(19)
(11)EP 2 970 396 B1

(12)EUROPEAN PATENT SPECIFICATION

(45)Mention of the grant of the patent:
23.02.2022 Bulletin 2022/08

(21)Application number: 14763229.3

(22)Date of filing:  15.03.2014
(51)International Patent Classification (IPC): 
C07K 14/095(2006.01)
C07K 19/00(2006.01)
C12N 5/10(2006.01)
A61P 31/16(2006.01)
C07K 14/005(2006.01)
C07K 16/10(2006.01)
C12N 15/63(2006.01)
A61K 39/12(2006.01)
A61K 39/125(2006.01)
A61K 39/00(2006.01)
(52)Cooperative Patent Classification (CPC):
A61K 39/12; C07K 14/095; C07K 16/1009; C07K 2317/33; C07K 2317/76; C12N 2770/32722; C12N 2770/32734; A61K 2039/5258; A61K 2039/58; A61P 31/16; Y02A 50/30
(86)International application number:
PCT/US2014/029891
(87)International publication number:
WO 2014/145174 (18.09.2014 Gazette  2014/38)

(54)

IMMUNOGENIC HUMAN RHINOVIRUS (HRV) COMPOSITIONS

IMMUNOGENE ZUSAMMENSETZUNGEN DES MENSCHLICHEN RHINOVIRUS (HRV)

COMPOSITIONS IMMUNOGÉNIQUES DE RHINOVIRUS HUMAIN (HRV)


(84)Designated Contracting States:
AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

(30)Priority: 15.03.2013 US 201361793788 P

(43)Date of publication of application:
20.01.2016 Bulletin 2016/03

(73)Proprietor: Biological Mimetics, Inc.
Frederick, MD 21702 (US)

(72)Inventors:
  • TOBIN, Gregory, J.
    Frederick, MD 21702 (US)
  • NARA, Peter, L.
    Frederick, MD 21702 (US)

(74)Representative: Bohmann, Armin K. 
Bohmann Anwaltssozietät Nymphenburger Straße 1
80335 München
80335 München (DE)


(56)References cited: : 
WO-A2-2008/057158
WO-A2-2008/057158
  
  • Michael J Francis ET AL: "Immunological properties of hepatitis B core antigen fusion proteins (peptide/virus/vaccine) Communicated by", Proc. Natl. Acad. Sci. USA, 1 April 1990 (1990-04-01), pages 2545-2549, XP055308067, Retrieved from the Internet: URL:http://www.pnas.org/content/87/7/2545. full.pdf [retrieved on 2016-10-06]
  • TOBIN G J ET AL: "Deceptive imprinting and immune refocusing in vaccine design", VACCINE, ELSEVIER LTD, GB, vol. 26, no. 49, 18 November 2008 (2008-11-18), pages 6189-6199, XP025632847, ISSN: 0264-410X, DOI: 10.1016/J.VACCINE.2008.09.080 [retrieved on 2008-10-11]
  • JOSHUA L KENNEDY ET AL: "Pathogenesis of rhinovirus infection", CURRENT OPINION IN VIROLOGY, vol. 2, no. 3, 1 June 2012 (2012-06-01), pages 287-293, XP055311472, United Kingdom ISSN: 1879-6257, DOI: 10.1016/j.coviro.2012.03.008
  • DATABASE Geneseq [Online] 25 November 2010 (2010-11-25), "Human rhinovirus 16 polyprotein sequence.", XP002766604, retrieved from EBI accession no. GSP:AYJ77291 Database accession no. AYJ77291 & US 2010/233677 A1 (LIGGETT STEPHEN B [US] ET AL) 16 September 2010 (2010-09-16)
  • DATABASE Geneseq [Online] 25 November 2010 (2010-11-25), "Human rhinovirus 39 polyprotein sequence.", XP002766605, retrieved from EBI accession no. GSP:AYJ77313 Database accession no. AYJ77313 & US 2010/233677 A1 (LIGGETT STEPHEN B [US] ET AL) 16 September 2010 (2010-09-16)
  • NARA P L ET AL: "Deceptive imprinting: a cosmopolitan strategy for complicating vaccination", VACCINE, ELSEVIER, AMSTERDAM, NL, vol. 16, no. 19, 1 November 1998 (1998-11-01), pages 1780-1787, XP004139007, ISSN: 0264-410X, DOI: 10.1016/S0264-410X(98)00168-6
  • DATABASE GENBANK [Online] 17 March 2004 'UNNAMED PROTEIN PRODUCT, PARTIAL [TETRAODON NIGROVIRIDIS]', XP055281828 Retrieved from NCBI Database accession no. CAG08266
  • UMESH KATPALLY: '«Antibodies to the Buried N Terminus of Rhinovirus VP4 Exhibit Cross-Serotypic Neutralization»?' JOURNAL OF VIROLOGY vol. 83, no. 14, 15 July 2009, pages 7040 - 7048, XP055066241 DOI: 10.1128/JVI.00557-09
  • Luciano Adorini: "Immunodominance" In: "Encyclopaedia of Immunology", 1 January 1998 (1998-01-01), Elsevier Ltd., London UK, XP055569171, pages 1290-1292,
  
Note: Within nine months from the publication of the mention of the grant of the European patent, any person may give notice to the European Patent Office of opposition to the European patent granted. Notice of opposition shall be filed in a written reasoned statement. It shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention).


Description

FIELD OF THE INVENTION



[0001] The present invention is related to an isolated polypeptide or a virus containing said polypeptide; an isolated nucleic acid molecule encoding said polypeptide; a fusion protein comprising said polypeptide; a recombinant expression vector comprising said nucleic acid molecule; a virus-like particle comprising said polypeptide, said fusion protein or a protein encoded by said expression vector; a recombinant virus comprising said polypeptide, said fusion protein, or a protein encoded by said recombinant expression vector; a host cell comprising said recombinant expression vector, said virus-like particle or said virus; an immunogenic composition comprising one or more of said polypeptides, said fusion protein, said virus-like particle or said virus; a vaccine comprising one or more of said polypeptides, said fusion protein, said virus-like particle, said virus or said immunogenic composition; a pharmaceutical composition comprising one or more of said polypeptides, said fusion protein, said virus-like particle, said virus or said immunogenic composition; and said immunogenic composition or said vaccine for use in a method of eliciting an immune response to an human rhinovirus (HRV) for use in a subject, in a method of treating a subject infected with a human rhinovirus (HRV), for use in a method of vaccinating a subject against multiple serotypes of human rhinovirus (HRV) and for use in therapy.

BACKGROUND



[0002] The current stable of licensed vaccines in the human and veterinary arenas is generally successful against what are termed "Class One pathogens." Class One pathogens (such as poliovirus, smallpox, measles, mumps and rubella viruses) are those pathogens, which, in general: (1) infect or cause the most serious disease in children/young adults, (2) carry a relatively stable microbial genome, (3) have a natural history of disease which results in spontaneous recovery; and (4) induce durable memory, associated with polyclonal and multi-epitope antigen recognition.

[0003] In contrast, Class Two pathogens, such as, human rhinovirus (HRV), Foot- and-Mouth-Disease Virus (FMDV), viral influenza, HIV-1, malaria, tuberculosis, trypanosomes, schistosomes, leishmania, anaplasma, enterovirus, astrovirus, Norwalk viruses, toxigenic/pathogenic E. coli, Neisseria, Streptomyces, nontypeable haemophilus influenza, hepatitis C, cancer cells etc. are characterized by quite opposite features. For example, Class Two pathogens: (1) tend to infect and are transmitted in a significantly extended host age range, with infections occurring and reoccurring from childhood through the geriatric period; (2) exhibit microbial genetic instability in defined regions of their genome (a hallmark of the successful evolution of such pathogens); (3) in some cases, include spontaneous recovery of disease that frequently still leaves the host vulnerable to multiple repeated annual infections and/or the establishment of either a chronic/active or chronic/latent infectious state; (4) induce oligoclonal, early immune responses that are directed to a very limited set of immunodominant epitopes which provide either narrow strain-specific protection, no protection and/or enhanced infection; and (5) cause immune dysregulation following infection or vaccination, e.g. epitope blocking antibody, atypical primary immune response Ig subclasses, anamnestic cross reactive recall and inappropriate TH1 and/or TH2 cytokine metabolism.

[0004] At the immunologic level, infection with HRV may stimulate strain-specific immunity, but the host remains susceptible to re-infection by other serotypes of the virus. Characterization of immune responses against HRV suggests that the immune system recognizes and reacts to only a small number of immunodominant epitopes. Because the immunodominant epitopes are in highly variable sites that distinguish the various HRV serotypes, the immune response is highly strain-specific. Thus, an effective cross-protective vaccine against HRV must stimulate immune responses that are directed against more highly conserved regions of the virus, some of which may have previously been subdominant. In the case of HRV, a successful vaccine must overcome strain-specific immune responses to stimulate cross-protective immunity against 1) multiple serotypes and 2) evolving antigenic determinants.

[0005] Although some advances with regard to antigen delivery and expression have improved the immunogenicity of some Class Two microbial pathogens, current vaccine technologies have not readily translated into new, broadly effective and safe licensed vaccines for use in humans or animals. That may be due, in large part, to a poor understanding of the fundamental laws governing the vertebrate host defense system origin, repertoire development, maintenance, activation, senescence and co-evolution in similar and dissimilar environments.

[0006] Antigenic variation is an evolved mechanism to ensure rapid sequence variation of specific pathogen gene(s) encoding homologues of an individual protein antigen, usually involving multiple, related gene copies, resulting in a change in the structure of an antigen on the surface of the pathogen. Thus, the host immune system during infection or re-infection is less capable of recognizing the pathogen and must make new antibodies to recognize the changed antigens before the host can continue to combat the disease. As a result, the host cannot stay completely immune to the viral disease. That phenomenon stands as one of the more, if not, most formidable problem challenging modern vaccine development today.

[0007] Thus, it is not surprising that natural infection and vaccination fail to yield a more functional cross-reactive primary and anamnestic immunity as the repertoire development against those less immunogenic epitopes, which may be more conserved and capable of generating cross-strain immunity, are lower on the antigenic hierarchy.

[0008] The immunologic phenomenon whereby immunodominant epitopes misdirect the immune response away from more conserved and less immunogenic regions on an antigen was initially termed "clonal dominance" (Kohler et al., J Acquir Immune Defic Syndr 1992; 5:1158-68), which later was renamed as "Deceptive Imprinting" (Kohler et al., Immunol Today 1994 (10):475-8).

[0009] The immunologic mechanisms for immunodominance behind deceptive imprinting are not fully understood, and no one mechanism yet fully explains how or why certain epitopes have evolved to be immunoregulatory and immunodominant. The range of immune responses observed in the phenomena include: the induction of highly strain/isolate-specific neutralizing antibody capable of inducing passive protection in experimental animal model-viral challenge systems all the way to the induction of a binding non-protective/non-neutralizing, blocking and even pathogen-enhancing antibody that in some cases prevents the host immune system from recognizing nearby adjacent epitopes, to interfering with CD4 T-cell help. The same decoying of the immune response through immunodominance resulting in a more narrowly focused set of epitopes is observed with T cells of the host in the development of helper and cytotoxic cell-mediated immunity. (Gzyl et al., Virology 2004; 318(2):493-506; Kiszka et al., J Virol. 2002 76(9):4222-32; and Goulder et al., J Virol. 2000; 74(12):5679-90).

[0010] Human Rhinoviruses (HRVs) are among the most common of human pathogens. It is estimated that each year the common cold is responsible for about 20 million missed work days, 22 million missed school days, and 27 million physician visits in the United States alone (Adams, Hendershot et al. 1999; Turner 2001; Mackay 2008). In addition, tens of billions of dollars per year are spent on prescription and over-the-counter medicines associated with treatments for the common cold (Bertino 2002). The estimated overall economic impact of colds in the U.S. in 2008 was nearly $40 billion a year composed of $17 billion from direct medical costs and $22.5 billion in indirect costs.

[0011] HRV is a highly contagious human pathogen that causes respiratory tract symptoms related to "the common cold" and exacerbates asthma and chronic pulmonary diseases. HRV is an unenveloped virus of the family Picornaviridae and is composed of 60 copies each of the viral capsid proteins VP-1, VP-2, VP-3, and VP4 and one copy of positive-sense RNA. The capsid proteins are translated in a genome-length polyprotein and cleaved to mature proteins by the viral protease-3C. The capsid proteins mediate binding to the cell receptor to facilitate virus entry and contain the primary virus neutralizing epitopes for immune targeting. HRV exists as a large number of serotypes dually classified based on 1) cell receptor usage and 2) antigenic relatedness. Viruses in the major group utilize the ICAM-1 receptor and those in the minor group use several members of the low density lipoprotein receptor that are almost ubiquitously expressed on many cell types. The serotypes are arranged within at least 3 clades (HRV-A, HRV-B, and HRV-C) based on genetic relationships.

[0012] To develop a strategy to overcome strain-specific immunity, it is necessary to understand the nature of native immune responses against HRV and other related members of the picornaviridae family. Within 2-3 weeks of infection or immunization with HRV virions, the immune system responds by developing humoral responses containing high titers of neutralizing antibody that are thought to help clear virus infections. However, the antibodies are directed against a small number of immune dominant epitopes that are located within genetically variable regions of the capsid proteins. Thus, infection or immunization with a virus or vaccine derived from one strain does not stimulate protective immunity against others. Because of the ubiquity of numerous HRV strains, vaccines that stimulate protection against one or a few serotypes are not effective.

[0013] Immune Refocusing Technology (IRT) was developed to overcome strain-specific immunity by reducing the antigenicity of immunodominant epitopes responsible for the strain-specific immune reactions. Using IRT, immunodominant epitopes are altered by site-specific mutagenesis to allow the immune system to develop responses to previously subdominant epitopes that participate in the development of more broadly protective immune responses.

