Title of Invention

STREPTOCOCCUS ANTIGENS

Abstract

An isolated polynucleotide chosen from: (a) an isolated polynucleotide encoding a polypeptide consisting of an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:258 (NEW43), which polypeptide is chosen from table E, wherein the polypeptide is capable of inducing an immune response to Streptococcus pneumoniae; (b) an isolated polynucleotide encoding a polypeptide consisting of the amino acid sequence set forth in SEQ ID NO:258 (NEW 43), which polypeptide is chosen from Table E; and (c) an isolated polynucleotide encoding a polypeptide consisting of an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:21 (10D7.5 epitope), SEQ ID NO:22 (10G9.3 epitope, B11B.2 epitope, and 10A2 epitope), or SEQ ID NO:23 (11B8.4 epitope), which polypeptide is chosen from Table F, wherein the polypeptide is capable of inducing an immune response to Streptococcus pneumoniae; (d) an isolated polynucleotide encoding a polypeptide consisting of the amino acid sequence set forth in SEQ ID NO:21 (10D7.5 epitope), SEQ ID NO:22 (10G9.3 epitope, B11B.2 epitope, and 10A2 epitope), or SEQ ID NO:23 (11B8.4 epitope), which polypeptide is chosen from Table F; and (e) an isolated polynucleotide complementary to the polynucleotide of(a)rfb), (c),or(d).

Full Text

FORM 2 THE PATENTS ACT 1970 [39 OF 1970] & The Patents Rule, 2003 COMPLETE SPECIFICATION [See Section 10 and Rule 13] "STREPTOCOCCUS ANTIGENS* ID BIOMEDICAL CORPORATION; of 525 Cartier Boulevard West, Laval, Quebec H7V 3S8, Canada; The following specification particularly describes the nature of the invention and the manner in which it is to be performed:- FIELD OF THE INVENTION The present invention is related to antigens, epitopes and 5 antibodies directed to these epitopes, more ■particularly polypeptide antigens of streptococcus pneumoniae pathogen which may be useful for. prophylaxis, diagnostic or treatment of streptococcal infection. 10 BACKGROUND OF THE INVENTION S. pneumoniae is an important agent of disease in man especially among infants, the elderly and immunocompromised persons. It is a bacterium frequently isolated from patients 15 with invasive . diseases such' as bacteraemia/septicaemia, pneumonia, meningitis with high morbidity and mortality throughout the world. Even with appropriate antibiotic therapy-, pneumococcal infections still result in many deaths. Although the advent of antimicrobial drugs has reduced the 20 overall mortality from pneumococcal disease, the presence of resistant pneumococcal organisms has become a major problem in the world today. Effective pneumococcal vaccines could have a major impact on the morbidity and mortality associated with S. pneumoniae disease. Such vaccines would also potentially be 25 useful to prevent otitis media in infants and young children.- Efforts to develop a pneumococcal vaccine have generally concentrated on generating immune responses to the pneumococcal capsular polysaccharide. More than 80 pneumococcal capsular 30 serotypes have been identified on the basis of antigenic differences. The currently available pneumococcal vaccine, comprising 23 capsular polysaccharides that, most frequently caused disease, has significant shortcomings related primarily to the poor immunogenicity of some capsular polysaccharides, 35 the diversity of the serotypes and the differences in the distribution of serotypes over time, geographic areas and age WO 01/98334 PCT/CA01/00908 groups. In particular, the failure of existing vaccines and capsular conjugate vaccines currently in development to protect young children against all serotypes spurres evaluation of other S^ pneumoniae components. Although immunogenicity of 5 capsular polysaccharides can be improved, serotype specificity will still represent a major limitation of polysaccharide-based vaccines. The use of a antigenically conserved immunogenic pneumococcal protein antigen, either by itself or in combination with additional components, offers the possibility 10 of a protein-based pneumococcal vaccine. K ^ ; PCT WO 98/1893& published May 7, 1998 entitled "Streptococcus' Pneumoniae antigens and vaccines" describes certain polypeptides which are claimed to be antigenic. However, no 15 biological activity of these polypeptides is reported. Similarly, no sequence conservation is reported, which is a necessary species common vaccine candidate. PCT /WO 00/39299'describes polypeptides and polynucleotides 20 encoding these polypeptides. PCT WO 00/39299 demonstrates that polypeptides designated as BVH-3 and BVH-11 provide protection against fatal experimental infection with pneumococci. Therefore there remains an unmet need for Streptococcus 25 antigens that may be used as components for the prophylaxis, diagnostic and/or therapy of Streptococcus infection. 30 SUMMARY OF THE INVENTION An isolated polynucleotide comprising a polynucleotide chosen from,- 35 (a) a polynucleotide encoding a polypeptide haying at least 70% identity to a second polypeptide chosen from: table A, B, D, E or H; WO 01/98334 PCT/CA01/00908 (b) a polynucleotide encoding a polypeptide having at least 95% identity to a second polypeptide chosen from: table A, B, D, E or H; 5 (c) a polynucleotide encoding a polypeptide having an amino sequence chosen from table A, B, D, E or H; or fragments, analogs or derivatives .thereof; (d) a polynucleotide encoding a polypeptide chosen from: table A, B, D, E or H; 10 (e) a polynucleotide encoding a polypeptide capable of generating antibodies having binding specificity for a polypeptide having a sequence chosen from: table A, B, D, E or H; (f) a polynucleotide encoding an epitope bearing portion of a 15 polypeptide chosen from table A, B, D, E or H; and (g) a polynycleotide complementary to a polynucleotide in (a), (b), (c), (d), (e) or (f) . ■ In other aspects, there are provided novel polypeptides 20 encoded by polynucleotides of the invention, pharmaceutical or vaccine composition, vectors comprising polynucleotides of the invention operably linked to an expression control region, as well as host cells transfected with said vectors and methods of producing polypeptides comprising culturing said host cells 25 under conditions suitable for expression. BRIEF DESCRIPTION OF THE DRAWINGS ACCOMPANYING Figure 1 is the DNA sequence of SP64 BVH-3 gene; SEQ ID NO: 1 30 Figure 2 is a DNA sequence containing the complete SP64 BVH-3 gene at nucleotides 1777 to 4896; SEQ ID NO: 2 Figure 3 is the DNA sequence of SP64 BVH-11 gene; SEQ ID NO: 3 35 Figure 4 is a DNA sequence containing the complete SP64 BVH-11 gene at nucleotides 45 to 2567; SEQ ID NO: 4 WO 01/98334 PCT/CA01/00908 Figure 5 is a DNA sequence containing the complete SP64 BVH-11-2 gene at nucleotides 114 to 2 630; SBQ ID NO: 5 Figure 6 is the amino acid sequence of SP64 BVH-3 polypeptide; SEQ ID NO: 6 Figure 7 is the amino acid sequence of. SP64 BVH-11 polypeptide; SEQ ID NO: 7 Figure 8 is the ' amino acid sequence of SP64 BVH-11-2 polypeptide; SEQ ID NO: 8 Figure 9 is the DNA sequence of SP63 BVH-3 gene; SEQ ID NO:9 Figure 10 is the amino acid sequence of SP63 BVH-3 polypeptide; SEQ ID NO: 10 Figure 11 is the amino acid sequence of 4D4.9 polypeptide; SEQ ID NO: 11 Figure 12 is the amino acid sequence of 7G11.7 polypeptide; SEQ ID NO: 12 Figure 13 is the amino acid sequence of 7G11.9 polypeptide; SEQ ID NO: 13 Figure 14 is the amino- acid sequence of 4D3.4 polypeptide; SEQ ID NO: 14 Figure 15 is the amino acid sequence of 8E3.1 polypeptide; SEQ ID NO: 15 Figure 16 is the amino acid sequence of 1G2.2 polypeptide; SEQ ID NO: 16 WO 01/98334 PCT/CA01/00908 Figure 17 is the amirio acid sequence of 10C12.7 polypeptide; SEQ ID NO: 17 Figure 18 is the amino acid sequence of 14F6.3 polypeptide; 5 SEQ ID NO: 18 Figure 19 is the amino acid sequence of B12D8.2 polypeptide; SEQ ID NO: 19 10 Figure 20 is the amino acid sequence of 7F4.1 polypeptide; SEQ ID NO: 20 Figure 21 is the amino acid sequence of 10D7.5 polypeptide; SEQ ID NO: 21 15 Figure 22 is the amino acid sequence of 10G9.3 polypeptide, 10A2.2 polypeptide and B11B8.1 polypeptide; SEQ ID NO: 22 Figure 23 is the amino acid sequence of 11B8.4 polypeptide; 20 SEQ ID NO: 23 Figure 24 is the amino acid sequence of Mab H11B-11B8 target epitope; SEQ ID 163 25 Figure 25 is a. schematic representation of the BVH-3 gene as well as location of gene sequences coding for the full length and truncated polypeptides. : The relationships between DNA fragments are shown with respect to each other. 30 Figure 26 is a schematic representation of the BVH-11 gene as well as location of gene sequences coding for the full length and truncated polypeptides. The relationships between DNA fragments are shown with respect to each other. 35 Figure 27 is a schematic representation of the BVH-11-2 gene as well as location of gene sequences coding for the full WO 01/98334 PCT/CA01/00908 length and truncated polypeptides. The relationships between DNA fragments are shown with respect to each other. Figure 2 8 is a schematic representation of the BVH-3 protein 5 and the location of internal and surface epitopes recognized by certain monoclonal antibodies. Figure 29 is a schematic representation of the BVH-11-2 protein and the location of protective surface epitopes JO recognized by certain monoclonal antibodies. Figure 30 is a' map of. plasmid pURV22.HIS. KanR, kahamycin-resistance coding region; cI857, bacteriophage "k cI857 temperature-sensitive repressor gene; lambda pL, bacteriophage 15 X transcription promotor; His-tag, 6-histidine coding region; terminator, Tl transcription terminator; ori, colEl origin of replication,. Figure 31 depicts the comparison of the amino acid sequences 20 of BVH-3M (sp64) and BVH-3 (Sp63) proteins by using the program Clustal W from MacVector sequence analysis software (version 6.5.3). Underneath the alignment, there is a consensus line whers * and . characters indicate identical and similar amino acid residues, respectively. 25 Figure 32 depicts the comparison of the amino acid sequences of BVH-3, BVH-11 and BVH-11-2 proteins by using the program Clustal W from MacVector sequence analysis software (version 6.5.3). Underneath the alignment, there is a consensus line 30 where * and . characters indicate identical and similar amino acid residues, respectively. Figure 33 is the DNA sequence of the NEW43 gene (SEQ ID No 257) . WO 01/98334 PCT/CA01/00908 Figure 34 is the deduced amino acid sequence of NEW43 polypeptide (SEQ ID No 258). 5 DETAILED DESCRIPTION OF THE INVENTION It was determined that portions of the BVH-3 and BVH-11 polypeptides were internal. Other portions were not present in important strains such as encapsulated s.pneumonia causing 10 disease strains. It would be advantageous to have a polypeptide that comprises a portion that is not internal. When large portions of a polypeptide are internal, these portions, are not exposed on the bacteria. However, these portions can be very immunogenic in a recombinant polypeptide 15 and will not confer protection against infections. It would also be advantageous to have a polypeptide that comprises a portion that is present in most strains. The present invention is concerned with polypeptides in which 20 undesired portions have been deleted and/or modified in order to obtain a specific immune response. In accordance with the present invention, there are also provided polypeptides or polynucleotides encoding such 25 polypeptides comprising protective domains. Surprisingly, when the undesired portion of the polypeptides are deleted or modified, the polypeptides have desired biological properties. This is surprising in view of the fact 30 that some of these portions were described as being epitope bearing portion in the patent application PCT WO 98/18930. In, other publications such as PCT WO 00/37105, portions- identified as histidine triad and coil coiled regions were said to be of importance. The present inventors have found that variants of 35 the polypeptide BVH-3 and BVH-11 in which certain portions were deleted and/or modified and chimeras of these polypeptides have WO 01/98334 PCT/CA01/00908 biological properties and generate a specific immune response. According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at.least 5 70% identity to a second polypeptide comprising a sequence as disclosed in the present application, the tables and figures. In accordance with one aspect of the present invention, there is provided an isolated .polynucleotide comprising a 10 polynucleotide chosen from; 15 (a) a polynucleotide encoding a polypeptide having at least 70% identity to a second polypeptide chosen from: table B, E or H; (b) a polynucleotide encoding a polypeptide having at least 95% identity to a second polypeptide chosen from: table B, E or.H; 20 (G) a polynucleotide encoding a polypeptide having an amino sequence chosen from table B, E or H or fragments, analogs or derivatives thereof; 25 (d) a polynucleotide encoding a polypeptide chosen from: table B, E or H; (e) a polynucleotide encoding a polypeptide capable of generating antibodies having binding specificity for a polypeptide having a aequence chosen from: table B, E or H, (f) a polynucleotide encoding an epitope bearing portion of a polypeptide chosen from table B, E or H; and 30 (g) a polynycleotide complementary to a polynucleotide in (a), (b), (c), (d),(e) or (f). According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 70% identity to a second polypeptide comprising a sequence 35 chosen from table A, B, D, E, G or H or fragments, analogues or derivatives thereof.' WO 01/98334 PCT/CA01/00908 According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 95% identity to a second polypeptide comprising a sequence 5 chosen from table A, B, D, E, G or H or fragments, analogues or derivatives thereof. According to one aspect, the present invention relates to polypeptides characterised by the amino acid sequence chosen 10 from table A, B, D, E, G or H or fragments, analogues or derivatives thereof. According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 15 70% identity to a second polypeptide comprising a sequence chosen from table A, B, D, E, G or H. According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 20 95% identity to a second polypeptide comprising a sequence chosen from table A, B, D, E, G or H. According to one aspect, the present invention relates to polypeptides characterised by the amino acid sequence chosen 25 from table A, B, D, E, G or H. According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 70% identity to a second polypeptide comprising a sequence 30 chosen . from table B, E or H or fragments, analogues or derivatives thereof. According to one aspect, the present invention provides • an isolated polynucleotide encoding a polypeptide having at least 35 95% identity to a second polypeptide comprising a sequence chosen from B, E or H or fragments, analogues or derivatives WO 01/98334 PCT/CA01/00908 thereof. According to one aspect, the present invention relates to polypeptides characterised by the amino acid sequence chosen 5 from table B, E or H or fragments, analogues or derivatives thereof-. According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 10 70% identity to a second polypeptide comprising a sequence chosen from table B, E or H. According to one aspect, the present invention provides an isolated polynucleotide encoding a polypeptide having at least 15 . 