibodies can be used for treating an infection with a coronavirus, e.g., SARS.
  • the invention therefore features a method of treating SARS, e.g., by administering to a subject in need thereof an effective amount of a polypeptide, an antibody, or a compound of the invention.
  • Subjects to be treated can be identified as having, or being at risk for acquiring, a condition characterized by SARS. This method can be performed alone or in conjunction with other drugs or therapy.
  • a pharmaceutical composition that contains a pharmaceutically acceptable carrier and an effective amount of a polypeptide, an antibody, or a compound of the invention.
  • the pharmaceutical composition can be used to treat coronavirus infection, such as SARS.
  • the pharmaceutically acceptable carrier includes a solvent, a dispersion medium, a coating, an antibacterial and antifungal agent, and an isotonic and absorption delaying agent.
  • a composition of this invention e.g., a composition containing a polypeptide, an antibody, or a compound of the invention
  • a pharmaceutically-acceptable carrier e.g., physiological saline
  • intravenous infusion or injected or implanted subcutaneously, intramuscularly, intrathecally, intraperitoneally, intrarectally, intravaginally, intranasally, intragastrically, intratracheally, or intrapulmonarily.
  • the dosage required depends on the choice of the route of administration; the nature of the formulation; the nature of the subject's illness; the subject's size, weight, surface area, age, and sex; other drugs being administered; and the judgment of the attending physician. Suitable dosages are in the range of 0.01-100.0 mg/kg. Wide variations in the needed dosage are to be expected in view of the variety of compositions available and the different efficiencies of various routes of administration. For example, oral administration would be expected to require higher dosages than administration by intravenous injection. Variations in these dosage levels can be adjusted using standard empirical routines for optimization as is well understood in the art. Encapsulation of the composition in a suitable delivery vehicle (e.g., polymeric microparticles or implantable devices) may increase the efficiency of delivery, particularly for oral delivery.
  • a suitable delivery vehicle e.g., polymeric microparticles or implantable devices
  • a pharmaceutical composition of the invention can be formulated into dosage forms for different administration routes utilizing conventional methods.
  • it can be formulated in a capsule, a gel seal, or a tablet for oral administration.
  • Capsules can contain any standard pharmaceutically acceptable materials such as gelatin or cellulose.
  • Tablets can be formulated in accordance with conventional procedures by compressing mixtures of the composition with a solid carrier and a lubricant. Examples of solid carriers include starch and sugar bentonite.
  • the composition can also be administered in a form of a hard shell tablet or a capsule containing a binder, e.g., lactose or mannitol, conventional filler, and a tableting agent.
  • the pharmaceutical composition can be administered via the parenteral route.
  • parenteral dosage forms include aqueous solutions, isotonic saline or 5% glucose of the active agent, or other well-known pharmaceutically acceptable excipient.
  • Cyclodextrins, or other solubilizing agents well known to those familiar with the art, can be utilized as pharmaceutical excipients for delivery of the therapeutic agent.
  • compositions of this invention can be evaluated both in vitro and in vivo. Briefly, the composition can be tested for its ability to inhibit the binding between a coronavirus and its target cell in vitro. For in vivo studies, the composition can be injected into an animal (e.g., a mouse model) and its therapeutic effects are then accessed. Based on the results, an appropriate dosage range and administration route can be determined.
  • an animal e.g., a mouse model
  • SARS-CoV TW1 A SARS CoV, designated as “SARS-CoV TW1,” was isolated from a SARS patient in Taiwan. Seven pairs of PCR primers were designed based on the sequence of the Urbani strain (SEQ ID NO: 1) or the SARS CoV TOR2 strain. The positions of the primers' 5′ ends within the Urbani genome were summarized below:
  • SARS CoV M and E proteins were also cloned and expressed.
  • the E-M fusion protein corresponds to residues 8751 to 9057 of the first open reading frame of SEQ ID NO: 1.
  • Construction of DNA plasmids containing genes for E and M proteins was performed by standard molecular biology methods (Sambrook et al (1989) Molecular cloning: a laboratory manual. 2 nd ed. Cold Spring Harbor Laboratory. Cold Spring Harbor, N.Y.). The constructs utilized a pUC-based expression vector, which was shown to result in optimal expression of reporter genes.
  • Each vector employed the human cytomegalovirus promoter, enhancer, intron A, and the bovine growth hormone termination and polyasenylation sequences.
  • the tissue plasminogen activator signal sequence was use to enhance the level of expression.
  • the M and E proteins were further expressed in host cells to generated virus like particles.
  • the above-described PUC19/S was transformed into E. coli . to express the S protein. It was found that the full-length recombinant S (rS) protein was not expressed in E. coli . Vectors encoding different S protein fragments fused to Myc-His tag were then constructed and transformed in E. coli . The fragments include the N-terminal amino acids 80-228 of the S protein (receptor binding domain 1; RBD1); the middle region encompassing amino acids 284-735 of the S protein (receptor binding domain 2; RBD2), the transmembrane domain (TM), and fusions of them.
  • RBD1 receptor binding domain 1
  • RBD2 transmembrane domain
  • SARS CoV polypeptides were synthesized by standard techniques:
  • RBD1-specific peptide (SEQ ID NO:29) KSGNFKHLREFVFKNKDGFLYVYKGQPIDV RBD2-specific peptide (SEQ ID NO:24) GNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPC TM-specific peptide (SEQ ID NO:30) DSFKEELDRY FKNHTSPDVD LGDISGINAS VV E-specific peptide (SEQ ID NO:31) ALRLCAYCCN IVNVSLVKPT VYVYSRVKNL NSSEG M-specific peptide (SEQ ID NO:32) MADNGTITVE ELKQLLEQWN LVICFLAW IML
  • a vector encoding RBD2 was also generated More specifically, PCR was conducted using the following two primers 5′ primer: GGATCCGCCACCATG gagattgaca (SEQ ID NO:35) and 3′ primer: aatatgg GCGGCCGC (SEQ ID NO:36) to generate a 14 kb fragment After being digested by BamH1H-Not1, the resulting fragment was also subcloned into pcDNA-A4 The resultant vector was used to express RBD2 in the same manner described above It was found that a 50-kDa protein was expressed at high levels in both soluble form and in inclusion bodies Western blot analysis revealed that this protein was recognized by the S-specific antisera This rRBD2 fragment was highly immunogenic too and elicited even stronger neutralizing antibodies that could block SARS CoV binding to Vero cell (see Example 9 below).
  • E. coli pellet from a 250 mL culture was resuspended in 40 mL of 50 mM Tris, pH 8.0, and disrupted by sonication (3 ⁇ 10 minutes, 70% duty circle).
  • the resultant mixture was centrifuged at 20,000 ⁇ g.
  • the pellet was re-extracted with 40 mL of 50 mM Tris, 0.5% Triton X-100, 10 mM EDTA, pH 8.0.
  • the suspension was then sonicated for 10 minutes at 70% duty circle and centrifuged at 300 ⁇ g for 5 minutes.
  • the resulting supernatant was centrifuged again at 20,000 ⁇ g for 30 minutes.
  • the pellet was resuspended in 50 mM Tris, 0.5% Triton X-100, 10 mM EDTA, pH 8.0 and mixed with PBS/8 M urea to a final urea concentration of 6 M urea. The mixture was then dialyzed against PBS to remove urea and centrifuged at 300 ⁇ g for 10 minutes. The supernatant was saved and stored at 4° C.
  • Ni-affinity chromatography was used to isolate rRBD1 and rRBD2 fusion proteins from inclusion body. The just described supernatant was loaded onto a Ni affinity column (2 mL) equilibrated with PBS containing 1% Triton X-100. The run-through of the column was discarded. After washing the column with 20 mL of PBS, the affinity column was eluted with 50 mM Tris-HCl buffer, pH 8.0, containing 5 mM EDTA. The protein-containing factions were collected and the purity was analyzed by SDS-PAGE.
  • rRBD2 was recovered from 1 L of E. coli bacterial culture.
  • the identity of rRBD2 was confirmed by both immunoblotting and protein sequencing.
  • the N-terminal sequence of this polypeptide was found to be Met-Ala-Glu-Leu-Lys-Cys, which corresponds to residues 284 to 288 of the sequence of S protein.
  • Nucleic acids encoding 1-333, 334-666, and 667-999 amino acid of the S protein were obtained by PCR with primer sets listed below, respectively, in the manner similar to that described in Example 1
  • the PCR products were inserted into the pCR2.1 vector by TA cloning.
  • the coding sequences were than released by BamHI digestions and ligated to BamHI-cutted pSecTagb/hIgG1.Fc vector, thereby in-frame fusing the S protein-encoding sequence to that encoding the human IgG1 Fc,
  • the resultant vectors encodes fusion proteins spike1-Fc, spike2-Fc, and spike3-Fc.
  • the three fusion genes were released by NheI/XhoI digestion and ligated to XbaI/XhoI-cutted pBacPAK9 vectors.
  • the just-described pBacPAK9 vectors were co-transfected into Sf21 cells with Bsu36 I-digested BacPAK6 viral DNA by Bacfectin (Clontech 6144-1). Each resulting viral plaque was picked by performing plaque assays on the co-transfection supernatant. The recombinant viruses were confirmed by PCR. Sf21 cells were then infected with virus at a small scale to characterize gene expression and to determine the optimum harvest time and infection ratio by standard methods. Recombinant viruses were amplified to high virus titer to obtain working stocks for large-scale infection.
  • Sf21 cells were cultured in spinner flask at a starting concentration of 2 ⁇ 10 5 /ml in the first 3-5 days. After reaching 1 ⁇ 2 ⁇ 10 6 cells/ml, the cells were infected with the above-described recombinant baculoviruses at M.O.I. of 5-10 and cultured for 4-5 days. The supernatants were then collected and cell debris was removed by centrifugation. The supernatant was loaded onto protein A Sepharose® 4 Fast Flow beads (Amersham Biosciences 17-0974). Finally, the bound Fc-fusion protein was eluted with a 0.1 M glycine buffer (pH 3.0), followed by dialysis against PBS. The purity and the concentration of purified proteins were assessed by a standard silver staining method.
  • S1-Fc fusion protein crude extract prepared in the manner described above were dissolved in 5 mL of phosphate buffer saline (PBS) containing 1% Triton X-100. The solution was then loaded onto a Protein A-Sepharose 4B column (2 mL) equilibrated with PBS containing 1% Triton X-100. The run-through of the column was discarded. The column was washed with 20 mL of PBS and the S1-FC fusion protein was eluted with 50 mM Gly-HCl buffer, pH 3.0. Elution was monitored by absorbance at 280 nm. Protein-containing fractions (2 mL/fraction) were collected and pooled. The purity of the protein was assessed by SDS-PAGE.
  • PBS phosphate buffer saline
  • the above-described recombinant RBD1, RBD2, S1-FC, and S2-Fc were used to produce of S-specific antisera.
  • the purified recombinant proteins were emulsified in the Freund's complete adjuvant (Difco) and injected intramuscularly (IM) into New Zealand White rabbits (Maple Lane) or guinea pigs (Charles River) at a dose of 10 to 100 ⁇ g/injection.
  • the animals were boosted on day 28 with another half of dose of the corresponding S fragment emulsified in Freund's incomplete adjuvant.
  • a blood sample was taken from each animal via the marginal ear vein for titer determination by standard methods. Animals that generated specific antibodies were bled to obtain more antisera.
  • guinea pigs or mice were immunized with RBD1 or 2 of various amounts.
  • the doses between 10 to 100 ⁇ g/injection RBD1 induced high IgG titers in guinea pigs when administered in the presence of either Freund's adjuvant or AlPO 4 .
  • RBD1 or 2 appeared to be immunogenic at a dose as low as 5 ⁇ g/injection in either Freund's adjuvant.
  • a ferret model was used to examine the protective ability of anti-RBD1 or 2 sera against a SARS CoV infection. It was found that ferrate passively immunized with guinea pig anti-RBD2 antisera, but not anti-RBD1 sera, were significantly protected than controls injected with pre-immune sera.
  • the above-described S1-Fc or S2-Fc fusion protein was used to purify S protein-specific polyclonal antibodies by affinity chromatography.
  • the recombinant S1-Fc or S2-Fc fusion protein was conjugated to cyanogen bromide-activated Sepharose to form an affinity column.
  • the affinity column was then used to purify antibodies from a rabbit hyperimmune anti-inactivated SARS CoV antiserum.
  • the affinity purified-antibodies were shown by immunoblotting to react with a 200-kDa component present in the lysates of SARS Cov isolates.
  • antisera raised against the recombinant fusion protein or the purified RBD1, RBD2, S1 and S2 can also be purified in the same manner.
  • S. pneumococcal oligosaccharides 14 14F
  • S. pneumococcal oligosaccharides 14 was prepared by controlled acid hydrolysis. The mean molecular size of the 14F molecules used for conjugation was determined as approximately 20,000 Daltons. The conjugation was carried out with or without a linker molecule. A 14/RBD2 molar ratio of approximately 7 was used to provide an excess of 14F hapten.
  • periodate-oxidized 14 25 mg in 1 mL of 0.1 M sodium phosphate buffer, pH 6.0
  • bovine serum albumin (BSA) (1.32 mg; 0.02 ⁇ mol) in 0.5 mL of 0.2 M sodium phosphate buffer, pH 8.0, followed by the addition of sodium cyanoborohydride (14 ⁇ g; 0.22 ⁇ mol; 10 eqv. to BSA). After incubation at 37° C.
  • reaction mixture was dialyzed against 4 L of 0.1 M phosphate buffer, pH 7.5.
  • the resulting solution was applied onto an analytical Superose 12 column (15 ⁇ 0.300 mm, Pharmacia) equilibrated with 0.2 M sodium phosphate buffer, pH 7.2, and eluted with the same buffer. Fractions were monitored for absorbance at 230 nm. The first major protein peak was pooled and concentrated in a Centriprep 30 to 2.2 mL. The amount of protein was found, by the Bio Rad protein assay, to be 300 ug/mL. The presence of 14 oligosccharides in the protein conjugate fraction was confirmed by the Orcinol test.
  • the peptides were synthesized by an ABI 433A peptide synthesizer and optimized F-Moc chemistry according to the manufacturer's manual.
  • the synthesized peptides were cleaved from the resin by Trifluoroacetic acid (TFA). They were then purified by reversed-phase high performance liquid chromatography (RP-HPLC) on a Vydac C4 semi-preparative column (1 ⁇ 30 cm) using a 15 to 55% acetonitrile gradient in 0.1% trifluoryl acetic acid (TFA) developed over 40 minutes at a flow rate of 2 mL/min. All synthetic peptides used in subsequent biochemical and immunological studies were >95% pure as determined by analytical HPLC. Amino acid compositions of these peptides were determined on a Waters Pico-Tag system. The results indicated a good agreement with their expected compositions.
  • ELISA was used to map B-cell epitopes.