[0014] Figure 1 shows a diagram that describes IRT using a model representing the trimeric influenza A/Aichi/68 hemagglutinin (HA) structure. In the molecule in Panel A, strain-specific antibodies (identified as naturally-occurring antibodies) are produced against highly variable immunodominant epitopes (shown as the blackened residues and identified with arrows). Using IRT, specific amino acid residues in the immunodominant epitopes are altered to reduce the antigenicity of the epitopes (depicted as light gray ovals). The rationally designed HA molecule stimulates the production of antibodies to previously subdominant epitopes. The newly refocused antibodies (shown as novel cross-neutralizing antibodies) have enhanced cross-protective antiviral activities against heterologous viruses. In addition, the rationally designed antigen can be used to derive novel therapeutic antibodies with enhanced cross-protective properties.

[0015] The IRT can be applied to derive improved HRV vaccines that stimulate enhanced cross-protective immunity against multiple strains. Rationally designed immunogens can be engineered with mutations in the immunodominant epitopes such that the immune system responds against more broadly protective subdominant epitopes. The novel immunogens can be incorporated into whole virus particles or expressed as recombinant subunit antigens for vaccine production.

[0016] WO 2008/057158 A2 is related to a neutralizing immunogen (NIMIV) of rhinovirus and its use for vaccine application.

[0017] Francis MJ et al. (Proc. Natl. Acad. Sci. USA, Vol. 87, pp 2545-2549, April 1990, Immunology) report on the immunological properties of hepatitis B core antigen fusion protein.

[0018] Tobin GJ et al. (Vaccine 26 (2008) 6189-6199) report on deceptive imprinting and immune refocusing in vaccine design.

SUMMARY OF THE INVENTION



[0019] The problem underlying the present invention is solved by the subject matter of the attached independent claims; preferred embodiments may be taken from the attached dependent claims.

[0020] More specifically, the problem underlying the present invention is solved in a first aspect by an isolated polypeptide or virus containing an amino acid sequence selected from the group consisting of SEQ ID NOs: 16-21, 35, 65-73 and 75-92.

[0021] More specifically, the problem underlying the present invention is solved in a second aspect by an isolated nucleic acid molecule encoding a polypeptide according to the first aspect, including any embodiment thereof.

[0022] More specifically, the problem underlying the present invention is solved in a third aspect by a fusion protein comprising the polypeptide according to the first aspect, including any embodiment thereof.

[0023] More specifically, the problem underlying the present invention is solved in a fourth aspect by a recombinant expression vector comprising the nucleic acid molecule according to the second aspect, including embodiment thereof, and optionally a heterologous nucleic acid molecule.

[0024] More specifically, the problem underlying the present invention is solved in a fifth aspect by a virus-like particle (VLP) comprising the polypeptide according to the first aspect, including any embodiment thereof, the fusion protein according to the third aspect, including any embodiment thereof, or a protein encoded by the recombinant expression vector according to the fourth aspect, including any embodiment thereof.

[0025] More specifically, the problem underlying the present invention is solved in a sixth aspect by a recombinant virus comprising the polypeptide according to the first aspect, including any embodiment thereof, the fusion protein according to the third aspect, including any embodiment thereof, or a protein encoded by the recombinant expression vector according to the fourth aspect, including any embodiment thereof.

[0026] In an embodiment of the fifth aspect and in an embodiment of the sixth aspect, the VLP and, respectively, the virus further comprises a toxic or therapeutic molecule.

[0027] More specifically, the problem underlying the present invention is solved in a seventh aspect by a host cell comprising the recombinant expression vector according to the fourth aspect, including any embodiment thereof, the VLP according to the fifth aspect, inculding any embodiment thereof, or the virus according to the sixth aspect, including any embodiment thereof.

[0028] More specifically, the problem underlying the present invention is solved in an eighth aspect by an immunogenic composition comprising one or more of the polypeptides according to the first aspect, inculding any embodiment thereof, the fusion protein according to the third aspect, including any embodiment thereof, the VLP according to the fifth aspect, including any embodiment thereof, or the virus according to the sixth aspect, including any embodiment thereof, optinally further comprising an adjuvant, wherein, preferably, the adjuvant is slected from a group consisting of an aluminum salt, a salt of calcium, a salt of iron, a salt of zinc, an insoluble suspension of acylated tyrosine, acetylated sugars, cationically or anionically derived polysaccharides, and polyphosphazenes.

[0029] More specifically, the problem underlying the present invention is solved in a ninth aspect by a vaccine comprising one or more of the polypetides according to the first aspect, including any embodiment thereof, the fusion protein according to the third aspect, including any embodiment thereof, the VLP according to the fifth aspect, including any embodiment thereof, the virus according to the sixth aspect, including any embodiment thereof, or the immunogenic composition according to the eighth aspect, including any embodiment therof.

[0030] More specifically, the problem underlying the present invention is solved in a tenth aspect by a pharmaceutical composition comprising one or more of the polypeptides according to the first aspect, including any embodiment thereof, the fusion protein according to the third aspect, including any embodiment thereof, the VLP according to the fifth aspect, including any embodiment thereof, the virus according to the sixth aspect, including any embodiment thereof, or the immunogenic composition according to the eighth aspect, including any embodiment thereof.

[0031] More specifically, the problem underlying the present invention is solved in an eleventh aspect by the immunogenic composition according to the eighth aspect, inculding any embodiment thereof, for use in a method of eliciting an immune response to a human rhinovirus (HRV) in a subject, wherein the method comprises administering to the subject an effective amount of the immunogenic composition, thereby eliciting an immune response to a human rhinovirus (HRV) in the subject.

[0032] More specifically, the problem underlying the present invention is solved in a twelfth aspect by the vaccine according to the ninth aspect, including any embodiment thereof for use in a method of eliciting an immune response to an human rhinovirus (HRV) in a subject, wherein the method comprises administering to the subject an effective amount of the vaccine, thereby eliciting an immune response to a human rhinovirus (HRV) in the subject.

[0033] More specifically, the problem underlying the present invention is solved in a 13th aspect by the immunogenic composition according to the eighth aspect, including any embodiment thereof, for use in a method of treating a subject infected with a human rhinovirus (HRV), wherein the method comprises administering to the subject a therapeutically effective amount of the immunogenic composition, thereby treating the subject infected with the human rhinovirus (HRV).

[0034] More specifically, the problem underlying the present invention is solved in a 14th aspect by the vaccine according to the ninth aspect, including any embodiment thereof, for use in a method of treating a subject infected with a human rhinovirus (HRV), wherein the method comprises administering to the subject a therapeutically effective amount of the vaccine, thereby treating the subject infected with the human rhinovirus (HRV).

[0035] More specifically, the problem underlying the present invention is solved in a 15th aspect by the immunogenic composition according to the eighth aspect, including any embodiment thereof, for use in a method of vaccinating a subject against multiple serotypes of human rhinovirus (HRV), wherein the method comprises administering to the subject an effective amount of the immunogenic composition.

[0036] More specifically, the problem underlying the present invention is solved in a 16th aspect by the vaccine accordign to the ninth aspect, inculding any embodiment thereof, for use in a method of vaccinating a subject against multiple serotypes of human rhinovirus (HRV), wherein the method comprises administering to the subject an effective amount of the the vaccine.

[0037] In an embodiment of the eleventh, twelfth, 13th, 14th, 15th and 16th aspect, the subject is a human, preferably the subject is an adult human, an adolescent human, or an infant human.

[0038] More specifically, the problem underlying the present invention is solved in a 17th aspect by the immunogenic composition according to the eighth aspect, including any embodiment thereof for use in therapy.

[0039] More specifically, the problem underlying the present invention is solved in an 18th aspect by the vaccine according to the ninth aspect, including any embodiment thereof, for use in therapy.

[0040] The invention as defined in the claims relates, in part, to novel HRV antigens with enhanced or novel immunogenicity. The HRV composition of the invention as defined in the claims can serve as an improved vaccine, resulting from modifications providing the virus or viral antigen with a different array of and/or newly recognizable epitopes. In addition, the HRV composition the invention as defined in the claims can serve as an antigen for the purpose of developing improved antibodies for therapeutic, diagnostic, or research reagent uses.

[0041] The more efficient and rapid use of recombinant technology coupled to a novel immune refocusing technology results in subunit compositions that greatly change the current practice of vaccine development by generating an HRV vaccine with improved effectiveness and an enhanced ability to stimulate increased cross-protective immune responses.

[0042] Recombinant proteins produced in bacteria, yeast, insect cells, or mammalian cells can incorporate the novel HRV antigens of the invention as defined in the claims. In addition, recombinant viruses, such as reverse engineered HRV virions, can serve as vehicles for production and delivery.

BRIEF DESCRIPTION OF THE DRAWINGS



[0043] 

Figure 1. Diagram of immune refocusing technology using HRV2 as an example. Cartoon depicting immune refocusing technology as applied to HRV. A. Structural cartoon of HRV2 with capsid antigens VP1, VP2, VP3, and VP4 shown in ribbon form. Amino acid residues in immunodominant epitopes that stimulate serotype-restricted antibodies are shown in surface smoothing black and identified with arrows. B. Structural cartoon with immune refocusing mutations introduced into immunodominant epitope(s) in VP1 shown as gray ovals. C. Immune refocused HRV2 antigen shown with novel broadly cross-neutralizing antibodies attached to conserved domains. Structure shown is adapted from structure IFPN.pdb from Verdaguer et al., 2000.

Figure 2. Location of selective pressure and known immunogenic sites in capsid genes. A. Capsid region of HRV genome. B. Location of HRV-A B-cell antigenic sites are shown as lines in th3e rectangle representing the3 capsid precursor protein based on studies of HRV2 (Appleyard et al., 1990; Hastings et al., 1990; Speller et al., 1993; Hewat and Blaas, 1996; Hewat et al., 1998). C, D. dN/dS plot for capsid genes of HRV-A and HRV-B, respectively. E. Location of HRV-B antigenic sites NimIA, NimIB, NimII and NimIII are show as lines in the rectangle representing the capsid precursor protein based on studies of HRV14 (Sherry and Rueckert, 1985; Sherry et al., 1986). Figure from Xiang et al., 2008.

Figure 3. Structure of HRV. A) Space-filled model showing arrangements of VP1, VP2, and VP3 forming a viral capsid. B and C) are crystal structure diagrams of capsids with the major antigenic sites accentuated using darker gray (1FPN.pdb). HRV39 has not been crystallized but is very closely related to HRV2 shown above. B is a ribbon structure with surface-filled contouring of the minimal immunodominant strain-specific antibody contact points. C is a ball model with exposed adjacent residues (dark gray) to the epitopes identified in B. Analysis of the structure along with comparison to HRV39 sequence assists in identifying residues for immune refocusing.

Figure 4 Alignment of portions of the HRV39 and HRV 2 capsid sequences with identification of antibody contact points (bold typeface) and amino acid residues adjacent to contact points (underlined). Identification of capsid epitopes A, B, and C is indicated above the lines. Amino acid numbering refers to the start of the mature capsid polyprotein. In SEQ NOs:1 and 2, the numbers in the parentheses indicate the number of amino acids deleted from the figure.

Figure 5 Examples of first generation HRV39 immune refocused mutations. Changed residues indicated by amino acid letters, unchanged residues represented by dashes. Sequences above can be localized in the polyprotein using residue numbers provided in Figure 4.

Figure 6. Transmission electron microscopic analysis of HRV39 virus-like-particles expressed in insect larvae using recombinant baculoviruses. Panel A shows native HRV as produced by HeLa cells. Panel B shows HRV39 VLPS. The two micrographs were taken at approximately equal magnification. The micrographs show structures consistent in size and appearance to VLPs.

Figure 7 provides a listing of the serotypes of HRV analyzed for cross-neutralization.

Figure 8. List of HRV serotypes neutralized by sera from rabbits immunized with HRV39 immune refocused subunit antigens. The sera from rabbits immunized with IRT antigens was incubated 1h with 1000 TCID50 of each virus at a final dilution of 1:8 in PBS. Sera from non-immune rabbits were used as negative controls for neutralization and incubated with virus at a final dilution of 1:2. The virus-serum mix was placed onto duplicate wells in a 48-well plate for 1h. The monolayers were washed with media, overlaid with media, incubated for 2-4 days at 35C, and examined microscopically for signs of virus infection. Wells were scored for cytopathic effects of the virus on a scale of 0 to 10. After at least three sessions of analysis, the scores were analyzed for difference from the scores obtained from non-immune sera using the Student's T test. HRV serotypes neutralized by the sera at a confidence level of 95% are listed.

Figure 9 Examples of immune refocused derivatives of HRV16. The upper line of each sequence presents the unmodified (WT) amino acid sequences in and around the major defined epitopes. The lower line shows examples of the IRT mutations with substituted residues

Figure 10 List of HRV serotypes neutralized by sera from rabbits immunized with HRV16 immune refocused virions. The sera from rabbits immunized with IRT antigens was incubated 1h with 1000 TCID50 of each virus at a final dilution of 1:8 in PBS. Sera from non-immune rabbits were used as negative controls for neutralization and incubated with virus at a final dilution of 1:2. The virus-serum mix was placed onto duplicate wells in a 48-well plate for 1h. The monolayers were washed with media, overlaid with media, incubated for 2-4 days at 35C, and examined microscopically for signs of virus infection. Wells were scored for cytopathic effects of the virus on a scale of 0 to 10. After at least three sessions of analysis, the scores were analyzed for difference from the scores obtained from non-immune sera using the Student's T test. HRV serotypes neutralized by the sera at a confidence level of 95% are listed.