95% identity to a second polypeptide comprising a sequence chosen from B, E or H. According to one aspect, the present invention relates to polypeptides characterised by the amino acid sequence chosen 20 from table B, E or H. In accordance with the present invention, all nucleotides encoding polypeptides and chimeric polypeptides are within the scope of the present invention. 25 In a further embodiment, the polypeptides or chimeric polypeptides in accordance with the present invention are antigenic. 30 In a further embodiment, the polypeptides or chimeric polypeptides in accordance with the present invention are immunogenic. In a further embodiment, the polypeptides or chimeric 35 polypeptides in accordance with the present invention can elicit an immune response in an individual. 11 WO 01/98334 PCT/CA01/00908 In a further embodiment, the present invention also relates to polypeptides which are able to raise antibodies having binding specificity to the .polypeptides or chimeric polypeptides of 5 the present invention as defined above. In one embodiment, the polypeptides of table A (BVH-3) or table D (BVH-11) comprise at least one epitope bearing portion. 10 In a further embodiment, the fragments of the polypeptides of the present invention will comprise one or more epitope bearing portion identified, in Table C and F. The-fragment will comprises at least 15 contiguous amino acid of the polypeptide 15 of table C and F. The fragment will comprises at least 20 contiguous amino acid of the polypeptide of table C and F. In a further embodiment, the epitope bearing portion of the polypeptide of table A(BVH-3) comprises at least one 20 polypeptide listed in.Table C. In a further embodiment, the epitope bearing portion of the polypeptide of table B(BVH-11) comprises at least one polypeptide listed in Table F. 25 An antibody that " has binding specificity" is an antibody . that recognises and binds the selected polypeptide but which does not substantially recognise and bind other molecules in a sample, such as a biological sample. Specific.binding can be 30 measured using an ELISA assay in which the selected polypeptide is used as an antigen. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by 35 one of ordinary skill in the art to which this invention belongs. All publications, patent applications, patents, and WO 01/98334 PCT/CA01/00908 other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are 5 illustrative only and not intended to be limiting. In accordance with the present invention, "protection" in the biological studies is defined by a significant increase in the survival curve, rate or period. Statistical analysis using the 10 Log rank test to compare survival curves, and Fisher exact test to compare survival rates and numbers of days to death, respectively, might be useful to calculate P values and determine whether the difference between the two groups is statistically significant. P values of 0.05 are regarded as 15 not significant. As used herein, "fragments", "derivatives" or "analogues" of the polypeptides of the invention include those polypeptides in which one or more of the amino acid residues are 20 substituted with a conserved or non-conserved amino acid residue (preferably conserved) and which may be natural or unnatural. In one embodiment, derivatives and analogues of polypeptides of the invention will have about 70% identity with those sequences illustrated in the figures or fragments 25 thereof. That is, 70% of the residues are the same. In a further embodiment, polypeptides will have greater than 75% homology. In a further embodiment, polypeptides will have greater than' 80% homology. In a further embodiment, polypeptides will have greater than 85% homology. In a further 30 embodiment, polypeptides will have greater than 90% homology. In a further embodiment, polypeptides will have greater than 95% homology. In a further embodiment, polypeptides will have greater than 99% homology. In a further embodiment, derivatives and analogues of polypeptides of the invention 35 will have less than about 20 amino acid residue substitutions, modifications or deletions and more Dreferably less than 10. WO 01/98334 PCT/CA01/00908 Preferred substitutions are those known in the art as conserved i.e. the substituted residues share physical, or chemical properties such as hydrophobicity, size, charge or functional groups. 5 The skilled person will appreciate that . analogues or derivatives of the proteins or polypeptides of the invention will also find use in the context of. the present invention, i.e. as antigenic/immunogenic material. Thus, for instance \ 15 amino acid. One carl use a program ,such as the CLUSTAL program to compare amino acid sequences. This program compares amino acid sequences and finds the optimal alignment by inserting spaces 20 in either sequence as appropriate. It is possible to calculate amino acid identity or similarity (identity plus conservation of amino acid type) for an optimal alignment. A program like BLASTx will align the longest stretch of similar sequences and assign a value to the fit. It is thus-possible 25 to obtain a comparison where several regions of similarity are found, each having a different score. Both types of identity analysis are contemplated in the present invention. In an alternative approach, the analogues or derivatives could 30 be fusion proteins, incorporating moieties which render purification easier, for example by effectively tagging the desired protein or polypeptide, It may be necessary to remove the "tag" or it may be the case'that the fusion protein itself retains sufficient antigenicity to be useful. WO 01/98334 PCT/CA01/00908 In an additional aspect of the invention there are provided antigenic/immunogenic fragments of the proteins or polypeptides of the invention, or of analogues or derivatives thereof. 5 The fragments of the present invention should include one or more such epitopic regions or be sufficiently similar to such regions to retain their antigenic/immunogenic properties. Thus, for fragments according to the present invention the 10 degree of identity is perhaps irrelevant, since they may be 100% identical to a particular part of a' protein or polypeptide, analogue or derivative as described herein. The key issue, once again, is that the fragment retains the antigenic/immunogenic properties. 15 Thus, what is important for analogues, derivatives and fragments is that they possess at least a degree of the antigenicity/immunogenic of the protein or polypeptide from which they are derived, 20 In accordance with the present invention, polypeptides of the invention include both polypeptides and chimeric polypeptides. Also included are polypeptides which have fused thereto other 25 compounds which alter the polypeptides biological or pharmacological properties i.e. polyethylene glycol (PEG) to increase half-life; leader or secretory amino acid sequences • for ease of purification; prepro- and pro- sequences; and (poly)saccharides. 30 Furthermore, in those situations where amino acid regions are found to be polymorphic, it may be desirable to vary one or more particular amino acids to more effectively mimic the different epitopes of the different streptococcus strains. 35 Moreover, the polypeptides of the present invention can be WO 01/98334 PCT/CA01/00908 modified by terminal -NH2 acylation (e.g. by acetylation, or thiogly'colic acid amidation, terminal carboxy amidation, e.g. with ammonia or methylamine) to provide stability, increased hydrophobicity for linking or binding to a support or other 5 molecule.. ' Also contemplated are hetero and homo polypeptide multimers of the polypeptide fragments, analogues and derivatives. These polymeric forms include, for example, one or more polypeptides 10 that have been cross-linked with cross-linkers such as ■avidin/biotin, gluteraldehyde or dimethylsuperimidate. Such polymeric forms also include polypeptides containing two or more tandem or inverted contiguous sequences, produced from ■multicistronic mRNAs'generated by recombinant DNA technology. 15 Preferably, a fragment, analogue or. derivative of a polypeptide of the invention will comprise at least one antigenic region i.e. at least one epitope. 20. In order to achieve the formation of antigenic polymers (i.e. synthetic multimers), polypeptides may be. utilised having bishaloacetyl groups, nitroarylhalides, or the like, where the .reagents being specific for thio groups. Therefore, the link between two mercapto groups of the different peptides may be a 25 single bond or may be' composed.of a linking group of at least two, typically at least four, and not more than 16, but usually not more than about 14 carbon atoms. In a particular embodiment, polypeptide fragments, analogues 30 and derivatives of the invention do not contain a methionine (Met) starting residue. Preferably, polypeptides will not • incorporate a leader or secretory sequence (signal sequence). The signal portion of a polypeptide of the invention may be determined according to established molecular biological 35 techniques. In general, the polypeptide of interest may be isolated from a streptococcus ' culture and subsequently WO 01/98334 PCT/CA01/00908 sequenced to determine the initial residue of the mature protein and therefore the sequence of the mature polypeptide. According to another aspect, there are provided vaccine 5 compositions comprising one or more streptococcus polypeptides of the invention in admixture with a pharmaceutically acceptable carrier diluent or adjuvant. Suitable adjuvants include oils. i.e. Freund's complete or incomplete adjuvant; salts i.e. AlK(S04)2, AlNa(S04)2, A1NH4(S04)2, silica, kaolin, 10 carbon polynucleotides i.e. poly IC and poly AU. Preferred adjuvants include QuilA and Alhydrogel. Vaccines of the invention may be administered parenterally by injection, rapid infusion, nasopharyngeal absorption, dermoabsorption, or bucal or oral. Pharmaceutically acceptable carriers also include 15 tetanus toxoid. The term vaccine is also meant to include antibodies. In accordance with the present invention, there is also provided the use of one or more antibodies having binding specificity 20 for the polypeptides of the present invention for the treatment or prophylaxis of streptococcus, infection and/or diseases and symptoms mediated by streptococcus infection. Vaccine compositions of the invention are used for the. 25 treatment or prophylaxis of streptococcus infection and/or diseases and symptoms mediated by streptococcus infection as described in' P.R. Murray (Ed, in chief),E.J. Baron, M.A. Pfaller, F.C. Tenover and R.H. Yolken. Manual of Clinical Microbiology, ASM Press, Washington, D.C. sixth edition, 1995, 30 I482p which are herein incorporated by reference. In one embodiment, vaccine compositions of the present invention are used for the treatment or prophylaxis of meningitis, otitis media, bacteremia or pneumonia. In one embodiment, vaccine compositions of the invention are used for the treatment or 35 prophylaxis of streptococcus infection and/or diseases and symptoms mediated by streptococcus infection, . in particular WO 01/98334 PCT/CA01/00908 S,pneumoniae, group A streptococcus {pyogenes), group B streptococcus (GBS or agalactiae) , dysgalactiae, uteris, nocardia as well as Staphylococcus aureus. In a further embodiment, the streptococcus infection is S.pneumoniae. 5 In a particular embodiment, .vaccines are administered to those individuals at risk of streptococcus infection such as infants, elderly and immunocompromised individuals. 10 As used in the present application, the term " individuals" include mammals. In a further embodiment, the mammal is human. Vaccine compositions are preferably in unit dosage form of about 0.001 to 100 ug/kg (antigen/body weight) and more 1,5 preferably 0.01 to 10 |ig/kg and most preferably 0.1 .to 1 ug/kg 1 to 3 times with an interval of about 1 to 6 week intervals between immunizations. Vaccine compositions, are preferably in unit dosage form of 20 about 0.1 ug to 10 mg and more preferably'l^g to 1 mg.and most preferably 10 to 100 ug 1 to 3 times with an interval of about 1 to 6 week intervals between immunizations. According to another aspect, there are provided 25 . polynucleotides encoding polypeptides characterised by the amino acid sequence chosen from table A, B, D, E, G or H or fragments, analogues or derivatives thereof. According to another aspect, there are provided 30 polynucleotides encoding polypeptides characterised by the amino acid sequence chosen from table B, E or H or fragments, analogues or derivatives thereof. In one embodiment, polynucleotides are those illustrated in 35 table A, B, D, E, G or H which encodes polypeptides of the WO 01/98334 PCT/CA01/00908 invention. In one embodiment, polynucleotides are those illustrated in table B, E or H which encodes polypeptides of the invention. 