  • Microtiter wells Nunc, Denmark
  • a coating buffer 15 mM Na 2 CO 3 , 35 mM NaHCO 3 , pH 9.6
  • 200 ng of purified recombinant S fragments or 500 ng of individual peptides listed in Table 3 below
  • the plates were then blocked in 0.1% (w/v) BSA in phosphate buffer saline (PBS) for 30 minutes at room temperature.
  • Serially diluted antisera were added to the wells and incubated for 1 hour at room temperature.
  • the plates were washed five times with PBS containing 0.1% (w/v) Tween-20 and 0.1% (w/v) BSA.
  • Fab′2 fragments from goat anti-rabbit, -guinea pig, -mouse, or -human IgG antibodies conjugated to horseradish peroxidase (Jackson ImmunoResearch Labs Inc., PA) were diluted (1/8,000) with a washing buffer, and added to the microtiter wells. After incubating for 1 hour at room temperature, the wells were washed five times with the washing buffer and then developed using the substrates tetramethylbenzidine (TMB) and H 2 O 2 (ADI, Toronto).
  • SRAS CoV binds to VERO E6 cells.
  • the above-described S protein fragments were tests for their ability to bind to VERO E6 cells.
  • Vero E6 cells (1 ⁇ 10 4 cells per mL) were incubated with S1-Fc, S2-Fc, S3-Fc, or human IgG1 at various concentrations in a volume of 1 mL for 2 hours at room temperature. The cells were then washed in PBS containing 0.5% BSA and 0.1% NaN3, incubated with FITC-labeled goat anti-human IgG Fc (Sigma), and analyzed by flow cytometry.
  • VERO E6 cell model was used to examine the ability of anti-S1-Fc or anti-S2-Fc serum to inhibit the binding of SARS CoV to VERO E6 cells.
  • VERO E6 cells were cultured on a 24-well plate until they reached approximately 50% confluent. The cells were then incubated with SARS-CoV Tw1 strain (MOI 1:10) and human sera that had a 1/128 virus neutralization titer in the presence or absence of 0.1 to 10 ⁇ g/mL corresponding S fusion proteins. After 24-48 hours, the cells were examined under a microscope. The presence of mltinucleated giant cells indicated infected cells. The results indicated that human sera blocked the viral infection, and that this blocking activity was repressed by the recombinant S fusion proteins.
  • S2-Fc fusion protein strongly bound to VERO E6 cell and inhibited human neutralizing antibody activity against SARS CoV, it was of interest to identify the protective epitope(s) of this S2 fragment.
  • Eighty-eight peptides from S2 (shown in Table 2 above) were synthesized based upon the sequence of the SARS CoV TW1 S protein.
  • Recombinant RBD2 was tested first. 104 of VERO E6 cells were incubated with 330 ng/mL of S2-Fc protein in the presence or absence of know amount of RBD2 protein solution. It was found that 1 ⁇ g of RBD2 significantly reduced the S2-Fc binding to VERO E6 cells.
  • the inhibition assays were repeated with 11 cocktails, each containing nine RBD2 fragment and covering(S28 to S115). More specifically, the VERO E6 cells were harvested and washed twice with a FACS staining/washing buffer. 2 ⁇ 10 5 cells were incubated with various peptides and then stained in a final volume of 100 ml with recombinant S-Fc protein (1 mg), S2-Fc protein (0.2-0.3 mg), or hIgG1 as isotype control for 30 minutes at 4° C. Cells were washed twice and stained with the RPE-conjugated anti-hIg Abs for 30 minutes at 4° C.
  • Blocking agents 1 10 100 Negative control (SEQ ID NOs:) 0 0 0 Gp(28-35) (SEQ ID NOs: 78-85) 0 0 0 Gp(36-43) (SEQ ID NOs: 86-93) 0 0 0 Gp(44-51) (SEQ ID NOs: 94-101) 0 0 0 Gp(52-59) (SEQ ID NOs: 102-109) 0 0 0 Gp(60-67) (SEQ ID NOs: 110-117) 0 0 0 Gp(68-75) (SEQ ID NOs: 118-125) 0 0 0 Gp(76-83) (SEQ ID NOs: 126-133) 0 0 0 Gp(84-91) (SEQ ID NOs: 134-141) 0 10% 30%
  • Blocking agents 1 10 100 Negative control (SEQ ID NOs:) 0 0 0 Gp(76-83) (SEQ ID NOs: 126-133) 0 0 0 Gp(84-91) (SEQ ID NO: 134-141) 0 10 30 S84 (SEQ ID NO: 134) 0 0 0 S85 (SEQ ID NO: 135) 0 0 0 S86 (SEQ ID NO: 136) 0 0 10 S87 (SEQ ID NO: 137) 0 0 0 S88 (SEQ ID NO: 138) 0 0 0 S89 (SEQ ID NO: 139) 0 0 10 S90 (SEQ ID NO: 140) 0 0 0 S91 (SEQ ID NO: 141) 0 0 0 0 S86 + S87 (SEQ ID NO: 140) 0 0 0 0 S91 (SEQ ID NO: 141) 0 0 0 0 S86 + S87 (SEQ ID NO: 140) 0 0
  • peptides were used to generate S peptide-specific antisera.
  • Guinea pigs and rabbits were immunized with peptides cocktail (50 to 200 ⁇ g) emulsified with the Freund's complete adjuvant and injected intramuscularly. The animals were boosted with the same amount of peptide cocktails in the incomplete Freund's adjuvant at days 14 and 28.
  • Antisera were collected on day 42 and tested by ELISAs and immunoblotting. Both rabbit and guinea pig antisera were shown to be monospecific for their respective immunizing peptides by the peptide-specific ELISAs.
  • T-cell lines' proliferative responses to S peptides were determined by conventional cytokine assays as described below.
  • mice (Charles River Animal Farm, Montreal, Canada) were primed subcutaneously with 20 ⁇ g of recombinant S adsorbed to 1.5 mg of aluminium phosphate (alum) in presence of 100 ⁇ g of CpG. The mice were boosted twice with the same dose of immunogen at 3-week intervals.
  • Splenocytes were isolated and cultured in 200 ⁇ L of RPMI 1640 medium (Flow Lab) at 5.75 ⁇ 10 5 cells per well of a microtiter plate.
  • the medium was supplemented with 10% heat-inactivated fetal calf serum (Gibson), 2 mM L-glutamine, 100 U/mL) penicillin, and 5 ⁇ 0.10 ⁇ 5 M 2-mercaptoethanol and contained varying concentrations (1, 10 and 100 ⁇ g per mL) of individual S peptides.
  • the cultures were kept in a humidified incubator in the presence of 5% CO 2 /air. Triplicate cultures were performed for each concentration of each peptide.
  • IL-2 Interleukin-2
  • T-cell epitopes can be used as carriers for pneumococcal polysaccharides and/or S B-cell epitopes to enhance the immunogenicity.
  • the Th1 cell epitopes identified above can be used in SARS CoV vaccine formulations to induce SARS-specific cellular immune responses.
  • mice were immunized intraperitoneally with 20 to 50 ⁇ g of RBD2 emulsified in the Freund's complete adjuvant. Two weeks later, the mice were injected with the same amount of immunogen in the incomplete Freund's adjuvant. The anti-S titers were examined. Positive mice were selected for making hybridomas by standard cell fusion techniques. Three days before the fusion, the mice were boosted again with the same amount of immunogen in the incomplete Freund's adjuvant. Hybridomas were produced by fusion of splenic lymphocytes from immunized mice with non-secreting Sp2/0 myeloma cells in the manner described in Hamel et al.
  • S-specific hybridomas were cloned by sequential limiting dilutions and screened for anti-S monoclonal antibody production. Eight S-specific hybridoma cell lines were identified, expanded, and frozen in liquid nitrogen by standard techniques.
  • S1-Fc and S2-Fc bind to VERO cells.
  • S3-Fc binds to any other cells.
  • a panel of cell lines were tested. About 1 ⁇ 10 4 cells/mL were incubated with 0.1, 0.3, and 1 ⁇ g of S3-Fc or the same amount of S1-Fc or S2-Fc in a volume of 1 mL for 2 hours at room temperature. The cells were washed in PBS with 0.5% BSA and 0.1% NaN 3 , incubated with FITC-labeled goat anti-human IgG Fc (Sigma), and analyzed by flow cytometry.
  • S3-Fc bound strongly to NIH 3T3 cells but not to Jarket cells.
  • S3-Fc showed strong binding to NIH 3T3 cells even at a concentration as low as 0.1 ⁇ g/mL.
  • S1-Fc did not bind to NIH3T3 cells even at 10 g/mL
  • S2-Fc showed some binding to NIH 3T3 cell at 1 ⁇ g/mL.
  • S protein also binds to HeLa, BHK-21, and COS-7 cells.
  • Three separated receptor-binding domains of S protein were identified: (1) the low affinity mapped to the N-terminal 333 residues, (2) a intermediate affinity receptor-binding domain (with 1 ⁇ M avidity) mapped to residues 334 to 666, and (3) a high affinity domain within residues 667 to 999.
  • Beside VERO E6 cells all these cell lines had not been reported before to be the hosts for SARS CoV replication. This explained why SARS CoV could infect patient via skin contact with infected solutions.

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Abstract

Isolated polypeptides containing fragments of SARS CoV S protein and functional equivalents thereof. Also disclosed are isolated nucleic acids encoding the polypeptides, related expression vectors, related host cells, related antibodies, and related compositions. Methods of producing the polypeptide, diagnosing infection with a coronavirus, and identifying a test compound for treating infection with a coronavirus are also disclosed.

Description

    RELATED APPLICATION
  • This application is a divisional of U.S. application Ser. No. 11/033,455, filed on Jan. 10, 2005, which_claims priority to U.S. Provisional Application Ser. No. 60/535,641, filed on Jan. 9, 2004, the contents of which are incorporated by reference in its entirety.
    • BACKGROUND
  • Virus is the cause of various disorders. For example, members of the coronavirus family cause hepatitis in mice, gastroenteritis in pigs, and respiratory infections in birds and humans. Among the more than 30 strains isolated so far, three or four infect humans. The severe acute respiratory syndrome (SARS), a newly found infectious disease, is associated with a novel coronavirus. This life-threatening respiratory coronavirus touched off worldwide outbreaks in 2003. Vaccines and drugs against SARS coronavirus (CoV) are being vigorously sought. Nevertheless, the progress has been rather slow due to safety concerns.
    • SUMMARY
  • This invention is based, at least in part, on the discovery of receptor binding domains of the SARS CoV Spike (S) protein. Genomic sequences of a number of SARS CoV strains can be found in GenBank. GenBank Accession No. AY278741 (SEQ ID NO: 1) represents the genomic sequence of the SARS CoV Urbani strain, which contains an open reading frame encoding a polypeptide that is 7,073 amino acid residues (aa.) in length (SEQ ID NO: 2). The nucleic acid encoding the S protein of this strain corresponds to nucleotides (nt) 21,492-25,259 of GenBank Accession No. AY278741. Listed below are the nucleic acid and amino acid sequences of the S protein:
  • (SEQ ID NO: 3)
    21492            atgtttatt ttcttattat ttcttactct cactagtggt agtgaccttg
    21541 accggtgcac cacttttgat gatgttcaag ctcctaatta cactcaacat acttcatcta
    21601 tgaggggggt ttactatcct gatgaaattt ttagatcaga cactctttat ttaactcagg
    21661 atttatttct tccattttat tctaatgtta cagggtttca tactattaat catacgtttg
    21721 gcaaccctgt catacctttt aaggatggta tttattttgc tgccacagag aaatcaaatg
    21781 ttgtccgtgg ttgggttttt ggttctacca tgaacaacaa gtcacagtcg gtgattatta
    21841 ttaacaattc tactaatgtt gttatacgag catgtaactt tgaattgtgt gacaaccctt
    21901 tctttgctgt ttctaaaccc atgggtacac agacacatac tatgatattc gataatgcat
    21961 ttaattgcac tttcgagtac atatctgatg ccttttcgct tgatgtttca gaaaagtcag
    22021 gtaattttaa acacttacga gagtttgtgt ttaaaaataa agatgggttt ctctatgttt
    22081 ataagggcta tcaacctata gatgtagttc gtgatctacc ttctggtttt aacactttga
    22141 aacctatttt taagttgcct cttggtatta acattacaaa ttttagagcc attcttacag
    22201 ccttttcacc tgctcaagac atttggggca cgtcagctgc agcctatttt gttggctatt
    22261 taaagccaac tacatttatg ctcaagtatg atgaaaatgg tacaatcaca gatgctgttg
    22321 attgttctca aaatccactt gctgaactca aatgctctgt taagagcttt gagattgaca
    22381 aaggaattta ccagacctct aatttcaggg ttgttccctc aggagatgtt gtgagattcc
    22441 ctaatattac aaacttgtgt ccttttggag aggtttttaa tgctactaaa ttcccttctg
    22501 tctacgcatg ggagagaaaa aaaatttcta attgtgttgc tgattactct gtgctctaca
    22561 actcaacatt tttttcaacc tttaagtgct atggcgtttc tgccactaag ttgaatgatc
    22621 tttgcttctc caatgtctat gcagattctt ttgtagtcaa gggagatgat gtaagacaaa
    22681 tagcgccagg acaaactggt gttattgctg attataatta taaattgcca gatgatttca
    22741 tgggttgtgt ccttgcttgg aatactagga acattgatgc tacttcaact ggtaattata
    22801 attataaata taggtatctt agacatggca agcttaggcc ccttgagaga gacatatcta
    22861 atgtgccttt ctcccctgat ggcaaacctt gcaccccacc tgctcttaat tgttattggc
    22921 cattaaatga ttatggtttt tacaccacta ctggcattgg ctaccaacct tacagagttg
    22981 tagtactttc ttttgaactt ttaaatgcac cggccacggt ttgtggacca aaattatcca
    23041 ctgaccttat taagaaccag tgtgtcaatt ttaattttaa tggactcact ggtactggtg
    23101 tgttaactcc ttcttcaaag agatttcaac catttcaaca atttggccgt gatgtttctg
    23161 atttcactga ttccgttcga gatcctaaaa catctgaaat attagacatt tcaccttgct
    23221 cttttggggg tgtaagtgta attacacctg gaacaaatgc ttcatctgaa gttgctgttc
    23281 tatatcaaga tgttaactgc actgatgttt ctacagcaat tcatgcagat caactcacac
    23341 cagcttggcg catatattct actggaaaca atgtattcca gactcaagca ggctgtctta
    23401 taggagctga gcatgtcgac acttcttatg agtgcgacat tcctattgga gctggcattt
    23461 gtgctagtta ccatacagtt tctttattac gtagtactag ccaaaaatct attgtggctt
    23521 atactatgtc tttaggtgct gatagttcaa ttgcttactc taataacacc attgctatac
    23581 ctactaactt ttcaattagc attactacag aagtaatgcc tgtttctatg gctaaaacct
    23641 ccgtagattg taatatgtac atctgcggag attctactga atgtgctaat ttgcttctcc
    23701 aatatggtag cttttgcaca caactaaatc gtgcactctc aggtattgct gctgaacagg
    23761 atcgcaacac acgtgaagtg ttcgctcaag tcaaacaaat gtacaaaacc ccaactttga
    23821 aatattttgg tggttttaat ttttcacaaa tattacctga ccctctaaag ccaactaaga
    23881 ggtcttttat tgaggacttg ctctttaata aggtgacact cgctgatgct ggcttcatga
    23941 agcaatatgg cgaatgccta ggtgatatta atgctagaga tctcatttgt gcgcagaagt
    24001 tcaatggact tacagtgttg ccacctctgc tcactgatga tatgattgct gcctacactg
    24061 ctgctctagt tagtggtact gccactgctg gatggacatt tggtgctggc gctgctcttc
    24121 aaataccttt tgctatgcaa atggcatata ggttcaatgg cattggagtt acccaaaatg
    24181 ttctctatga gaaccaaaaa caaatcgcca accaatttaa caaggcgatt agtcaaattc
    24241 aagaatcact tacaacaaca tcaactgcat tgggcaagct gcaagacgtt gttaaccaga
    24301 atgctcaagc attaaacaca cttgttaaac aacttagctc taattttggt gcaatttcaa
    24361 gtgtgctaaa tgatatcctt tcgcgacttg ataaagtcga ggcggaggta caaattgaca
    24421 ggttaattac aggcagactt caaagccttc aaacctatgt aacacaacaa ctaatcaggg
    24481 ctgctgaaat cagggcttct gctaatcttg ctgctactaa aatgtctgag tgtgttcttg
    24541 gacaatcaaa aagagttgac ttttgtggaa agggctacca ccttatgtcc ttcccacaag
    24601 cagccccgca tggtgttgtc ttcctacatg tcacgtatgt gccatcccag gagaggaact
    24661 tcaccacagc gccagcaatt tgtcatgaag gcaaagcata cttccctcgt gaaggtgttt
    24721 ttgtgtttaa tggcacttct tggtttatta cacagaggaa cttcttttct ccacaaataa
    24781 ttactacaga caatacattt gtctcaggaa attgtgatgt cgttattggc atcattaaca
    24841 acacagttta tgatcctctg caacctgagc tcgactcatt caaagaagag ctggacaagt
    24901 acttcaaaaa tcatacatca ccagatgttg atcttggcga catttcaggc attaacgctt
    24961 ctgtcgtcaa cattcaaaaa gaaattgacc gcctcaatga ggtcgctaaa aatttaaatg
    25021 aatcactcat tgaccttcaa gaattgggaa aatatgagca atatattaaa tggccttggt
    25081 atgtttggct cggcttcatt gctggactaa ttgccatcgt catggttaca atcttgcttt
    25141 gttgcatgac tagttgttgc agttgcctca agggtgcatg ctcttgtggt tcttgctgca
    25201 agtttgatga ggatgactct gagccagttc tcaagggtgt caaattacat tacacataa
    25259
    MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSD
    TLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRG
    WVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTM
    IFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQP
    IDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYF
    VGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSN
    FRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVL
    YNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVI
    ADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDI
    SNVPFSPDGKPCTPPALNCYWPLNDYGEYTTTGIGYQPYRVVVLSFELLN
    APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDV
    SDFTDSVRDPKTSEILDISPCAFGGVSVITPGTNASSEVAVLYQDVNCTD
    VSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGI
    CASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTE
    VMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDR
    NTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLENKVT
    LADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALV
    SGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNK
    AISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDI
    LSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSE
    CVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAIC
    HEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGII
    NNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEI
    DRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLC
    CMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT (SEQ ID NO: 4; the
    two underlines segments represent two receptor binding
    domains.)
    MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSD
    TLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRG
    WVFGSTMNNKSQVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTM
    IFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQP
    IDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYF
    VGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSN
    FRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVL
    YNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVI
    ADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDI
    SNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLN
    APATVCGPTLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDV
    SDFTDSVRDPKTSEILDISPCAFGGVSVITPGTNASSEVAVLYQDVNCTD
    VSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGI
    CASYHTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTE
    VMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDR
    NTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVT
    LADAGFMKQYGECLCDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALV
    SGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNK
    AISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDI
    LSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSE
    CVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAIC
    HEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGII
    NNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEI
    DRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLC
    CMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT (SEQ ID NO: 4; the
    two underlines segments represent two receptor binding
    domains.)
  • One aspect of the invention features an isolated polypeptide containing SEQ ID NO: 4 or an immunogenic fragment derived from SEQ ID NO: 4. The immunogenic fragment is at least 10 amino acid residues in length, i.e., any number between 10 and 1255 (the length of SEQ ID NO: 4), inclusive. Examples of such an immunogenic fragment include the domains listed below:
  • Corresponding aa.
    position within
    Domain Name SEQ ID NO: 4 SEQ ID NO
    Receptor binding domain 1  80-227 SEQ ID NO: 6
    (RBD1)
    Receptor binding domain 2 284-735 SEQ ID NO: 8
    (RBD2)
    S1  1-333 SEQ ID NO: 18
    S2 334-666 SEQ ID NO: 20
    S3  667-1000 SEQ ID NO: 22
    RBD2-consensus (RBD2-C) 434-467 SEQ ID NO: 24
    RBD-55 564-613 SEQ ID NO: 26
    Transmembrane domain (TM) 1128-1255 SEQ ID NO: 28

    Examples also include the fusions of two or more of the above-listed domains, e.g., RBD1-(Gly)8-TM (SEQ ID NO: 10), RBD2-(Gly)8-TM (SEQ ID NO: 12), RBD1-(Gly)8-RBD2 (SEQ ID NO: 14), and RBD1-(Gly)8-RBD2-(Gly)8-TM (SEQ ID NO: 16). In these fusions, different S protein fragments are joined by a linker of 8 glycines. Additional examples include those listed in Table 2 shown in Example 6 below. Preferably, the polypeptide of this invention contains SEQ ID NO: 24 or 26. In one embodiment, the polypeptide is a glycoprotein containing a polysaccharide, e.g., a polysaccharide from S. pneumococcal. In another embodiment, the polypeptide is a fusion protein including a heterologous polypeptide that contains an Fc portion of an immunoglobin, e.g., an IgG. Preferably, the immunoglobin is IgG1, and more preferably, a human IgG1. The fusion protein can also include a heterologous polypeptide that contains a surface portion of a protein of a pathogen, such as the HA or NA of an influenza virus.
  • An “isolated polypeptide” refers to a polypeptide substantially free from naturally associated molecules, i.e., it is at least 75% (i.e., any number between 75% and 100%, inclusive) pure by dry weight. Purity can be measured by any appropriate standard method, for example, by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. An isolated polypeptide of the invention can be purified from a natural source, produced by recombinant DNA techniques, or by chemical methods. A “heterologous” protein or nucleic acid is one that originates from a foreign species, or, if from the same species, is substantially modified from its original form.
  • The invention also features an isolated nucleic acid that contains a sequence encoding one of the above-mentioned polypeptides. Examples of the sequence include (1) those encoding S, RBD1, RBD2, S1, S2, S3, RBD-2C, RBD-55, and TM, which, respectively, correspond to nt. 21492-25259, 21729-22172,—22341-23696, 21492-22490, 22491-23489, 23490-24491, 22791-22892, 23181-23330, and 24873-25256 of GenBank Accession No. AY278741 (SEQ ID NOs: 3, 5, 7, 17, 19, 21, 23, 25, and 27, respectively)
  • Listed below are exemplary sequences that encode fusion proteins RBD1-(Gly)8-TM, RBD2-(Gly)8-TM, RBD1-(Gly)8-RBD2, and RBD1-(Gly)8-RBD2-(Gly)8-TM (SEQ ID NOs: 9, 11, 13, and 15, respectively; linkers shown in the upper case):
  • SEQ ID NO: 9
    catacgtttg gcaaccctgt catacctttt aaggatggta tttattttgc tgccacagag
    aaatcaaatg ttgtccgtgg ttgggttttt ggttctacca tgaacaacaa gtcacagtcg
    gtgattatta ttaacaattc tactaatgtt gttatacgag catgtaactt tgaattgtgt
    gacaaccctt tctttgctgt ttctaaaccc atgggtacac agacacatac tatgatattc
    gataatgcat ttaattgcac tttcgagtac atatctgatg ccttttcgct tgatgtttca
    gaaaagtcag gtaattttaa acacttacga gagtttgtgt ttaaaaataa agatgggttt
    ctctatgttt ataagggcta tcaacctata gacgtagttc gtgatctacc ttctggtttt
    aacactttga aacctatttt taagttgcct ctcggtatta acattacaaa ttttagagcc
    GAATTCGGGG GCGGGGGTGG AGGTGGTGGC tcatt      caaagaagag ctggacaagt
    acttcaaaaa tcatacatca ccagatgttg atcttggcga catttcaggc attaacgctt
    ctgtcgtcaa cattcaaaaa gaaattgacc gcctcaatga ggtcgctaaa aatttaaatg
    aatcactcat tgaccttcaa gaattgggaa aatatgagca atatattaaa tggccttggt
    atgtttggct cggcttcatt gctggactaa ttgccatcgt catggttaca atcttgcttt
    gttgcatgac tagttgttgc agttgcctca agggtgcatg ctcttgtggt tcttgctgca
    agtttgatga ggatgactct gagccagttc tcaagggtgt caaattacat tacaca
    SEQ ID NO: 11
    gagattgaca aaggaattta ccagacctct aatttcaggg ttgttccctc aggagatgtt
    gtgagattcc ctaatattac aaacttgtgt ccttttggag aggtttttaa tgctactaaa
    ttcccttctg tctatgcatg ggagagaaaa aaaatttcta attgtgttgc tgattactct
    gtgctctaca actcaacatt tttttcaacc tttaagtgct atggcgtttc tgccactaag
    ttgaatgatc tttgcttctc caatgtctat gcagattctt ttgtagtcaa gggagatgat
    gtaagacaaa tagcgccagg acaaactggt gttattgctg attataatta taaattgcca
    gatgatttca tgggttgtgt ccttgcttgg aatactagga acattgatgc tacttcaact
    ggtaattata attataaata taggtatctt agacatggca agcttaggcc ctttgagaga
    gacatatcta atgtgccttt ctcccctgat ggcaaacctt gcaccccacc tgctcttaat
    tgttattggc cattaaatga ttatggtttt tacaccacta ccggcattgg ctaccaacct
    tacagagttg tagtactttc ttttgaactt ttaaatgcac cggccacggt ttgtggacca
    aaatcatcca ctgaccttat taagaaccag tgtgtcaatt ttaattttaa tggactcact
    ggtactggtg tgttaactcc ttcttcaaag agatttcaac catttcaaca atttggccgt
    gatgcttctg atttcactga ttccgttcga gatcctaaaa catctgaaat attagacatt
    tcaccttgct cttttggggg tgtaagtgta attacacctg gaacaaatgc ttcatctgaa
    gttgctgttc tatatcaaga tgttaactgc actgatgttt ctacagcaat tcatgcagat
    caactcacac cagcttggcg catatattct actggaaaca atgtattcca gactcaagca
    ggctgtctta taggagctga gcatgtcgac acttcttatg agtgcgacat tcctattgga
    gctggcattt gtgctagtta ccatacagtt tctttattac gtagtactag ccaaaaatct
    attgtggctt atactatgtc tttaggtgct gatagttcaa ttgcttactc taataacacc
    attgctatac ctactaactt ttcaattagc attactacag aagtaatgcc tgtttctatg
    gctaaaacct ccgtagattg taatatgtac atctgcggag attctactga atgtgctaat
    ttgcttctcc aatatggGCG GCCGCCTGGG GGCGGGGGTG GAGGTGGTGG Ctcatt
    caaagaagag ctggacaagt acttcaaaaa tcatacatca ccagatgttg atcttggcga
    catttcaggc attaacgctt ctgtcgtcaa cattcaaaaa gaaattgacc gcctcaatga
    ggtcgctaaa aatttaaatg aatcactcat tgaccttcaa gaattgggaa aatatgagca
    atatattaaa tggccttggt atgtttggct cggcttcatt gctggactaa ttgccatcgt
    catggttaca atcttgcttt gttgcatgac tagttgttgc agttgcctca agggtgcatg
    ctcttgtggt tcttgctgca agtttgatga ggatgactct gagccagttc tcaagggtgt
    caaattacat tacaca
    SEQ ID NO: 13
    catacgtttg gcaaccctgt catacctttt aaggatggta tttattttgc tgccacagag
    aaatcaaatg ttgtccgtgg ttgggttttt ggttctacca tgaacaacaa gtcacagtcg
    gtgattatta ttaacaattc tactaatgtt gttatacgag catgtaactt tgaattgtgt
    gacaaccctt tctttgctgt ttctaaaccc atgggtacac agacacatac tatgatattc
    gataatgcat ttaattgcac tttcgagtac atatctgatg ccttttcgct tgatgtttca
    gaaaagtcag gtaattttaa acacttacga gagtttgtgt ttaaaaataa agatgggttt
    ctctatgttt ataagggcta tcaacctata gatgtagttc gtgatctacc ttctggtttt
    aacactttga aacctatttt taagttgcct cttggtatta acattacaaa ttttagagcc
    GAATTCGGGG GCGGGGGTGG AGGTGGTGGC gagattgaca aaggaattta ccagacctct
    aatttcaggg ttgttccctc aggagatgtt gtgagattcc ctaatattac aaacttgtgt
    ccttttggag aggtttttaa tgccactaaa ttcccttctg tctatgcatg ggagagaaaa
    aaaatttcta attgtgttgc tgactactct gtgctctaca actcaacatt tttttcaacc
    tttaagtgct atggcgtttc tgccactaag ttgaatgatc tttgcttctc caatgtctat
    gcagattctt ttgtagtcaa gggagatgat gtaagacaaa tagcgccagg acaaactggt
    gttattgctg attataatta taaattgcca gatgatttca tgggttgtgt ccttgcttgg
    aatactagga acattgatgc tacctcaact ggtaattata attataaata taggtatctt
    agacatggca agcttaggcc ctttgagaga gacatatcta atgtgccttt ctcccctgat
    ggcaaacctt gcaccccacc tgctcttaat tgttattggc cattaaatga ttatggtttt
    tacaccacta ctggcattgg ctaccaacct tacagagttg tagtactttc ttttgaactt
    ttaaatgcac cggccacggt ttgtggacca aaattatcca ctgaccttat taagaaccag
    tgtgtcaatt ttaattttaa tggactcact ggtactggtg tgttaactcc ttcttcaaag
    agatttcaac catttcaaca atttggccgt gatgtttctg atttcactga ttccgttcga
    gatcctaaaa catctgaaat attagacatt tcaccttgct cttttggggg tgtaagtgta
    attacacctg gaacaaatgc ttcatctgaa gttgctgttc tatatcaaga tgttaactgc
    actgatgttt ctacagcaat tcatgcagat caactcacac cagcttggcg catatattct
    actggaaaca atgtattcca gactcaagca ggctgtctta taggagctga gcatgtcgac
    acttcttatg agtgcgacat tcctattgga gctggcattt gtgctagtta ccatacagtt
    tctttattac gtagtactag ccaaaaatct attgtggctt atactatgtc tttaggtgct
    gatagttcaa ttgcttactc taataacacc attgctatac ctactaactt ttcaattagc
    attactacag aagtaatgcc tgtttctatg gctaaaacct ccgtagattg taatatgtac
    atctgcggag attctactga atgtgctaat ttgcttctcc aatatgg
    SEQ ID NO: 15
    catacgtttg gcaaccctgt catacctttt aaggatggta tttattttgc tgccacagag
    aaatcaaatg ttgtccgtgg ttgggttttt ggttctacca tgaacaacaa gtcacagtcg
    gtgactatta ttaacaattc tactaatgtt gttatacgag catgtaactt tgaattgtgt
    gacaaccctt tctttgctgt ttctaaaccc atgggtacac agacacatac tatgatattc
    gataatgcat ttaattgcac tttcgagtac atatctgatg ccttttcgct tgatgtttca
    gaaaagtcag gtaattttaa acacttacga gagtttgtgt ttaaaaataa agatgggttt
    ctctatgttt ataagggcta tcaacctata gatgtagttc gtgatctacc ttctggtttt
    aacactttga aacctatttt taagttgcct cttggtatta acattacaaa ttttagagcc
    GAATTCGGGG GCGGGGGTGG AGGTGGTGGC gagattgaca aaggaattta ccagacctct
    aattccaggg ttgttccctc aggagatgtt gtgagattcc ctaatattac aaacttgtgt
    ccttttggag aggtttttaa tgctactaaa ttcccttctg tctatgcatg ggagagaaaa
    aaaatttcta attgtgttgc tgattactct gtgctctaca actcaacatt tttttcaacc
    tttaagtgct atggcgtttc tgccactaag ttgaatgatc tttgcttctc caatgtctat
    gcagattctt ttgtagtcaa gggagatgat gtaagacaaa tagcgccagg acaaactggt
    gttattgctg attataatta taaattgcca gatgatttca tgggttgtgt ccttgcttgg
    aatactagga acattgatgc tacttcaact ggtaattata attataaata taggtatctt
    agacatggca agcttaggcc ctttgagaga gacatatcta atgtgccttt ctcccctgat
    ggcaaacctt gcaccccacc tgctcttaat tgttattggc cattaaatga ttatggtttt
    tacaccacta ctggcattgg ctaccaacct tacagagttg tagtactttc ttttgaactt
    ttaaatgcac cggccacggt ttgtggacca aaattatcca ctgaccttat taagaaccag
    tgtgtcaatt ttaattttaa tggactcact ggtactggtg tgttaactcc ttcttcaaag
    agatttcaac catttcaaca atttggccgt gatgtttctg atttcactga ttccgttcga
    gatcctaaaa catctgaaat attagacatt tcaccttgct cttttggggg tgtaagtgta
    attacacctg gaacaaatgc ttcatctgaa gttgctgttc tatatcaaga tgttaactgc
    actgatgttt ctacagcaat tcatgcagat caactcacac cagcttggcg catatattct
    actggaaaca atgtattcca gactcaagca ggctgtctta taggagctga gcatgtcgac
    acttcttatg agtgcgacat tcctattgga gctggcattt gtgctagtta ccatacagtt
    tctttattac gtagtactag ccaaaaatct attgtggctt atactatgtc tttaggtgct
    gatagttcaa ttgcttactc taataacacc attgctatac ctactaactt ttcaattagc
    attactacag aagtaatgcc tgtttctatg gctaaaacct ccgtagattg taatatgtac
    atctgcggag attctactga atgtgctaat ttgcttctcc aatatggGCG GCCGCCTGGG
    GGCGGGGGTG GAGGTGGTGG Ctcatt     caaagaagag ctggacaagt acttcaaaaa
    tcatacatca ccagatgttg atcttggcga catttcaggc attaacgctt ctgtcgtcaa
    cattcaaaaa gaaattgacc gcctcaatga ggtcgctaaa aatttaaatg aatcactcat
    tgaccttcaa gaattgggaa aatatgagca atatattaaa tggccttggt atgtttggct
    cggcttcatt gctggactaa ttgccatcgt catggttaca atcttgcttt gttgcatgac
    tagttgttgc agttgcctca agggtgcatg ctcttgtggt tcttgctgca agtttgatga
    ggatgactct gagccagttc tcaagggtgt caaattacat tacaca
  • Additional examples of the nucleic acid of this invention include nucleic acids encoding the peptides listed in Table 2. In a preferred embodiment, the nucleic acid contains SEQ ID NO: 23 or 25.