Figure 11 Use of antibody escape mutants to identify epitopes for immune refocusing and to design immune refocused antigens. HRV14 was pre-incubated with either polyclonal anti-HRV sera raised in rabbits against purified HRV14 or monoclonal antibody (MoAb-17) directed to the immunodominant epitope (B Sherry, A G Mosser, R J Colonno, R R Rueckert. Use of monoclonal antibodies to identify four neutralization immunogens on a common cold picornavirus, human rhinovirus 14. J Virol. 1986 January; 57(1): 246-257; B Sherry, R Rueckert. Evidence for at least two dominant neutralization antigens on human rhinovirus 14. J Virol. 1985 January; 53(1): 137-143.) After 3 or 6 days, virus progeny was harvested from the monolayers, plaque purified, and sequenced in the capsid gene region. The panels report the sequence divergences observed in comparison to the parental HRV14 capsid sequences. Numbering of amino acids is from the start of each capsid protein. Dashes or blank cells indicate no change from the parental sequence. Panel A: 3 passages with incubation of HRV14 with MoAb-17. Panel B: 6 passages with incubation of HRV14 with MoAb-17. Panel C: 3 passages with incubation of HRV14 with polyclonal anti-HRV14. The results identifies amino acids that can be targeted for immune refocusing.


DETAILED DESCRIPTION OF THE INVENTION



[0044] "Wild type" refers to a naturally occurring organism. The term also relates to nucleic acids and proteins found in a natural occurring organism of a naturally occurring population arising from natural processes, such as seen in polymorphisms arising from natural mutation and maintained by genetic drift, natural selection and so on, and does not include a nucleic acid or protein with a sequence obtained by, for example, purposeful modification of the sequence either through a biologically or chemically selective process or through molecular mutagenesis methods..

[0045] "Immunogen" and "antigen" are used interchangeably herein as a molecule that elicits a specific immune response, for example, containing an antibody that binds to that molecule or eliciting T cells capable of destroying or recognizing an HRV-infected cell. That molecule can contain one or more sites to which a specific antibody binds. As known in the art, such sites are known as epitopes or determinants. An antigen can be polypeptide, polynucleotide, polysaccharide, a lipid and so on, as well as a combination thereof, such as a glycoprotein or a lipoprotein. An immunogenic compound or product, or an antigenic compound or product is one which elicits a specific immune response, which can be a humoral, cellular or both.

[0046] A vaccine is an immunogen or antigen used to generate an immunoprotective response, that is, the antibody reduces the negative impact of the immunogen or antigen found on an infectious virus, or entity expressing same, in a host. The dosage is derived, extrapolated and/or determined from preclinical and clinical studies, as known in the art. Multiple doses can be administered as known in the art, and as needed to ensure a prolonged prophylactic or anamestic (memory) state. The successful endpoint of the utility of a vaccine for the purpose of this invention is the resulting presence of an induced immune response (e.g. humoral and/or cell-mediated) resulting, for example, in the production of serum antibody, or antibody made by the host in any tissue or organ, that binds the antigen or immunogen of interest or a cellular response that recognizes the intended antigen. The induced antibody in some way may combine with a compound, molecule and the like carrying the cognate antigen or immunogen or directs the host to neutralize, reduce or prevent and/or eliminate a viral pathogen from infecting and causing serious clinical disease. Immunoprotection for the purposes of the instant invention is the surrogate marker of inducing presence of such circulating anti-viral antibody that binds the immunogen. That can be determined using any known immunoassay, such as an ELISA. Alternatively, one can use a viral neutralization assay to ascertain presence of circulating anti-viral antibody. For the purposes of the instant invention, observing immunoprotection, that is, presence of circulating anti-HRV antibody, of at least thirty days is evidence of efficacy of a vaccine of interest. The time of immunoprotection can be at least 45 days, at least 60 days, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years or longer. Preferably the immunoprotection is observed in out-bred populations, different geographic populations, clades and so on. Successful measurements of vaccine outcomes may include, but are not exclusively confined to, immunity that either protects against infection or reduces disease or infectivity upon infection.

[0047] "Immunodominant epitope" is an epitope that selectively provokes an immune response in a host organism to the effective or functional exclusion, which may be partial or complete, of other epitopes on that antigen. A, "subdominant epitope," is one which is not immunodominant and often is not immunogenic because the host preferentially reacts solely to the immunodominant epitope(s).

[0048] "To immunodampen an epitope" or "to immune dampen an epitope" is to modify an epitope to substantially prevent the immune system of the host organism from producing antibodies, helper or cytotoxic T cells against the dampened epitope. However, immunodampen does not necessarily result in the complete removal of said epitope. Immunodampening can exert influence on epitopes located away from the site of dampening.

[0049] Immunodampening of an immunodominant epitope of an antigen can result in the production in a host organism of high titer antibodies or T cell responses against non-dominant epitopes on that antigen and/or new titers of antibodies or T cell responses to otherwise relatively immune silent epitopes. Such immunodampened antigens can serve as effective vaccines against organisms that have an antigen with a moderately or highly variable and/or conserved immunodominant epitope(s) or as antigens for the development of novel antibodies with broadened specificities and/or therapeutic or diagnostic uses.

[0050] An immunodominant epitope can be identified by examining serum or T-cell reactivity from a host organism infected with the pathogenic organism. The serum is evaluated for content of antibodies that bind to the identified antigens, usually either as pre-existing antibodies (naive human or animal) or occurring within a short amount of time after exposure or immunization that are likely to cause an immune response in a host organism. If an immunodominant epitope is present, substantially many antibodies in the serum will bind to and/or T cells will recognize the immunodominant epitope(s), with reduced to no binding/recognition to other epitopes present in the antigen.

[0051] After an immunodominant epitope has been identified, the immunodominant epitope is immunodampened as taught herein using the materials and methods taught herein and as known in the art as a design choice. The process of immunodampening can be performed through a variety of methods including, but not limited to, site-specific mutagenesis, antibody-induced evolution, or other in vitro or in vivo selection methods using native or recombinant reagents.

[0052] A particular amino acid of the immunodominant epitope can be replaced, substituted or deleted to dampen immunogenicity. Immunodampening can occur by replacing, substituting or eliminating one amino acid, two amino acids, three amino acids or more of the immunodominant epitope, for example, by site directed mutagenesis of the nucleic acid encoding the antigen with another amino acid(s) which are less immunogenic or which changes the pattern or hierarchy of immunogenicity. Methods for altering nucleic acids and/or polypeptides are provided herein, and are known in the art.

[0053] Alternatively, a sequence that leads to a post-translational modification of an amino acid such as glycosylation, acetylation, or other modification can be introduced or eliminated to immunodampen an immunodominant epitope. Methods for altering nucleic acids to introduce or remove post-translational modifications are provided herein, and are known in the art.

[0054] The phrases and terms, as well as combinations thereof, "functional fragment, portion, variant, derivative or analog" and the like, as well as forms thereof, of an HRV antigen, component, subunit, VP-1, VP-2, VP-3, VP-4, protease, capsomer, virus-like particle, and the like thereof relate to an element having qualitative biological activity in common with the wild-type or parental element from which the variant, derivative, analog and the like was derived. For example, a functional portion, fragment or analog of HRV is one which stimulates an immune response as does native HRV, although the response may be to different epitopes on virus.

[0055] The invention as defined in the claims encompasses functional equivalents of a virus, or portion or derivative thereof, of interest. The term "functional equivalents" includes the virus and portions thereof with the ability to stimulate an immune response to HRV.

[0056] Parts of an HRV of interest, such as a whole virions or subunits carrying, for example, capsid proteins, as well as preparations of any other HRV antigens can be obtained practicing methods known in the art. The parts can be produced through purification of materials from either native virus infections or from recombinant methods using a variety of nucleic acid expression vectors or recombinant virus vectors known in the art. When one or more immunodominant, strain specific epitopes are removed or dampened, for example, by intramolecular modifications (e.g. deletions, charge changes, altering post-translational modifications and so on) and given as an antigen to a naive animal, the novel immunogen can induce a new hierarchy of immune responses at either or both the B and T cell levels (Garrity et al., J Immunol. (1997) 159(1):279-89) against subdominant or previously silent epitopes. That technology as described herein is known the "Immune Refocusing" method of rational antigen design.

[0057] Thus, a vaccine derived from a recombinant HRV capsid subunit protein, an engineered virus-like particle, a recombinant virus vector or vehicle (e.g., adenovirus, vaccinia virus, bacteriophage or other virus-derived system) can be sufficient to protect against challenge from plural strains of HRV.

[0058] Immunodampening can be affected by any of a variety of techniques such as, altering or deleting specific amino acids of the epitope, or adding or removing, for example, a glycosylation site at or near the epitope. The changes can be effected at the level of the polypeptide or at the level of the polynucleotide, practicing methods known in the art. Immunodampening can also be affected by genetic methods such as selection of naturally occurring or experimentally induced mutations from nucleic acid or protein libraries.

[0059] Once a change is made, one then determines whether the change alters, such as, reduces the reactivity of the immunodominant epitope now modified, the "dampened epitope, antigen and so on." That can be tested in vitro by determining the reactivity of the dampened antigen with defined antisera known to react with the dominant epitope, such as by an ELISA or Western blot, for example. Candidates demonstrating reduced reactivity with those defined antisera are chosen for testing in vivo to determine whether those dampened antigens are immunogenic and the host generates an immune response thereto. Hence, for example, a mouse or other animal is immunized to the dampened antigen as known in the art, serum obtained and tested in an in vitro assay for reactivity therewith. That antiserum then can be tested on wild-type virus to determine if the antibody still recognizes the wild type epitope or the wild type antigen. That can be done, for example, in an ELISA or a Western blot. The latter can be informative, revealing whether the particular immunodominant epitope is bound, and if the antiserum remains reactive with HRV, the size and possibly, the identity of the molecule carrying the epitope reactive with the mouse antiserum.

[0060] Those candidate immunodampened antigens less or no longer reactive with known antisera that bind to the parent immunodominant antigen, yet remain immunogenic in hosts, are selected as candidate vaccines for further testing. For example, if the altered molecule is administered to a mouse, the mouse antiserum thereto can be tested for reactivity with a number of HRV strains in standardized anti-viral-based assays to determine how generic that antibody is, that is, whether the newly recognized epitopes on the dampened antigen are generic to a wide range of HRV strains and if the antibody has antiviral activity.

[0061] Many techniques are available to one of ordinary skill in the art to permit manipulation of immunogenic structures. The techniques can involve substitution of various amino acid residues at a site of interest, followed by a screening analysis of binding of the mutein to defined, known antibody that binds to one or more immunodominant epitopes of HRV. For example, a polypeptide can be synthesized to contain one or more changes to the primary amino acid sequence of the immunodominant epitope. Alternatively, the nucleic acid sequence of the immunodominant epitope can be modified to express an immunodampened epitope. Hence, the nucleic acid sequence can be modified by, for example, site directed mutagenesis to express amino acid substitutions, insertions, additions, deletions and the like, some of which may introduce further modification at or near the immunodominant epitope, such as, altering sites that lead to post-translational modifications such as addition or subtraction of carbohydrate, fatty acids and so on. Mutations to the nucleotide, and resulting polypeptide, sequences can also be made through in vitro or in vivo selection processes, also known in the art.

[0062] One procedure for obtaining epitope mutants (a mutant epitope that varies from wildtype) and the like is "alanine scanning mutagenesis" (Cunningham & Wells, Science 244:1081-1085 (1989); and Cunningham & Wells, Proc Nat. Acad Sci USA 84:6434-6437 (1991)). One or more residues are replaced by alanine or polyalanine residue(s). Those residues demonstrating functional sensitivity to the substitutions then can be refined by introducing further or other mutations at or for the sites of substitution. Thus, while the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined. Similar substitutions can be attempted with other amino acids, depending on the desired property of the scanned residues.

[0063] A more systematic method for identifying amino acid residues to modify comprises identifying residues involved in immune system stimulation or immunodominant antibody recognition and those residues with little or no involvement with immune system stimulation or immunodominant antibody recognition. An alanine scan of the involved residues is performed, with each ala mutant tested for reducing immune system stimulation to an immunodominant epitope or immunodominant antibody recognition. Alternatively, those residues with little or no involvement in immune system stimulation are selected to be modified. Modification can involve deletion of a residue or insertion of one or more residues adjacent to a residue of interest. However, normally the modification involves substitution of the residue by another amino acid. A conservative substitution can be a first substitution. If such a substitution results in reduction of immune system stimulation or reduced reactivity with known immunodominant antibody, then another conservative substitution can be made to determine if more substantial changes are obtained.

[0064] Even more substantial modification in the ability to alter the immune system response away from the immunodominant epitope can be accomplished by selecting an amino acid that differs more substantially in properties from that normally resident at a site. Thus, such a substitution can be made while maintaining: (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation; (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.

[0065] A more rational design strategy, used by immune refocusing, takes into account the key residues in the epitopes that are most responsible for the immune responses and for antibody-antigen binding. Substitution of these key residues enables a more efficient analysis as the mutational strategy focuses on the most important elements of an epitope rather than inserting random substitutions in random sites. Immune refocusing mutations typically focus on these key residues with substitutions of amino acids of similar nature, such as a substitution of glutamine (Gin, Q) for glutamic acid (Glu, E), and the like.

[0066] For example, the naturally occurring amino acids can be divided into groups based on common side chain properties:
  1. (1) hydrophobic: methionine (M or met), alanine (A or ala), valine (V or val), leucine (L or leu) and isoleucine (I or ile);
  2. (2) neutral, hydrophilic: cysteine (C or cys), serine (S or ser), threonine (T or thr), asparagine (N or asn) and glutamine (Q or gln);
  3. (3) acidic: aspartic acid (D or asp) and glutamic acid (E or glu);
  4. (4) basic: histidine (H or his), lysine (K or lys) and arginine (R or arg);
  5. (5) residues that influence chain orientation: glycine (G or gly) and proline (P or pro), and
  6. (6) aromatic: tryptophan (W or trp), tyrosine (Y or tyr) and phenylalanine (F or phe).


[0067] Non-conservative substitutions can entail exchanging an amino acid with an amino acid from another group. Conservative substitutions can entail exchange of one amino acid for another within a group.