5 It will be appreciated that the polynucleotide sequences illustrated in the figures may be altered with degenerate codons yet still encode the polypeptides of the invention. Accordingly the present invention further provides 10 polynucleotides which hybridise to the polynucleotide sequences herein above described (or the complement sequences thereof) having 50% identity between sequences. In one ■embodiment, at least 70% identity between sequences. In one embodiment, at least 75% identity between sequences. In one 15 embodiment, at least 80% identity between sequences. In one embodiment, at least 85% identity between sequences. In one embodiment, at least 90% identity between sequences. In a further embodiment, polynucleotides are hybridizable under stringent conditions i.e. having at least 95% identity. In a 20 further embodiment, more than 97% identity. Suitable stringent conditions for hybridation can be readily determined by one of skilled in the art (see for example Sambrook et al., (1989) Molecular cloning : A Laboratory 25 Manual, 2nd ed, Cold Spring Harbor, N.Y.; Current Protocols in Molecular Biology, (1999) Edited by Ausubel F.M. et al., John Wiley & Sons, Inc., N.Y.). In a further embodiment, the present invention provides 30 polynucleotides that hybridise under stringent conditions to either (a) a DNA sequence encoding a polypeptide or (b) the complement of a ' DNA sequence encoding a polypeptide ,- 35 wherein said polypeptide comprising a sequence chosen from table A, B, D, E, G or H or fragments or analogues thereof. WO 01/98334 PCT/CA01/00908 In a further embodiment, the present invention provides polynucleotides that hybridise under stringent conditions to 5 e.ither ■ (c) a DNA sequence encoding a polypeptide or (d) the complement of a DMA sequence encoding a polypeptide; wherein said polypeptide comprising a sequence chosen from 10 table B, E or H or fragments*or analogues thereof. In a further embodiment, the present invention .provides polynucleotides that hybridise under stringent conditions to either 15 (a) a DNA sequence encoding a polypeptide or (b) the complement of a DNA sequence encoding a polypeptide; wherein said polypeptide comprises at least 10 contiguous amino acid residues from a polypeptide comprising a sequence chosen 20 from table A, B, D, E, 'G or H or fragments or analogues thereof. In a further embodiment, the present invention provides polynucleotides that hybridise under stringent conditions to 25 either (c) a DNA sequence encoding a polypeptide or (d) the complement of a DNA sequence encoding a polypeptide,- wherein said polypeptide comprises at least 10 contiguous amino 30 acid residues from a polypeptide comprising a sequence chosen from table B, E or H or fragments or analogues thereof. In a further embodiment, polynucleotides are those' encoding polypeptides of the invention illustrated in table A, B, D, E, 35 G or H. WO 01/98334 PCT/CA01/00908 As will be readily appreciated by one skilled in the art, polynucleotides include, both DNA.and RNA. The present invention also includes . polynucleotides 5 complementary to the polynucleotides described in the present application. In a further aspect, polynucleotides encoding polypeptides of the invention, or fragments, analogues or derivatives thereof, \§ may be used' in a UNA immarn.'zat.ion "tneV/iod. That is, tYifey cari be incorporated into a vector which is replicable and expressible upon injection thereby producing the antigenic polypeptide in vivo- For example polynucleotides may be incorporated into a plasmid vector under the control of the 15 CMV promoter which is functional in eukaryotic cells. Preferably the vector is injected intramuscularly. According to another aspect, there is provided a process for producing polypeptides of the invention . by recombinant 20 techniques by expressing a polynucleotide encoding said polypeptide in a hc?st cell and recovering the expressed polypeptide product. Alternatively, the' polypeptides can be produced according to established synthetic chemical techniques i.e. solution phase or solid phase synthesis of 25 oligopeptides which are ligated to produce the full polypeptide (block ligation). General methods f polynucleotides and polypeptides are described in the 30 following references: Sambrook et al, Molecular Cloning: A Laboratory Manual, 2ild ed, Cold Spring Harbor, N.Y., 1989; Current Protocols in Molecular Biology, Edited by Ausubel F.M. et al,, John Wiley and Sons, Inc. New York; PCR Cloning Protocols, from Molecular Cloning to Genetic Engineering, 35 Edited by White B.A., Humana Press, Totowa, New Jersey, 1997, 490 Pages: Protein Purification, Principles and Practices WO 01/98334 PCT/CA01/00908 Scopes R.K. , Springer-Verlag, New York. 3rd Edition, 1993, 380 pages; Current Protocols in Immunology/ Edited by Coligan J.E. et al., John Wiley & Sons Inc., New York which are herein incorporated by reference. . 5 For recombinant production, host cells are • transfected with vectors which encode the polypeptide, and then cultured iri a nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the genes. 10 Suitable vectors are those that are viable and replicable in the chosen host and include chromosomal, non-chromosomal and synthetic DNA sequences e.g. bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA. The polypeptide sequence may be 15 incorporated in the vector at the appropriate site using restriction enzymes such that it is operably linked to an expression control region comprising a promoter, ribosome binding' site (consensus region or Shine-Dalgarno sequence), and optionally an operator (control element). One can select 20 individual components of the expression control region that are appropriate for a given host and vector according to established molecular biology principles (Sambrook et al. Molecular Cloning: A Laboratory Manual/ 2nd ed, Cold Spring Harbor, N.Y., 1989; Current Protocols in Molecular Biology, 25 Edited by Ausubel F.M. et al. , John Wiley and Sons, Inc. New York incorporated herein by reference). Suitable promoters include but are not limited to LTR or SV40 promoter, E.coli lac/ tac or trp promoters and the phage lambda Pi, promoter. Vectors will preferably incorporate an origin of replication 30 as well as selection markers i.e. ampicilin resistance gene. Suitable bacterial vectors include pET, pQE70, pQE60, pQE-9, pbs, PD10 phagescript, psixl74, pbluescript SK, pbsks, pNH8A, pNHl6a, pNHlSA, pNH46A, ptrc99a, pKK223-3, pKK233-3, pDR540, PRIT5 and eukaryotic vectors pBlueBadll, pWLNEO, pSV2CAT, 35 pOG44, pXTl, pSG, pSVK3, pBPV, pMSG and pSVL. Host cells may be bacterial i.e. E. coli, Bacillus subtilis., Streptomycee; WO 01/98334 PCT/CA01/00908 fungal i.e. Aspergillus niger, Aspergillus nidulins; yeast i.e. Saccharomyces or eukaryotic i.e. CHO, COS. Upon expression of the polypeptide in culture, cells are 5 typically harvested by centrifugation then disrupted by physical or chemical means (if the expressed polypeptide is not secreted into the media) and the resulting crude extract retained to isolate the polypeptide of interest. Purification of the polypeptide from culture media or lysate may be 10 achieved by established techniques depending on the properties of the polypeptide i.e. using ammonium sulfate or ethanol precipitation , acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, hydroxylapatite chromatography and 15 lectin chromatography. Final purification may be achieved using HPLC. The polypeptide may be expressed with or without a leader or secretion sequence. In the former case the leader may be 20 removed using post-translational processing (see US 4,431,739; US 4,425,437; and US 4,338,397 incorporated herein by reference) or be chemically removed subsequent to purifying the expressed polypeptide. 25 According to a further aspect, the streptococcus polypeptides of the invention may be used in a diagnostic test for streptococcus infection, in particular S._ pneumoniae infection. Several diagnostic methods are possible, for example detecting streptococcus organism in a biological 30 sample, the following procedure may be followed: a)obtaining a biological sample from a patient; b)incubating an antibody or fragment thereof reactive with a streptococcus polypeptide of the invention with the biological sample to form a mixture; and 35 c)detecting specifically bound antibody or bound fragment in the. mixture which indicates the presence of streptococcus. WO 01/98334 PCT/CA01/00908 Alternatively, a method for the detection of antibody specific to a streptococcus antigen in a biological sample containing or suspected of containing said antibody may be performed as 5 follows: a)obtaining a biological sample from a patient; b) incubating one or more streptococcus polypeptides of the invention or fragments thereof with the biological sample to form a mixture; and 10 c)detecting specifically bound antigen or bound fragment in the mixture which indicates the presence of antibody specific to streptococcus. One of skill in the art will recognize that this diagnostic 15 test may take several forms, including an immunological test such as an enzyme-linked immunosorbent assay (ELISA) , a radioimmunoassay or a latex agglutination assay, essentially to determine whether antibodies specific for the polypeptide are present in an organism. 20 The DNA sequences encoding polypeptides of the invention may also be used to design DNA probes for use in detecting the presence of streptococcus in a biological sample suspected of containing such bacteria. The detection method of this 25 invention comprises: a)obtaining the biological sample from a patient; b)incubating one or • more DNA probes having a DNA sequence encoding a polypeptide of the invention or fragments thereof with the biological sample to form a mixture; and 30 c)detecting specifically bound DNA probe in the mixture which indicates the presence of streptococcus bacteria. The DNA probes of this invention may also be used. for detecting circulating streptococcus i.e. S.pneumoniae nucleic 35 acids in a sample, for example using a polymerase chain reaction, as a method of diagnosing streptococcus infections. WO 01/98334 PCT/CA01/00908 The probe may be synthesized using conventional techniques and may be immobilized on a solid phase, or may be labelled with a detectable label. A preferred DNA probe for this application is an oligomer having a sequence complementary to at least 5 about 6 contiguous nucleotides of the streptococcus pneumoniae polypeptides of the invention. 1 Another diagnostic method for the detection of streptococcus in a patient comprises: 10 a)labelling an antibody reactive with a polypeptide of the invention or fragment thereof with a detectable label; b)administering the labelled antibody or labelled fragment to the patient; 'and c)detecting specifically bound labelled antibody or labelled 15 fragment in the patient which indicates the presence of streptococcus. A further aspect of the invention is the use. of the' streptococcus polypeptides of the invention as immunogens for 20 the production of specific antibodies for the diagnosis and in particular the treatment of streptococcus infection. Suitable antibodies may be determined using appropriate screening methods, for example by measuring the ability of a particular antibody to passively protect against streptococcus infection 25 in a test model. One example of an animal model is the mouse model described in the examples herein. The antibody may be a whole antibody or an antigen-binding fragment thereof and may belong to any immunoglobulin class. The antibody or fragment may be of animal origin, specifically of mammalian origin and 30 more specifically of murine, rat or human origin. It may be a natural antibody or a fragment thereof, or if desired, a recombinant antibody or antibody fragment. The term recombinant antibody or antibody fragment means antibody or antibody fragment which was produced using molecular biology 35 techniques. The antibody or antibody fragments' may be polyclonal, or preferably monoclonal. It may be specific for WO 01/98334 PCT/CA01/00908 a number of epitopes associated with the streptococcus pneumoniae polypeptides but is preferably specific for one. A further aspect of the invention is the use of the antibodies 5 directed to the streptococcus polypeptides of the invention for passive immunization. .One could use the antibodies described in the present application. Suitable antibodies may be determined using appropriate screening methods, for example by measuring the ability of a particular antibody to passively [0 protect against streptococcus infection in a test model. One example of an animal model is the mouse model described in the examples herein. The antibody may be a whole antibody or an antigen-binding fragment thereof and may belong to any immunoglobulin class. The antibody or fragment may be of 1'5 animal origin, specifically of • mammalian origin and more specifically of murine, rat or human origin. It may be a natural antibody or a fragment thereof, or if desired, a recombinant antibody or antibody fragment. The term recombinant antibody or antibody fragment means antibody or 10 antibody fragment which was produced using molecular biology techniques. The antibody or antibody fragments may be polyclonal, or preferably monoclonal. It may be specific for a number of epitopes associated with the streptococcus pneumoniae polypeptides but is preferably specific for one. 25 The following are reference tables summarizing the sequences disclosed in the present application: TABLE A, B and C Variants and Epitope of BVH-3- 30 Table A New 21 aa 396-1039 of SEQ ID. 6 New 25 aa 233-1039 of SEQ ID.6 New 40 aa 408-1039 of SEQ ID.6 WO 01/98334 PCT/CA01/00908 TABLE B NEWl-mutl** 235 NEW35A 236 NEW42 237 NEW49 238 NBW50 239 NEW51 240 NEW52 241 NEW53 242 NEW54 243 NEW55 244 NEW56 245 NEW56-mut2** 245 NEW56-mut3** 245 NEW57 246 NEW63 247 NEW64 248 NEW65 249 NEW66 250 NEW76 251 NEW105 252 NEW106 253 NEW107 254 5 ** silent mutation, i.e. the polypeptide is the same as Newl or New 56 TABLE C- Epitopes of BVH-3 7G11.7 12 7G11.9 13 B12D8.2 19 7F4 .1 20 14F6.3 18 4D3.4 14 10C12.7 17. 