  • A “nucleic acid” refers to a DNA molecule (e.g., a cDNA or genomic DNA), an RNA molecule (e.g., an mRNA), or a DNA or RNA analog. A DNA or RNA analog can be synthesized from nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA. An “isolated nucleic acid” is a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid or to that of any fragment of a naturally occurring genomic nucleic acid. The term therefore covers, for example, (a) a DNA which has the sequence of part of a naturally occurring genomic DNA molecule but is not flanked by both of the coding sequences that flank that part of the molecule in the genome of the organism in which it naturally occurs; (b) a nucleic acid incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion protein. The nucleic acid described above can be used to express the polypeptide of this invention. For this purpose, one can operatively linked the nucleic acid to suitable regulatory sequences to generate an expression vector.
  • A “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. The vector can be capable of autonomous replication or integrate into a host DNA. Examples of the vector include a plasmid, cosmid, or viral vector. The vector of this invention includes a nucleic acid in a form suitable for expression of the nucleic acid in a host cell. Preferably the vector includes one or more regulatory sequences operatively linked to the nucleic acid sequence to be expressed. A “regulatory sequence” includes promoters, enhancers, and other expression control elements (e.g., polyadenylation signals). Regulatory sequences include those that direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and/or inducible sequences. The design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vector can be introduced into host cells to produce the polypeptide of this invention. Also within the scope of this invention is a host cell that contains the above-described nucleic acid. Examples include E. coli cells, insect cells (e.g., using baculovirus expression vectors), yeast “effective amount” is an amount of the composition that is capable of producing a medically desirable result, e.g., as described above, in a treated subject.
  • The details of one or more embodiments of the invention are set forth in the accompanying description below. Other advantages, features, and objects of the invention will be apparent from the detailed description and the claims.
    • DETAILED DESCRIPTION
  • This invention relates to receptor binding domains or immunogenic fragments of the S protein of a coronavirus, such as SARS. Since these domains mediate target cell binding and entry of the coronavirus or induce immune response, they can be targeted for diagnosing or treating an infection with the coronavirus.
  • A polypeptide of this invention contains the sequence of the S protein, such as SEQ ID NO: 4 or an immunogenic fragment thereof. It can also contain the sequence of the S protein of SARS CoV TW1, Tor-2, SIN2500, SIN2774, SIN2748, SIN2677, SIN2679, CUHK-W1, HKU39849, GZO1, BJO1, BJO2, BJO3 BJO4, and other strains. In a particular embodiment, the polypeptide contains a receptor-binding domain of the S protein or a functional equivalent. A functional equivalent of the a protein receptor binding domain refers to a polypeptide derived from the coronavirus S protein, e.g., a fusion polypeptide or a polypeptide having one or more point mutations, insertions, deletions, truncations, or a combination thereof. In particular, such functional equivalents include polypeptides, whose sequences differ from the S protein by one or more conservative amino acid substitutions or by one or more non-conservative amino acid substitutions, deletions, or insertions. Such a functional equivalent can be encoded by a nucleic acid that hybridizes under high stringency conditions to a probe the sequence of which consists of SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, or 25. The term “hybridizes under stringent conditions” refers to conditions for hybridization in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 50-65° C. All of the above-described functional equivalents retain substantially the receptor binding activity of coronavirus, e.g., SRAS CoV S protein, i.e., binding to target cells including VERO E6, NIH3T3. This activity can be determined by the assays described in the examples presented below.
  • A polypeptide of the invention can be obtained as a synthetic polypeptide or a recombinant polypeptide. To prepare a recombinant polypeptide, a nucleic acid encoding it can be linked to another nucleic acid encoding a fusion partner, e.g., Glutathione-S-Transferase (GST), 6×-His epitope tag, or M13 Gene 3 protein. The resultant fusion nucleic acid expresses in suitable host cells a fusion protein that can be isolated by methods known in the art. The isolated fusion protein can be further treated, e.g., by enzymatic digestion, to remove the fusion partner and obtain the recombinant polypeptide of this invention.
  • A polypeptide of the invention can be used to generate antibodies in animals (for production of antibodies) or humans (for treatment of diseases). Methods of making monoclonal and polyclonal antibodies and fragments thereof in animals are known in the art. See, for example, Harlow and Lane, (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. The term “antibody” includes intact molecules as well as fragments thereof, such as Fab, F(ab′)2, Fv, scFv (single chain antibody), and dAb (domain antibody; Ward, et. al. (1989) Nature, 341, 544). These antibodies can be used for detecting the S polypeptide, e.g., in determining whether a test sample from a subject contains coronavirus or in identifying a compound that binds to the polypeptide. As these antibodies interfere with the cell binding and entry of the coronavirus, they are also useful for treating a coronavirus infection.
  • In general, to produce antibodies against a polypeptide, the polypeptide is coupled to a carrier protein, such as KLH, mixed with an adjuvant, and injected into a host animal. Antibodies produced in the animal can then be purified by peptide affinity chromatography. Commonly employed host animals include rabbits, mice, guinea pigs, and rats. Various adjuvants that can be used to increase the immunological response depend on the host species and include Freund's adjuvant (complete and incomplete), mineral gels such as aluminum hydroxide, CpG, surface-active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol. Useful human adjuvants include BCG (bacille Calmette-Guerin) and Corynebacterium parvum.
  • Polyclonal antibodies, heterogeneous populations of antibody molecules, are present in the sera of the immunized subjects. Monoclonal antibodies, homogeneous populations of antibodies to a polypeptide of this invention, can be prepared using standard hybridoma technology (see, for example, Kohler et al. (1975) Nature 256, 495; Kohler et al. (1976) Eur. J. Immunol. 6, 511; Kohler et al. (1976) Eur J Immunol 6, 292; and Hammerling et al. (1981) Monoclonal Antibodies and T Cell Hybridomas, Elsevier, N.Y.). In particular, monoclonal antibodies can be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture such as described in Kohler et al. (1975) Nature 256, 495 and U.S. Pat. No. 4,376,110; the human B-cell hybridoma technique (Kosbor et al. (1983) Immunol Today 4, 72; Cole et al. (1983) Proc. Natl. Acad. Sci. USA 80, 2026, and the EBV-hybridoma technique (Cole et al. (1983) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD, and any subclass thereof. The hybridoma producing the monoclonal antibodies of the invention may be cultivated in vitro or in vivo. The ability to produce high titers of monoclonal antibodies in vivo makes it a particularly useful method of production.
  • In addition, techniques developed for the production of “chimeric antibodies” can be used. See, e.g., Morrison et al. (1984) Proc. Natl. Acad. Sci. USA 81, 6851; Neuberger et al. (1984) Nature 312, 604; and Takeda et al. (1984) Nature 314:452. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region. Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. Nos. 4,946,778 and 4,704,692) can be adapted to produce a phage library of single chain Fv antibodies. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge. Moreover, antibody fragments can be generated by known techniques. For example, such fragments include, but are not limited to, F(ab′)2 fragments that can be produced by pepsin digestion of an antibody molecule, and Fab fragments that can be generated by reducing the disulfide bridges of F(ab′)2 fragments. Antibodies can also be humanized by methods known in the art. For example, monoclonal antibodies with a desired binding specificity can be commercially humanized (Scotgene, Scotland; and Oxford Molecular, Palo Alto, Calif.). Fully human antibodies, such as those expressed in transgenic animals are also features of the invention (see, e.g., Green et al. (1994) Nature Genetics 7, 13; and U.S. Pat. Nos. 5,545,806 and 5,569,825).
  • A polypeptide of the invention can also be used to prepare an immunogenic composition (e.g., a vaccine) for generating antibodies against coronavirus (e.g., SRAS CoV) in a subject susceptible to the coronavirus. Such compositions can be prepared, e.g., according to the method described in the examples below, or by any other equivalent methods known in the art. The composition contains an effective amount of a polypeptide of the invention, and a pharmaceutically acceptable carrier such as phosphate buffered saline or a bicarbonate solution. The carrier is selected on the basis of the mode and route of administration, and standard pharmaceutical practice. Suitable pharmaceutical carriers and diluents, as well as pharmaceutical necessities for their use, are described in Remington's Pharmaceutical Sciences. An adjuvant, e.g., a cholera toxin, Escherichia coli heat-labile enterotoxin (LT), liposome, immune-stimulating complex (ISCOM), or immunostimulatory sequences oligodeoxynucleotides (ISS-ODN), can also be included in a composition of the invention, if necessary. The S protein, fragments or analogs thereof or peptides may be components of a multivalent composition of vaccine against respiratory diseases. This multivalent composition contains at least one immunogenic fragment of S protein described above, along with at least one protective antigen isolated from influenza virus, para-influenza virus 3, Strentococcus pneumoniae, Branhamella (Moroxella) gatarhalis, Staphylococcus aureus, or respiratory syncytial virus, in the presence or absence of adjuvant.
  • Methods for preparing vaccines are generally well known in the art, as exemplified by U.S. Pat. Nos. 4,601,903; 4,599,231; 4,599,230; and 4,596,792. Vaccines may be prepared as injectables, as liquid solutions or emulsions. The S protein, fragments or analogs thereof or peptides corresponding to portions of S protein may be mixed with physiologically acceptable and excipients compatible. Excipients may include, water, saline, dextrose, glycerol, ethanol, and combinations thereof. The vaccine may further contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or adjuvants to enhance the effectiveness of the vaccines. Methods of achieving adjuvant effect for the vaccine includes use of agents, such as aluminum hydroxide or phosphate (alum), commonly used as 0.05 to 0.1 percent solutions in phosphate buffered saline. Vaccines may be administered parenterally, by injection subcutaneously or intramuscularly. Alternatively, other modes of administration including suppositories and oral formulations may be desirable. For suppositories, binders and carriers may include, for example, polyalkalene glycols or triglycerides. Oral formulations may include normally employed incipients such as, for example, pharmaceutical grades of saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10-95% of the S protein, fragment analogs, or peptides.
  • The vaccines are administered in a manner compatible with the dosage formulation, and in an amount that is therapeutically effective, protective and immunogenic. The quantity to be administered depends on the subject to be treated, including, for example, the capacity of the individual's immune system to synthesize antibodies, and if needed, to produce a cell-mediated immune response. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner. However, suitable dosage ranges are readily determinable by one skilled in the art and may be of the order of micrograms of the polypeptide of this invention. Suitable regimes for initial administration and booster doses are also variable, but may include an initial administration followed by subsequent administrations. The dosage of the vaccine may also depend on the route of administration and varies according to the size of the host.