[0068] Preferred amino acid substitutions are those which dampen an immunodominant epitope, but can also include those which: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter immune system stimulating activity and/or (4) confer or modify other physico-chemical or functional properties of such analogs. Analogs can include various muteins of a sequence other than the naturally occurring peptide sequence. For example, single or multiple amino acid substitutions (preferably conservative amino acid substitutions) may be made in the naturally-occurring sequence. A conservative amino acid substitution generally should not substantially change the structural characteristics of the parent sequence (e.g., a replacement amino acid should not tend to break a helix that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence) unless of a change in the bulk or conformation of the R group or side chain (Proteins, Structures and Molecular Principles (Creighton, ed., W. H. Freeman and Company, New York (1984); Introduction to Protein Structure, Branden & Tooze, eds., Garland Publishing, New York, NY (1991)); and Thornton et al. Nature 354:105 (1991)).

[0069] Ordinarily, the epitope mutant with altered biological properties will have an amino acid sequence having at least 75% amino acid sequence identity or similarity with the amino acid sequence of the parent molecule, at least 80%, at least 85%, at least 90% and often at least 95% identity. Identity or similarity with respect to parent amino acid sequence is defined herein as the percentage of amino acid residues in the candidate sequence that are identical (i.e., same residue) or similar (i.e., amino acid residue from the same group based on common side-chain properties, supra) with the parent molecule residues, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.

[0070] Covalent modifications of the molecules of interest are included within the scope of the invention. Such may be made by chemical synthesis or by enzymatic or chemical cleavage of the molecule, if applicable. Other types of covalent modifications of the molecule can be introduced into the molecule by reacting targeted amino acid residues of the molecule with an organic derivatizing agent that is capable of reacting with selected side chains or with the N-terminal or C-terminal residue.

[0071] Cysteinyl residues can be reacted with α-haloacetates (and corresponding amines), such as chloroacetic acid or chloroacetamide, to yield carboxylmethyl or carboxyamidomethyl derivatives. Cysteinyl residues also can be derivatized by reaction with bromotrifluoroacetone, α-bromo-β-(5-imidozoyl)propionic acid, chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyl disulfide, p-chloromercuribenzoate, 2-chloromercura-4-nitrophenol or chloro-7-nitrobenzo-2-oxa-1,3-diazole, for example.

[0072] Histidyl residues can be derivatized by reaction with diethylpyrocarbonate at pH 5.5-7.0. p-bromophenacyl bromide also can be used, the reaction is preferably performed in 0.1 M sodium cacodylate at pH 6.0.

[0073] Lysinyl and α terminal residues can be reacted with succinic or other carboxylic acid anhydrides to reverse the charge of the residues. Other suitable reagents for derivatizing α-amino-containing residues include imidoesters, such as, methyl picolinimidate, pyridoxal phosphate, pyridoxal, chloroborohydride, trinitrobenzenesulfonic acid, O-methylisourea and 2,4-pentanedione, and the amino acid can be transaminase-catalyzed with glyoxylate.

[0074] Arginyl residues can be modified by reaction with one or several conventional reagents, such as, phenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione and ninhydrin. Derivatization of arginine residues often requires alkaline reaction conditions. Furthermore, the reagents may react with lysine as well as the arginine ε-amino group.

[0075] The specific modification of tyrosyl residues can be made with aromatic diazonium compounds or tetranitromethane. For example, N-acetylimidizole and tetranitromethane can be used to form O-acetyl tyrosyl species and 3-nitro derivatives, respectively. Tyrosyl residues can be iodinated using 125I or 131I to prepare labeled proteins for use in a radioimmunoassay or with other radionuclides to serve as an imaging means.

[0076] Carboxyl side groups (aspartyl or glutamyl) can be modified by reaction with carbodiimides (R-N=C=C-R'), where R and R' can be different alkyl groups, such as 1-cyclohexyl-3-(2-morpholinyl-4-ethyl) carbodiimide or 1-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide. Furthermore, aspartyl and glutamyl residues can be converted to asparaginyl and glutaminyl residues by reaction with ammonium ions.

[0077] Glutaminyl and asparaginyl residues are frequently deamidated to the corresponding glutamyl and aspartyl residues, respectively, under neutral or basic conditions. The deamidated form of those residues falls within the scope of this invention.

[0078] Other modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of serinyl or threonyl residues, methylation of the α-amino groups of lysine, arginine, and histidine side chains (Creighton, Proteins: Structure and Molecular Properties, W.H. Freeman & Co., San Francisco, pp. 79-86 (1983)), and acetylation of the N-terminal amine and amidation of any C-terminal carboxyl group.

[0079] Another type of covalent modification involves chemically or enzymatically coupling glycosides to the molecules of interest. Depending on the coupling mode used, the sugar(s) may be attached to: (a) arginine and histidine; (b) free carboxyl groups; (c) free sulfhydryl groups, such as those of cysteine; (d) free hydroxyl groups, such as those of serine, threonine or hydroxyproline; (e) aromatic residues such as those of phenylalanine, tyrosine or tryptophan; or (f) the amide group of glutamine. Such methods are described in WO 87/05330 and in Aplin & Wriston, CRC Crit Rev Biochem, pp. 259-306 (1981).

[0080] Removal of any carbohydrate moieties present on the molecule of interest may be accomplished chemically or enzymatically. Chemical deglycosylation, for example, can require exposure of the molecule to the compound, trifluoromethanesulfonic acid, or an equivalent compound, resulting in cleavage of most or all sugars except the linking sugar (N-acetylglucosamine or N-acetylgalactosamine), while leaving the remainder of the molecule intact. Chemical deglycosylation is described, for example, in Hakimuddin et al., Arch Biochem Biophys 259:52 (1987) and in Edge etal., Anal Biochem 118:131 (1981). Enzymatic cleavage of carbohydrate moieties on molecules can be achieved by any of a variety of endoglycosidases and exoglycosidases as described, for example, in Thotakura et al., Meth Enzymol 138:350(1987).

[0081] RNA or DNA encoding the VP-1, VP-2, VP-3, VP-4, protease, and the like of HRV is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to the relevant genes, Innis et al. in PCR Protocols. A Guide to Methods and Applications, Academic (1990), and Sanger et al., Proc Natl Acad Sci 74:5463 (1977)). Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells, including but not restricted to E. coli cells, NS0 cells, COS cells, Chinese hamster ovary (CHO) cells or myeloma cells, to obtain synthesis of the protein of interest in the recombinant host cells. The RNA or DNA also may be modified, for example, by substituting bases to optimize for codon usage in a particular host or by covalently joining to the coding sequence of a heterologous polypeptide. Such an approach would be the basis for developing a subunit vaccine.

[0082] Thus, in one example, the capsid proteins of HRV39 were selected as a target for refocusing the host immune response to other non-dominant sites on the virus particle as novel targets for an immunoprotective response, preferably one of broad scope and spectrum active on a wide variety of strains and so on.

[0083] The above alterations to immunodominant sites can be obtained by cloning, site directed mutagenesis, amplification, immune or drug selection, and so on, using a molecular method, a biological method or both, as known in the art.

[0084] To streamline approval from regulatory agencies, such as the US Food and Drug Administration or European Medicines Agency for human products and the US Department of Agriculture for veterinary products, biological pharmaceutics must meet purity, safety and potency standards defined by the pertinent regulatory agency. To produce a vaccine that meets those standards, the recombinant organisms can be maintained in culture media that is, for example, certified free of transmissible spongiform encephalopathies (herein referred to as "TSE").

[0085] Typically, plasmids harboring the vaccine-encoding sequence carry a non-antibiotic selection marker, since it is not always ideal to use antibiotic resistance markers for selection and maintenance of plasmids in mycobacteria that are designed for use in humans and veterinary pharmaceutics, although use of a recombinant subunit vaccine may be favorable. Therefore, a selection strategy is provided in which, for example, a catabolic enzyme is utilized as a selection marker by enabling the growth of bacteria in medium containing a substrate of said catabolic enzyme as a carbon source. An example of such a catabolic enzyme includes, but is not restricted to, lacYZ encoding lactose uptake and β-galactosidase (Genbank Nos. J01636, J01637, K01483 or K01793). Other selection markers that provide a metabolic advantage in defined media include, but are not restricted to, galTK (GenBank No. X02306) for galactose utilization, sacPA (GenBank No. J03006) for sucrose utilization, trePAR (GenBank No. Z54245) for trehalose utilization, xylAB (GenBank No. CAB13644 and AAB41094) for xylose utilization etc. Alternatively, the selection can involve the use of antisense mRNA to inhibit a toxic allele, such as the sacB allele (GenBank No. NP _391325).

[0086] The immunogen of the present invention as defined in the claims may be used to treat a human. The immunogen as defined in the claims may be administered to a nonhuman mammal for the purpose of obtaining preclinical data, for example. Exemplary nonhuman mammals include nonhuman primates, dogs, cats, rodents and other mammals. Such mammals may be established animal models for a disease to be treated with the formulation, or may be used to study toxicity of the immunogen of interest. In each of those cases, dose escalation studies may be performed in the mammal. A product of the invention as defined in the claims can be used to treat same.

[0087] The specific method used to formulate the novel vaccines and formulations described herein is not critical to the present invention and can be selected from or can include a physiological buffer (Feigner et al., U.S. Pat. No. 5,589,466 (1996)); aluminum phosphate or aluminum hydroxyphosphate (e.g. Ulmer et al., Vaccine, 18:18 (2000)), monophosphoryl-lipid A (also referred to as MPL or MPLA; Schneerson et al. J. Immunol., 147:2136-2140 (1991); e.g. Sasaki et al. Inf. Immunol., 65:3520-3528 (1997); and Lodmell et al. Vaccine, 18:1059-1066 (2000)), QS-21 saponin (e.g. Sasaki et al., J. Virol., 72:4931 (1998)); dexamethasone (e.g., Malone et al., J. Biol. Chem. 269:29903 (1994)); CpG DNA sequences (Davis et al., J. Immunol., 15:870 (1998)); interferon-a (Mohanty et al., J. Chemother. 14(2):194-197, (2002)), lipopolysaccharide (LPS) antagonist (Hone et al., J. Human Virol., 1: 251-256 (1998)) and so on.

[0088] The formulation herein also may contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely impact each other. For example, it may be desirable to further provide an adjuvant. Such molecules suitably are present in combination in amounts that are effective for the purpose intended. The adjuvant can be administered sequentially, before or after antigen administration. Adjuvants are known and examples include aluminum salts, salts of calcium, salts of iron, salts of zinc, insoluble suspensions of acylated tyrosine, acetylated sugars, cationically or anionically derived polysaccharides and polyphosphazenes

[0089] The immunogen of the invention as defined in the claims can be used with a second component, such as a therapeutic moiety conjugated to or mixed with same, administered as a conjugate, separately in combination, mixed prior to use and so on as a therapeutic, see, for example, Levine et al., eds., New Generation Vaccines. 2nd Marcel Dekker, Inc., New York, NY, 1997). The therapeutic agent can be any drug, vaccine and the like used for an intended purpose. Thus, the therapeutic agent can be a biological, a small molecule and so on. The immunogen of the invention as defined in the claims can be administered concurrently or sequentially with a second HRV immunogenic composition, immunodampened or not, for example. Thus, an immunodampened antigen of the invention as defined in the claims can be combined with an existing vaccine, although that approach would minimize the use thereof if the existing vaccine is made in eggs.

[0090] The term "small molecule" and analogous terms include, but are not limited to, peptides, peptidomimetics, amino acids, amino acid analogues, polynucleotides, polynucleotide analogues, carbohydrates, lipids, nucleotides, nucleotide analogues, organic or inorganic compounds (i.e., including heterorganic and/organometallic compounds) having a molecular weight less than about 10,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 5,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 1,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 500 grams per mole, and salts, esters, combinations thereof and other pharmaceutically acceptable forms of such compounds which stimulate an immune response or are immunogenic, or have a desired pharmacologic activity.

[0091] Thus, the immunogen of the invention as defined in the claims may be administered alone or in combination with other types of treatments, including a second immunogen or a treatment for the disease being treated. The second component can be an immunostimulant.

[0092] In addition, the immunogen of the instant invention as defined in the claims may be conjugated to various effector molecules such as heterologous polypeptides, drugs, radionucleotides and so on, see, e.g., WO 92/08495; WO 91/14438; WO 89/12624; U.S. Pat. No. 5,314,995; and EPO 396,387. An immunogen may be conjugated to a therapeutic moiety such as an antibiotic (e.g., a therapeutic agent or a radioactive metal ion (e.g., α emitters such as, for example, 213Bi)) or an adjuvant.

[0093] Therapeutic compounds of the invention alleviate at least one symptom associated with a target disease, disorder, or condition amenable for treatment with an immunogen of interest. The products of the invention may be provided in pharmaceutically acceptable compositions as known in the art or as described herein. The terms "physiologically acceptable," "pharmacologically acceptable" and so on mean approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals and more particularly in humans.

[0094] The products of interest can be administered to a mammal in any acceptable manner. Methods of introduction include, but are not limited to, parenteral, subcutaneous, intraperitoneal, intrapulmonary, intranasal, epidural, inhalation and oral routes, and if desired for immunosuppressive treatment, intralesional administration. Parenteral infusions include intramuscular, intradermal, intravenous, intraarterial or intraperitoneal administration. The products or compositions may be administered by any convenient route, for example, by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. In addition, it may be desirable to introduce the therapeutic products or compositions of the invention into the central nervous system by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir. In addition, the product can be suitably administered by pulse infusion, particularly with declining doses of the products of interest. Preferably the dosing is given by injection, preferably intravenous or subcutaneous injections, depending, in part, on whether the administration is brief or chronic.

[0095] Various other delivery systems are known and can be used to administer a product of the present invention, including, e.g., encapsulation in liposomes, microparticles or microcapsules (see Langer, Science 249:1527 (1990); Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein et al., eds., (1989)).