8E3.1 15 1G2.2 16 WO 01/98334 PCT/CA01/00908 TABLE D, E and F Variants and Epitope of BVH-11- TABLE D- TABLE E- New 43 NEW60 258 293 NEW61 294 NEW62 295 NEW80 296 NEW81 297 NEW82 298 NEW83 299 NEW84 300 NEW85 301 NEW88D1 302 NEW88D2 303 NEW88 304 10 15 TABLE F- epitopes of BVH-11 10D7.5 21 10G9.3 22 B11B8.1 22 • 10A2.2 22 libs.4 23 3A4.1 24 TABLE G and H Chimeras- TABLE G WO 01/98334 PCT/CA01/00908 . chlmeras. with BVH-l.r,': '.and ••BVH^3-*:. " • '-..'. i!P Newl7 M*-NEW5-G*P*-NEW1 New 20 M*-NEW1-G*P*-NEW5 New26 M*-NEW10-G*P*-NEW25 New27 M*-NEW19-G*P*-NEW25 New28 M*-NEW10-G*P*-NEWl New29 ^M*-NEW5-G*P*-NEW25 New30 M*-NEW4-G*P*-KEW25 New31 M*-NEW4~G*P*-NEWl NEW32 M*-NE19-G*P*-NEW1 * OPTIONAL AMINO ACID TABLE H VP 89 VP 90 VP 91 VP 92 VP 93 VP 94 VP 108 VP109 VP 110 VP 111 VP112 VP113 VP114 VP115 VP116 VP117 VP119 VP120 VP121 VP122 VP123 VP124 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 EXAMPLE 1 This example describes the bacterial strains, plasmids, PCR primers, recombinant proteins and hybridoma antibodies used 10 herein. WO 01/98334 PCT/CA01/00908 S.pneumoniae SP64 (serogroup 6) and SP63 (serogroup 9) clinical isolates were provided by the Laboratoire de la Sante1 Publique du Quebec, Sainte-Anne-de-Bellevue; Rxl strain, a nonencapsulated derivative of the type 2 strain D39 and the 5 type 3 strain WU2 were provided by David E. Briles from University of Alabama, Birmingham and the type 3 clinical isolate P4241 was provided by the Centre de Recherche en Infectiologie du Centre Hospitaller de 1'University Laval, Sainte-Foy. E_^ coli strains DH5oc (Gibco BRL, Gaithesburg, 10 MD) ; AD494 (XDE3) (Novagen, Madison, WI) and BL21 (XDE3) (Novagen) as well as plasmid superlinker pSL301 vector (Invitrogen, San Diego, CA) ; pCMV-GH vector (gift from Dr. Stephen A. Johnston, Department for Biochemistry, University of Texas, Dallas, Texas); pET32 and pET21 (Novagen) and 15 pURV22.HIS expression vectors (Figure 30) were used in this study. The pURV22.HIS vector contains a cassette of the bacteriophage X CI857 temperature-sensitive repressor gene from which the functional PR promoter has been deleted. The inactivation of the CI857 repressor by. a temperature increase 20 from the range of 30-37°C to 3 7-42°C results in the induction of the gene under the control of promoter A,PL. The PCR primers used for the generation of the recombinant plasmids had a restriction endonuclease site at the 5'end, thereby allowing directional cloning of the amplified product into the 25 digested plasmid vector. The PCR oligonucleotide primers used are listed in the following Table 1. The location of the gene sequences coding for BVH-3, BVH-11 and BVH-11-2 gene products is summarized in the Figure 25, Figure 26 and Figure 27, respectively. 30 WO 01/98334 PCT/CA01/00908 Table 1. List of PCR oligonucleotide primers Primer SEQ ID NO Sequence 5' - 3' Nucleotide position Restriction sites OCRR 479 25 cagtagatctgtgcctatgcact aaac SEQ ID 1: 61-78 SEQ ID 9: 1-18 Bglll OCRR 480 26 gatctctagactactgctattec ttacgctatg SEQ ID 2: 4909-4887 SEQ ID 9: 2528-2519' Xbal OCRR 497 27 atcactcgagcattacctggata atcctgt SEQ ID 1: 1525-1506 Xhol OCRR 498 28 ctgctaagcttatgaaagattta gat SEQ ID 1: 1534-1548 HindiII- OCRR 499 29 gatactcgagctgctattcctta c SEQ ID 2: 4906-4893 Xhol- HAMJ 172 30 gaatctcgagttaagctgctgct aattc SEQ ID 1: 675-661 Xhol HAMJ 247 31 gacgctcgagcgctatgaaatca gataaattc SEQ ID 1: 3117-3096 Xhol HAMJ 248 32 gacgctcgagggcattacctgga taatcctgttcatg SEQ ID 1: 1527-1501. Xhol HAMJ-249 33 cagtagatctcttcatcatttat tgaaaagagg SEQ ID 2: 1749-1771 Bglll HAMJ 278 34 ttatttcttccatatggacttga cagaagagcaaattaag SEQ ID 1: 1414-1437 Ndel HAMJ 279 35 cgccaagcttcgctatgaaatca gataaattc SEQ ID 1: 3117-3096 HindiII HAMJ 280 36 cgccaagcttttccacaatataa gtcgattgatt SEQ ID 1: 2400-2377 HindiII HAMJ 281 37 ttatttcttccatatggaagtac ctatcttggaaaaagaa SEQ ID 1: 2398-2421 Ndel HAMJ 300 38 ttatttcttccatatggtgccta tgcactaaaccagc SEQ ID 1: 62-82 Ndel 31 SUBSTITUTE SHEET (RULE 26) WO 01/98334 PCT/CA01/00908 Primer SEQ ID NO Sequence 5' - 3' Nucleotide position Restriction sites HAMJ 313 39 ataagaatgcggccgcttccaca atataagtcgattgatt SEQ ID 1: 2400-2377 Not I OCRR 487 40 cagtagatctgtgcttatgaact aggtttgc SEQ ID 3: 58-79 Bglll OCRR 488 41 gatcaagcttgctgctaccttta cttactctc SEQ ID 4: 2577-2556 HindiII HAMJ 171 42 ctgagatatccgttatcgttcaa ace SEQ ID 3: 1060-1075 EcoRV HAMJ 251 43 ctgeaagcttttaaaggggaata atacg SEQ ID 3:" 1059-1045 HindiII HAMJ 264 44 cagtagatctgcagaagccttcc tatctg SEQ ID 3: 682-700 Bglll HAMJ 282 45 tcgccaagcttcgttatcgttca aaccattggg SEQ ID 3: 1060-1081 HindiII HAMJ 283 46 ataaga'atgcggccgccttactc tcctttaataaagccaatagtt SEQ ID 3: 2520-2492 NotI HAMJ 284 47 catgccatggacattgatagtct cttgaaacagc SEQ ID 3: 856-880 Ncol HAMJ 285 48 cgccaagcttcttactctccttt aataaagecaatag SEQ ID 3: 2520-2494 HindiII HAMJ 286 49 cgacaagcttaacatggtcgcta gcgttacc SEQ ID 3: 2139-2119 SEQ ID 5: 2210-2190 HindiII HAMJ 287 50 cataccatgggcctttatgaggc acctaag SEQ ID 3: 2014-2034 Ncol HAMJ 288 51 cgacaagcttaagtaaatcttca gcctctctcag SEQ ID 3: 2376-2353 HindiII HAMJ 289 52 gataccatggctagcgaccatgt tcaaagaa SEQ ID 3: 2125-2146 Ncol HAMJ 290 53 cgccaagcttatcatccactaac ttgactttatcac SEQ ID 3: 1533-1508 HindiII SUBSTITUTE SHEET (RULE 26) WO 01/98334 PCT/CA01/00908 Primer SEQ ID NO Secjuence 5' - 3# Nucleotide position Restriction sites HAMJ-291 54 cataccatggatattcttgcctt cttagctccg SEQ ID 3: 1531-1554 Ncol HAMJ 301 55 catgccatggtgcttatgaacta ggtttgc SEQ ID 3: 59-79 Ncol HAMJ 302 56 cgecaagctttagcgttaccaaa acdattatc SEQ ID 3: 2128-2107 HindiII HAMJ 160 57 gtattagatctgttcctatgaac ttggtcgtcacca . SEQ ID 5: 172-196 Bglll HAMJ 186 58 cgcctctagactactgtatagga gccgg SEQ ID 5:'" 2613-2630 Xbal HAMJ 292 59 catgccatggaaaacatttcaag ccttttacgtg SEQ ID 5: 925-948 Ncol HAMJ 293 60 cgacaagcttctgtataggagcc ggttgactttc SEQ ID 5: 2627-2604 HindiII HAMJ 294 61 catgccatggttcgtaaaaataa ggdagaccaag SEQ ID 5: 2209-2232 Ncol HAMJ 297 62 catgccatggaagcctattggaa tgggaag SEQ ID 5: 793-812 Ncol HAMJ 352 63 catgccatggaagcctattggaa tgggaagc SEQ ID 5: 793-813 Ncol HAMJ 353 64 cgccaagcttgtaggtaatttgc gcatttgg SEQ ID 5: 1673-1653 HindiII HAMJ 354 65 cgccaagcttctgtataggagcc ggttgac SEQ ID 5: 2627-2608 HindiII HAMJ 355 66 catgccatggatattcttgcctt cttagctcc SEQ ID 5: 1603-1624 Ncol HAMJ 404 67 ttatttcttccatatgcatggtg atcatttccattaca SEQ ID 1: 1186-1207 Ndel HAMJ 4 64 68 gatgcatatgaatatgcaaccga gtcagttaagc SEQ,ID 1: 697-720 Ndel HAMJ 465 69 gatgctcgagagcatcaaatccg tatccatc SEQ ID 1: 1338-1318 Xhol 33 SUBSTITUTE SHEET (RULE 26) WO 01/98334 PCT/CA01/00908 Primer SEQ ID NO Sequence 5' - 3' Nucleotide position Restriction sites HAMJ 466 70 gatgcatatggatcatttccatt acattcca SEQ ID 1: 1192-1212 Ndel HAMJ 467 71 gacaagcttggcattacctggat aatcctg SEQ ID 1: 1527-1507 HindiII HAMJ 352 72 catgccatggaagcctattggaa tgggaagc SEQ ID 5: 793-813 Ncol HAMJ 470 73 ataagaatgcggccgccgctatg aaatcagataaattc SEQ ID 1: 3096-3117 Not I HAMJ 471 168 atatgggcccctgtataggagcc ggttgactttc SEQ ID 5: 2626-2604 Apa I HAMJ 472 169 atatgggcccaatatgcaaccga gtcagttaagc SEQ ID 1: 720-697 Apa I HAMJ 350 170 atatgggcccaacatggtcgcta gcgttacc SEQ ID 3: 2139-2119 Apa I HAMJ 351, 171 tcccgggcccgacttgacagaag agcaaattaag SEQ ID 1: 1414-1437 Apa I HAMJ 358 172 catgccatgggacttgacagaag agcaaattaag SEQ ID 1: 1415-1437 Ncol HAMJ 359 173 tcccgggccccgctatgaaatca gataaattc SEQ ID 1: 3116-3096 Apa I HAMJ 403 174 atatgggcccgacattgatagtc tcttgaaacagc SEQ ID 3: 856-880 Apa I HAMJ 361 175 cgccaagcttaacatggtcgcta gcgttacc SEQ ID 3: 2139-2119 Hind III HAMJ 483 176 atatgggccccttactctccttt aataaagccaatag SEQ ID 3: 2520-2494 Apa I Molecular biology techniques were performed according to standard methods. See for exanple, Sanbrook, J.-, Fritsch, E.F., Maniatis, T., "Molecular cloning. A laboratory manual" Vol. 1-2-3 (second edition) Cbld Spring Harbour Laboratory Press, 1989, New York, which is herein incorporated by reference. PCR- anplified products were digested with restriction endcnucleases and ligated to either linearized plasmid pSL301, pCMV-GH, pET or ptKV22.HIS expression ■vector digested likewise or digested with enzymes that produce conpatible cohesive ends. Recombinant pSL301 and recorbinant pCMV-GH plasmids were digested with restriction enzymes for the in-frams cloning in pET expression vector. when pET SUBSTITUTE SHEET (RULE 26) WO 01/98334 PCT/CA01/00908 ■vectors "were used, clones were first stabilized in E;. ooli EH5a before introduction into EL coli BL21$EE3) or AD494 (?£E3) for egression of full-length or truncated BVH-3, BVH-11 or BVH-11-2 molecules. Each of the resultant plasmid constructs was confirmed by nucleotide sequence analysis. The 5 recctibinant proteins were expressed as N-terminal fusions with the thioredoxin and His-tag (pEI32 expression system); as C-terminal fusions with an His-tag (pEI21 expression system); or as N-terminal fusions with an His-tag (pURV22 .HIS expression system). The expressed recombinant proteins were purified from supernatant fractions obtained after centrifugation of sonicated IPIG- (pET 10 systems) or heat- (pURV22.HIS) induced K ooli using a His-Bind metal chelation resin (Qlflgen, Chatsworth, CA). The gene products generated from £L pneumoniae SP64 are listed in the following Table 2. Ihe gene fragment enocding BVH-3-Sp63 protein (amino acid residues 21 to 840 on SEQ ID NO: 10) was generated from ^ rmeumaniae SP63 using the PCR-primar sets 0CRR479-OCRR480 and the 15 cloning vector pSL301. The reccmbinant pSL301-BVH-3Sp63 was digested for the in-frame cdoning in pEI32 vector for the expression of the BVH-3-SpS3 molecule. SUBSTITUTE SHEET (RULE 26) Table 2. Lists of truncated BVH-3, BVH-11, BVH-11-2 and Chimsric gene 20 products generated from S^. pneumoniae SP64 WO 01/98334 PCT/CA01/00908 HAMJ171-OCRR488 BVH- BVH-11 C'end 354-840 pET-32 a(+) HAMJ264-OCRR488 BVH- BVH-11 C'end 228-840 pET-32 a(+) HAMJ278-HAMJ279 NEW1 BVH-3 C'end 472-1039 .pET-21b(+) HAMJ278-HAMJ280 NEW2 BVH-3 C'end 472-800 pET-21b(+) HAMJ281-HAMJ279 NEW3 BVH-3 C'end 800-1039 pET-21b(+) HAMJ284-HAMJ285 NEW4 BVH-11 C'end 286-840 pET-21d(+) HAMJ284-HAMJ286 NEW5 BVH-11 286-713 pET>21d(+) HAMJ287-HAMJ288 NEW6 BVH-11 672-792 pET-21d(+) HAMJ285-HAMJ289 NEW7 BVH-U C'end 709-840 pET-21d(+) HAMJ284-HAMJ290 NEWS BVH-11 286-511 pET-21d(+) HAMJ286-HAMJ291 NEW9 BVH-11 511-713 pET-21d(+) HAMJ160-HAMT186 BVH- BVH-11-2 w/o 20-838 pSUOl HAMJ292-HAMJ293 NEW10 BVH-11-2 271-838 pET-21d(+) HAMJ293-HAMJ294 NEW11 BVH-11-2 699-838 pET-21d(+) HAMJ282-HAMJ283 NEW13 BVH-11 C'end 354-840 pET-21b(+) HAMJ286-HAMJ297 NEW14 BVH-11-2 227-699 pET-21d(+) HAMJ300-HAMJ313 NEW15 BVH-3 N'end 21-800 pET-21b(+) HAMJ301-HAMJ302 NEW16 BVH-11 N'end w/oss 20-709 pET-21d(+) HAMJ352-HAMJ353 NEW18 BVH-11-2 internal 227-520 pET21d(+) HAMJ354-HAMJ355 NEW19 BVH-11-2 C'end 497-838 PET21d(+) HAMJ404-HAMJ279 NEW21 BVH-3 C'end 396-1039 pET21b(+) HAMJ464-HAMJ465 NEW22 BVH-3 internal 233-446 pET-21a(+) HAMJ466-HAMJ467 NEW23 BVH-3 internal 398-509 pET-21b(+) HAMJ352-HAMJ293 NEW24 BVH-11-2 C'end 227-838 pET-21d(+) HAMJ464-HAMJ470 • NEW25 BVH-3 C'end 233-1039 pET-21b(+) HAMJ278-HAMJ279 (NEW 1) HAMJ282-HAMJ283 (NEW 13) NEW1 2 Chimera* M-NEW 1 -KL -NEW 13 pET 21 b (+) HAMJ284-HAMJ350 (NEW 5) HAMJ351-HAMJ279 (NEW 1) NEW1 7 Chimera* M- NEW 5 -GP -NEW1 pET21d(+) HAMJ358-HAMJ359 (NEW 1) HAMJ403- NEW2 0 Chimera* M- NEW 1 -GP -NEW 5 pET21d(+) SUBSTITUTE SHEET (RULE 26) WO 01/98334 PCT/CA01/00908 HAMI361(NEW5) | HAMD292-HAMI471 (NEW 10) HAMJ472-HAMT470(NEW25) NEW26 Chimera* M- NEW 10 -GP - NEW25 pET2ld(+) HAMJ355-HAMJ471 (NEW 19) HAMT472-HAMJ470(NEW25) NEW27 Chimera* M- NEW 19 -GP -NEW25 pET21d(+) BAMJ292-HAMI471 (NEW 10) HAMB51 -HAM)279(NEW1) NEW28 Chimera* M- NEW 10 -GP -NEW1 pET21d(+) HAMJ2&1-HAMB50 (NEW 5) HAMJ472-HAM3470(NEW25) NEW29 Chimera* M- NEW 5 -GP - NEW25 pET21d(+) HAMD284-HAM34S3 (NEW 4) HAMI472-HAM1470(NEW25) NEW30 Qnmaa* M- NEW 4 -GP -NEW25 piET21d(+) HAMJ284-HA1VD483 (NEW 4) HAMB51-HAM3279(NEW1) NEW31 Chimera* M- NEW 4 -GP - NEW1 pET21d(+) HAMB55flAM3471 (NEW 19) HAM3351-HAM)279(NEW1) NEW32 Chimera* M- NEW 19 -GP - NEW1 pET21d(+) w/o ss : without signal sequence. Analysis of the BVH-3, BVH-11 and BVH-11-2 protein sequences suggested the presence of putative hydrophobic leader sequences. * encoded amino acids for the chimeras are expressed as the gene product, additional non essential amino acids residue were added M is methionine, K is lysine, L is leucine, G is glycine and P is proline. Monoclonal antibody (Mab)-secreting hybridomas were obtained by fusions of spleen cells from immunized mice and non-secreting, HGPRT-deficient mouse myeloma SP2/0 cells by the methods of Fazekas De St-Groth and Scheidegger (J Immunol Methods 35 : 1-21, 1980) with modifications (J. Hamel et al. J Med Microbiol 23 : 163-170, 1987). Female BALB/c mice (Charles River, St-Constant, Quebec, Canada) were immunized with either BVH-3M (thioredoxin-His»Tag-BVH-3M fusion protein/ pET32 SUBSTITUTE SHEET (RULE 26) WO 01/98334 PCT/CA01/00908 system), BVH-11M (thioredoxin-His»Tag-BVH-llM fusion protein/ pET32 system), BVH-11-2M (thioredoxin-His»Tag-BVH-ll-2M fusion protein/ pET32 system) , BVH-11B (thioredoxin-His«Tag-BVH-HB fusion protein/ pET32 system), BVH-3M (His«Tag-BVH-3 fusion 5 protein/ pURV22^HIS system) or NEW1 (NEWl-His«Tag fusion protein/ pET21 system) gene products from S_^ pneumoniae strain SP64 to generate the tfab series H3-, H11-, H112-, HUB-, H3V-, and HN1-, respectively- Culture supernatants of hybridomas were initially screened hy enzyme- linked- immunoassay (ELISA). 10 according to the procedure described by Hamel et al. (Supra) using plates coated with preparations of purified recombinant BVH-3, BVH-11 and/or 0VH-11-2 proteins or suspensions of heat-killed S^ pneumoniae? cells. The Mab-secreting hybridomas selected for further characterization are listed in Table 3 15 and Table 4 from the following Example 2. The class and subclass of Mab immunoglobulins were determined by ELISA using commercially available reagents (Southern Biotechnology Associates, Birmingham/ AL). 20 Furthermore, the cloning and expression of chimeric gene(s) encoding for chimeric polypeptides and the protection observed after vaccination with these chimeric polypeptides are described. 