  • Use of polypeptide in vivo may first require chemical modification of the peptides since they may not have a sufficiently long half-life. A chemically modified peptide or a peptide analog includes any functional chemical equivalent of the peptide characterized by its increased stability and/or efficacy in vivo or in vitro in respect of the practice of the invention. The term peptide analog also refers to any amino acid derivative of a peptide as described herein. A peptide analog can be produced by procedures that include, but are not limited to, modifications to side chains, incorporation of unnatural amino acids and/or their derivatives during peptide synthesis and the use of cross-linkers and other methods that impose conformational constraint on the peptides or their analogs. Examples of side chain modifications include modification of amino groups, such as by reductive alkylation by reaction with an aldehyde followed by reduction with NaBH4; amidation with methylacetimidate; acetylation with acetic anhydride; carbamylation of amino groups with cyanate; trinitrobenzylation of amino groups with 2, 4, 6, trinitrobenzene sulfonic acid (TNBS); alkylation of amino groups with succinic anhydride and tetrahydrophthalic anhydride; and pyridoxylation of lysine with pyridoxa-5′-phosphate followed by reduction with NABH4. The guanidino group of arginine residues may be modified by the formation of heterocyclic condensation products with reagents such as 2,3-butanedione, phenylglyoxal and glyoxal. The carboxyl group may be modified by carbodiimide activation via o-acylisourea formation followed by subsequent derivatization, for example, to a corresponding amide. Sulfhydryl groups may be modified by methods, such as carboxymethylation with iodoacetic acid or iodoacetamide; performic acid oxidation to cysteic acid; formation of mixed disulphides with other thiol compounds; reaction with maleimide; maleic anhydride or other substituted maleimide; formation of mercurial derivatives using 4-chloromercuribenzoate, 4-chloromercuriphenylsulfonic acid, phenylmercury chloride, 2-chloromercuric-4-nitrophenol and other mercurials; carbamylation with cyanate at alkaline pH. Tryptophan residues may be modified by, for example, oxidation with N-bromosuccinimide or alkylation of the indole ring with 2-hydroxy-5-nitrobenzyl bromide or sulphonyl halides. Tryosine residues may be altered by nitration with tetranitromethane to form a 3-nitrotyrosine derivative. Modification of the imidazole ring of a histidine residue may be accomplished by alkylation with iodoacetic acid derivatives or N-carbethoxylation with diethylpyrocarbonate. Examples of incorporating unnatural amino acids and derivatives during peptide synthesis include, but are not limited to, use of norleucine, 4-amino butyric acid, 4-amino-3-hydroxy-5-phenylpentanoic acid, 6-aminohexanoic acid, t-butylglycine, norvaline, phenylglycine, ornithine, sarcosine, 4-amino-3-hydroxy-6-methylheptanoic acid, 2-thienyl alanine and/or D-isomers of amino acids.
  • A nucleic acid molecule of this invention may also be used directly for immunization by administration of the nucleic acid directly to a subject via a live vector, such as Salmonella, BCG, adenovirus, poxvirus or vaccinia. Immunization methods based on nucleic acids are well known in the art.
  • A subject susceptible to coronavirus infection can be identified and administered a polypeptide-containing composition of the invention. The dose of the composition depends, for example, on the particular polypeptide, whether an adjuvant is co-administered with the polypeptide, the type of adjuvant co-administered, the mode and frequency of administration, as can be determined by one skilled in the art. Administration is repeated as necessary, as can be determined by one skilled in the art. For example, a priming dose can be followed by three booster doses at weekly intervals. A booster shot can be given at 4 to 8 weeks after the first immunization, and a second booster can be given at 8 to 12 weeks, using the same formulation. Sera or T-cells can be taken from the subject for testing the immune response elicited by the composition against the coronavirus S protein or infection. Methods of assaying antibodies or cytotoxic T cells against a protein or infection are well known in the art. Additional boosters can be given as needed. By varying the amount of polypeptide, the dose of the composition, and frequency of administration, the immunization protocol can be optimized for eliciting a maximal immune response. Before a large scale administering, efficacy testing is desirable. In an efficacy testing, a non-human subject can be administered via an oral or parenteral route with a composition of the invention. After the initial administration or after optional booster administration, both the test subject and the control subject (receiving mock administration) are challenged with an LD95 dose of a coronavirus. End points other than lethality can also be used. Efficacy is determined if subjects receiving the composition dies at a rate lower than control subjects. The difference in death rates should be statistically significant.
  • The above-described S protein and its fragment can be used as a carrier and linked to other antigens of interest to generate antibodies against the antigens. The S protein or its fragment can be generally utilized to prepare chimeric molecules and conjugate compositions against pathogenic bacteria, including encapsulated bacteria. For example, the glycoconjugates of the present inventions may be applied to immunize a subject to generate antibodies against the bacteria and confer protection against infection with any bacteria having polysaccharide antigens, e.g., Haemophilus influenzae, Streptococcus pneumoniae, Escherichia coli, Neisseria meningitidis, Salmonella typhi, Streptococcus mutans, Cryptococcus neoformans, Klebsiella, Staphylococcus aureus, and Pseudomonas aeruginosa. In addition, as a carrier, the S protein or fragment may be used to induce immunity toward abnormal polysaccharides of tumor cells, thereby to produce anti-tumor antibodies for chemotherapy or diagnosis.
  • Also within the scope of this invention is a diagnosing method using the above-described polypeptides or antibodies. Presence of the polypeptides or antibodies in a subject indicates that the subject is infected with a coronavirus. To detect the antibodies or polypeptides, one can obtain a test sample from a subject and detect the presence or absence of the antibodies or polypeptides using standard techniques, including ELISAs, immunoprecipitations, immunofluorescence, EIA, RIA, and Western blotting analysis.
  • The nucleic acid of this invention is useful as a hybridization probe for identifying coronavirus, e.g., SARS CoV, in a sample. The sample can be a clinical sample, including exudates, body fluids (e.g., serum, amniotic fluid, middle ear effusion, sputum, bronchoalveolar lavage fluid) and tissues. A variety of hybridization conditions may be employed to achieve varying degrees of selectivity of the probe toward the target sequences. A high degree of selectivity requires stringent conditions, such as that described in the Summary section
  • A hybridization reaction can be performed both in a solution or on a solid phrase. In a solid phase, a test sequence from a sample is affixed to a selected matrix or surface. The fixed nucleic acid is then subjected to specific hybridization with selected probes comprising the nucleic acid of the present invention under desired conditions. The selected conditions will depend on the particular circumstances based on the particular criteria required depending on, for example, on the G+C contents, type of target nucleic acid, source of nucleic acid, size of hybridization probe etc. Following washing of the hybridization surface to remove non-specifically bound probe molecules, specific hybridization is detected or quantified, by means of the label. The selected probe should be at least 18 bp and may be in the range of 30 bp to 90 bp long.
  • In addition, A small interference RNA (SiRNA) corresponding to the nucleotide sequences of the present invention comprising the sequence of the S protein receptor binding domains such as RBD1 and RBD2, can be useful to block SARS CoV replication in vivo.
  • A polypeptide of this invention can also be used in a screening method of identifying a compound for treating an infection with a coronavirus, e.g., SARS CoV. The method includes (1) contacting a polypeptide of this invention with a suitable cell, to which the coronavirus binds to; and (2) determining a binding level between the polypeptide and the cell the presence or absence of a test compound. The binding level in the presence of the test compound, if lower than that in the absence of the test compound, indicates that the test compound can be used to treat an infection with the coronavirus. Examples of the cell include VERO E6 cells, NIH3T3 cells, HeLa cells, BHK-21 cells, and COS-7 cells. One can also use other cells that are capable of binding to a coronavirus.
  • The above-described polypeptides and antibodies can be used for treating an infection with a coronavirus, e.g., SARS. The invention therefore features a method of treating SARS, e.g., by administering to a subject in need thereof an effective amount of a polypeptide, an antibody, or a compound of the invention. Subjects to be treated can be identified as having, or being at risk for acquiring, a condition characterized by SARS. This method can be performed alone or in conjunction with other drugs or therapy.
  • Thus, also within the scope of this invention is a pharmaceutical composition that contains a pharmaceutically acceptable carrier and an effective amount of a polypeptide, an antibody, or a compound of the invention. The pharmaceutical composition can be used to treat coronavirus infection, such as SARS. The pharmaceutically acceptable carrier includes a solvent, a dispersion medium, a coating, an antibacterial and antifungal agent, and an isotonic and absorption delaying agent.
  • In one in vivo approach, a composition of this invention (e.g., a composition containing a polypeptide, an antibody, or a compound of the invention) is administered to a subject. Generally, the antibody or the compound is suspended in a pharmaceutically-acceptable carrier (e.g., physiological saline) and administered orally or by intravenous infusion, or injected or implanted subcutaneously, intramuscularly, intrathecally, intraperitoneally, intrarectally, intravaginally, intranasally, intragastrically, intratracheally, or intrapulmonarily.
  • The dosage required depends on the choice of the route of administration; the nature of the formulation; the nature of the subject's illness; the subject's size, weight, surface area, age, and sex; other drugs being administered; and the judgment of the attending physician. Suitable dosages are in the range of 0.01-100.0 mg/kg. Wide variations in the needed dosage are to be expected in view of the variety of compositions available and the different efficiencies of various routes of administration. For example, oral administration would be expected to require higher dosages than administration by intravenous injection. Variations in these dosage levels can be adjusted using standard empirical routines for optimization as is well understood in the art. Encapsulation of the composition in a suitable delivery vehicle (e.g., polymeric microparticles or implantable devices) may increase the efficiency of delivery, particularly for oral delivery.
  • A pharmaceutical composition of the invention can be formulated into dosage forms for different administration routes utilizing conventional methods. For example, it can be formulated in a capsule, a gel seal, or a tablet for oral administration. Capsules can contain any standard pharmaceutically acceptable materials such as gelatin or cellulose. Tablets can be formulated in accordance with conventional procedures by compressing mixtures of the composition with a solid carrier and a lubricant. Examples of solid carriers include starch and sugar bentonite. The composition can also be administered in a form of a hard shell tablet or a capsule containing a binder, e.g., lactose or mannitol, conventional filler, and a tableting agent. The pharmaceutical composition can be administered via the parenteral route. Examples of parenteral dosage forms include aqueous solutions, isotonic saline or 5% glucose of the active agent, or other well-known pharmaceutically acceptable excipient. Cyclodextrins, or other solubilizing agents well known to those familiar with the art, can be utilized as pharmaceutical excipients for delivery of the therapeutic agent.
  • The efficacy of a composition of this invention can be evaluated both in vitro and in vivo. Briefly, the composition can be tested for its ability to inhibit the binding between a coronavirus and its target cell in vitro. For in vivo studies, the composition can be injected into an animal (e.g., a mouse model) and its therapeutic effects are then accessed. Based on the results, an appropriate dosage range and administration route can be determined.
  • The specific examples below are to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. Without further elaboration, it is believed that one skilled in the art can, based on the description herein, utilize the present invention to its fullest extent. All publications cited herein are hereby incorporated by reference in their entirety.
    • EXAMPLE 1
  • In this example, the gene encoding S protein of SARS CoV was cloned. A SARS CoV, designated as “SARS-CoV TW1,” was isolated from a SARS patient in Taiwan. Seven pairs of PCR primers were designed based on the sequence of the Urbani strain (SEQ ID NO: 1) or the SARS CoV TOR2 strain. The positions of the primers' 5′ ends within the Urbani genome were summarized below:
  • 5′ primer 3′ primer
    Pair 1 21,492 22,000
    Pair 2 22,000 22,600
    Pair 3 22,600 23,100
    Pair 4 23,075 23,780
    Pair 5 23,765 24,320
    Pair 6 24,300 24,875
    Pair 7 24,850 25,244
  • Seven products were generated by PCR reactions respectively and ligated together to form a sequence that encoded the S protein. The sequence was then subcloned into pUC19 to produce pUC19/S and used to transform E. coli HB101. Plasmid DNA was prepared from two E. coli HB101 colonies and sequenced on an ABI 370A DNA sequencer. Subsequent sequence analysis revealed that the sequence differed from that of the TOR2 strain by 3 base pairs and that it is about 30.1% identical to that of human coronavirus 229E.
  • SARS CoV M and E proteins (GenBank Accession Nos. AAP13443 and 13444) were also cloned and expressed. The E-M fusion protein corresponds to residues 8751 to 9057 of the first open reading frame of SEQ ID NO: 1. Construction of DNA plasmids containing genes for E and M proteins was performed by standard molecular biology methods (Sambrook et al (1989) Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory. Cold Spring Harbor, N.Y.). The constructs utilized a pUC-based expression vector, which was shown to result in optimal expression of reporter genes. Each vector employed the human cytomegalovirus promoter, enhancer, intron A, and the bovine growth hormone termination and polyasenylation sequences. The tissue plasminogen activator signal sequence was use to enhance the level of expression. The M and E proteins were further expressed in host cells to generated virus like particles.
    • EXAMPLE 2
  • It is known that, in SARS CoV, the S native protein is expressed in small quantities. To obtain a large amount of the S protein, there is a need to either express it in a heterologous system, such as E. coli, or to modify SARS CoV to increase the native S protein expression.
  • The above-described PUC19/S was transformed into E. coli. to express the S protein. It was found that the full-length recombinant S (rS) protein was not expressed in E. coli. Vectors encoding different S protein fragments fused to Myc-His tag were then constructed and transformed in E. coli. The fragments include the N-terminal amino acids 80-228 of the S protein (receptor binding domain 1; RBD1); the middle region encompassing amino acids 284-735 of the S protein (receptor binding domain 2; RBD2), the transmembrane domain (TM), and fusions of them.
  • To examine the expressed protein, antisera against various SARS CoV proteins were generated The following SARS CoV polypeptides were synthesized by standard techniques:
  • RBD1-specific peptide
    (SEQ ID NO:29)
    KSGNFKHLREFVFKNKDGFLYVYKGQPIDV
    RBD2-specific peptide
    (SEQ ID NO:24)
    GNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPC
    TM-specific peptide
    (SEQ ID NO:30)
    DSFKEELDRY FKNHTSPDVD LGDISGINAS VV
    E-specific peptide
    (SEQ ID NO:31)
    ALRLCAYCCN IVNVSLVKPT VYVYSRVKNL NSSEG
    M-specific peptide
    (SEQ ID NO:32)
    MADNGTITVE ELKQLLEQWN LVICFLFLAW IML
  • More specifically, 200 μg of each peptide was mixed with the completed Fruend's adjuvant and injected at day 0 and injected into rabbits by standard techniques At day 14 and 56, the rabbits were boosted with half of the amount of the peptide in the incomplete Fruend's adjuvant At day 78, the rabbits were bleed, and the blood were tested for antiserum titer by ELISA The results are shown in Table 1
  • TABLE 1
    Rabbit immunogenicity of SARS CoV peptides
    Reactivity of Anti-peptide sera to target peptide
    Peptides Pre-Immune Post-booster Final Bleed
    RBD1-specific 0 5120 10240
    RBD2-specific 0 10240 41440
    TM-specific 0 5120 10240
    E-specific 0 1280 5120
    M-specific 0 5120 10240
  • To generate a vector encoding RBD1, the following two primers were used for PCR: 5′ primer: GGATCCGCCACC ATG catacgtttg g (SEQ ID NO:33); and 3′ primer: aa ttttagagcc GAATTC (SEQ ID NO:34) The two primers contained EcoRI and BamHI sites to facilitate subsequent cloning of PCR products A ˜500 base pair (bp) fragment was obtained and subcloned into pcDNA-A4 to generate pcDNA-A4-D1 plasmid, which encoded a fusion protein of Myc-His-RBD This plasmid was transformed into E coli HB101 to express recombinant RBD1 (rRBD1) It was found that, upon induction, the transformed clones expressed a 20 kDa protein This protein was expressed at high levels in inclusion bodies and was recognized by anti-RBD-1 antisera and anti-His tag antibody on Western blot analysis It was also found that protein was highly immunogenic, but not able to elicit protective antibodies against live virus challenge.