[0096] The active ingredients may be entrapped in a microcapsule prepared, for example, by coascervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nanoparticles and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, 16th edition, A. Osal, Ed. (1980).

[0097] Respiratory tract or pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent. The composition of interest may also be administered into the upper respiratory tract lungs of a patient in the form of a dry powder composition, see e.g., U.S. Pat. No. 6,514,496.

[0098] It may be desirable to administer the therapeutic products or compositions of the invention as defined in the claims locally to the area in need of treatment; that may be achieved by, for example, and not by way of limitation, local infusion, topical application, by injection, by means of a catheter, by means of a suppository or by means of an implant, said implant being of a porous, non-porous or gelatinous material, including hydrogels or membranes, such as sialastic membranes or fibers. Preferably, when administering a product of the invention, care is taken to use materials to which the protein does not absorb or adsorb.

[0099] In yet another embodiment of the invention as defined in the claims, the product can be delivered in a controlled release system. In one embodiment of the invention as defined in the claims, a pump may be used (see Langer, Science 249:1527 (1990); Sefton, CRC Crit Ref Biomed Eng 14:201 (1987); Buchwald et al., Surgery 88:507 (1980); and Saudek et al., N Engl J Med 321:574 (1989)). In another embodiment of the invention as defined in the claims, polymeric materials can be used (see Medical Applications of Controlled Release, Langer et al., eds., CRC Press (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen et al., eds., Wiley (1984); Ranger et al., J Macromol Sci Rev Macromol Chem 23:61 (1983); see also Levy et al., Science 228:190 (1985); During et al., Ann Neurol 25:351 (1989); and Howard et al., J Neurosurg 71:105 (1989)). In yet another embodiment of the invention as defined in the claims, a controlled release system can be placed in proximity of the therapeutic target.

[0100] The compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations, depots and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulations can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate etc. Examples of suitable carriers are described in "Remington's Pharmaceutical Sciences," Martin. Such compositions will contain an effective amount of the immunogen preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. As known in the art, the formulation will be constructed to suit the mode of administration.

[0101] Sustained release preparations may be prepared for use with the products of interest. Suitable examples of sustained release preparations include semi-permeable matrices of solid hydrophobic polymers containing the immunogen, which matrices are in the form of shaped articles, e.g., films or matrices. Suitable examples of such sustained release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethylmethacrylate), poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers (such as injectable microspheres composed of lactic acid-glycolic acid copolymer) and poly-D-(-)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release cells, proteins and products for and during shorter time periods. Rational strategies can be devised for stabilization depending on the mechanism involved.

[0102] Therapeutic formulations of the product may be prepared for storage as lyophilized formulations or aqueous solutions by mixing the product having the desired degree of purity with optional pharmaceutically acceptable carriers, diluents, excipients or stabilizers typically employed in the art, i.e., buffering agents, stabilizing agents, preservatives, isotonifiers, non-ionic detergents, antioxidants and other miscellaneous additives, see Remington's Pharmaceutical Sciences, 16th ed., Osol, ed. (1980). Such additives are generally nontoxic to the recipients at the dosages and concentrations employed, hence, the excipients, diluents, carriers and so on are pharmaceutically acceptable.

[0103] An "isolated" or "purified" immunogen is substantially free of contaminating proteins from the medium from which the immunogen is obtained, or substantially free of chemical precursors or other chemicals in the medium used which contains components that are chemically synthesized. The language "substantially free of subcellular material" includes preparations of a cell in which the cell is disrupted to form components which can be separated from subcellular components of the cells, including dead cells, and portions of cells, such as cell membranes, ghosts and the like, from which the immunogen is isolated or recombinantly produced. Thus, an immunogen that is substantially free of subcellular material includes preparations of the immunogen having less than about 30%, 20%, 25%, 20%, 10%, 5%, 2.5% or 1%, (by dry weight) of subcellular contaminants.

[0104] As used herein, the terms "stability" and "stable" in the context of a liquid formulation comprising an immunogen refer to the resistance of the immunogen in a formulation to thermal and chemical aggregation, degradation or fragmentation under given manufacture, preparation, transportation and storage conditions, such as, for one month, for two months, for three months, for four months, for five months, for six months or more. The "stable" formulations of the invention retain biological activity equal to or more than 80%, 85%, 90%, 95%, 98%, 99% or 99.5% under given manufacture, preparation, transportation and storage conditions. The stability of said immunogen preparation can be assessed by degrees of aggregation, degradation or fragmentation by methods known to those skilled in the art, including, but not limited to, physical observation, such as, with a microscope, particle size and count determination and so on, compared to a reference.

[0105] The term, "carrier," refers to a diluent, adjuvant, excipient or vehicle with which the therapeutic is administered. Such physiological carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a suitable carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions also can be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.

[0106] Buffering agents help to maintain the pH in the range which approximates physiological conditions. Buffers are preferably present at a concentration ranging from about 2 mM to about 50 mM. Suitable buffering agents for use with the instant invention include both organic and inorganic acids, and salts thereof, such as citrate buffers (e.g., monosodium citrate-disodium citrate mixture, citric acid-trisodium citrate mixture, citric acid-monosodium citrate mixture etc.), succinate buffers (e.g., succinic acid-monosodium succinate mixture, succinic acid-sodium hydroxide mixture, succinic acid-disodium succinate mixture etc.), tartrate buffers (e.g., tartaric acid-sodium tartrate mixture, tartaric acid-potassium tartrate mixture, tartaric acid-sodium hydroxide mixture etc.), fumarate buffers (e.g., fumaric acid-monosodium fumarate mixture, fumaric acid-disodium fumarate mixture, monosodium fumarate-disodium fumarate mixture etc.), gluconate buffers (e.g., gluconic acid-sodium glyconate mixture, gluconic acid-sodium hydroxide mixture, gluconic acid-potassium gluconate mixture etc.), oxalate buffers (e.g., oxalic acid-sodium oxalate mixture, oxalic acid-sodium hydroxide mixture, oxalic acid-potassium oxalate mixture etc.), lactate buffers (e.g., lactic acid-sodium lactate mixture, lactic acid-sodium hydroxide mixture, lactic acid-potassium lactate mixture etc.) and acetate buffers (e.g., acetic acid-sodium acetate mixture, acetic acid-sodium hydroxide mixture etc.). Phosphate buffers, carbonate buffers, histidine buffers, trimethylamine salts, such as Tris, HEPES and other such known buffers can be used.

[0107] Preservatives may be added to retard microbial growth, and may be added in amounts ranging from 0.2%-1% (w/v). Suitable preservatives for use with the present invention include phenol, benzyl alcohol, m-cresol, octadecyldimethylbenzyl ammonium chloride, benzyalconium halides (e.g., chloride, bromide and iodide), hexamethonium chloride, alkyl parabens, such as, methyl or propyl paraben, catechol, resorcinol, cyclohexanol and 3-pentanol.

[0108] Isotonicifiers are present to ensure physiological isotonicity of liquid compositions of the instant invention and include polyhydric sugar alcohols, preferably trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol. Polyhydric alcohols can be present in an amount of between about 0.1% to about 25%, by weight, preferably 1% to 5% taking into account the relative amounts of the other ingredients.

[0109] Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the therapeutic agent or helps to prevent denaturation or adherence to the container wall. Typical stabilizers can be polyhydric sugar alcohols; amino acids, such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, threonine etc.; organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, arabitol, erythritol, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol and the like, including cyclitols such as inositol; polyethylene glycol; amino acid polymers; sulfur containing reducing agents, such as urea, glutathione, thioctic acid, sodium thioglycolate, thioglycerol, α-monothioglycerol and sodium thiosulfate; low molecular weight polypeptides (i.e., <10 residues); proteins, such as human serum albumin, bovine serum albumin, gelatin or immunoglobulins; hydrophilic polymers, such as polyvinylpyrrolidone, saccharides, monosaccharides, such as xylose, mannose, fructose or glucose; disaccharides, such as lactose, maltose and sucrose; trisaccharides, such as raffinose; polysaccharides, such as, dextran and so on. Stabilizers can be present in the range from 0.1 to 10,000 w/w per part of immunogen.

[0110] Additional miscellaneous excipients include bulking agents, (e.g., starch), chelating agents (e.g., EDTA), antioxidants (e.g., ascorbic acid, methionine or vitamin E) and cosolvents.

[0111] As used herein, the term "surfactant" refers to organic substances having amphipathic structures, namely, are composed of groups of opposing solubility tendencies, typically an oil-soluble hydrocarbon chain and a water-soluble ionic group. Surfactants can be classified, depending on the charge of the surface-active moiety, into anionic, cationic and nonionic surfactants. Surfactants often are used as wetting, emulsifying, solubilizing and dispersing agents for various pharmaceutical compositions and preparations of biological materials.

[0112] Non-ionic surfactants or detergents (also known as "wetting agents") may be added to help solubilize the therapeutic agent, as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stresses without causing denaturation of the protein. Suitable non-ionic surfactants include polysorbates (20, 80 etc.), polyoxamers (184, 188 etc.), Pluronic® polyols and polyoxyethylene sorbitan monoethers (TWEEN-20®, TWEEN-80® etc.). Non-ionic surfactants may be present in a range of about 0.05 mg/ml to about 1.0 mg/ml, preferably about 0.07 mg/ml to about 0.2 mg/ml.

[0113] As used herein, the term, "inorganic salt," refers to any compound, containing no carbon, that results from replacement of part or all of the acid hydrogen or an acid by a metal or a group acting like a metal, and often is used as a tonicity adjusting compound in pharmaceutical compositions and preparations of biological materials. The most common inorganic salts are NaCl, KC1, NaH2PO4 etc.

[0114] The present invention as defined in the claims can provide liquid formulations of an immunogen having a pH ranging from about 5.0 to about 7.0, or about 5.5 to about 6.5, or about 5.8 to about 6.2, or about 6.0, or about 6.0 to about 7.5, or about 6.5 to about 7.0.

[0115] The instant invention as defined in the claims encompasses formulations, such as, liquid formulations having stability at temperatures found in a commercial refrigerator and freezer found in the office of a physician or laboratory, such as from about -20° C to about 5° C, said stability assessed, for example, by microscopic analysis, for storage purposes, such as for about 60 days, for about 120 days, for about 180 days, for about a year, for about 2 years or more. The liquid formulations of the present invention as defined in the claims also exhibit stability, as assessed, for example, by particle analysis, at room temperatures, for at least a few hours, such as one hour, two hours or about three hours prior to use.

[0116] Examples of diluents include a phosphate buffered saline, buffer for buffering against gastric acid in the bladder, such as citrate buffer (pH 7.4) containing sucrose, bicarbonate buffer (pH 7.4) alone, or bicarbonate buffer (pH 7.4) containing ascorbic acid, lactose, or aspartame. Examples of carriers include proteins, e.g., as found in skim milk, sugars, e.g., sucrose, or polyvinylpyrrolidone. Typically, these carriers would be used at a concentration of about 0.1-90% (w/v) but preferably at a range of 1-10% (w/v).

[0117] The formulations to be used for in vivo administration must be sterile. That can be accomplished, for example, by filtration through sterile filtration membranes. For example, the subcellular formulations of the present invention may be sterilized by filtration.

[0118] The immunogen composition will be formulated, dosed and administered in a manner consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners. The "therapeutically effective amount" of the immunogen thereof to be administered will be governed by such considerations, and can be the minimum amount necessary to prevent, ameliorate or treat a targeted disease, condition or disorder.

[0119] The amount of antigen is not critical to the present invention as defined in the claims but is typically an amount sufficient to induce the desired humoral and cell mediated immune response in the target host. The amount of immunogen of the present invention to be administered will vary depending on the species of the subject, as well as the disease or condition that is being treated. Generally, the dosage employed can be about 10-1500 µg/dose.

[0120] As used herein, the term "effective amount" refers to the amount of a therapy (e.g., a prophylactic or therapeutic agent), which is sufficient to reduce the severity and/or duration of a targeted disease, ameliorate one or more symptoms thereof, prevent the advancement of a targeted disease or cause regression of a targeted disease, or which is sufficient to result in the prevention of the development, recurrence, onset, or progression of a targeted disease or one or more symptoms thereof. For example, a treatment of interest can increase survivability of the host, based on baseline or a normal level, by at least 5%, preferably at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 100%. In another embodiment of the invention as defined in the claims, an effective amount of a therapeutic or a prophylactic agent reduces the symptoms of a targeted disease, such as a symptom of HRV by at least 5%, preferably at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 100%. Also used herein as an equivalent is the term, "therapeutically effective amount."

[0121] Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lidocaine or other "caine" anesthetic to ease pain at the site of the injection.

[0122] Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water-free concentrate in a sealed container, such as an ampule or sachet indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampule of sterile water for injection or saline can be provided, for example, in a kit, so that the ingredients may be mixed prior to administration.

[0123] An article of manufacture containing materials useful for the treatment of the disorder described above is provided. The article of manufacture can comprise a container and a label. Suitable containers include, for example, bottles, vials, syringes and test tubes. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is effective for preventing or treating a targeted condition or disease and may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The label on or associated with the container indicates that the composition is used for treating the condition of choice. The article of manufacture may further comprise a second container comprising a pharmaceutically acceptable buffer, such as phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes and package inserts with instructions for use.

[0124] The instant disclosure also includes kits, e.g., comprising an immunogenic composition of the invention as defined in the claims, homolog, derivative thereof and so on, for use, for example, as a vaccine, and instructions for the use of same and so on. The instructions may include directions for using the composition, derivative and so on. The composition can be in liquid form or presented as a solid form, generally, desiccated or lyophilized. The kit can contain suitable other reagents, such as a buffer, a reconstituting solution and other necessary ingredients for the intended use. A packaged combination of reagents in predetermined amounts with instructions for use thereof, such as for a therapeutic use is contemplated. In addition, other additives may be included, such as, stabilizers, buffers and the like. The relative amounts of the various reagents may be varied to provide for concentrates of a solution of a reagent, which provides user flexibility, economy of space, economy of reagents and so on.