25 BVH-3 and BVH-11 gene fragments corresponding to the 3'end of the genes were amplified by PCR using pairs of oligonucleotides engineered to amplify gene fragments to be included in the chimeric genes. The primers used had a restriction endonuclease site at the 5' end, thereby allowing 30 directional in-frame cloning of the amplified product into digested plasmid vectors (Table 1 and Table 2). PCR-amplified products were digested with restriction endonucleases and ligated to linearized plasmid pET21 or pSL301 vector. The resultant plasmid constructs were confirmed by nucleotide 35 sequence analysis. The recombinant pET21 plasmids containing WO 01/98334 PC17CAD1/00908 10 15 20 25 a PCR product were linearized by digestion with restriction enzymes for the in-frame cloning of a second DNA fragment and the generation of a chimeric gene encoding for a chimeric pneumococcal protein molecule. Recombinant pSL301 plasmids containing a PCR product were digested with restriction enzymes fox the attention of the DNA inserts. The resulting insert DNA fragments were purified and inserts corresponding to a given chimeric gene were ligated into pET21 vector for the generation of a chimeric gene. The recombinant chimeric polypeptides listed in Table 2 were as C-terminal fusion with an His-tag. The expressed recombinant proteins were purified from supernatant fractions obtained from centrifugation of sonicated IPTG-induced E._ coli cultures using a His-Bind metal chelation resin (QIAgen, Chatsworth, CA). Groups of 8 female BALB/c mice (Charles River) were immunizied subcutaneously two times at three-week intervals with 25 p.g of either affinity purified His.Tag-fusion protein identifed in presence of 15-20 jig of QuilA adjuvant. Ten to 14 days following the last immunization, the mice were challenged challenged intravenously with 10E5-10E6 CFU of S. pneumoniae type 3 strain WJ2. The polypeptides and fragments are capable of eliciting a protective immune response. Table 2A WO 01/98334 PCT7CA01/00908 EXAMPLE 2 5 This example describes the identification of peptide domains carrying target epitoPes using Mabs and recombinant truncated proteins described in example 1. Hybridomas were tested by ELISA against truncated BVH-3, BVH- 10 3JL or BVH-11-2 gene products in order to characterize the epitopes recognized by the Mabs. The truncated gene products were generated from S- pneumoniae SP64 strain except for BVH- 3-Sp63 which was generated from S. pneumoniae SP63 strain. As a positive control, the reactivity of each antibody was 15 examined with full-length BVH-3, BVH-11 or BVH-11-2 recombinant proteins. In some cases, the Mab reactivity was evaluated by Western immunoblotting after separation of the gene product by SDS-PAGE and transfer on nitrocellulose paper. The reactivities obse:Tved is set forth in the following Table 20 3 and Table 4. Table 3. ELISA reactivity of BVH-3-reactive Maba with a panel of eleven BVH-3 gene products the BVH-llM molecule Gene products tested Mabs (IgG isotype) BVH-3M BVH-3AD BVH-3B BVH-3C NEW 1 NEW 2 NEW 3 NEW 21 NEW .22 NEW 23 BVH- 3 Sp63 BVH-llM H3-4F9 (1) + + - + - - - - - - + + H3-4D4 (1) + + - + - - - - - + + H3-9H12 (1) + + - - + - - - - - + + H3-7G2 (1) + + - - - - - - + - - - H3-10A1 (1) + + - - - - - +■ - + + - H3-4D3 (1) + .- + - + - + + - - + - H11-6E7 (1) + + - + - - . - NT NT NT + + H11-10H10 (2a) + + + NT NT NT + + H11-7G11 (2b) + + • + + + + NT NT NT + + H3V-4F3 (1) + - + - + - - + - - + - H3V-2F2 (1) + - + - + + - +■ - - + - H3V-7F4 (1) + - + - + + - + - - + - H3V-7H3 (1) + - + - + - + + - " + - Gene products tested Mabs (IgG isotype) BVH-3M ■ BVH-3AD i BVH-3B BVH-3C NEW 1 NEW 2 NEW 3 NEW. 21 NEW 22 NEW 23 BVH- 3 Sp63 BVH- 11M H3V-13B8 (1) + + + + + + H3V-9C2 (1) + + - +/- - ■- - - + - + /- +/- H3V-9C6 (1) + + - - "- - - - + - - - H3V-16A7 (1) + +" + + H3V-15A10 (1) + + + +/- + + + + + + + /- H3V-6B3 (1/2) + + NT NT + + + + NT HN1-5H3 (2b) + + NT + + + HN1-8E3 (2a) + + NT + + + HN1-14P6 (2a) + + NT + + + ■ HN1-2G2 (1) + - + NT + + - + - - . + - Gene products tested Mabs (IgG isotype) BVH-3M BVH-3AD BVH-3B BVH-3C NEW 1 NEW 2 NEW 3 NEW 21 NEW 22 NEW 23 BVR- 3 Sp63 BVH-11M HN1-12D8 (2a) •f + NT + + + + HN1-14B2 (2a) + + NT + + + + HN1-1G2 (2a) + - + NT + + + + HN1-10C12 (1) + + NT + + + + HN1-3E5 (1) + + - - + + - + - + + NT : not.tested +/- : very low reactivity but higher than background, possible non-specific Mab binding Table 4. ELISA reactivity of BVH-11 and/or BVH-11-2-reactive Mabs with a panel of fourteen BVH-11 and BVH-11-2 gene products and the BVH-3M molecule X Gene products tested Mabs {igG isotype) BVH-11M BVH-11A BVH-11B BVH-11C NEW 5 NEW 6 NEW 7 NEW 8 NEW 9 NEW 10 NEW 11 NEW 14 NEW 18 NEW 19 BVH- 11- 2-M BVH-3M H3-4F9 (1) + + + + H3-4D4 (1) + + + + H3-9H12 (1) + + + + H11-6E7 (1) + + + + Hll- 10H10 (2a) + + + + H11-7G11 (2b) + + + + H11-1B12 (1) + + + H11-7B9 |+ + - - - " i - - - - - - + " to 00 (*> H O > I V- Gene, products tested Mabs BVH- BVH- BVH- BVH- NEW NEW NEW NEW NEW NEW NEW .NEW NEW NEW BVH-11- BVH- (IgG 11M 11A 11B 11C 5 6 7 8 9 10 11 14 18 19 2-M 3M isotype) (2a) H11-3H5 + - + + + - - _* - + - + + - + - (1) H11-10B8 + , - . + + + - - _* - + - + + - + - (1) H11-1A2 + - + + + - - _* - + - + + - + - (1) H112-3A1 + - + NT + - - + - + - + + - + - (1) H112- + + /- + NT + - - + - + - + + - + - 13C11 (1) H112- + + - NT + - - + - + - + + - +. - 10H10 (1) H112-1D8 + + - NT + - - + - + - + + - + - (2a) .. 3 o I o H n > I Gene products tested Mabs BVH- BVH- BVH- BVH- NEW . NEW NEW NEW NEW MEW NEW- NEW NEW NEW BVH-11- BVH- (IgG 11M 11A 11B 11C 5 6 7 8 9 10 11 14 18 19 2-M 3M isotype) H112- + - + NT + - - - + + - + - + + - 10G9 (2b) H112- + - + NT + - - ■+/- + + - +' - + + - 10A2 (1) H112-3E8 + - + NT •+ - - + /- - + - + - + + - (2a) H112- + - + NT + - -. - - + - + - - + ■ - 10D7 (2a) H112-2H7 + + - NT - - - - - - - - - - + - (2a) H112-6H7 .+ + - NT - - '- - . - - - - - - + - (1) H112-3A4 - - - NT - - - - + + - - + + - (2a) H112- - - - NT - - - - • - + + - - + ■h " 3 o n H n > I o Gene products tested Mabs (IgG isotype) BVH-11M BVH-11A BVH-11B BVH-11C NEW 5 NEW 6 NEW 7 NEW 8 NEW 9 NEW 10 ' NEW 11 NEW 14 NEW 18 NEW 19 BVH- 11- 2-M BVH-3M 10C5 (1) H112-14H6 (1) NT + + + + H112-7G2 (1) NT + + + + H112-13H10 (2a) NT + + + H112-7E8 (2b) +/- NT +/- + H112-7H6 (1). +/- NT +/- + HUB- 5F10 (1) + + + + + + + + + H11B-15G2 (1) + + + + + + + + + H11B- + - + + + - + + - + - + + " 00 Ui ■u. n H P o >—. o o Gene products tested Mabs (igG isotype) BVH-11M BVH-11A BVH-11B BVH-11C NEW 5 NEW 6 NEW 7 NEW 8 NEW 9 NEW 10 NEW 11 NEW 14 NEW 18 NEW 19 BVH- 11- '2-M BVH-3M 13D5-(2) H11B-11B8 (1) + 4- + + -t- + + 4- + HUB- • 7E11 (1) .+- + + + + + +- H11B-1C9 (1) + + + + + + + H11B-5E3 (2) + + + + H11B-6E8 (1) • + + + + NT : not tested ■ +/- : very low reactivity but higher than background, possible non-specific Mab binding * : a strong signal was detected when tested by Western iratttunoblotting WO 01/98334 PCT/CA01/00908 The deduced locations of the epitopes are summarized in Figure 28 and Figure 29. As can be seen from the data in Table 3, 5 BVH-3-reactive Mabs can be divided into two groups : BVH-3A-and BVH-3B-reactive Mabs with the exception of Mabs H11-7G11 and H3V-15A10 which reacted with both, BVH-3A and BVH-3B molecules. The BVH-3A-reactive Mabs can be subdivided in two subgroups of antibodies depending of their reactivity or lack 10 of reactivity with BVH-3C recombinant protein. Mab reactive with BVH-3C protein recognized epitopes shared by both, BVH-3 and BVH-11 proteins. As can be seen in Table 4, these BVH-3-and BVH-11-cross-reactive Mabs were also reactive with BVH-11A and BVH-11-2M recombinant proteins. BVH-3B-reactive Mabs can 15 be subdivided into three subgroups according to their reactivity with NEW1, NEW2 and NEW3 recombinant proteins. Some Mabs were only reactive with the NEW1 protein while other Mabs were reactive with either, NBW1 and NEW2 or NEW1 and NEW3 recombinant proteins. 20 Mabs H11-7G11 and H3V-15A10 react with epitopes in more than one position on BVH-3. The reactivity of H11-7G11 with BVH-3AD, BVH-3B, BVH-3C, BVH-11A and BVH-11-2M molecules suggests that H11-7G11 epitope might comprised HXXHXH sequence. This 25 sequence is repeated, respectively, 6 and 5 times in BVH-3 and BVH-ll/BVH-11-2 protein sequences. The lack of reactivity of Mab H11-7G11 with NEW 10 molecule suggests that the epitope includes the HGDHXH sequence. Multiple-position mapping of H3V-15A10 epitope on BVH-3 is suggested by the reactivity of 30 the Mab with two BVH-3 fragments that do not overlap. Interestingly, Mabs H3-7G2, H3V-9C6 and H3V-16A7 were not reactive with BVH-3 Sp63 thus allowing the location of their corresponding epitopes on a 177-amino acid fragment comprised 35 between amino acids 244 and 420 on BVH-3 molecule of S. pneumoniae SP64 (Figure 31). WO 01/98334 PCT/CA01/00908 As can be seen from the data in Table 4, the Mabs that are reactive with BVH-11- and/or BVH-11-2 and that do not recognize BVH-3 molecules can be divided into three groups 5 according to their reactivities with BVH-11A and NEW10 recombinant proteins. Some Mabs reacted exclusively with either BVH-11A or NEW10 protein while other Mabs were reactive with both, BVH-11A and NEW10 recombinant proteins. 10 EXAMPLE 3 This example describes the construction of BVH-3 and BVH-11-2 gene libraries for the mapping of epitopes. 15 BVH-3 and BVH-11-2 gene libraries were constructed using recombinant pCMV-GH and PSL301 plasmid DNA containing respectively, BVH-3 gene sequence spanning nucleotides 1837 to 4909 (SEQ ID NO: 2) or BVH-11-2 gene sequence spanning nucleotides 172 to 2630 (SEQ ID NO: 5) and the Novatope® 20 library construction and screening system (Novagen) . The recombinant plasmids containing BVH-3 or BVH-11-2 gene fragment were purified Using QIAgen kit (Chatsworth, CA) and digested with the restriction enzymes Bglll and Xbal respectively. The resulting Bglll-Xbal DNA fragments were 25 purified using the QlAquick gel extraction kit from QIAgen and digested with Dnase I for the generation of randomly cleaved DNA. DNA fragments of 50 to 200 bp were purified, treated with T4 DNA polymerase to blunt the target DNA ends and add a single 3'dA residue, and ligated into pSCREEN-T-Vector 30 (Novagen) following the procedures suggested by the manufacturer (Novatope® System, Novagen). The gene libraries of E^ coli clones, each of which expressing a small peptide derived from BVH-3 or BVH-11-2 genes were screened by standard colony lift methods using Mabs as immunoprobes. The colony 35 screening was not successful with Mabs producing very high backgrounds on colony lifts. Moreover, in some cases, Mabs WO 01/98334 PCT/CA01/00908 failed to detect epitope-expressing-colonies. The lack of reactivity can possibly be explained by the small amount of recombinant proteins produced or the recognition of conformation-dependent epitopes consisting of different 5 protein domains. Sequencing of DNA inserts from positive clones determined the location of the segment that encodes the target epitope. The data are presented in Table 5. The peptides encoded by DNA inserts into the recombinant pSCREEN-T vector can be purified and used as immunogens as described 10 below in Example 6. The peptide sequences obtained from the screening of BVH-3 and BVH-11-2 gene libraries with the Mabs are in agreement with the Mab ELISA reactivities against the truncated gene 15 products. As expected, the amino acid sequences obtained from H11-7G11 contained the sequence HGDHXH. These findings provide additional evidence for the location of epitopes recognized with the Mabs. Interestingly, although the Mabs H112-10G9, H112-10A2 and H11B-11B8 were reactive against the 20 same peptide, sequence (amino acid residues 594 to 679 on BVH-11-2 protein sequence) , clones corresponding to the sequence spanning from amino acid residues 658 to 698 were only picked up by Mab H11B-11B8 thus revealing the location of H11B-11B8 epitope between amino acid residues 658 to 679 (SEQ ID NO: 25 163). Mabs H112-10G9, H112-10A2, and H11B-11B8 are directed against 3 distinct non overlapping epitopes located closely on the peptide sequence corresponding to amino acid residues 594 to 679 (SEQ ID NO: 22). 30 Table Mabs 5. Peptide sequences obtained from the screening of BVH-3 and BVH-11-2 gene libraries CO c 00 CO Mab Clone/ Protein designat ion Nucleotide position Amino acid position Amino acid sequence SEQ ID NO H3-4D4 4D4.9 SEQ ID 1: 226-509 SEQ ID 6: 76-169 DQGYVTSHGDHyHYYNGKVPYDALFSEELLMKDPNYQLKDA DIVNEVKGGYIIKVDGKYYVYLKDAAHADNVRTKDEINRQK QEHVKDNEKVNS 11 Hll-7G11 7G11.7 SEQ ID 1: 193-316 SEQ ID 6: 64-105 GIQAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDALFSEEL L 12 Hll- 7G11 7G11.9 SEQ ID 1: 1171-1284 SEQ ID 6: 390-428 TAYIVRHGDHFHYIPKSNQIGQPTLPNNSLATPSPSLPI 13 H3-4D3 4D3.4 SEQ ID 1: 2565-2670 SEQ ID 6: 855-890 TSNSTLEEVPTVDPVQEKVAKFAESYGMKLENVLFN 14 HN1-8E3 8E3.1 SEQ ID 1: 3004-3120 SEQ ID 6: 1016-1039 MDGTIELRLPSGEVIKKNLSDFIA- 15 HN1-1G2 1G2.2 SEQ ID 1: 3017-3120 SEQ ID 6: 1005-1039 YGLGLDSVIFNMDGTIELRLPSGEVIKKNLSDFIA 16 HN1-10C12 10C12.7 SEQ ID 1: 2936-3120 SEQ ID 6: 983-1039 PALEEAPAVDPVQEKLEKFTASYGLGLDSVIFNMDGTIELR LPSGEVIKKNLSDFIA 17 HN1- 14F6 14F6.3 SEQ ID 1: 2501-2618 SEQ ID 6: 833-872 KVEEPKTSEKVEKEKLSETGNSTSNSTLEEVPTVDPVQEK 18 Mab Clone/ Protein designat ion Nucleotide position Amino acid position Amino acid sequence SEQ ID NO HN1-12D8 B12D8.2 SEQ ID 1:1433- 1767 SEQ ID 6: 512-589 MKDLDKKIEEKIAGIMKQYGVKRESIVVNKEKNAIIYPHGD HHHADPIDEHKPVGIGHSHSNYELFKPEEGVAKKEGN 19 H3V-7F4 7F4 .1 SEQ ID 1: 1633-1785 SEQ ID 6: 545-595 AI lYPHGDHHHADP IDEHKPVGIGHSHSNYELFKPEEGVAK KEGNKVYTGE 20 H112- 10D7 10D7.5 SEQ ID 5: 1685-1765 SEQ ID 8: 525-553 IQVAKLAGKYTTEDGYIFDPRDITSDEGD 21 H112-10G9 10G9.3 SEQ ID 5: 1893-2150 SEQ ID 8: 594-679 DHQDSGNTEAKGAEAIYNRVKAAKKVPLDRMPYNLQYTVEV KNGSLI I PHYDHYHNIKFEWFDEGLYEAPKGYSLEDLLATV KYYV 22 H112-10A2 10A2.2 SEQ ID 5 : 1893-2150 SEQ ID 8 : 594-679 DHQDSGNTEAKGAEAIYNRVKAAKKVPLDKMPYNLQYTVEV KNGSLIIPHYDHYHNIKFEWFDEGLYEAPKGYSLEDLLATV KYYV 22 H11B-11B8 B11B8.1 SEQ ID 5: 1893-2150 SEQ ID 8: 594-679 DHQDSGNTEAKGAEAIYNRVKAAKKVPLDRMPYNLQYTVEV KNGSLIIPHYDHYHNIKFEWFDEGLYEAPKGYSLEDLLATV KYYV 22 H11B-11B8 11B8.4 SEQ ID 5: 2085-2217 SEQ ID 8: 658-698 GLYEAPKGYSLEDLLATVKYYVEHPNERPHSDNGFGNASDH 23 Mab Clone/ Protein desigrnat ion Nucleotide position Amino acid position Amino acid sequence SEQ ID NO H112-3A4 3A4.1 SEQ ID 5: 2421-2626 SEQ ID 8 : 769-837 