  • A vector encoding RBD2 was also generated More specifically, PCR was conducted using the following two primers 5′ primer: GGATCCGCCACCATG gagattgaca (SEQ ID NO:35) and 3′ primer: aatatgg GCGGCCGC (SEQ ID NO:36) to generate a 14 kb fragment After being digested by BamH1H-Not1, the resulting fragment was also subcloned into pcDNA-A4 The resultant vector was used to express RBD2 in the same manner described above It was found that a 50-kDa protein was expressed at high levels in both soluble form and in inclusion bodies Western blot analysis revealed that this protein was recognized by the S-specific antisera This rRBD2 fragment was highly immunogenic too and elicited even stronger neutralizing antibodies that could block SARS CoV binding to Vero cell (see Example 9 below).
  • The above-described recombinant proteins were isolated from E. coli. More specifically, E. coli pellet from a 250 mL culture was resuspended in 40 mL of 50 mM Tris, pH 8.0, and disrupted by sonication (3×10 minutes, 70% duty circle). The resultant mixture was centrifuged at 20,000×g. The pellet was re-extracted with 40 mL of 50 mM Tris, 0.5% Triton X-100, 10 mM EDTA, pH 8.0. The suspension was then sonicated for 10 minutes at 70% duty circle and centrifuged at 300×g for 5 minutes. The resulting supernatant was centrifuged again at 20,000×g for 30 minutes. The pellet was resuspended in 50 mM Tris, 0.5% Triton X-100, 10 mM EDTA, pH 8.0 and mixed with PBS/8 M urea to a final urea concentration of 6 M urea. The mixture was then dialyzed against PBS to remove urea and centrifuged at 300×g for 10 minutes. The supernatant was saved and stored at 4° C.
  • Ni-affinity chromatography was used to isolate rRBD1 and rRBD2 fusion proteins from inclusion body. The just described supernatant was loaded onto a Ni affinity column (2 mL) equilibrated with PBS containing 1% Triton X-100. The run-through of the column was discarded. After washing the column with 20 mL of PBS, the affinity column was eluted with 50 mM Tris-HCl buffer, pH 8.0, containing 5 mM EDTA. The protein-containing factions were collected and the purity was analyzed by SDS-PAGE.
  • It was estimated that about 10 mg of rRBD2 was recovered from 1 L of E. coli bacterial culture. The identity of rRBD2 was confirmed by both immunoblotting and protein sequencing. The N-terminal sequence of this polypeptide was found to be Met-Ala-Glu-Leu-Lys-Cys, which corresponds to residues 284 to 288 of the sequence of S protein.
    • EXAMPLE 3
  • In this example, additional fragments of the SARS coronavirus S protein were expressed in baculovirus and SF21 insect cell.
  • Nucleic acids encoding 1-333, 334-666, and 667-999 amino acid of the S protein (spike1, spike2, and spike3; S1, S2, and S3, respectively) were obtained by PCR with primer sets listed below, respectively, in the manner similar to that described in Example 1
  • Amplified Primer
    fragment name Sequence (5′ to 3′) Sense
    Spike1 S1F AGGGGATCCATGTTTATTTTCT S
    (1-333 aa) TATTATTTCTTACTC
    S1R CCTGGATCCTTTAGTAGCATTA AS
    AAAACCTCTCCA
    Spike2 S2F AGGGGATCCTTCCCTTCTGTCT S
    (334-666 aa) ATGCATGGGAGA
    S2R CCTGGATCCTAATAAAGAAACT AS
    GTATGGTAACTA
    Spike3 S3F AGGGGATCCCGTAGTACTAGCC S
    (667-999 aa) AAAAATCTATTG
    S3R CCTGGATCCTTCAGCAGCCCTG AS
    ATTAGTTGTTGT
    RBD1 RBD1F CATACGTTTGGCAACCCTGTC S
    (74-253 aa) RBD1R AACATTACAAATTTTAGAGCC AS
    RBD2 RBD2F GAGATTGACAAAGGAATTTAC S
    (294-739 aa) RBD2R CTAATTTGCTTCTCCAATATGG AS
    RBD3 RBD3F ATGGCTAAAACCTCCGTAGAT S
    (713-1113 aa) RBD3R AATTGTGATGTCGTTATTGGC AS
    TM TM1F ACTTCAAAAATCATACATCA S
    (1130-1255 aa) TM1R GGTGTCAAATTACATTACACAT AS
    AA
    SEQ ID NOs 37-50, respectively
  • The PCR products were inserted into the pCR2.1 vector by TA cloning. The coding sequences were than released by BamHI digestions and ligated to BamHI-cutted pSecTagb/hIgG1.Fc vector, thereby in-frame fusing the S protein-encoding sequence to that encoding the human IgG1 Fc, The resultant vectors encodes fusion proteins spike1-Fc, spike2-Fc, and spike3-Fc. To generate corresponding baculovirus transfer vectors, the three fusion genes were released by NheI/XhoI digestion and ligated to XbaI/XhoI-cutted pBacPAK9 vectors.
  • The just-described pBacPAK9 vectors were co-transfected into Sf21 cells with Bsu36 I-digested BacPAK6 viral DNA by Bacfectin (Clontech 6144-1). Each resulting viral plaque was picked by performing plaque assays on the co-transfection supernatant. The recombinant viruses were confirmed by PCR. Sf21 cells were then infected with virus at a small scale to characterize gene expression and to determine the optimum harvest time and infection ratio by standard methods. Recombinant viruses were amplified to high virus titer to obtain working stocks for large-scale infection.
  • To purify recombinant proteins, Sf21 cells were cultured in spinner flask at a starting concentration of 2×105/ml in the first 3-5 days. After reaching 1−2×106 cells/ml, the cells were infected with the above-described recombinant baculoviruses at M.O.I. of 5-10 and cultured for 4-5 days. The supernatants were then collected and cell debris was removed by centrifugation. The supernatant was loaded onto protein A Sepharose® 4 Fast Flow beads (Amersham Biosciences 17-0974). Finally, the bound Fc-fusion protein was eluted with a 0.1 M glycine buffer (pH 3.0), followed by dialysis against PBS. The purity and the concentration of purified proteins were assessed by a standard silver staining method.
  • Five milligrams of S1-Fc fusion protein crude extract prepared in the manner described above were dissolved in 5 mL of phosphate buffer saline (PBS) containing 1% Triton X-100. The solution was then loaded onto a Protein A-Sepharose 4B column (2 mL) equilibrated with PBS containing 1% Triton X-100. The run-through of the column was discarded. The column was washed with 20 mL of PBS and the S1-FC fusion protein was eluted with 50 mM Gly-HCl buffer, pH 3.0. Elution was monitored by absorbance at 280 nm. Protein-containing fractions (2 mL/fraction) were collected and pooled. The purity of the protein was assessed by SDS-PAGE.
  • Certain plasmids described above was deposited with the American Type Culture Collection (ATCC) located at 10801 University Boulevard, Manassas, Va. 20110-2209 U.S.A. pursuant to the Budapest Treaty and prior to the filing of this application. Samples of the deposited plasmids will become available to the public upon grant of a patent based upon this United States patent application.
    • EXAMPLE 4
  • The above-described recombinant RBD1, RBD2, S1-FC, and S2-Fc were used to produce of S-specific antisera. The purified recombinant proteins were emulsified in the Freund's complete adjuvant (Difco) and injected intramuscularly (IM) into New Zealand White rabbits (Maple Lane) or guinea pigs (Charles River) at a dose of 10 to 100 μg/injection. The animals were boosted on day 28 with another half of dose of the corresponding S fragment emulsified in Freund's incomplete adjuvant. On day 42, a blood sample was taken from each animal via the marginal ear vein for titer determination by standard methods. Animals that generated specific antibodies were bled to obtain more antisera.
  • To examine the immunogenicity of the RBD1 or 2 fusion protein, guinea pigs or mice were immunized with RBD1 or 2 of various amounts. The doses between 10 to 100 μg/injection RBD1 induced high IgG titers in guinea pigs when administered in the presence of either Freund's adjuvant or AlPO4. In the mice, RBD1 or 2 appeared to be immunogenic at a dose as low as 5 μg/injection in either Freund's adjuvant.
  • A ferret model was used to examine the protective ability of anti-RBD1 or 2 sera against a SARS CoV infection. It was found that ferrate passively immunized with guinea pig anti-RBD2 antisera, but not anti-RBD1 sera, were significantly protected than controls injected with pre-immune sera.
  • The above-described S1-Fc or S2-Fc fusion protein was used to purify S protein-specific polyclonal antibodies by affinity chromatography. The recombinant S1-Fc or S2-Fc fusion protein was conjugated to cyanogen bromide-activated Sepharose to form an affinity column. The affinity column was then used to purify antibodies from a rabbit hyperimmune anti-inactivated SARS CoV antiserum. The affinity purified-antibodies were shown by immunoblotting to react with a 200-kDa component present in the lysates of SARS Cov isolates.
  • Similarly, antisera raised against the recombinant fusion protein or the purified RBD1, RBD2, S1 and S2 can also be purified in the same manner.
    • EXAMPLE 5
  • Purified recombinant RBD2 were conjugated with S. pneumococcal oligosaccharides 14 (14F) by periodate oxidation in the manner described in U.S. Pat. No. 4,356,170. S. pneumococcal oligosaccharides 14 was prepared by controlled acid hydrolysis. The mean molecular size of the 14F molecules used for conjugation was determined as approximately 20,000 Daltons. The conjugation was carried out with or without a linker molecule. A 14/RBD2 molar ratio of approximately 7 was used to provide an excess of 14F hapten.
  • To prepare 14-BSA conjugates, 0.5 mL of periodate-oxidized 14 (25 mg in 1 mL of 0.1 M sodium phosphate buffer, pH 6.0), prepared from native 14F treated with aqueous periodic acid (Carlone et al, 1986 J. Clin. Microbiol. 24:330-331.), was added to bovine serum albumin (BSA) (1.32 mg; 0.02 μmol) in 0.5 mL of 0.2 M sodium phosphate buffer, pH 8.0, followed by the addition of sodium cyanoborohydride (14 μg; 0.22 μmol; 10 eqv. to BSA). After incubation at 37° C. for 5 days, the reaction mixture was dialyzed against 4 L of 0.1 M phosphate buffer, pH 7.5. The resulting solution was applied onto an analytical Superose 12 column (15×0.300 mm, Pharmacia) equilibrated with 0.2 M sodium phosphate buffer, pH 7.2, and eluted with the same buffer. Fractions were monitored for absorbance at 230 nm. The first major protein peak was pooled and concentrated in a Centriprep 30 to 2.2 mL. The amount of protein was found, by the Bio Rad protein assay, to be 300 ug/mL. The presence of 14 oligosccharides in the protein conjugate fraction was confirmed by the Orcinol test.
  • The above-described RBD2-14 S. pneumococcal polysaccharide conjugate was then used to produce anti-14 S. pneumococcal polysaccharide antisera in animals. Rabbits were immunized intramuscularly with 14-RBD2 conjugates (5 to 50 μg 14 equivalent) mixed with 3 mg AlPO4 per mL, followed by two booster doses (half amount of the same immunogen) at 2-week intervals. Antisera were collected every 2 weeks after the first injection, heat-inactivated at 56° C. for 30 minutes and stored at −20° C. It was found that the immunization elicited both primary and secondary immune responses against PRP-IgG and S protein. Rabbit anti-RBD2-14F antisera also strongly reacted with both native S and rS as determined by immunoblot analysis. These results indicate that RBD2 can be used as a carrier protein in a conjugate vaccine. Since RBD2-14 S. pneumococcal polysaccharide conjugate elicited antibodies against both 14F and S, it can be used to d thus should enhance the level of protection against S. pneumococcal-related diseases, especially in infants.
    • EXAMPLE 6
  • To map the linear B-cell epitopes of the SARS S protein, overlapping synthetic peptides covering the entire S protein were synthesized. These peptides were listed in Table 2 below.