Example 1



[0125] Cross-protective HRV antigens can be designed and developed using an immune refocusing strategy. Strain-specific epitopes of HRV can be deduced through analysis of sequence variation, serology, and structural characterizations.

[0126] A significant body of published information is available on the structure, antigenic sites, and sequence of picornaviruses including rhinoviruses.

[0127] Figure 2 presents an analysis of variation and antigenic sites based on a global alignment of all HRV-A and HRV-B serotypes (Xiang et al. 2008). Line A shows a linear representation of the PI region which encodes the fragment of the polyprotein which is processed into VP4, VP2, VP3, and VP1 capsid proteins. Line B identifies the B cell epitopes in HRV-A strains which stimulate the dominant antibodies. C and D graphically present diversity between the serotypes in A and B strains, respectively. Line E shows he epitopes of HRV-B serotype viruses. Although the viruses differ greatly in primary amino acid sequence, the areas of diversity and B cell epitopes align.

[0128] Structural data aid in understanding the mechanisms of virus attachment to cell receptors, antibodies, and antiviral molecules. These data can also be utilized to identify immunodominant epitopes in an effort to localize the likely position of immunodominant antigenic sites within the HRV39 capsid sequence. This algorithm weights various parameters such as sequence alignments, hydrophilicity, hydrophobicity, free energy of hydrophilic side chains, mobility, and charge.

[0129] Identification of immunodominant, strain-specific sites on the HRV capsid proteins can be facilitated by analysis of structural data. Although the structural analysis for each serotype has not been completed, sufficient conservation of structure between serotypes permits identification of variable regions, epitopes, and other sites. For example, structural models of HRV2 and other serotypes can be used to predict the epitopes of other serotypes such as HRV39. In Figure 3, the antigenic sites of HRV2 have been modeled using published structures and antigenic data for all available serotypes. Although HRV2 uses the LDL receptor, it is genetically close to HRV39 (Palmenberg et al., 2009), shares 75.4% similarity with HRV39 capsids (compared to 50.4% for HRV14) and can serve as a model for identifying HRV39 antigenic sites. Panel A shows the general arrangement of the capsid proteins on HRV2 virus particle. Panel B presents a ribbon diagram of VP1, VP2, VP3, and VP4 with the position of the antibody binding residues. Panel C presents the capsids in a space-filled, ball, model. In Panel C, the residues adjacent to the antibody binding sites have been distinguished to identify amino acids that may contribute to the antigenicity of the epitopes.

[0130] Once the amino acid residues participating in epitope are identified in HRV2, they can be used to predict similar residues in other HRV-A strains after aligning the sequences. Amino acid alignments of the capsid regions of all HRV-A and HRV-B serotypes reveal that the sites of the highest degree of variability co-localize with immunodominant epitopes discovered through antibody-binding and antibody-escape studies. Figure 4 shows a linear representation of portions of the capsid region of the HRV2 and HRV39 polyproteins. Figure 4 identifies the most highly variable regions and the underlined residues are located within the known epitopes. Residues shown in enlarged and bold typeface indicate the most variable residues within the epitopes. In Figure 4, the number system starts at the N-terminal residue of the PI polyprotein. Additional structural and antigenic site analysis of HRV39 was done using HRV A and B homologues (e.g. 16, 14, 2, 2a, 2b, and 3) and has led to the identification of three major immunodominant B cell epitopes in the capsid proteins (Verdaguer, Blaas et al. 2000).

[0131] Sites identified for engineering immune refocused mutations are presented in Figure 4. The minimal epitope residues are indicated by enlarged and bold type and the adjacent amino acids are underlined. The preponderance of charged residues in epitopes is noted. The alignment with HRV2 is used to identify amino acid residues of HRV39 that are likely components of immunodominant epitopes. In Figure 4, the bold, underlined residues correspond to the surface smoothed amino acids in Figure 3B and the underlined (but not bold) letters correspond to flanking residues shown as gray balls in Figure 3C.

[0132] Examples of immune refocusing mutations are shown in Figure 5. Several of the mutations target specific residues in the minimal epitopes as defined by antibody footprints. Thus, M1, M2, M7, M8, M9, and M14 are designed to assess immune dampening at sites thought to be most important in antibody binding in antigenic sites corresponding to HRV2 sites A, B, and C. Additional mutations are presented to assess the additive or multiplicative effects of combining the mutations within epitopes to derive M5, M12, and M16. Because it is possible that mutations to one or more of these sites may not have the most optimum effect of stimulating broadened immunity or may be essential for protein folding and capsid assembly, a second set of mutations are shown that target the flanking residues (dark gray balls in Figure 3C, mutants, M3, M4, M10, M11, and M15).

[0133] Using similar logical strategies, mutations that target additional sites within the HRV-39 capsid molecules or those that target immunodominant sites in other HRV serotypes can be designed.

[0134] IRT mutations can be introduced into the capsid gene fragment of HRV39 for the purposes of analyzing cross-neutralizing immune responses using site-directed mutagenesis methods known to the art. The capsid genes can be expressed using a variety of systems known for the expression of recombinant proteins such as bacteria, yeast, mammalian, and insect cell vectors. In the present example, the IRT mutations were introduced into HRV39 capsid genes that were co-expressed with the viral protease protein, 3C, using recombinant baculoviruses. Alternative strategies to produce VLPs of HRV include the use of a single polyprotein containing both the capsid and 3C proteins, separate baculoviruses expressing the capsid and 3C fragments, and other methods known to the art. Further, VLPs of HRV and other rhinoviruses can be stabilized by substituting amino acids that are proximal to the interface between capsid proteins that form capsomers and assemble into virions or virus-like particles. Such amino acid residue can be substituted with cysteine residues to permit disulfide bonds to form between the two proteins and thereby strengthen or stabilize the capsid structure.

[0135] Insect cells and insect larva were infected with the recombinant baculoviruses for the purpose of producing the IRT antigens as virus-like particles (VLPs). Figure 6 shows electron micrographs comparing the structure of the HRV39 VLPs (right panel) with HeLa cell-produced HRV virions (left panel). The VLPs are consistent in size and appearance with empty particles.

[0136] Rabbits were immunized with HRV39 IRT VLP antigens. After two boosts, sera were collected for analysis of immune responses.

[0137] Virus neutralization assays were performed to assess stimulation of cross-protective immunity conveyed by the IRT antigens. Sixty-one serotypes of HRV were propagated to derive reagent stocks that were standardized to 100-1,000 tissue-culture infectious dose-50 (TCID50) of each virus per microliter, for example, depending on the CPE and the replication time of a serotype. Figure 7 lists the viruses prepared for the cross-neutralization tests. Standard neutralization assays were done to identify serotypes of viruses that were neutralized by sera from IRT antigens as compared to non-immune sera. Briefly, 100-1,000 TCID50 doses of virus were incubated with test sera. To ensure that IRT sera could be distinguished from non-immune rabbit sera on the basis of neutralizing heterologous, final concentrations of IRT sera at 1:8 were compared to 1:2 dilutions of non-immune sera. IRT sera (1:8) were incubated with each heterologous virus (100-1000 TCID50) for 1h and then placed onto MRC-5 cells for 1h at room temperature using duplicate wells. The monolayers were rinsed with media to remove unattached virus, overlaid with standard growth media, and incubated for 2-4 days at 35°C. The monolayers were observed microscopically until cytopathic effects (CPE) due to virus infection were visible in the negative control wells in which the virus had been incubated with non-immune sera. The intensity of the CPE in each well was scored at least three times over the next 48 hours to assess virus propagation. Scoring was based on a scale of 0 to 10 in which wells showing no, slight, moderate, strong, or complete CPE were assigned a value of 0, 1-2, 3-4, 5-9, or 10, respectively. The scores of the duplicate wells were aggregated as a set and analyzed to determine whether they were statistically higher than the scores assigned to the wells in which the virus had been incubated with non-immune sera instead of sera from rabbits immunized with IRT antigens. The Student's T test was used to determine which HRV serotypes were neutralized better by sera from IRT antigens as compared with non-immune sera. Figure 8 presents the serotypes that were neutralized by HRV39 IRT sera with a confidence level equal to or greater than 95% for each serum. The column under the heading "39WT" lists the HRV serotypes neutralized by serum from rabbits immunized with unmodified (WT) HRV39 antigen. It is important to note that the sera from WT antigen neutralizes only the homologous HRV39 antigen and the sera from the IRT antigens neutralize multiple serotypes of HRV. The right-most column presents an aggregate of all tested HRV serotypes that were shown to be neutralized.

Example 2



[0138] In addition to separate mutations, immune refocused immunogens may be composed of combinations of mutations at different sites. Thus, immune refocused antigens may contain multiple mutations to epitopes A, B, or C (see Figure 4) or other antigenic, structural, or functional sites located in other parts of the virus. HRV39 IRT mutants M12, 13, 17, and 18 are examples of antigens containing IRT mutations at multiple epitopes. After engineering the combination sites into the antigen, the second-generation antigens are tested for stimulation of enhanced cross-protective immune responses as described in Example 2.

Example 3



[0139] Reverse genetics systems have been developed for HRV and other viruses for the purpose of introducing site-specific mutations into the genomes of the viruses (Lee and Wang, 2003). Immune refocusing mutations can be engineered into recombinant, replication-competent HRV virions. Figure 9 presents examples of IRT modifications made in the context of the HRV-16 virus sequence. After introduction of the IRT mutations into the proviral plasmid clones, viral RNA transcripts were synthesized from the plasmids using RNA-dependent RNA polymerase and transfected into HeLa cells to derive novel strains of HRV16. The recombinant viruses were propagated in HeLa cells and purified using standard HRV purification methods. Rabbits were immunized with the HRV16 IRT variants and serum samples tested for cross-neutralization of the panel of HRV serotypes shown previously in Figure 7. Using a similar neutralization assay as in Example 1, sera from rabbits immunized with immune refocused HRV16 virions were compared to non-immune sera to identify heterologous serotypes of virus that could be cross-neutralized by the IRT sera. Figure 10 lists the viruses that were neutralized by the five HRV16 IRT sera at a confidence level equal to or greater than 95%. The column under the heading "16WT" shows that sera from unmodified HRV16 neutralized homologous virus (HRV16) but did not cross-neutralize heterologous serotypes of HRV. In contrast sera from IRT antigens demonstrated robust cross-neutralization of multiple serotypes of HRV.

Example 4



[0140] The above examples demonstrate that the immune refocusing technology is independent of vector or antigen format for stimulated improved cross-reactive immune responses.

[0141] IRT antigens of HRV can be incorporated into alternative expression platforms including recombinant viruses such as adenovirus or vaccinia viruses, bacterial or yeast expression systems, and DNA expression molecules.

Example 5



[0142] The immune refocusing mutations can be designed rationally using the algorithms described above which include but are not restricted to sequence alignments to identify variable and conserved regions; structural analyses to identify flexible loops, residues associated with functional requirements of the virus, and other features; biochemical analysis of charge, hydrophathy, physical size and other chemical features of amino acids; and the like. Alternatively, IRT mutations can be designed through the use of escape mutations.

[0143] In the present example, antibody escape mutations were derived from cultures infected with HRV14. The virus was pre-incubated with varying concentrations of monoclonal or polyclonal antibodies, placed onto cells for 1h to allow attachment to occur, and washed off. The cells were overlaid with standard culture media and incubated for 1 day at 35°C to permit replication of viruses that were not neutralized by the antibodies. The process was repeated with increasing concentrations of antibody to derive virus strains that were resistant to the antibody.

[0144] Figure 11 shows an example of virus escape mutants derived using HRV14 and either polyclonal rabbit sera raised against HRV14 virions or monoclonal antibody MoAb17 directed against the NIM-1A epitope. Virus progeny were plaque purified and sequenced to identify amino acids in the virus that survived the antibody pressure. After 3 passages, four plaques were analyzed (Panel A). Two had no mutations in the capsid region, one had a mutation that lead to E94D in residue #94 of VP1, and one had a mutation that led to E90N. After 6 passages, six plaques were analyzed (Panel B). Again, mutations were observed in residues 90 and 94 of VP1. In addition, mutations were observed in residues 120, 124, 125, 126, and 127 of VP2. The result suggests that the antibody contacts the virus at or near these residues. A similar result was observed after 3 passages of virus following incubation with polyclonal rabbit antisera. Panel C shows the sequences in the capsid gene fragment found to contain mutations following pressure with polyclonal antibody. As can be seen, the predominant mutations were in VP2 and the sites overlapped those observed with MoAb #17 shown in Panel B. This result suggests that the polyclonal antibody response contains a low diversity of antibody species and that these species of antibody molecules primarily recognize one or two epitopes.

[0145] The results in antibody escape studies can be used to design IRT antigens having the mutations of the escape variants.

[0146] Similar studies can be performed using sera from human subjects experimentally infected with FDA-approved stocks of HRV16 and HRV39 or from natural infections.

Example 6



[0147] The above examples utilize HRV-A (HRV16 and HRV39) and HRV-B (HRV14) serotypes as examples of immune refocusing of HRV. HRV-C serotypes can also be used as the parental virus for immune refocusing.

[0148] HRV-C has been shown to cause disease and exacerbate asthma and chronic lung disease. Efforts to understand the biology and immunology of HRV-C viruses have been complicated by the difficulties encountered in propagating the HRV-C viruses in standard cell lines other than primary human tissue explants.

[0149] Fragments and complete genomes of HRV-C viruses have been cloned and nucleic acid and protein sequences determined. Alignments of the HRV-C capsid sequences in the PI fragment are used to identify regions of variation and conservation. Like HRV-A and HRV-B viruses (and other Class II pathogens such as HIV-1 and influenza), the regions of maximum variation correlate with serotype-specific epitopes. Regions of diversity between the HRV-C viruses are targeted for immune refocusing to design and engineer antigens that stimulate antibodies that neutralize multiple serotypes of HRV-C viruses.