VENSVINAKIADAEALLEKVTDPS IRQNAMETLTGLKSSLL LGTKDNNTISAEVDSLLALLKESQPAPI 24 WO 01/98334 PCT/CAO1/00908 EXAMPLE 4 This example describes the immunization of animals with recombinant proteins for the generation of antibody reactive 5 with BVH-3, BVH-11 and/or BVH-11-2. NZW rabbits (Charles River Laboratories, St-Constant, Quebec, Canada) were immunized subcutaneously at multiple sites with 50 \iq or 100 £ig of the purified BVH-3M, L-BVH-3AD, NEW1, 10 NEW13, or L-BVH-11 recombinant protein in presence of 80 /ig of QuilA adjuvant (Cedarlane Laboratoratories Ltd, Hornby, Canada). The rabbits were boosted two times at three-week intervals with the same antigen and blood samples were collected before each immunization and 6 to 28 days following 15 the last immunization. The sera samples were designated preimmune, post lBt, post 2nd or post 3rd injection. The rabbit immune response to immunization was evaluated by ELISA using recombinant BVH-3M (BVH-3M-His»Tag fusion protein/ pET21 system) or BVH-11M (BVH-llM-His»Tag fusion protein/ pET21 20 system) proteins or suspensions of heat-killed • S^_ pneumoniae Rx-1 cells as coating antigens. ELISA titer was defined as the reciprocal of the highest sera dilution at which absorbance A4io value was 0.1 above the background value. Antibodies reactive with BVH-3 and/or BVH-11 epitopes were 25 elicited following immunization in all animals as shown in the following Table 6. Antibody reactive with recombinant or pneumococcal antigens was not present in the preimmune sera. The immune response to immunization was detectable in the sera of each rabbit after a single injection of recombinant 30 antigen. The antibody response following the second injection with either antigen tested was characterized by a strong increase in antibody titer. Interestingly, good titers of antibody reactive with S^ pneumoniae cells, with an average titer of 52,000 after the third immunization, were obtained, 35 thus establishing that native pneumococcal epitopes are expressed on the recombinant E_;_ coli gene products. These ■55 WO 01/98334 PCT/CA01/00908 data support the potential use of BVH-3, BVH-11 and/or BVH-11-2 gene products and the antibody raised to BVH-3, .BVH-11 and/or BVH-11-2 gene products as vaccines for the prevention and the treatment of pneumococcal disease, respectively. Table 6. Rabbit Antibody response to immunization with BVH-3 and BVH-11 gene products i ELISA Titer with coating antigen Rabbit Immunogen Sera sample BVH-3M BVH-11M pneumoniae #15 BVH-3M (50jig) Preimmune NT NT 200 Post-lac NT NT 1,600 Post-2na NT NT 20,000 Post-3ra 512,000 NT 40,000 #16 BVH-3M ■(lOOfig) Preimmune NT NT 200 post lsc NT NT 1,600 post 2na NT NT 40,000 post 3rQ 10b #112 L-BVH-3AD (50 pg) Preimmune post 1BC 16,000 NT NT post 2™ 512,000 NT NT post 3ra 2x10" NT 32,000 #113 New 1 (50 fig) Preimmune post 1BC 16,000 NT NT post 2M 512,000 NT NT post 3ra 10* NT #114 New 13 (50 ixg) Preimmune NT post lac NT 16,000 NT post 2na NT 64,000 NT post 3tQ NT NT 256,00 0 32,000 Preimmune WO 01/98334 FCT/CAW00908 #116 L-BVH-11 (50 /zg) post lsc NT 64,000 NT post 2na NT I0b NT post 3ra NT 2x10" 64,000 NT : not tested EXAMPLE 5 5 This example describes the protection of animals against fatal experimental pneumococcal infection by administration of antibody raised to BVH-3, BVH-11 or BVH-11-2 gene products. 10 High-titer Mab preparations were obtained from ascites fluid of mice inoculated intraperitoneally with Mab-secreting hybridoma cells according to the method described by Brodeur et al (J Immunol Methods 71 :265-272, 1984) • Sera samples were collected from rabbits immunized with BVH-3M as described 15 in Example 4. The. rabbit sera collected after the third immunization and ascites fluid were used for the purification of antibodies by precipitation using • 45 to 50% saturated ammonium sulfate. The antibody preparations were dissolved and dialyzed against phosphate-buffered saline (PBS). 20 CBA/N (x'id). mice (National Cancer Institute, Frederick, MA) were injected intraperitoneally with either 0.1 ml of purified rabbit antibodies or 0.2 ml of ascites fluid before intravenous challenge with approximately 200 CFU of the type 3 25 S^ pneumoniae strain WU2. Control mice received sterile PBS or antibodies purified from preimmune rabbit sera or sera from rabbits immunized with an unrelated N._ meningitidis recombinant protein antigen. One group of mice was challenged with S^ pneumoniae before the administration of anti-BVH-3 30 antibody. Samples of the S. pneumoniae challenge inoculum were plated on chocolate agar plates to determine the number of CFU and verify the challenge dose. The CBA/N mice were chosen because of their high susceptibility to S_;_ pneumoniae WO 01/98334 PCT/CA01/00908 infection. The LD50 of WU2 injected intravenously to CBA/N mice is estimated to be S1Q CFU. Deaths were recorded at 24-h intervals for a period of. at least 7 days. 5 The protection data obtained from mice injected with rabbit anti-BVH-3 antibody are set forth in the following Table 7. Nine' out of 10 mice receiving the anti-BVH-3 antibody survived the challenge in contrast to none of 10 mice injected with control antibody or PBS buffer. The observation that antibody 10 raised to the BVH-3-M molecule passively protected even when administered after the challenge demonstrated the ability of anti-BVH-3 antibody to prevent death even from an already established infection. 15 Table 7. Protective effects of rabbit antibody to BVH-3-M gene in CBA/N mice challenged i.v. with WU2 pneumococci Antibody preparation Time of antibody administration Alive s Dead Days to death post-infection Anti-BVH3M 1 h before infection 5 : 0 >14, >14, >14, >14, >14 Anti-N. meningitidis 1 h before infection 0 : 5- £. f £* f wf * / ** Anti-BVH-3M 0.5 h post¬infection 4 : 1 2, >14, >14, >14, >14 None (PBS) 1 h before infection 0 : 5 1 f J* f £> § £■ t ** CBA/N mice were infected with 1000 CFU of WU2 S. pneumoniae before or after intraperitoneal administration of 0.1 ml of rabbit antibody. 20 In an other experiment, 0.1 ml of rabbit antibody prepared from preimmune and immune sera were administered intraperitoneally to CBA/N mice four hours before intranasal challenge with 280 CFU of S^ pneumoniae P4241 type 3 strain. 25 As seen in the following Table 8, all immunized mice survived WO 01/98334 PCT/CA01/00908 the challenge while none of 9 mice receiving preimmune sera antibody or buffer alone were alive on day 6 post-infection. S. pneumoniae hemocultures on day 11 post-challenge were negative for all surviving mice. Furthermore, 100% protection 5 was observed in mice receiving monoclonal antibodies H112-10G9 or a mixture of H112-10G9 and H11B-7E11 which are' directed against. BVH-ll/BVH-11-2. 10 Table 8. Protective effects of passive transfer of rabbit antibody to BVH-3-M gene product or anti-BVH-ll/BVH-ll-2 specific Mabs in CBA/N mice challenged i.n. with P4241 pneumocbcci Antibody preparation Alive : Dead Days to death post-infection Anti-BVH-3M 5 : 0 >11, >11, >11, >11, Antibody from preimmune sera 0 : 5 3,3,3/6/6 H112-10G9 4 : 0 >11, >11, >11, >11 H112-10G9+H11B-7E11 5 : 0 >11, >11, >11, >11, >11 None (PBS) 0 : 4 3, '3, 3, 3 15 Altogether, the results from' Table 7 and Table 8 clearly establish that immunization of animals with a BVH-3 gene product such as BVH-3M elicited protective antibodies capable of preventing experimental ' bacteremia and pneumonia 20 infections. The protection data obtained for mice injected with ascites fluid are set forth in the following Table 9. Administration of a volume of 0.2 ml of ascites fluid of 0.2 ml of some sets 25 of ascites fluid prevented death from experimental infection. For example, H112-3A4 + H112-10G9 and H112-10G2 + H112-10D7 WO 01/98334 PCT/CA01/00908 sets of 2 Mabs conferred complete protection against experimental infection. These data indicated that antibody targetting BVH-11 and/or BVH-11-2 epitopes gave efficient protection. The Mabs H112-3A4, H112-10G9, H112-10D7, H112-5 10A2, H112-3E8, H112-10C5, H11B-11B8, H11B-15G2, H11B-1C9, H11B-7E11, H11B-13D5 and H11-10B8 were present in at least one protective pair of Mabs and were said to be protective and reactive against protective epitopes. The locations of protection-conferring epitopes on BVH-11-2 molecules are 10 summarized in Table 10 and Figure 29 . Protective Mabs H112-3A4, H112-10G9, . H112-10D7, H112-10A2, H112-3E8, H112-10C5, H11B-11B8, H11B-15G2, H11B-1C9, H11B-7E11, H11B-13D5 and Hll-10B8 were all reactive with New 10 protein corresponding to amino'acid residues 271 to 838 on the BVH-11-2 molecule. Six 15 out of these 12 Mabs were directed against epitopes present in the NEW 19 protein and 3 protective Mabs recognized NEW 14. Interestingly, Mab H112-3A4 and H112-10C5 reacted with distinct epitopes exclusive to BVH-11-2 located at the carboxyl end comprised between amino acid residues 769 and 20 837. Also, Mabs H11-7G11, H11-6E7 and H3-4F9 reactive with epitopes shared by pneumococcal BVH-3, BVH-11 and BVH-11-2 molecules did not succeed to protect even if given in combination with protective H112-10G9 or H112-11B8 Mab. These Mabs recognized epitopes located at the amino end of the BVH- 25 3, BVH-11 and BVH-11-2 molecules comprising, respectively, the first 225, 228 and 226 amino acid residues. The comparison of the BVH-3, BVH-11 and BVH-11-2 protein sequences revealed that a large number of amino acids were conserved in the amino end portion comprising these 225-228 residues with 30 a-global 72.8 % identity (Figure 32). Altogether the data set forth in Table 9 and Table 10 suggest that the protection eliciting BVH-11- and BVH-ll-2-epitopes is comprised in the carboxy terminal product containing amino 35 acids 229 to 840 and 227 to 838, on BVH-11 and BVH-11-2 proteins, respectively. WO 01/98334 PCT/CA01/00908 Table 9. Passive immunization with BVH-11- and/or BVH-11-2-specific Mabs can protect mice from lethal experimental pneumococcal infection. Experim ent Mab Alive : Dead Days to death post-infection 1 H112 3A4 + H112-10O9 6 : 0 6 X >10 H112-3A4 + H112-10D7 5 : 1 4, 5X >10 None 0 : 6 2, 2, 2, 2, 2, 6 2 H112-10 A2 + H112-10D7 5 : 1 3, 5X >10 H112-3E8 + H112-10G9 6 : 0 6 X >10 None 0 : 6 2/ 2/ 2, 2, 2/ 2 3 H112-10D7 + H11B-11B8 6:0 6 X >10 H112-10G9 + H11B-15G2 3 : 3 2, 6,6, 3 X >10 None 0 : 6 £* f & f JSM / "/ ** i ** 4 H112-10G9 + H112-10D7 5 : 0 5 X >11 None 0 : 5 £t f £t / A f £i t £ .5 H112-10G9 + H11-10B8 4 : 1 8, 4 X >14 H112-Z0G9 + H11B-7E11 5 : 0 5 X >14 None 0 : 3 1, 2, 2 6 H112-10G9 + H11B-1C9 4 : 1 4, 4 X >14 None 0 : 3 2, 2, 2' 7 H112-10C5 + H11B-13D5 5 :0 5 X >14 None 3 :3 2,2,2 CBA/N mice were injected intraperitoneally with a total of 0.2 ml of ascites fluid 4 hours before intravenous challenge with S, pneumoniae WU2. WO 01/98334 PCT/CAO1/00908 Table 10. Deduced locations of protection-conferring epitopes on BVH-11-2 molecules. Mabs Protection Gene products carrying Mab-epitope H112-3A4 + NEW 19 and NEW 11 H112-10G9 + NEW 19 H112-10D7 + NEW 14 and NEW 10 H112-10A2 + NEW 19 H112-3E8 + NEW 19 H11B-11B8 + NEW 19 H11B-15G2 + NEW 18 H11B-7E11 + NEW 14 and NEW 10 H11-10B8 + NEW 18 H11B-1C9 •V NEW 14 and NEW 1Q HU2-3A1 - NEW 18 and NEW 8 H112-10H10 - NEW 18 and NEW 8 H112-2H7 - BVH-11-2M H112-6H7 - BVH-11-2M H11-7G11 - BVH-11A and BVH-3C H11-6E7 - BVH-11A and BVH-3C H112-10C5 + NEW 19, NEW11 and 3A4.1 H11B-13D5 + NEW 19 H112-7G2 - NEW 18 H112-7E8 - BVH-11-2M H3-4F9 - BVH-11A and BVH-3C 5 Altogether the data presented in this example substantiate the potential use of antibodies raised to BVH-3, BVH-11 or BVH-11-2 molecules as therapeutic means to prevent, diagnose or treat S_^ pneumoniae diseases. 10 EXAMPLE 6 WO 01/98334 PCT/CAO1/00908 This example describes the localization of surface-exposed peptide domains using Mabs described in Example 1. 8. pneumoniae type 3 strain WU2 was grown in Todd Hewitt (TH) 5 broth (Difco Laboratories, Detroit MI) enriched with 0.5% Yeast extract (Difco Laboratories) at 37°C in a 8% C02 atmosphere to give an OD60o of 0.260 (-108 CFU/ml) . The bacterial suspension was then aliquoted in 1 ml samples and the S_;_ pneumoniae cells.were pelletted by centrifugation and 10 resuspended in hybridoma culture supernatants. The bacterial suspensions were then incubated for 2 h at 4°C. Samples were washed twice in blocking buffer [PBS containing 2% bovine serum albumin (BSA) ] , and then 1 ml of goat fluorescein (FITC)-conjugated anti-mouse IgG + IgM diluted in, blocking 15 buffer was added. After, an additional incubation of 60 min at room temperature, samples were washed twice in blocking buffer and fixed with 0.25 % formaldehyde in PBS buffer for 18-24 h at 4°C. Cells were washed once in PBS buffer and resuspended in 500 fil of PBS buffer. Cells were kept in the dark at 4°C 20 until analyzed by flow cytometry (Epics® XL; Beckman Coulter, Inc.). Ten thousands (10,000) cells were analyzed per sample and the results were expressed as % Fluorescence and Fluorescence index (FI) values. The % Fluorescence is the number of fluorescein-labelled S_;_ pneumoniae cells divided by 25 100 and the FI value is the median fluorescence value of pneumococci treated with Mab supernatant divided by the fluorescence value of pneumococci treated with the conjugate, alone or with a control unrelated Mab. ■ A FI value of 1 indicated that the Mab has not been detected at the surface of 30 the bacteria whereas a FI value higher than 2 was considered positive when at least 10 % of the pneumococcal cells were labelled and indicated that the Mab was ' reactive with cell-surface exposed epitopes. The following Table 11 summarized the data obtained with the Mabs tested by flow cytometry. 