  • TABLE 2
    Synthetic SARS CoV S peptides
    Peptide SEQ ID
    ID No MW Sequence NO:
    RBD1-related fragments
      1 1,6812 VIPFKDGIYFAATEK 51
      2 1,6520 DGIYFAATEKSNVVR 52
      3 1,6029 AATEKSNVVRGWVFG 53
      4 1,6499 SNVVRGWVFGSTMNN 54
      5 1,6238 GWVEGSTMNNKSQSV 55
      6 1,6449 STMNNKSQSVIIINN 56
      7 1,5978 KSQSVIIINNSTNVV 57
      8 1,6261 IIINNSTNVVIRACN 58
      9 1,6661 STNVVIRACNFELCD 59
     10 1,7423 IRACNFELCDNPFFA 60
     11 1,7272 FELCDNPFFAVSKPM 61
     12 1,6439 NPFFAVSKPMGTQTH 62
     13 1,6750 VSKPMGTQTHTMIFD 63
     14 1,6820 GTQTHTMIFDNAFNC 64
     15 1,8113 TMIFDNAFNCTFEYI 65
     16 1,7111 NAFNCTFEYISDAFS 66
     17 1,7050 TFEYISDAFSLDVSE 67
     18 1,5849 SDAFSLDVSEKSGNF 68
     19 1,7412 LDVSEKSGNFKHLRE 69
     20 1,8334 KSGNFKHLREFVFKN 70
     21 1,8605 KHLREFVFKNKDGFL 71
     22 1,8074 FVFKNKDGFLYVYKG 72
     23 1,7882 KDGFLYVYKGYQPID 73
     24 1,8101 YVYKGYQPIDVVRDL 74
     25 1,7019 YQPIDVVRDLPSGFN 75
     26 1,6381 VVRDLPSGFNTLKPI 76
     27 1,6543 PSGFNTLKPIFKLPL 77
    RBD2-related fragments
     28 1,6362 AELKCSVKSFEIDKG 78
     29 1,6840 SVKSFEIDKGIYQTS 79
     30 1,7510 EIDKGIYQTSNFRVV 80
     31 1,6638 IYQTSNFRVVPSGDV 81
     32 1,6849 NFRVVPSGDVVRFPN 82
     33 1,6140 PSGDVVRFPNITNLC 83
     34 1,6881 VRFPNITNLCPFGEV 84
     35 1,6361 ITNLCPFGEVFNATK 85
     36 1,6850 PFGEVFNATKFPSVY 86
     37 1,8262 FNATKFPSVYAWERK 87
     38 1,8103 FPSVYAWERKKISNC 88
     39 1,7522 AWERKKISNCVADYS 89
     40 1,6581 KISNCVADYSVLYNS 90
     41 1,6960 VADYSVLYNSTFFST 91
     42 1,7593 VLYNSTFFSTFKCYG 92
     43 1,6692 TFFSTFKCYGVSATK 93
     44 1,6443 FKCYGVSATKLNDLC 94
     45 1,6561 VSATKLNDLCFSNVY 95
     46 1,6891 LNDLCFSNVYADSFV 96
     47 1,6449 FSNVYADSFVVKGDD 97
     48 1,6018 ADSFVVKGDDVRQIA 98
     49 1,5226 VKGDDVRQIAPGQTG 99
     50 1,5697 VRQIAPGQTGVIADY 100
     51 1,6179 PGQTGVIADYNYKLP 101
     52 1,7432 VIADYNYKLPDDFMG 102
     53 1,7543 NYKLPDDFMGCVLAW 103
     54 1,7372 DDFMGCVLAWNTRNI 104
     55 1,6470 CVLAWNTRNIDATST 105
     56 1,6859 NTRNIDATSTGNYNY 106
     57 1,8112 DATSTGNYNYKYRYL 107
     58 1,9276 GNYNYKYRYLRHGKL 108
     59 2,0017 KYRYLRHGKLRPFER 109
     60 1,8063 RHGKLRPFERDISNV 110
     61 1,7580 RPFERDISNVPFSPD 111
     62 1,5589 DISNVPFSPDGKPCT 112
     63 1,5229 PFSPDGKPCTPPALN 113
     64 1,6422 GKPCTPPALNCYWPL 114
     65 1,7522 PPALNCYWPLNDYGF 115
     66 1,7832 CYWPLNDYGFYTTTG 116
     67 1,6789 NDYGFYTTTGTGYQP 117
     68 1,6989 YTTTGIGYQPYRVVV 118
     69 1,7651 IGYQPYRVVVLSFEL 119
     70 1,6731 YRVVVLSFELLNAPA 120
     71 1,5140 LSFELLNAPATVCGP 121
     72 1,4689 LNAPATVCGPKLSTD 122
     73 1,5990 TVCGPKLSTDLIKNQ 123
     74 1,7191 KLSTDLIKNQCVNFN 124
     75 1,7071 LIKNQCVNFNFNGLT 125
     76 1,5380 CVNFNFNGLTGTGVL 126
     77 1,4609 FNGLTGTGVLTPSSK 127
     78 1,6039 GTGVLTPSSKRFQPF 128
     79 1,7928 TPSSKRFQPFQQFGR 129
     80 1,8558 RFQPFQQFGRDVSDF 130
     81 1,7387 QQFGRDVSDFTDSVR 131
     82 1,6508 DVSDFTDSVRDPKTS 132
     83 1,6710 TDSVRDPKTSEILDI 133
     84 1,6181 DPKTSEILDISPCAF 134
     85 1,4890 EILDISPCAFGGVSV 135
     86 1,3748 SPCAFGGVSVITPGT 136
     87 1,3576 GGVSVITPGTNASSE 137
     88 1,5038 ITPGTNASSEVAVLY 138
     89 1,5937 NASSEVAVLYQDVNC 139
     90 1,6087 VAVLYQDVNCTDVST 140
     91 1,5707 QDVNCTDVSTAIHAD 141
     92 1,5217 TDVSTAIHADQLTPA 142
     93 1,7241 AIHADQLTPAWRIYS 143
     94 1,7019 QLTPAWRIYSTGNNV 144
     95 1,7668 WRIYSTGNNVFQTQA 145
     96 1,5047 TGNNVFQTQAGCLIG 146
     97 1,5708 FQTQAGCLIGAEHVD 147
     98 1,5791 GCLIGAEHVDTSYEC 148
     99 1,6310 AEHVDTSYECDIPIG 149
    100 1,4951 TSYECDIPIGAGICA 150
    101 1,4991 DIPIGAGICASYHTV 151
    102 1,5602 AGICASYHTVSLLRS 152
    103 1,6760 SYHTVSLLRSTSQKS 153
    104 1,6360 SLLRSTSQKSIVAYT 154
    105 1,5389 TSQKSIVAYTMSLGA 155
    106 1,4810 IVAYTMSLGADSSIA 156
    107 1,5129 MSLGADSSIAYSNNT 157
    108 1,5489 DSSIAYSNNTIAIPT 158
    109 1,6240 YSNNTIAIPTNFSIS 159
    110 1,5880 IAIPTNFSISITTEV 160
    111 1,6380 NFSISITTEVMPVSM 161
    112 1,5759 ITTEVMPVSMAKTSV 162
    113 1,6591 MPVSMAKTSVDCNMY 163
    114 1,5891 AKTSVDCNMYICGDS 164
    115 1,6211 DCNMYICGDSTECAN 165
    TM-related Fragments
    116 1,8833 DSFKEELDKYFKNHT 166
    117 1,7901 ELDKYFKNHTSPDVD 167
    118 1,6270 FKNHTSPDVDLGDIS 168
    119 1,4418 SPDVDLGDISGINAS 169
    120 1,4818 LGDISGINASVVNIQ 170
    121 1,6379 GINASVVNIQKEIDR 171
    122 1,7219 VVNIQKEIDRLNEVA 172
    123 1,7671 KEIDRLNEVAKNLNE 173
    124 1,6671 LNEVAKNLNESLIDL 174
    125 1,6961 KNLNESLIDLQELGK 175
    126 1,7941 SLIDLQELGKYEQYI 176
    127 2,0132 QELGKYEQYIKWPWY 177
    128 2,0604 YEQYIKWPWYVWLGF 178
    129 1,8315 KWPWYVWLGFIAGLI 179
    130 1,5843 VWLGFIAGLIAIVMV 180
    131 1,5254 IAGLIAIVMVTILLC 181
    132 1,5834 AIVMVTILLCCMTSC 182
    133 1,6046 TILLCCMTSCCSCLK 183
    134 1,4824 CMTSCCSCLKGACSC 184
    135 1,4354 CSCLKGACSCGSCCK 185
    136 1,5221 GACSCGSCCKFDEDD 186
    137 1,6260 GSCCKFDEDDSEPVL 187
    138 1,6730 FDEDDSEPVLKGVKL 188
    S3 Fragments
    S3-1 GDSTECANLLLQYGS 189
    S3-2 LQYGSFCTQLNRALS 190
    S3-3 NRALSGIAAEQDRNT 191
    S3-4 QDRNTREVFAQVKQM 192
    S3-5 QVKQMYKTPTLKYFG 193
    S3-6 LKYFGGFNFSQILPD 194
    S3-7 QILPDPLKPTKRSFI 195
    S3-8 KRSFIEDLLFNKVTL 196
    S3-9 KVTLLADAGFMKQYG 197
    S3-10 MKQYGECLGDINARD 198
    S3-11 INARDLICAQKFNGL 199
    S3-12 KFNGLTVLPPLLTDD 200
    S3-13 LLTDDMIAAYTAALV 201
    S3-14 TAALVSGTATAGWTF 202
    S3-15 AGWTFGAGAALQIPF 203
    S3-16 LQIPFAMQMAYRFNG 204
    S3-17 YRFNGIGVTQNVLYE 205
    S3-18 NVLYENQKQTANQFN 206
    S3-19 ANQFNKAISQIQESL 207
    S3-20 IQESLTTTSTALGKL 208
    S3-21 ALGKLQDVVNQNAQA 209
    S3-22 QNAQALNTLVKQLSS 210
    S3-23 KQLSSNFGAISSVLN 211
    S3-24 SSVLNDILSRLDKVEA 212
    S3-25 LDKVEAEVQIDRLITG 213
    S3-26 RLITGRLQSLQTYVTQQLIRA 214
    (SEQ ID NO:24)
    RBD2 GNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPC
    (SEQ ID NO:26)
    RBD55 DPKTSEILDISPCAFGGVSVITPGTNASSEVAVLYQD
    VNCTDVSTAIHAD
    Note:
    RBD-55 includes the amino acids covering S84 to S91
  • The peptides were synthesized by an ABI 433A peptide synthesizer and optimized F-Moc chemistry according to the manufacturer's manual. The synthesized peptides were cleaved from the resin by Trifluoroacetic acid (TFA). They were then purified by reversed-phase high performance liquid chromatography (RP-HPLC) on a Vydac C4 semi-preparative column (1×30 cm) using a 15 to 55% acetonitrile gradient in 0.1% trifluoryl acetic acid (TFA) developed over 40 minutes at a flow rate of 2 mL/min. All synthetic peptides used in subsequent biochemical and immunological studies were >95% pure as determined by analytical HPLC. Amino acid compositions of these peptides were determined on a Waters Pico-Tag system. The results indicated a good agreement with their expected compositions.
  • ELISA was used to map B-cell epitopes. Microtiter wells (Nunc-Immunoplate, Nunc, Denmark) were coated with 50 μL of a coating buffer (15 mM Na2CO3, 35 mM NaHCO3, pH 9.6) containing 200 ng of purified recombinant S fragments or 500 ng of individual peptides (listed in Table 3 below) for 16 hours at room temperature. The plates were then blocked in 0.1% (w/v) BSA in phosphate buffer saline (PBS) for 30 minutes at room temperature. Serially diluted antisera were added to the wells and incubated for 1 hour at room temperature. After removal of the antisera, the plates were washed five times with PBS containing 0.1% (w/v) Tween-20 and 0.1% (w/v) BSA. Fab′2 fragments from goat anti-rabbit, -guinea pig, -mouse, or -human IgG antibodies conjugated to horseradish peroxidase (Jackson ImmunoResearch Labs Inc., PA) were diluted (1/8,000) with a washing buffer, and added to the microtiter wells. After incubating for 1 hour at room temperature, the wells were washed five times with the washing buffer and then developed using the substrates tetramethylbenzidine (TMB) and H2O2 (ADI, Toronto). The reaction was stopped by adding 1N H2 SO4 and the optical density was measured at 450 nm by a Titretek Multiskan TI (Flow Labs., Virginia). Two irrelevant peptides were used as negative controls. All assays were performed in triplicate, and the reactive titer of each antiserum was defined as the dilution consistently showing 2-fold increase absorbance value over those obtained from the negative controls. Immunodomiant B-cell epitopes were identified to residues 125-146, 334-348, 409-423, 449-468, 589-603, and 1232-1246. These results indicate that these regions contain the linear B-cell epitope sequences and that they can be used as target antigens in, e.g., diagnostic kits to detect the presence of anti-S and anti-SARS CoV antibodies in samples.
    • EXAMPLE 7
  • It is known that SRAS CoV binds to VERO E6 cells. The above-described S protein fragments were tests for their ability to bind to VERO E6 cells. Vero E6 cells (1×104 cells per mL) were incubated with S1-Fc, S2-Fc, S3-Fc, or human IgG1 at various concentrations in a volume of 1 mL for 2 hours at room temperature. The cells were then washed in PBS containing 0.5% BSA and 0.1% NaN3, incubated with FITC-labeled goat anti-human IgG Fc (Sigma), and analyzed by flow cytometry. It was found that S1-Fc and S2-Fc bound to VERO E6 cells at 1 μg/ml and 0.1 g/ml, respectively. In contrast, S3-fc and human IgG1 did not bind to VERO E6 cell even at 10 μg/ml.
  • The just-described VERO E6 cell model was used to examine the ability of anti-S1-Fc or anti-S2-Fc serum to inhibit the binding of SARS CoV to VERO E6 cells. VERO E6 cells were cultured on a 24-well plate until they reached approximately 50% confluent. The cells were then incubated with SARS-CoV Tw1 strain (MOI 1:10) and human sera that had a 1/128 virus neutralization titer in the presence or absence of 0.1 to 10 μg/mL corresponding S fusion proteins. After 24-48 hours, the cells were examined under a microscope. The presence of mltinucleated giant cells indicated infected cells. The results indicated that human sera blocked the viral infection, and that this blocking activity was repressed by the recombinant S fusion proteins.
    • EXAMPLE 8
  • Since S2-Fc fusion protein strongly bound to VERO E6 cell and inhibited human neutralizing antibody activity against SARS CoV, it was of interest to identify the protective epitope(s) of this S2 fragment. Eighty-eight peptides from S2 (shown in Table 2 above) were synthesized based upon the sequence of the SARS CoV TW1 S protein.
  • Five convalescent sera were obtained from patients infected with SARS CoV and three sera were obtained from guinea pigs immunized with RBD2 in the manner described in Examples 5 and 6 above. These antisera were mixed with the peptides shown in Table 3. These peptides covered residues 522 to 600 of the S protein. The reactive titer of each antiserum was determined. The results are summarized in Table 3
  • TABLE 3
    Reactivity of human or guinea pig anti-RBD2
    antisera with synthetic peptides
    Reactive
    Titers
    Peptide ID No. Synthetic Guinea
    (SEQ ID NO:) peptides Human pig
    76 (SEQ ID NO: 126) CVNFNFNGLTGTGVL 1/5 0/3
    77 (SEQ ID NO: 127) FNGLTGTGVLTPSSK 1/5 0/3
    78 (SEQ ID NO: 128) GTGVLTPSSKRFQPF 0/5 0/3
    79 (SEQ ID NO: 129) TPSSKRFQPFQQFGR 0/5 0/3
    80 (SEQ ID NO: 130) RFQPFQQFGRDVSDF 0/5 0/3
    81 (SEQ ID NO: 131) QQFGRDVSDFTDSVR 1/5 0/3
    82 (SEQ ID NO: 132) DVSDFTDSVRDPKTS 2/5 1/3
    83 (SEQ ID NO: 133) TDSVRDPKTSEILDI 15 1/3
    84 (SEQ ID NO: 134) DPKTSEILDISPCAF 0/5 0/3
    85 (SEQ ID NO: 135) EILDISPCAFGGVSV 1/5 0/3
    86 (SEQ ID NO: 136) SPCAFGGVSVITPGT 0/5 0/3
    87 (SEQ ID NO: 137) GGVSVITPGTNASSE 0/5 0/3
    88 (SEQ ID NO: 138) ITPGTNASSEVAVLY 5/5 3/3
    89 (SEQ ID NO: 139) NASSEVAVLYQDVNC 5/5 3/3
    90 (SEQ ID NO: 140) VAVLYQDVNCTDVST 4/5 1/3
    91 (SEQ ID NO: 141) QDVNCTDVSTAIHAD 1/5 0/3
    RBD-55 5/5 3/3
    (SEQ ID NO: 26)
  • As shown in Table 3, most of the peptides successfully detected the presence of anti-S protein antibody in the samples.