[0150] Immune refocusing mutation similar to those provided in the examples above are used. In general, charged amino acids can be substituted by uncharged residues to reduce the strain-restricted antigenicity without destroying structural features such as conformational epitopes. HRV-C viruses of known sequence, such as strain W10-C15, can be used as parental antigens to derive immune refocused antigens.

[0151] The resultant immune refocused HRV-C antigens can be used as vaccine components, diagnostic reagents, or to derive novel antibodies.

Example 7



[0152] Immune refocused HRV antigens can be used as vectors to deliver heterologous epitopes, or therapeutic or toxic molecules.

[0153] The structural models of HRV serotypes can be used to identify flexible loops that can accept the insertion of heterologous epitopes or other molecules. Epitopes from other viruses, such as but not limited to HRV-1 V3 loop peptides, influenza HA epitopes, and the like can be molecularly engineered to be expressed in recombinant virions or VLPs of immune refocused HRV antigens. Using a similar strategy, toxic or therapeutic molecules can be incorporated into the structures for the purpose of providing therapy for cancer or other diseases for which an HRV carrier vector may provide advantages.

[0154] The immune refocused HRV VLPs and viruses can also be used to encapsulate small molecules for therapeutic uses. If for example, HRV VLPs can be show to preferentially attach to and enter specific target cells such as cancer cells, the antigens can be used as carrier vectors for delivery of small therapeutic molecules or toxins. The VLP can be readily disrupted in various denaturants known in the art such as but not limited to 5M urea, 6M guanidine-HCL and others. After denaturation, additional small molecules can be added to the solution and the denaturant removed by dialysis or other method. Upon removal of the denaturant, the VLPs and virus particles re-associate into virus-like structures. Because the small molecules were included in the solution, they can be incorporated within the virion or VLP. When the virion or VLP is introduced into a human, it can attach to a cell bearing a virus receptor. Upon entry into the cell, the virus will deliver the payload for therapeutic or toxic uses.

Example 8



[0155] The safety, toxicity and potency of recombinant immunogens are evaluated according to the guidelines in 21 CFR 610, which include: (i) general safety test; (ii) stringent safety test in immunocompetent mice; (iii) guinea pig safety test; and (iv) acute and chronic toxicity tests, as described below.

[0156] Groups of eight BALB/c mice are inoculated intraperitoneally with 100 µl of immunogen containing 300 µg of the immunogen of interest. Suitable negative and positive controls are used.

[0157] The animals are monitored for general health and body weight for 14 days post infection. Similar to animals that receive placebo, animals that receive the immunogen remain healthy, and do not lose weight or display overt signs of disease during the observation period.

[0158] For the more stringent safety test, groups of 15 healthy BALB/c mice are injected with 300 µg of the immunogen.

[0159] One day after inoculation, 3 mice in each group are euthanized and the spleen, lung and liver homogenates are analyzed for immunogen. At week 4, 8, 12, and 16 post infection, 3 mice in each group are euthanized and spleen, live and lung homogenates are obtained and analyzed to assess presence of the immunogen.

[0160] The safety of immunogen is also assessed in the guinea pig model. First, the effect of the immunogen on the general health status of the animals is examined, including weight gain.

[0161] Groups of 8 guinea pigs are inoculated intramuscularly with 300 µg of the immunogen.

[0162] The general health and body weight of the animals are monitored for six weeks post inoculation. If any animals are euthanized before the six-week period concludes due to serious adverse effects, each euthanized animal will be subjected to a detailed post-mortem examination. All animals are euthanized at the end of six weeks post-inoculation and gross pathology is performed. The immunogen is deemed safe if no adverse health effects are observed and the animals gain weight at the normal rate compared to animals inoculated with placebo as an internal control.

[0163] To evaluate the acute and chronic toxicity of an immunogen, groups of 16 guinea pigs are inoculated intradermally with 300 µg of the immunogen at graded doses or saline.

[0164] Three days post-inoculation, 8 animals in each group are euthanized to access the acute effects of the immunogen on the animals. At 28 days post-inoculation, the remaining 8 animals in each group are euthanized to evaluate any chronic effects on the animals. At both time points, the body weight of each animal is obtained. In addition, the gross pathology and appearance of the injection sites are examined. Blood is taken for blood chemistry, and the histopathology of the internal organs and injection sites are performed at each time point.

[0165] The mice are given a total of 3 doses of vaccine at 0, 14 and 60 days and the immune response to HRV is measured by ELISA using sera collected from individual mice at 10 day intervals, as described. The neutralization of HRV is measured in the collected sera 80 days after the first vaccination. The results of the study show that the vaccine of interest has the capacity to substantially increase the magnitude and potency of the humoral response to HRV and therefore possesses useful adjuvant properties.

Example 9



[0166] Immune refocused antigens can be used as immunogens to raise novel antibodies useful as diagnostics, laboratory reagents, and/or therapeutics. The novel antibodies can be derived as polyclonal antibodies, monoclonal antibodies, or recombinant antibodies derived from immune cells of immunized humans, animals, or in vitro immune systems.

[0167] Cross-neutralizing antibodies are rarely observed when an individual has been infected with an HRV serotype or when an animal has been immunized with a naturally-occurring HRV antigen. Because immune refocused antigens contain mutations to serotype-specific epitopes, immunization with immune refocused antigens can enrich the percentage of antibodies or monoclonal antibodies that contain cross-neutralizing activities.

[0168] In a similar manner, immune refocused antigens can be used to identify cross-neutralizing antibodies. Immune refocused antigens have mutations in the serotype-restricted epitopes. Antibodies in the population or monoclonal antibodies produced by any method known to the art that are specific to the serotype-restricted epitope that was altered in the immune refocused antigen will not be detected. In the event that the serotype-restricted antibodies are in the majority, the use of immune refocused antigens in the screening steps will improve the efficiency of identifying antibodies that bind the antigen at sites other than those that were altered.

[0169] The Sequence Listing filed concurrently herewith herein is incorporated by reference in entirety.

REFERENCES CITED



[0170] 
  1. 1. Kohler H, Goudsmit, J. Nara P. Clonal dominance: cause for a limited and failing immune response to HIV-1 infection and vaccination. J. Acquir Immune Defic Syndr. 1992; 5(11): 1158-68.
  2. 2. Lee, W. -M., and Wang, W. (2003). Human rhinovirus type 16: mutant V1210A requires capsid-binding drug for assembly of pentamers to form virions during morphogenesis. J. Virology. 77, 6235-6244.
  3. 3. Kiszka, I., D. Kmieciak, J. Gzyl, T. Naito, E. Bolesta, A. Sieron, S. P. Singh, A. Srinivasan, G. Trinchieri, Y. Kaneko, and D. Kozbor. 2002. Effect of the V3 loop deletion of envelope glycoprotein on cellular responses and protection against challenge with recombinant vaccinia virus expressing gp160 of primary human immunodeficiency virus type 1 isolates. J Virol 76:4222-32.
  4. 4. Adams, P. F., G. E. Hendershot, et al. (1999). "Current estimates from the National Health Interview Survey, 1996." Vital Health Stat 10(200): 1-203.
  5. 5. Appleyard, G., S. M. Russell, et al. (1990). "Neutralization epitopes of human rhinovirus type 2." J Gen Virol 71 (Pt 6): 1275-82.
  6. 6. Bertino, J. S. (2002). "Cost burden of viral respiratory infections: issues for formulary decision makers." Am J Med 112 Suppl 6A: 42S-49S.
  7. 7. Garrity, R. R., G. Rimmelzwaan, et al. (1997). "Refocusing neutralizing antibody response by targeted dampening of an immunodominant epitope." J Immunol 159(1): 279-89.
  8. 8. Hastings, G. Z., S. A. Speller, et al. (1990). "Neutralizing antibodies to human rhinovirus produced in laboratory animals and humans that recognize a linear sequence from VP2." J Gen Virol 71 (Pt 12): 3055-9.
  9. 9. Hewat, E. A. and D. Blaas (1996). "Structure of a neutralizing antibody bound bivalently to human rhinovirus 2." EMBO J 15(7): 1515-23.
  10. 10. Hewat, E. A., T. C. Marlovits, et al. (1998). "Structure of a neutralizing antibody bound monovalently to human rhinovirus 2." J Virol 72(5): 4396-402.
  11. 11. Mackay, I. M. (2008). "Human rhinoviruses: the cold wars resume." J Clin Virol 42(4): 297-320.
  12. 12. Paranhos-Baccalà, K. Shen, Q. Jin, and J. Wang Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 14, No. 10, October 2008 pgs 1665-1667.
  13. 13. Palmenberg, A. C., D. Spiro, et al. (2009). "Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveals Structure and Evolution." Science. 324(5923):55-9.
  14. 14. Turner, R. B. (2001). "The treatment of rhinovirus infections: progress and potential." Antiviral Res 49(1): 1-14.
  15. 15. Verdaguer, N., D. Blaas, et al. (2000). "Structure of human rhinovirus serotype 2 (HRV2)." J Mol Biol 300(5): 1179-94.
  16. 16. Z. Xiang, R. Gonzalez, Z. Xie, Y. Xiao, L. Chen, Y. Li, C. Liu, Y. Hu, Y. Yao, S. Qian, R. Geng, G. Vernet, G. (2008) www.cdc.gov/eid , vol. 14, No. 10 pgs. 1665-1667.
  17. 17. Speller et al. (1993) "The nature and spatial distribution of amino acid substitutions conferring resistance to neutralizing monoclonal antibodies in human rhinovirus type 2." J Gen Virol 74(2)193-200.

HRV16 WT (SEQ ID N0:64

HRV16 M1 (SEQID N0:65)

HRV16 M2 (SEQ ID N0:66)

HRV16 M3 (SEQID N0:67)

HRV16 M4 (SEQID N0:68)

HRV16 MS (SEQID N0:69)

HRV16 M6 (SEQID N0:70)

HRV16 M7 (SEQID N0:71)

HRV16 MS (SEQID N0:72)

HRV16 M9 (SEQID N0:73)

HRV39 Attn WT (SEQID N0:74)

HRV39 Attn M1 (SEQID N0:75)

HRV39 Attn M2 (SEQID N0:76)

HRV39 Attn M3 (SEQID N0:77)

HRV39 Attn M4 (SEQID N0:78)

HRV39 Attn MS (SEQID N0:79)

HRV39 Attn M6 (SEQID N0:80)

HRV39 Attn M7 (SEQID N0:81

HRV39 Attn MS (SEQID N0:82)

HRV39 Attn M9 (SEQID N0:83)

HRV39 Attn M1O (SEQID N0:84)

HRV39 Attn M11 (SEQID N0:85)

HRV39 Attn M12 (SEQID N0:86)

HRV39 Attn M13 (SEQID N0:87)

HRV39 Attn M14 (SEQID N0:88)

HRV39 Attn M15 (SEQID N0:89)

HRV39 Attn M16 (SEQID N0:90)

HRV39 Attn M17 (SEQID N0:91)

1 HRV39 Attn M18 (SEQ ID N0:92)

2


SEQUENCE LISTING



[0171] 

<110> BIOLOGICAL MIMETICS, INC.

<120> IMMUNOGENIC HUMAN RHINOVIRUS (HRV) COMPOSITION

<130> 020812-02131201

<140>
<141>

<150> 61/793,788
<151> 2013-03-15

<160> 92

<170> PatentIn version 3.5

<210> 1
<211> 77
<212> PRT
<213> Human rhinovirus

<220>
<221> MOD_RES
<222> (5)..(46)
<223> Any amino acid

<220>
<221> MOD_RES
<222> (50)..(65)
<223> Any amino acid

<400> 1

<210> 2
<211> 77
<212> PRT
<213> Human rhinovirus

<220>
<221> MOD_RES
<222> (5)..(46)
<223> Any amino acid

<220>
<221> MOD_RES
<222> (50)..(65)
<223> Any amino acid

<400> 2

<210> 3
<211> 32
<212> PRT
<213> Human rhinovirus

<400> 3

<210> 4
<211> 31
<212> PRT
<213> Human rhinovirus

<400> 4

<210> 5
<211> 20
<212> PRT
<213> Human rhinovirus

<400> 5

<210> 6
<211> 20
<212> PRT
<213> Human rhinovirus

<400> 6

<210> 7
<211> 11
<212> PRT
<213> Human rhinovirus

<400> 7

<210> 8
<211> 11
<212> PRT
<213> Human rhinovirus

<400> 8

<210> 9
<211> 18
<212> PRT
<213> Human rhinovirus

<400> 9

Val Trp

<210> 10
<211> 18
<212> PRT
<213> Human rhinovirus

<400> 10



<210> 11
<211> 13
<212> PRT
<213> Human rhinovirus

<400> 11

<210> 12
<211> 13
<212> PRT
<213> Human rhinovirus

<400> 12

<210> 13
<211> 31
<212> PRT
<213> Human rhinovirus

<400> 13

<210> 14
<211> 31
<212> PRT
<213> Human rhinovirus

<400> 14

<210> 15
<211> 20
<212> PRT
<213> Human rhinovirus

<400> 15



<210> 16
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 16

<210> 17
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 17

<210> 18
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 18

<210> 19
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 19

<210> 20
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 20

<210> 21
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 21

<210> 22
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 22



<210> 23
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 23

<210> 24
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 24

<210> 25
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 25

<210> 26
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 26

<210> 27
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 27

<210> 28
<211> 40
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 28

<210> 29
<211> 13
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 29

<210> 30
<211> 13
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 30

<210> 31
<211> 13
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 31

<210> 32
<211> 73
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 32

<210> 33
<211> 73
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic polypeptide