35 WO 01/98334 PCT/CA01/00908 Flow cytometric analysis revealed that the Mabs reactive with BVH-3C and/or BVH-11A molecules did not bind to the cell surface. In contrast, with the exception of Mabs H3V-9C6 and H3V-16A7, the Mabs reactive with NEW 1, NEW 2, NEW 3, NEW 22 or NEW 23 BVH-3 gene products were detected at the surface of pneumococci. These data indicated that the first 225 amino acid residues located at the amino end of BVH-3 are internal. The lack of binding of Mabs H3V-9C6 and H3V-16A7 suggest some portions of the sequence corresponding to the 177-amino acids absent from the BVH-3 molecule of S^ pneumoniae SP63 appears not to be accessible to antibodies. Results from BVH-ll- and/or BVH-11-2-reactive Mabs revealed that there is a good correlation between surface-exposure and protection. All Mabs reactive with internal epitopes as determined by the flow cytometry assay were not protective whereas all the protective Mabs described in Example 5 gave a positive signal in flow cytometry. Although an FI value of 9.0 and a % Fluorescence of 81.2 were obtained with Mab Hll-7G11, this Mab was not shown to protect. Additional assays can be used to further evaluate whether this Mab and its corresponding epitope might participate in anti-infectious immunity. Table 11. Results from the binding of Mabs at the surface of S. pneumoniae by flow cytometry analysis Mab % Fluoresce nee FI Bindin g Gene products carrying Mab-epitope H3-4F9 3.4 1.2 - BVH-3C and BVH-11A H3-4D4 3.4 1.2 BVH-3C and BVH-11A. H3-9H12 2.5 1.1 BVH-3C and BVH-11A H3-7G2 66.2 6.3 + NEW 22 H3-10A1 58.8 5.6 + NEW 23 WO 01/98334 PCT/CA01/00908 Mab % Fluoresce nee FI Bindin 3 Gene products carrying Mab-epitope H3-4D3 33.2 3.5 + NEW 3 H3V-4F3 24.4 2.9 + NEW 1 H3V-2F2 15.6 2.4 + NEW 2 H3V-7F4 58.7 5.6 + NEW 2 H3V-7H3 68.8 6.9 + NEW 3 H3V-13B8 75.0 7.7 + NEW 3 . H3V-9C2 66.4 6.2 + NEW 22 H3V-9C6 2.9 1.0 - NEW 22 H3V-1SA7 6.6 1.7 - NEW 23 H3V-15A10 58.7 5.7 + NEW 22 and NEW 23 HN1-5H3 43.4 5.3 + NEW 1 HN1-8E3 57.4 6.6 + NEW 1 HN1-14F6 57.8 . 6.7 + NEW 1 HN1-2G2 54.8 6.3 + NEW 2 HN1-12D8 14.3 3.0 + NEW 2 HN1-14B2 11.5 2.7 + NEW 2 HN1-1G2 59.9 7.0 + NEW 3 HN1-10C12 13.6 2.8 + NEW 3 H11-6E7 4.9 1.2 - BVH-3C and BVH-llA Hll-10H1O 6.5 1.6 BVH-3C and BVH-llA H11-7G11 81.2 9.0 + BVH-3C and NEW 2 H11-1B12 3.1 1.2 . - BVH-llA H11-7B9 2.4 1.1 - BVH-llA H11-10B8 81.1 9.1 + NEW 18 and NEW 8 H11-1A2 84.4 10 + NEW 18 and NEW 8 H11-3H5 84.0 9.8 + NEW 18 and NEW 8 H112-13C11 49.3 5.9 + NEW 18 and NEW 8 H112- 0.4 1.0 - BVH-llA and NEW 18 WO 01/98334 PCT/CA01/00908 Mab % Fluoresce nee FI Bindin g Gene products carrying Mab-epitope 10H10 H112-1D8 0.4 1.0 - BYH-llA and NEW 18 H112-10G9 78.9 10.4 + NEW 19 H112-10A2 . 75.5 9.6 + NEW 19 H112-3E8 62.5 7.5 + NEW 19 H112-10D7 64.5 7.7 + NEW 14 H112-2H7 0.7 1.1 - BVH-11A' H112-6H7 0.3 1.0 - BVH-11A H112-3A4 70.1 8.9 + NEW 11 H112-10C5 86.3 9.2 + NEW 11 AND 3A4.1 H112- ■ 14H6 89.6 11 + NEW 11 H112-14H6 0.8 1.4 NEW 11 H112-7G2 4.7 2.0 - NEW 18 H112-13H10 0.5 1.0 NEW 18 H112-7E8 0.4 1.0 - BVH-11-2M H112-7H6 0.2 1.0 ■ - BVH-11-2M H11B-5P10 3.1 1.1 NEW 18 H11B-15G2 60.2 5.7 + NEW 18 and NEW 8 H11B-13D5 75.7 8.3 + ■ NEW 19 H11B-11B8 78.4 8.3 + NEW 19 H11B- 32.3 3.5 + ■ NEW X4 WO 01/98334 PCT/CA01/00908 Mab % Fluoresce nee FI Bindin g Gene products carrying Mab-epitope 7E11 H11B-1C9 57.3 5.5 + NEW 14 H11B-5E3 1.8 1.0 - NEW 7 H11B-6E8 2.4 1.0 - NEW 7 EXAMPLE 7 5 This example describes the immunization of animals ' with peptide epitopes of BVH-3 and BVH-11-2. The recombinant pSCREEN-T vector (Novagen, Madison, WI) containing DNA fragment (nucleotides 2421 to 2626 on SEQ ID 10 NO :. 5). encoding the Mab 3A4-epitope (SEQ ID NO: 24) was transformed by electrbporation (Gene Pulser II apparatus, BIO- . RAD Labs, Mississauga, Canada) into E^ coli Tuner (A.DE3) pLysS [BL21 (F' ompT hsdSB (rB"mB_) gal dem lacYI pLysS (Cmr)] (Novagen) . In this strain, the expression of the fusion 15 protein is controlled by the T7 promoter which is recognized by the T7 RNA polymerase (present on the XDE3 prophage, itself under the control of the lac promoter inducible by isopropyl-P-D-thiogalactopyranoside (IPTG). The pLysS plasmid reduces the basal fusion protein expression level by coding for a T7 20 lysozyme, which is a natural inhibitor of the T7 RNA polymerase. The transformants were grown at 37°C with 250 RPM agitation- in LB broth (peptone lOg/1, yeast extract 5g/l, NaCl 5g/l) 25 supplemented with 50mM glucose, I00jig/ml carbenicillin and 34/zg/ml chloramphenicol, until the absorbance at 600nm reached a value of 0,7. The overexpression of T7gene 10 protein-His»Tag-3A4.1 fusion protein was then induced by the addition of IPTG to a final concentration of lmM • and further WO 01/98334 PCT/CA01/00908 incubation at 25°C with 250 RPM agitation for 3 hours. Induced cells from a 800-ml culture were pelleted by centrifugation and frozen at -70°C. The fusion protein was purified from the soluble cell fraction by affinity chromatography based on the 5 binding of a six histidine residues sequence (His-Tag) to divalent cations (Ni2+) immobilized on a metal chelation Ni-NTA resin (Qiagen, Mississauga, Canada). Briefly, the pelleted cells were thawed and resuspended in Tris buffered sucrose solution (50mM Tris, 25%(w/v) sucrose) and frozen at - 10 70°C for 15 minutes. Cells were incubated 15 minutes on ice in the presence of 2mg/ml lysozyme before disruption by sonication. The lysate was centrifuged at 12000 RPM for 30 • minutes and Nickel charged Ni-NTA resin (QIAgen) was added to the supernatant for an overnight incubation at 4°C, with 100 15 RPM agitation. After washing the resin with a buffer consisting of 20mM Tris, 500mM NaCl, 20mM imidazole pH 7,9, the fusion 3A4.1 protein was eluted with the same buffer supplemented with 250mM imidazole. The removal of the salt and imidazole was done by dialysis against PBS at 4°C. The 20 protein concentration was determined with BCA protein assay reagent kit (Perce, Rockford,IL) and adjusted to 760 ^g/ml. . To evaluate whether immunization with an epitope peptide sequence could confer protection against disease, groups of 6 25 female CBA/N (xid) mice (National Cancer Institute) are immunized subcutaneously three times at three-week intervals with affinity purified T7genel0 protein-His«Tag-3A4.1 fusion protein or, as control, with QuilA adjuvant alone in PBS. Twelve to fourteen days following the third immunization, the 30 mice are challenged intravenously with S^ pneumoniae WU2 strain or intranasally with P4241 strain. Samples of the S. pneumoniae challenge inoculum are plated on chocolate agar plates to determine the number of CFU and to verify the challenge dose. The challenge dose are approximalety 300 CFU. 35 Deaths are recorded daily for a period of 14 days and on day WO 01/98334 PCT/CA01/00908 14 post-challenge, the surviving mice are sacrificed and blood samples tested for the presence of S^ pneumoniae organisms. The 3A4.1 protein or other tested protein is said protective when the number of mice surviving the infection or the median 5 number of days to death is significantly greater in the 3A4.1-immunized group compared to the .control mock-immunized group. EXAMPLE 8 10 This example illustrates the improvement of the antibody response to pneumococci using BVH-3 fragments and variants thereof. The combined results obtained from studies of Mab reactivity 15 with truncated gene products, epitope-expressing colonies and live intact pneumococci presented in examples 2, 3 and 6, allowed to delineate between surface-exposed and internal epitopes'. The epitopes detected by Mabs that efficiently bound to pneumococci cells mapped to a region comprised 20 between amino acid residues 223 to 1039 of BVH-3 described in SEQ ID NO 6. The existence of protective epitopes in the BVH-3-carboxyl half was confirmed by demonstrating that mice immunized with NEWl molecule were protected from fatal infection with P4241 strain. 25 Gene sequence comparison revealed that in some strains, the region of BVH-3 encoding for amino acids 244 to 420 as described in SEQ ID N06 is absent thus suggesting the lack of utility of this sequence in vaccine to prevent disease caused 30 by such strains (SEQ ID NO: 9 versus SEQ ID NO: 1) . Further BVH-3 fragments or variants thereof were designed in the purpose to develop a universal highly effective vaccine that would target the immune response to ubiquitous surface-exposed protective epitopes. BVH-3 gene fragments designated NEWl 35 (encoding amino acid residues 4 72 to 103 9 from SEQ ID NO: 6) and NEW40 (encoding amino acid residues 4 08 to 103 9 from SEQ WO 01/98334 PCT/CA01/00908 ID NO: 6) were amplified from the S^ pneumoniae strain SP64 by PCR using pairs of oligonucleotides engineered •for the amplification of the appropriate gene fragment. Each of the primers had a restriction endonuclease site at the 5'end, 5 thereby.allowing directional in-frame cloning of the amplified product into the digested plasmid vector. pCR-amplified products were, digested with restriction endonucleases and ligated to linearized plasmid pET21 (Novagen) expression vector digested likewise. Oligonucleotide primers HAMJ489 10 (ccgaattccatatgcaaattgggcaaccgactc,- Ndel) and HAMJ279 (cgccaagcttcgctatgaaatcagataaattc; Hindlll) were used for the NEW 40 construction. Clones were first stabilized in E^ coli DH5a before introduction into E_;_ coli BL21 (ADE3) for expression of the truncated gene products. Variants from NEW1 15 and NEW40 were generated by mutagenesis using the Quickchange Site-Directed Mutagenesis kit ' from Stratagene and the oligonucleotides designed to incorporate the appropriate mutation. The presence of 6 histidine tag residues on the C~ terminus of the recombinant molecules simplified the 20 purification of the proteins by nickel chromatography. The following tables 12 and 13 describe the sequences of the primers used for the mutagenesis experiments and the variant gene products generated, respectively. Mutagenesis experiments using primer sets 39, 40, 46, 47 or 48 resulted in silent 25. changes and were performed in the purpose of improving the expression of the desired gene or gene fragment since it was observed that during the course of expression, BVH-3 gene and fragments . of, shorter secondary translation initiation products were coexpressed. 12. List of PCR oligonucleotide primer sets used for site-directed mutagenesis truncates Primer set: Primer identification SEQ ID Ho Primer SEQUENCE 5' > 3' 9 HAMJ513 ' HAMJ514 177 17S GAATCAGGTTTTGTCATGAGTTCCGGAGACCACAATCATTATTTC GAAATAATGATTGTGGTCTCCGGAACTCATGACAAAACCTGATTC 10 HAMJ515 HAMJ516 179 180 GTCATGAGTTCCGGAGACTCCAATCATTATTTCTTCAAGAAGG CCTTCTTGAAGAAATAATGATTGGAGTCTCCGGAACTCATGAC 11 HAMJ517 HAMJ518 181 182 ATGAGTTCGGAGACTCCAATTCTTATTTCTTCAAGAAGGACTTG a^GTCCTTCTTGAAGAAATAAGAATTGGAGTCTCCGGAACTCAT 14 CHANS1 CHAN52 183 184 GCGATTATTTATCCGTCTGGAGATCACCATCATGC GCATGATGGTGATCTCCAGACGGATAAATAATCGC 17 CHAN53 CHAN54 185 186 CCGTCTGGAGATGGCCATCATGCAGATCCG CGGATCTGCATGATGGCCATCTCCAGACGG 19 CHAN47 CHAN48 187 188 CCGCAGGGAGATAAGCGTCATGCAGATCCGATTG CAATCGGATCTGCATGACGCTTATCTCCCTGCGG 20 CHANS5 CHAN56 189 190 CCGTCTGGAGATGGCACTCATGCAGATCCGATTG CAATCGGATCTGCATGAGTGCGATCTCCAGACGG 22 CHAN57 CHANS8 191 192 CCGTCTGGAGATGGCACTTCTGCAGATCCGATTGATG CATCAATCGGATCTGCAGAAGTGCCATCTCCAGACGG 23 HAMJ523 HAMJ524 193 194 CCGCATGGAGATGGCCATCATGCAGATCCG CGGATCTGCATGATGGCCATCTCCATGCGG 24 HAMJ526 HAMJ527 195 196 GTCATGAGTCACGGAGACTCCAATCATTATTTCTTCAAGAAGG CCTTCTTGAAGAAATAATGATTGGAGTCTCCGTGACTCATGAC 25 HAMJ528 HAMJ529 197 198 ATGAGTCACGGAGACCACAATTCTTATTTCTTCAAGAAGGACTTG CAAGTCCTTCTTGAAGAAATAAGAATTGTGGTCTCCGTGACTCAT 29 HAMJ569 HAMJ570 199 200 TACCTCATTATGACTCTTACTCTAACATCAAATTTGAGTGGTTTG CAAACCACTCAAATTTGATGTTAGAGTAAGAGTCATAATGAGGTA 30 HAMJ571 HAMJ572 201 202 TACCTTCTTATGACCATtACTCTAACATCAAATTTGAGTGGTTTG AAACCACTCAAATTTGATGTTAGAGTAATGGTCATAAGAAGGTA 31 HAMJS73 HAMJ574 1 _ — 203 204 AACGGTAGTTTAATCATACCTTCTAAAGACCATTACCATAACATC GATGTTATGGTAATGGTCTTTAGAAGGTATGATTAAACTACCGTT Primer set Primer identification SEQ ID NO Primer SEQUENCE 5' > 3' 32 HAMJ575 HAMJ576 205 206 -CGGTAGTTTAATCATACCTCATAAGGACTCTTACCATAACATCAAA TTTGATGTTATGGTAAGAGTCCTTATGAGGTATGATTAAACTACCG 33 HAMJ577 HAMJ578 207 208 AACGGTAGTTTAATCATACCTGACCATTACCATAACATCAAATTTG CAAATTTGATGTTATGGTAATGGTCAGGTATGATTAAACTACCGTT 34 HAMJ579 HAMJ580 209 210 AACGGTAGTTTAATCATACCTTACCATAACATCAAATTTGAGTGG CCACTCAAATTTGATGTTATGGTAAGGTATGATTAAACTACCGTT 35 HAMJ581 HAMJ582 211 212 ACCGGTAGTTTAATCATACCTAACATCAAATTTGAGTGGTTTGAC GTCAAACCACTCAAATTTGATGTTAGGTATGATTAAACTACCGTT 37 HAMJ53 6 HAMJ53 7 213 214 CCTATGTAACTCCACATATAACCCATAGCCACTGG CCAGTGGCTATGGGTTATATGTGGAGTTACATAGG 39 HAMJ550 HAMJ551 215 216 .CGTGAAAGTATTGTCGTAAATAAAGAAAAAAATGCG CGCATTTTTTTCTTTATTTACGACAATACTTTCACG 40 HAMJ586 HAMJ587 217 218 CATGAAGAAGATGGTTACGGTTTCGATGCTAACCGTATTATCGCTGAAG CTTCAGCGATAATACGGTTAGCATCGAAACCGTAACCATCTTCTTCTG 41 HAMJ588 HAMJ589 219 220 GAATCAGGTTTTGTCATGAGTGACCACAATCATTATTTCTTC GAAGAAATAATGATTGTGGTCACTCATGACAAAACCTGATTC 42 HAMJ590 HAMJ591 221 222 GAAGATGAATCAGGTTTTGTCATGAGTAATCATTATTTCTTCAAG CTTGAAGAAATAATGATTACTCATGACAAAACCTGATTCATCTTC 43 HAMJ592 HAMJ593 223 224 GAAGATGAATCAGGTTTTGTCATGAGTTATTTCTTCAAGAAGGAC GTCCTTCTTGAAGAAATAACTCATGACAAAACeTGATTCATCTTC 44 HAMJ594 HAMJ595 225 226 AAAATGCGATTATTTATCCGCACCATCATGCAGATCCGATTG CAATCGGATCTGCATGATGGTGCGGATAAATAATCGCATTTT 45 HAMJ600 HAMJ601 227 228 AAAATGCGATTATTTATCCGGCAGATCCGATTGATGAACATAAAC GTTTATGTTCATCAATCGGATCTGCCGGATAAATAATCGCATTTT 46 HAMJ604 HAMJ605 229 230 GATGCTAACCGTATAATCGCCGAAGACGAATCAGGTTTTGTCATG CATGACAAAACCTGATTCGTCTTCGGCGATTATACGGTTAGCATC 47 HAMJ606" HAMJ607 231 232 CGCCGAAGACGAATCCGGCTTTGTAATGAGTCACGGAGACTCC GGAGTCTCCGTGACTCATTACAAAGCCGGATTCGTCTTCGGCG 48 . HAMJ608 HAMJ609 233 234 CATCTCATGAACAGGATTATCCCGGCAACGCCAAAGAAATGAAAG CTTTCATTTCTTTGGCGTTGCCGGGATAATCCTGTTCATGAGATG 13. Lists of truncated variant BVH-3 gene products generated from S. pneumoniae SP64 Protein designation Gene/ Protein SBQ XD NO Protein Identification* PCR primer set (ref. table 12) Gene used for mutagenesis NEW1-mutl** 255 NEW1 39 NEW1 NEW35A 256 NEW1 550-SGDGTS-555 14,17,20,22 NEW1 NEW42 257 NEW40 55-SGDSNS-60 144-SGDGTS-149 9, 10, 11, 14, 17, 20, 22 NEW40 NEW49 258 NEW40 55-SGDHNH-60 9 NEW4 0 NEW50 259 NEW40 55-SGDSNH-60 10 NEW49 NEW51 260 NEW40 55-SGDHNH-60 144-SGDHHH-149 14 NEW49 NEWS 2 261 NEW40 55-SGDSNH-60 144-SGDGHH-149 10, 17 NEW51 NEW 5 3 262 NEW40 55-HGDHNH-60 144-SGDHHH-149 14 NEW40 NEWS 4 263 NEW40 55-SGDHNH-60 144-SGDGHH-149 17 NEW53 NEW55 264 NEW1 550-HGDGHH-555 23 NEW1 NEWS 6 265 NEW40 55-HGDSNH-60 144-SGDHHH-149 24 NEWS 3 NEW56-mut2** 266 KEW56 40 NEW56 NEWS6- . mut3** 267 NEW56 46,47,48 NEW56 NEW57 268 NEW40 55-HGDHNE3-60 144-SGDHHH-149 25 NEW53 NEW63 269 NEW40 55-HGDSNH-60 144-HGDHHH-149 24 NEW40 NEW64 270 NEW40 55-HGDHNS-60 144-HGDHHH-149 25 NEW40 NEW65 271 NEW40 55-HGDSNH-60 