    • EXAMPLE 9
  • Further studies were performed to determine whether the binding of S2-Fc to VERO E6 cells could be neutralized by S protein or its fragments.
  • Recombinant RBD2 was tested first. 104 of VERO E6 cells were incubated with 330 ng/mL of S2-Fc protein in the presence or absence of know amount of RBD2 protein solution. It was found that 1 μg of RBD2 significantly reduced the S2-Fc binding to VERO E6 cells.
  • The inhibition assays were repeated with 11 cocktails, each containing nine RBD2 fragment and covering(S28 to S115). More specifically, the VERO E6 cells were harvested and washed twice with a FACS staining/washing buffer. 2×105 cells were incubated with various peptides and then stained in a final volume of 100 ml with recombinant S-Fc protein (1 mg), S2-Fc protein (0.2-0.3 mg), or hIgG1 as isotype control for 30 minutes at 4° C. Cells were washed twice and stained with the RPE-conjugated anti-hIg Abs for 30 minutes at 4° C. After washing, cells were fixed with fixation buffer for 30 minutes at 4° C., and then the fluorescence was detected with FACS Calibur (Becton Dickinson). The results are summarized in Table 4 below. The inhibition level by RBD2 was designated as 100%.
  • TABLE 4
    Inhibition S2-Fc/VERO E6 cell Binding by S Peptides
    Percent of Inhibition
    Concentration of
    Synthetic peptides
    (μg/mL)
    Blocking agents 1 10 100
    Negative control (SEQ ID NOs:) 0 0 0
    Gp(28-35) (SEQ ID NOs: 78-85) 0 0 0
    Gp(36-43) (SEQ ID NOs: 86-93) 0 0 0
    Gp(44-51) (SEQ ID NOs: 94-101) 0 0 0
    Gp(52-59) (SEQ ID NOs: 102-109) 0 0 0
    Gp(60-67) (SEQ ID NOs: 110-117) 0 0 0
    Gp(68-75) (SEQ ID NOs: 118-125) 0 0 0
    Gp(76-83) (SEQ ID NOs: 126-133) 0 0 0
    Gp(84-91) (SEQ ID NOs: 134-141) 0  10% 30%
    Gp(92-99) (SEQ ID NOs: 142-149) 0 0 0
    Gp(100-107) (SEQ ID NOs: 150-157) 0 0 0
    Gp(108-115) (SEQ ID NOs: 158-165) 0 0 0
    RRBD2 (SEQ ID NO: 24) 100% 100% NA
  • As shown in Table 4, the peptide cocktail containing S peptides 84 to 91 (group #8) strongly inhibited the binding between S2-Fc and VERO-6 cells by 30% as compared with those in the RBD2. These results indicate that the major B-cell epitopes of S2 were located within the region covering these 9 peptides, i.e., residues 540 to 600 of S protein.
  • To more clearly define the protective epitope(s) of the S2 fragment, individual peptides S84-91 were also tested. 104 of VERO E6 cells were incubated with 330 ng per mL of S2-Fc protein in the presence or absence of the peptides, respectively. The inhibitions of the binding of S-Fc to VERO E6 cells were determined in the same manner described above. The same experiment was repeated using a polypeptide containing with 50 amino acids covering S84 to S91 (“RBD-55” shown in Table 2 above). The results are summarized in Table 5 below.
  • TABLE 5
    Inhibition Activity of S Synthetic Peptides against
    S2-Fc/VERO E6 cell Binding
    Percent of Inhibition
    Concentration of
    Synthetic peptides
    (μg/mL)
    Blocking agents 1 10 100
    Negative control (SEQ ID NOs:) 0 0 0
    Gp(76-83) (SEQ ID NOs: 126-133) 0 0 0
    Gp(84-91) (SEQ ID NO: 134-141) 0 10 30
    S84 (SEQ ID NO: 134) 0 0 0
    S85 (SEQ ID NO: 135) 0 0 0
    S86 (SEQ ID NO: 136) 0 0 10
    S87 (SEQ ID NO: 137) 0 0 0
    S88 (SEQ ID NO: 138) 0 0 0
    S89 (SEQ ID NO: 139) 0 0 10
    S90 (SEQ ID NO: 140) 0 0 0
    S91 (SEQ ID NO: 141) 0 0 0
    S86 + S87 (SEQ ID NOs: 136 and 137) 0 20 40
    S86 + S88 (SEQ ID NOs: 136 and 138) 0 0 0
    S86 + S89 (SEQ ID NOs: 136 and 139) 0 20 40
    S86 + S90 (SEQ ID NOs: 136 and 140) 0 0 0
    S86 + S91 (SEQ ID NOs: 136 and 141) 0 0 0
    RBD-55 (SEQ ID NO: 26) 10 30 60
    rRBD2 (SEQ ID NOs: 24) 100 100 Not test
  • As shown in Table 5, both S86 and S89 statistically significantly inhibited the S2-Fc/VERO cell binding. Furthermore, S86 and S87, or S86 and S89 exhibited synergetic effect and could inhibit 30% of S2-Fc/Vero cell binding. Each of S86 and S89 contains two cysteine residues on both termini, which could form a disulfide bridge and might lead to strong inhibition. RBD-55 inhibited the S2-FC/VERO E6 cell binding more significantly than S86 or S89 peptide (60% inhibition vs 10% inhibition). These results indicate that RBD-55 could be used as an immunogen to induce protective antibodies against SARS CoV.
    • EXAMPLE 10
  • The above-described peptides were used to generate S peptide-specific antisera. Guinea pigs and rabbits were immunized with peptides cocktail (50 to 200 μg) emulsified with the Freund's complete adjuvant and injected intramuscularly. The animals were boosted with the same amount of peptide cocktails in the incomplete Freund's adjuvant at days 14 and 28. Antisera were collected on day 42 and tested by ELISAs and immunoblotting. Both rabbit and guinea pig antisera were shown to be monospecific for their respective immunizing peptides by the peptide-specific ELISAs. In addition, both guinea pig and rabbit antisera raised against S peptides reacted with SARS CoV on immunoblot analyses. Since most S peptides induced strong anti-peptide antibody responses in at least one animal species, they are appropriate immunogens to be included in immunogenic compositions, e.g., vaccines.
    • EXAMPLE 11
  • Infant ferrets were used to examine the protective activity of S-specific antisera against SARS CoV challenge as described by NIH (Yang et al., Nature (2004) 428:561-564.). Five-day old infant ferrates were inoculated subcutaneously (SC) on the dorsum with 0.15 mL of two different rabbit anti-S fragments. Pre-immune sera were used as negative controls. One day after this passive immunization, the infant ferrets were injected intraperitoneally (IP) with 4000 plaque-forming units (cfu) of SARS CoV Tor2 strain (0.1 ml) freshly grown and isolated from a Vero cell culture medium supplemented with cofactors and diluted in PBS containing 0.5 mM MgCl2 and 0.15 mM CaCl2. One day later, blood samples were collected via cardiac puncture under methoxyflurane anaesthesia and cultured in the Vero cell media. The number of virus per mL of blood was determined after 24 hours. The Student's t-test was used to analyze differences observed in the levels of viramia relative to controls. The results indicate that the antibodies protect against SARS CoV challenge The protective ability of anti-RBD1 sera against SARS CoV infection was examined in the ferret model. It was that ferret passively immunized with guinea pig anti-RBD1 antisera were not more protective than pre-bleed serum control.
    • EXAMPLE 12
  • Little is known about the cellular immune response to SARS CoV and its role in protecting against SARS CoV infection. To examine the cellular response elicited by SARS CoV, T-cell lines' proliferative responses to S peptides were determined by conventional cytokine assays as described below.
  • S-specific T-cell lines were generated. BALB/c (H-2d) mice (Charles River Animal Farm, Montreal, Canada) were primed subcutaneously with 20 μg of recombinant S adsorbed to 1.5 mg of aluminium phosphate (alum) in presence of 100 μg of CpG. The mice were boosted twice with the same dose of immunogen at 3-week intervals.
  • Ten days after the final boost, the spleen of each immunized mouse was removed. Splenocytes were isolated and cultured in 200 μL of RPMI 1640 medium (Flow Lab) at 5.75×105 cells per well of a microtiter plate. The medium was supplemented with 10% heat-inactivated fetal calf serum (Gibson), 2 mM L-glutamine, 100 U/mL) penicillin, and 5×0.10−5 M 2-mercaptoethanol and contained varying concentrations (1, 10 and 100 μg per mL) of individual S peptides. The cultures were kept in a humidified incubator in the presence of 5% CO2/air. Triplicate cultures were performed for each concentration of each peptide. Five days later, 150 μL of 10% rat concanavalin A culture supernatant diluted in the culture medium was added to the microtiter plate wells. The supernatant contained Interleukin-2 (IL-2), which expand peptide-specific T-cells.
  • Six days later, 150 μL of the supernatant were removed from each microculture, and 150 μL of a fresh IL-2 containing culture supernatant added to further expand and maintain the viability of the peptide-specific T-cells. After another 6 day-incubation, the cells were washed with 200 μL culture medium for three times. Each set of cultures were then stimulated with a peptide at concentrations of 1, 10, and 100 μg/mL, respectively in the presence of 2×0.105 irradiated (1,500 rad) BALB/c spleen cells in a final volume of 200 μL culture medium. Sixty microliters of the supernatant were then removed from each triplicate culture and pooled. All supernatants were then assayed for IL-2, IL-4, and Interferon-gamma (IFN-gamma) using murine IL-2 and IL-4 ELISA kits (Endogen Inc, MA, U.S.A.) and a mouse IFN-gamma ELISA kit (Genzyme Corporation. MA, U.S.A.). Test culture supernatants were assayed at 1 in 5 dilution according to the manufacturers' instructions.
  • The results indicated that peptides corresponding to residues 120-134, 649-688, and 699-713 elicited proliferative responses and the release of specific cytokines. Because of this strong ability to induce cellular immune response, these immunodominant T-cell epitopes can be used as carriers for pneumococcal polysaccharides and/or S B-cell epitopes to enhance the immunogenicity. The Th1 cell epitopes identified above can be used in SARS CoV vaccine formulations to induce SARS-specific cellular immune responses.
    • EXAMPLE 13
  • In this example, murine anti-S monoclonal antibodies were generated. BALB/c mice were immunized intraperitoneally with 20 to 50 μg of RBD2 emulsified in the Freund's complete adjuvant. Two weeks later, the mice were injected with the same amount of immunogen in the incomplete Freund's adjuvant. The anti-S titers were examined. Positive mice were selected for making hybridomas by standard cell fusion techniques. Three days before the fusion, the mice were boosted again with the same amount of immunogen in the incomplete Freund's adjuvant. Hybridomas were produced by fusion of splenic lymphocytes from immunized mice with non-secreting Sp2/0 myeloma cells in the manner described in Hamel et al. 1987, J. Med. Microbiol. 23:163-170. S-specific hybridomas were cloned by sequential limiting dilutions and screened for anti-S monoclonal antibody production. Eight S-specific hybridoma cell lines were identified, expanded, and frozen in liquid nitrogen by standard techniques.
    • EXAMPLE 14
  • The mechanism of SARS CoV infection is unclear although it was reported that infection took place through enteric route, respiratory tract, and skin. As discussed above, S1-Fc and S2-Fc, but not S3-Fc, bind to VERO cells. To test whether S3-Fc binds to any other cells, a panel of cell lines were tested. About 1×104 cells/mL were incubated with 0.1, 0.3, and 1 μg of S3-Fc or the same amount of S1-Fc or S2-Fc in a volume of 1 mL for 2 hours at room temperature. The cells were washed in PBS with 0.5% BSA and 0.1% NaN3, incubated with FITC-labeled goat anti-human IgG Fc (Sigma), and analyzed by flow cytometry.
  • It was unexpected that S3-Fc bound strongly to NIH 3T3 cells but not to Jarket cells. S3-Fc showed strong binding to NIH 3T3 cells even at a concentration as low as 0.1 μg/mL. In contrast, S1-Fc did not bind to NIH3T3 cells even at 10 g/mL, and S2-Fc showed some binding to NIH 3T3 cell at 1 μg/mL. These results indicate that S3-Fc had specificity toward receptors in NIH 3T3 cells.
  • It was also unexpected that S protein also binds to HeLa, BHK-21, and COS-7 cells. Three separated receptor-binding domains of S protein were identified: (1) the low affinity mapped to the N-terminal 333 residues, (2) a intermediate affinity receptor-binding domain (with 1 μM avidity) mapped to residues 334 to 666, and (3) a high affinity domain within residues 667 to 999. Beside VERO E6 cells, all these cell lines had not been reported before to be the hosts for SARS CoV replication. This explained why SARS CoV could infect patient via skin contact with infected solutions.
    • OTHER EMBODIMENTS
  • All of the features disclosed in this specification may be combined in any combination. Each feature disclosed in this specification may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, each feature disclosed is only an example of a generic series of equivalent or similar features.
  • From the above description, one skilled in the art can easily ascertain the essential characteristics of the present invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions. Thus, other embodiments are also within the scope of the following claim.

Claims (13)

1-11. (canceled)
12. An isolated nucleic acid comprising a sequence encoding a polypeptide or a complement thereof, wherein the polypeptide comprises SEQ ID NO: 4 or an immunogenic fragment thereof, and the immunogenic fragment is at least 10 amino acid residues in length.
13. The nucleic acid of claim 12, wherein the sequence contains SEQ ID NO: 3, 5, 6, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, or 27; or encodes one of the peptide sequences listed in Table 2.
14. The nucleic acid of claim 13, wherein the sequence contains SEQ ID NO: 23 or 25.
15. An expression vector comprising a nucleic acid of claim 12.
16. A host cell comprising a nucleic acid of claim 12.
17. A method of producing a polypeptide, comprising culturing the host cell of claim 16 in a medium under conditions permitting expression of a polypeptide encoded by the nucleic acid, and purifying the polypeptide from the cultured cell or the medium of the cell, wherein the polypeptide comprises SEQ ID NO: 4 or an immunogenic fragment thereof, and the immunogenic fragment is at least 10 amino acid residues in length.
18. (canceled)
19. A method of generating an antibody against a polypeptide, the method comprising administering to a non-human animal a polypeptide or a nucleic acid encoding the polypeptide, wherein the polypeptide comprises SEQ ID NO: 4 or an immunogenic fragment thereof, and the immunogenic fragment is at least 10 amino acid residues in length.
20. A method of inducing an immune response in a subject against a coronavirus, the method comprising administering to the subject a polypeptide or a nucleic acid encoding the polypeptide, wherein the polypeptide comprises SEQ ID NO: 4 or an immunogenic fragment thereof, and the immunogenic fragment is at least 10 amino acid residues in length.
21-24. (canceled)
25. A method of treating an infection with a coronavirus, the method comprising administering to a subject in need thereof an effective amount of a polypeptide, wherein the polypeptide comprises SEQ ID NO: 4 or an immunogenic fragment thereof, and the immunogenic fragment is at least 10 amino acid residues in length.
26-29. (canceled)
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