<400> 33

<210> 34
<211> 19
<212> PRT
<213> Human rhinovirus

<400> 34



<210> 35
<211> 19
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 35

<210> 36
<211> 20
<212> PRT
<213> Human rhinovirus

<400> 36

<210> 37
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 37

<210> 38
<211> 19
<212> PRT
<213> Human rhinovirus

<400> 38



<210> 39
<211> 19
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 39

<210> 40
<211> 10
<212> PRT
<213> Human rhinovirus

<400> 40

<210> 41
<211> 10
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 41

<210> 42
<211> 21
<212> PRT
<213> Human rhinovirus

<400> 42

<210> 43
<211> 21
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 43

<210> 44
<211> 20
<212> PRT
<213> Human rhinovirus

<400> 44

<210> 45
<211> 20
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 45

<210> 46
<211> 19
<212> PRT
<213> Human rhinovirus

<400> 46

<210> 47
<211> 19
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 47

<210> 48
<211> 8
<212> PRT
<213> Human rhinovirus

<400> 48

<210> 49
<211> 8
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 49

<210> 50
<211> 25
<212> PRT
<213> Human rhinovirus

<400> 50

<210> 51
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 51

<210> 52
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 52

<210> 53
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 53

<210> 54
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 54



<210> 55
<211> 25
<212> PRT
<213> Human rhinovirus

<400> 55

<210> 56
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 56

<210> 57
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 57

<210> 58
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 58

<210> 59
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 59

<210> 60
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 60

<210> 61
<211> 25
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic peptide

<400> 61

<210> 62
<211> 40
<212> PRT
<213> Human rhinovirus

<400> 62

<210> 63
<211> 13
<212> PRT
<213> Human rhinovirus

<400> 63

<210> 64
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 64







<210> 65
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 65







<210> 66
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 66







<210> 67
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 67







<210> 68
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 68









<210> 69
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 69







<210> 70
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 70









<210> 71
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 71







<210> 72
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 72









<210> 73
<211> 859
<212> PRT
<213> Human rhinovirus

<400> 73







<210> 74
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 74









<210> 75
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 75







<210> 76
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 76









<210> 77
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 77







<210> 78
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 78









<210> 79
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 79







<210> 80
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 80









<210> 81
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 81







<210> 82
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 82









<210> 83
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 83







<210> 84
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 84







<210> 85
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 85







<210> 86
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 86







<210> 87
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 87







<210> 88
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 88







<210> 89
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 89









<210> 90
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 90







<210> 91
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 91









<210> 92
<211> 863
<212> PRT
<213> Human rhinovirus

<400> 92










Claims

1. An isolated polypeptide or virus containing an amino acid sequence selected from the group consisting of SEQ ID NOs: 16-21, 35, 65-73 and 75-92.
 
2. An isolated nucleic acid molecule encoding a polypeptide of claim 1.
 
3. A fusion protein comprising the polypeptide of claim 1.
 
4. A recombinant expression vector comprising the nucleic acid molecule of claim 2 and optionally a heterologous nucleic acid molecule.
 
5. A virus-like particle (VLP) comprising the polypeptide of claim 1, the fusion protein of claim 3, or a protein encoded by the recombinant expression vector of claim 4.
 
6. A recombinant virus comprising the polypeptide of claim 1, the fusion protein of claim 3, or a protein encoded by the recombinant expression vector of claim 4.
 
7. The VLP of claim 5 or the virus of claim 6, further comprising a toxic or therapeutic molecule.
 
8. A host cell comprising the recombinant expression vector of claim 4, the VLP of claim 5 or 7, or the virus of claim 6 or 7.
 
9. An immunogenic composition comprising one or more of the polypeptides of claim 1, the fusion protein of claim 3, the VLP of claim 5, or the virus of claim 6, optinally further comprising an adjuvant, wherein, preferably, the adjuvant is sleeted from a group consisting of an aluminum salt, a salt of calcium, a salt of iron, a salt of zinc, an insoluble suspension of acylated tyrosine, acetylated sugars, cationically or anionically derived polysaccharides, and polyphosphazenes.
 
10. A vaccine comprising one or more of the polypetides of claim 1, the fusion protein of claim 3, the VLP of claim 5, the virus of claim 6, or the immunogenic composition of claim 9.
 
11. A pharmaceutical composition comprising one or more of the polypeptides of claim 1, the fusion protein of claim 3, the VLP of claim 5, the virus of claim 6, or the immunogenic composition of claim 9.
 
12. The immunogenic composition of claim 9 or the vaccine of claim 10 for use in a method of eliciting an immune response to an human rhinovirus (HRV) in a subject, wherein the method comprises administering to the subject an effective amount of the immunogenic composition or the vaccine, thereby eliciting an immune response to a human rhinovirus (HRV) in the subject.
 
13. The immunogenic composition of claim 9 or the vaccine of claim 10 for use in a method of treating a subject infected with a human rhinovirus (HRV), wherein the method comprises administering to the subject a therapeutically effective amount of the immunogenic composition or the vaccine, thereby treating the subject infected with the human rhinovirus (HRV).
 
14. The immunogenic composition of claim 9 or the vaccine of claim 10 for use in a method of vaccinating a subject against multiple serotypes of human rhinovirus (HRV), wherein the method comprises administering to the subject an effective amount of the immunogenic composition or the vaccine.
 
15. The immunogenic composition or the vaccine for use of any one of claims 12-14, wherein the subject is a human, preferably the subject is an adult human, an adolescent human, or an infant human.
 
16. The immunogenic composition of claim 9 or the vaccine of claim 10 for use in therapy.
 


Ansprüche

1. Isoliertes Polypeptid oder Virus enthaltend eine Aminosäuresequenz ausgewählt aus der Gruppe bestehend aus SEQ ID NOs: 16-21, 35, 65-73 und 75-92.
 
2. Isoliertes Nukleinsäuremolekül codierend für ein Polypeptid nach Anspruch 1.
 
3. Fusionsprotein umfassend das Polypeptid nach Anspruch 1.
 
4. Rekombinanter Expressionsvektor umfassend das Nukleinsäuremolekül nach Anspruch 2 und optional ein heterologes Nukleinsäuremolekül.
 
5. Virus-ähnliches Partikel (VLP) umfassend das Polypeptid nach Anspruch 1, das Fusionsprotein nach Anspruch 3 oder ein durch den Expressionsvektor nach Anspruch 4 codiertes Protein.
 
6. Rekombinates Virus umfassend das Polypeptid nach Anspruch 1, das Fusionsprotein nach Anspruch 3 oder ein durch den rekombinanten Expressionsvektor nach Anspruch 4 codiertes Protein.
 
7. VLP nach Anspruch 5 oder Virus nach Anspruch 6, weiter umfassend ein toxisches oder therapeutisches Molekül.
 
8. Wirtszelle umfassend den rekombinanten Expressionsvektor nach Anspruch 4, das VLP nach Anspruch 5 oder 7 oder das Virus nach Anspruch 6 oder 7.
 
9. Immunogene Zusammensetzung umfassend ein oder mehrere von den Polypeptiden nach Anspruch 1, dem Fusionsprotein nach Anspruch 3, dem VLP nach Anspruch 5 oder dem Virus nach Anspruch 6, optional weiter umfassend ein Adjuvans, wobei, bevorzugterweise, das Adjuvans ausgewählt ist aus der Gruppe bestehend aus einem Aluminiumsalz, einem Calciumsalz, einem Eisensalz, einem Zinksalz, einer unlöslichen Suspention von acyliertem Tyrosin, acetylierten Zuckern, kationisch- oder anionisch-gewonnenen Polysacchariden und Polyphosphazenen.
 
10. Vakzin umfassend ein oder mehrere von den Polypeptiden nach Anspruch 1, dem Fusionsprotein nach Anspruch 3, dem VLP nach Anspruch 5, dem Virus nach Anspruch 6, oder der immunogenen Zusammensetzung nach Anspruch 9.
 
11. Pharmazeutische Zusammensetzung umfassend ein oder mehrere von den Polypeptiden nach Anspruch 1, dem Fusionsprotein nach Anspruch 3, dem VLP nach Anspruch 5, dem Virus nach Anspruch 6 oder der immunogenen Zusammensetzung nach Anspruch 9.
 
12. Immunogene Zusammensetzung nach Anspruch 9 oder Vakzin nach Anspruch 10 zur Verwendung in einem Verfahren zum Auslösen einer Immunantwort auf ein humanes Rhinovirus (HRV) in einem Lebewesen, wobei das Verfahren umfasst Verabreichen an das Lebewesen einer wirksamen Menge der immunogenen Zusammensetzung oder des Vakzins, wodurch eine Immunantwort auf ein humanes Rhinovirus (HRV) in dem Lebewesen ausgelöst wird.
 
13. Immunogene Zusammensetzung nach Anspruch 9 oder Vakzin nach Anspruch 10 zur Verwendung in einem Verfahren zum Behandeln eines mit einem humanen Rhinovirus (HRV) infizierten Lebewesens, wobei das Verfahren umfasst Verabreichen an das Lebewesen einer therapeutisch wirksamen Menge der immunogenen Zusammensetzung oder des Vakzins, wodurch das mit dem humanen Rhinovirus (HRV) infizierte Lebewesen behandelt wird.
 
14. Immunogene Zusammensetzung nach Anspruch 9 oder Vakzin nach Anspruch 10 zur Verwendung in einem Verfahren zum Vakzinieren eines Lebewesens gegen multiple Serotypen von menschlichem Rhinovirus (HRV), wobei das Verfahren umfasst Verabreichen an das Lebewesen einer wirksamen Menge der immunogenen Zusammensetzung oder des Vakzins.
 
15. Immunogene Zusammensetzung oder Vakzin zur Verwendung nach einem der Ansprüche 12 bis 14, wobei das Lebewesen ein Mensch ist, bevorzugterweise ist das Lebewesen ein erwachsener Mensch, ein heranwachsender Mensch oder ein menschliches Kleinkind.
 
16. Immunogene Zusammensetzung nach Anspruch 9 oder Vakzin nach Anspruch 10 zur therapeutischen Verwendung.
 


Revendications

1. Polypeptide ou virus isolé contenant une séquence d'acides aminés choisie dans le groupe constitué des SEQ ID NO: 16 à 21, 35, 65 à 73 et 75 à 92.
 
2. Molécule d'acide nucléique isolée codant pour un polypeptide selon la revendication 1.
 
3. Protéine de fusion comprenant le polypeptide selon la revendication 1.
 
4. Vecteur d'expression recombinant comprenant la molécule d'acide nucléique selon la revendication 2 et éventuellement une molécule d'acide nucléique hétérologue.
 
5. Particule pseudo-virale (PPV) comprenant le polypeptide selon la revendication 1, la protéine de fusion selon la revendication 3, ou une protéine codée par le vecteur d'expression recombinant selon la revendication 4.
 
6. Virus recombinant comprenant le polypeptide selon la revendication 1, la protéine de fusion selon la revendication 3, ou une protéine codée par le vecteur d'expression recombinant selon la revendication 4.
 
7. PPV selon la revendication 5 ou virus selon la revendication 6, comprenant en outre une molécule toxique ou thérapeutique.
 
8. Cellule hôte comprenant le vecteur d'expression recombinant selon la revendication 4, la PPV selon la revendication 5 ou 7, ou le virus selon la revendication 6 ou 7.
 
9. Composition immunogène comprenant un ou plusieurs des polypeptides selon la revendication 1, la protéine de fusion selon la revendication 3, la PPV selon la revendication 5, ou le virus selon la revendication 6, comprenant éventuellement en outre un adjuvant, dans laquelle, de préférence, l'adjuvant est choisi dans un groupe constitué d'un sel d'aluminium, d'un sel de calcium, d'un sel de fer, d'un sel de zinc, d'une suspension insoluble de tyrosine acylée, de sucres acétylés, de polysaccharides dérivés de manière cationique ou anionique et de polyphosphazènes.
 
10. Vaccin comprenant un ou plusieurs des polypeptides selon la revendication 1, la protéine de fusion selon la revendication 3, la PPV selon la revendication 5, le virus selon la revendication 6 ou la composition immunogène selon la revendication 9.
 
11. Composition pharmaceutique comprenant un ou plusieurs des polypeptides selon la revendication 1, la protéine de fusion selon la revendication 3, la PPV selon la revendication 5, le virus selon la revendication 6 ou la composition immunogène selon la revendication 9.
 
12. Composition immunogène selon la revendication 9 ou vaccin selon la revendication 10 à utiliser dans un procédé destiné à induire une réponse immunitaire à un rhinovirus humain (RVH) chez un sujet, dans laquelle le procédé comprend l'administration au sujet d'une quantité efficace de la composition immunogène ou du vaccin, induisant ainsi une réponse immunitaire à un rhinovirus humain (RVH) chez le sujet.
 
13. Composition immunogène selon la revendication 9 ou vaccin selon la revendication 10 à utiliser dans un procédé de traitement d'un sujet infecté par un rhinovirus humain (RVH), dans laquelle le procédé comprend l'administration au sujet d'une quantité thérapeutiquement efficace de la composition immunogène ou du vaccin, traitant ainsi le sujet infecté par le rhinovirus humain (RVH).
 
14. Composition immunogène selon la revendication 9 ou vaccin selon la revendication 10 à utiliser dans un procédé de vaccination d'un sujet contre de multiples sérotypes de rhinovirus humain (RVH), dans laquelle le procédé comprend l'administration au sujet d'une quantité efficace de la composition immunogène ou du vaccin.
 
15. Composition immunogène ou vaccin à utiliser selon l'une quelconque des revendications 12 à 14, dans laquelle le sujet est un être humain, de préférence le sujet est un adulte, un adolescent ou un nourrisson.
 
16. Composition immunogène selon la revendication 9 ou vaccin selon la revendication 10 à utiliser dans le cadre d'un traitement.
 




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Cited references

REFERENCES CITED IN THE DESCRIPTION



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Patent documents cited in the description




Non-patent literature cited in the description