144-HGDGHH-149 23 NEW63 00 3 g o o 00 Protein designation Gene/ Protein SEQ IB NO Protein Identification* PCR primer set (ref. table 12 > Gene used mutagenesis for NEW66 272 NEW40 55-HGDHNS-60 144-HGDGHH-149 23 NEW64 NEW 7 6 273 NEW40 55-HGDHNS-60 144-SGDGHH-149 17 NEW64 NEW105 274 NEW40 55- -60 41,42,43 NEW40 NEW106 275 New40 144- -149 44,45 NEW40 NEW107 276 NEW40 55- -60 144- -149 44,45 NEW105 * The underlined amino acid residues represent the modification in protein sequence. Nucleotides/amino acid residues are deleted in NEW105, NEW106 and NEW107 constructs. ** silent mutation, i.e. the polypeptide is the same as Newl. WO 01/98334 PCT/CA01/00908 Groups of 7 or 8 female BALB/c mice (Charles River) immunized as described earlier in example 1 were used for protection experiments against intranasal challenge with virulent S_;_ 5 pneumoniae P4241 strain. The mice were observed for 10 to 14 days post-infection. Data from Table 15 clearly indicate that the NEW35A molecule was equivalent to the parental NEW1 in term of protection. Interestingly, high survival rates where obtained for NEW40- and NEW56-immunized groups with 7 and 8 10 survivors out of 8 animals, respectively. Similarly, NEW25 comprising amino acid residues 233 to 1039 protected 7 out of 8 animals from lethal infection. Table 14. Protection mediated by BVH-3 fragments or variants 15 thereof in experimental pneumonia Expe rime nt Immunogen Alive : Dead Days to death post-infection 1 Quil A NEW 1 NEW 35A NEW 40 BVH-3M 0 : 8 5 : 3 5 : 2 7 : 1 4 : 4 4, 4, 4, 4, 4, 4, 4, 4 5, 7, 7, >14, >14, >14, >14, >14 9, 10, >14, >14, >14, >14, >14 13, >14, >14, >14, >14, >14, >14, >14 7, 8, 10, 12, >14, >14, >14, >14 2 Quil A NEW 52 NEW56 NEW 4 0 0 : 8 4:4 8 : 0 7 : 1 3, 3, 4, 4, 4, 4, 4, 4 7, -7, 8, 9, >10, >10, ?10, >10 8 X >10 6, >10, >10, >10, >10, >10, >10, >10 3 QuilA NEW25 0 : 8 7 : 1 3, 3, 4, 4, 4, 4, 4, 4 6, >13, >13, >13, >13, >13, >13, >13 Additionally, flow cytometry analyses of the binding capacity of the sera antibodies from the vaccinated animals revealed that NEW4 0 and NEW56 antibodies labelled live intact 20 pneumococci more efficiently than antibodies raised to BVH-3M (Table 15). WO 01/98334 PCT/CA01/00908 Table 15. Binding of mouse sera antibodies at the surface of S. pneumoniae type 3 strain WU2 as measured by flow cytometry. Antisera Fluorescence index Experiment Experiment Experiment Mean ± SE 1 2 3 BVH-3M 9.2 11.4 14.5 11.7 ± 1.5 NEWl 11.5 10.1 nd* 10.8 ± 0.7 NEW35A 14.3 12.9 nd 13.6 ± 0.7 NEW40 20.4 19.1 20.2 19.9 ± 0.4 NEW56 nd 16.7 20.2 18.5 ± 1.8 NEW52 nd 16.6 19.3. 18.0 ± 1.4 Adj uvant 1.9 1.6 1.2 1.6 ± 0.2 alone * nd: not done 5 cytometry results are expressed as fluorescence index value where the fluorescence index is the median fluorescence value of pneumococci treated with test sera divided by the background fluorescence value of pneumococci treated with the fluorescein conjugate alone, in these flow cytometric assays, 10 all sera were used at a dilution of 1 :50 and the sera from mice immunized with BVH-3C fragment or QuilA adjuvant alone gave a value similar to the background value. Altogether the protection and pneumococci antibody binding 15 data indicate that vaccination using NEWl or NEW40 molecules and variants thereof, directs the immune response to conserved protective surface-exposed epitopes. EXAMPLE 9 20 This example describes the cloning and expression of a chimeric deletant BVH-11-2 gene encoding, for a chimeric .polypeptide corresponding to BVH-ll-2 conserved protective surface-exposed epitopes present in most if not all S. pneumoniae strains. 76 " WO 01/98334 PCT/CA01/00908 BVH-ll-2 gene fragments corresponding to 4 gene regions, were amplified by PCR using pairs of oligonucleotides engineered to amplify fragments originating from SEQ ID NO :5 spanning . 5 nucleotides 1662 to 1742, 1806 to 2153, 2193 to 2414 and' 2484 to 2627 from S. pneumoniae strain Sp64 BVH-11-2 gene. The primers used, HAMJ490-491, HAMJ492-HAMJ493, HAMJ494-HAMJ495, HAMJ496-HAMJ354 had. a restriction endonuclease site 10 at the 5' end, thereby allowing directional in-frame cloning of the amplified product into the digested pET21b(+) plasmid vector (Table 16) . PCR-amplified products were digested with restriction endonucleases and ligated to linearized plasmid pSL301 vector digested likewise except for the PCR-amplified 15 fragment obtained with the primer pair HAMJ490-HAMJ491. The HAMJ490-HAMJ491 PCR-amplified product was purified from agarose, gel using a QIAquick gel extraction kit from QIAgen (Chatsworth, CA) and ligated into pGEM-T plasmid vector without any prior restriction endonuclease digestion. The 20 resultant plasmid constructs were confirmed by nucleotide sequence analysis. The recombinant plasmids containing each of the four were digested with restriction endonucleases corresponding with the 5' end of each primer pair used for the PCR-amplification. The fragments were purified from agarose 25 gel like described earlier and were all ligated to linearized plasmid pET2lb ( + ) digested with the restriction enzymes Ndel and Hindlll for the in-frame cloning of .the four different regions of the BVHll-2 gene. Clones were first stabilized in E.coli DH5ot before introduction into E.coli BL21 (ADE3) for .30 expression of a chimeric pneumococcal protein molecule. The resulting NEW43 gene sequence (SEQ ID No 257) is described in Figure 33. WO 01/98334 The deduced amino acid sequence 258) is described in Figure 34. PCT/CAOl/00908 of NEW43 pxotein (SEQ ID No WO 01/98334 PCT/CAO1/00908 Table 16. List of PCR oligonucleotide primers used to construct the NEW43 , VP43S and NEW86 Primer SEQ ID NO Sequence 5' - 3' Nucleotide position Restrictio n sites HAMJ490 259 ccgaattccatatgcaaat tacctacactgatgatg SEQ ID 5 :1662-1683 Ndel HAMJ491 260 ggactagtatcaaagatat aaccgtcttc SEQ ID 5 :1742-1722 Spel HAMJ492 261 ggactagttggattaaaaa agatagtttgtctg SEQ ID 5 :1806-1830 Spel HAMJ493 262 ttcccgcggttcgacatag tacttgacagtcg SEQ ID 5 :2153-2131 SacII HAMJ494 263 ttcccgcggaacgctagtg accatgttcg SEQ ID 5 :2193-2212 SacII HAMJ495 264 cggggtaccaggaatttca gcctcatctgtg SEQ ID 5 :2414~ 2393 Kpnl HAMJ496 265 cccggtacccctagtatta gacaaaatgctatggag SEQ ID 5 :2484-2510 Kpnl HAMJ 354 65 cgccaagcttctgtatagg agccggttgac SEQ ID 5 :2627-2608 HindiII HAMJ 583 266 ggatcccgggaggtatgat taaactaccg SEQ ID 5 :2039-2021 Smal HAMJ 584 267 catgcccgggaacatcaaa tttgagtggtttgac SEQ ID 5 :2058-2081 Smal HAMJ 610 . 268 cttgatcgacatatgttgg caggcaagtacacaacag SEQ ID. 5 :1701-1722 Ndel WO 01/98334 PCT/CAO1/00908 Table 17. List of truncated BVH-ll-2 gene fragments generated from S. pneumoniae SP64 for the construction of NEW43 PCR-primer sets Gene fragment designation Correspondin g amino acid residues on SEQ ID NO: 8 Cloning vector HAMJ490-HAMJ491 NEW43a 517-543 pGEM-T HAMJ492-HAMJ493 NEW43b 565-680 pSL301 HAMJ494-HAMJ495 NEW43C 694-767 pSL301 HAMJ496-HAMJ354 NEW43d 791-838 pSL301 Table 18. Properties of NEW86 and VP43S genes generated from NEW43 gene PCR-primer sets Gene/ Protein designation Identification HAMJ610-HAMJ354 VP43S NEW43 C'end corresponding to residues 15-272) HAMJ490-HAMJ583 HAMJ584-.HAMJ354 NEW 8 6 NEW43 109- PG -114 10 NEW43-derived molecules designated VP43S and NEW86 were generated from gene amplification- and cloning experiments using PCR primers described in Tables 16 and 18 and pET21 expression plasmid vector. Variants from NEW43 were generated by mutagenesis using the Quickchange Site-Directed Mutagenesis 15 kit from Stratagene and the oligonucleotides designed to incorporate the appropriate mutation. The presence of 6 histidine tag residues on the C-terminus of the recombinant molecules simplified the purification of the proteins by nickel chromatography. The following tables 19 and 20 20 describe the sequences of the primers used for the mutagenesis experiments and the NEW43 variant gene products generated, respectively. WO 01/98334 PCT/CA01/00908 5 Table 19. List of PCR oligonucleotide primer sets used for aite-directed mutagenesis on NEW43 gene Prim er set Primer idexiti -fication SEQ ID NO Primer SEQUENCE 5' ---> 3' 1 HAMJ 497 HAMJ 49B 269 270 AACGGTAQTTTAATCATACCTTCTTATGACCATTACCATAACATC GATQTTATGGTAATGGTCATAAGAAGGTATGATTAAACTACCGTT 2 HAMJ499 HAMJ500 271 272 AATCATACCTTCTTATGACTCTTACCATAACATCAAATTTGAGTG GACTCAAATTTaATGTTATGGTAAaAGTCATAAGAAGGTATGATT 3 HAMJ501 HAMJ502 273 274 TACCTTCTTATGACTCTTACTCTAACATCAAATTTGAaTGGTTTG CAAACCACTCAAATTTGATGTTAGAGTAAGAGTCATAAGAAGGTA 26 HAMJ530 HAMJ531 275 276 AATCATACCTCATTATGACTCTTACCATAACATCAAATTTGAGTG CACTCAAATTTGATGTTATGGTAAGAGTCATAATGAGGTATGATT 27 HAMJ532 HAMJ533 277 278 TACCTCATTATGACCATTACTCTAACATCAAATTTGAGTGGTTTG CAAACCACTCAAATTTGATGTTAGAGTAATGGTCATAATGAGGTA 29 HAMJ569 HAMJ570 279 280 TACCTCATTATGACTCTTACTCTAACATCAAATTTGAGTGGTTTG CAAACCACTCAAATTTGATGTTAGAGTAAGAGTCATAATGAGGTA 30 HAMJ571 HAMJ572 281 282 TACCTTCTTATGACCATTACTCTAACATCAAATTTGAGTGGTTTG AAACCACTCAAATTTGATGTTAGAGTAATGGTCATAAGAAGGTA 31 HAMJ573 HAMJ574 283 284 AACGGTAGTTTAATCATACCTTCTAAAGACCATTACCATAACATC GATGTTATGGTAATGGTCTTTAGAAGGTATGATTAAACTACCGTT 32 HAMJ575 HAMJ576 285 286 CGGTAGTTTAATCATACCTCATAAGGACTCTTACCATAACATCAAA TTTGATGTTATGGTAAGAGTCCTTATGAGGTATGATTAAACTACCG 33 HAMJ577 HAMJ578 287 288 AACGGTAGTTTAATCATACCTGACCATTACCATAACATCAAATTTG CAAATTTGATGTTATGGTAATGGTCAGGTATGATTAAACTACCGTT 34 HAMJ579 HAMJ580 289 290 AACGGTAGTTTAATCATACCTTACCATAACATCAAATTTGAGTGG CCACTCAAATTTGATGTTATGGTAAGGTATGATTAAACTACCGTT 35 HAMJ581 HAMJ582 291 292 ACCGGTAGTTTAATCATACCTAACATCAAATTTGAGTGGTTTGAC GTCAAACCACTCAAATTTGATGTTAGGTATGATTAAACTACCGTT WO 01/98334 PCT/CA01/00908 Table 20. List of NEW43 variant gene products generated from S. pneumoniae SP64 Polypeptide designation Polypep tide SEQ ID NO Polypeptide identification* PCR primer set (ref. table 22) Gene used for mutagenesis NEW60 293 NEW43 109-SYDHYH-114 1 NEW43 NEW61 294 NEW43 109-HYDSYH-114 26 NEW43 NEW62 295 NEW43 109-HYDHYS-114 27 NEW43 NEW80 296 NEW43 109-SYDSYH-114 2 NEW60 NEW81 297 NEW43 109-SYDSYS-114 3 NEW80 NEWS 2 298 NEW43 109-HYDSYS-114 29 NEW61 NEW83 . 299 NEW43 109-SYDHYS-114 30 NEW60 NEW84 300 NEW43 109-SKDHYH-114 31 NEW60 NEW85 301 NEW43 109-HKDSYH-114 32 NEW61 NEW88D1 302 NEW43 109- DHYH-114 33 NEW43 NEW88D2 303 NEW43 109- YH-114 34 NEW88D1 NEW88 304 NEW43 109- -114 35 NEW88D2 * The underlined amino acid residues represent the modification in protein sequence. Nucleotides/amino acid •residues are deleted in NEW88D1, NEW88D2 and NEW88 constructs. 10 Groups of 7 or 8 female BALB/c mice (Charles River) immunized as described earlier in example 1 were used for protection experiments against intranasal challenge with virulent S. pneumoniae P4241 strain. Data from Table 21 clearly indicate that NEW 19, NEW43 and variants thereof provided protection against experimental pneumonia. 15 WO 01/98334 PCT/CA01/00908 Table 21. Protection mediated by NEW19 and NEW43 fragments or variants thereof in experimental pneumonia Exper iment Immunogen Alive : Dead Median day alive 1 Quil A NEW 19 NEW 43 0 : 8 7 : 1 8 : 0 4, 4, 4, 4, 4, 4, 4, 5 5, 7X >14 8X >14 2 Quil A NEW 43 NEW 80 NEW 83 0 : 8 7 : 1 6 : 2 6 : 2 4, 4, 4, 4, 4, 5, 5, 5 8, 7X >14 5, 6, 6 X >14 8, 10, 6.X >14 3 Quil A NEW 43 NEW 88D1 NEW 88D2 NEW 88 0 : 8 7 : 1 5 : 3 5:3 7 : 1 4, 4, 4, 4, 5, 5, 5, 5 5, 7X >8 5, 6, 6, 6 X >8 6, 6, 6, 6 X >8 6, 7X >8 3 Quil A NEW 60 NEW 84 NEW 85 NEW 86 0 : 8 8 : 0 8 : 0 5 : 3 5 : 3 4, 4, 4, 5, 5, 5, 5, 6 8 X >8 8 X >8 5, 7, 7, 5 X >8 5, 6, 6, 5 X >8 EXAMPLE 10 This example describes the cloning and expression of chimeric genes encoding for a chimeric protein corresponding to the carboxy-terminal region of, BVH-3 or variants thereof in fusion, at either the carboxyl end or the amino end, to NEW43 # or variants thereof. The chimeric genes comprising a BVH-3 truncate variant gene and a NEW43 or NEW43 variant gene have been designed following WO 01/98334 PCT/CAO1/00908 the procedure described in example 1. The polypeptides encoded by these chimeric genes are listed in the table 22. Briefly, gene fragments to be included in a chimeric gene were amplified by PCR using pairs of oligonucleotides engineered so 5 that the primers had a restriction endonuclease site at the 5' end, thereby allowing directional in-frame cloning of the amplified product into digested plasmid vectors (Table 23 and Table 24) . PCR-amplified products were digested with restriction endonucleases and ligated to linearized plasmid 10 pSL301 vector. The resultant plasmid construct were confirmed by nucleotide sequence analysis. The recombinant pSL301 plasmids containing a PCR product were redigested with the same endonuclease restriction enzyme for the obtention of the DNA inserts. The resulting insert DNA fragments were purified 15 and inserts corresponding to a given chimeric gene were ligated into pURV22-NdeI vector for the generation of a chimeric gene. The expressed recombinant proteins were purified from supernatant fractions obtained from centrifugation of sonicated heat-induced E^_ coli cultures 20 using multiple chromatographic purification steps. Table 22. List of polypeptides encoded by chimeric genes comprising a BVH-3 truncate variant gene and a NEW43 or NEW43 variant gene 25 Polypeptide designation SEQIDNO Identificatio n VP 89 327 M-New56 -GP- New43* VP 90 328 M-New43 -GP- New56 VP 91 329 M-New52 -GP- New43 VP 92 330 M-New43 -GP- New52 VP 93 331 M-New56 -GP- New60 VP 94 332 M-New60 -GP- New56 VP 108 333 M-New56 -GP- New88 VP109 334 M-New88 -GP- New56 WO 01/98334 PCT/CAO1/00908 Polypeptide designation SEQIDNO Identificatio n VP 110 335 M-New60 -GP- Newl05 VP 111 336 M-New60 -GP- Newl07 VP112 337 M-New88 -GP- Newl05 VP113 338 M-New88 -GP- Newl07 VP114 339 M-New80-GP- NewlOS VP115 340 M-New80 -GP- Newl07 VP116 341 M-New83 -GP- Newl05 VP117 342 M-New83 -GP- Newl07 VP119 343 M-New43S- GP-Newl05 VP120 344 M-New43S- GP-Newl07 VP121 345 M-New80S- GP-Newl05 VP122 346 M-New80S- GP-Newl07 VP123 347 M-New88S~ GP-Newl05 VP124 348 M-New88S- GP-Newl07 * Encoded amino acids for the chimeras are expressed as the gene product, additional amino acid residues were added. M is methionine, G is glycine and P is proline. WO 01/98334 PCT/CA01/00908 Table 23. List of PCR oligonucleotide primer pairs designed for the generation of the chimeric genes encoding the polypeptides listed in Table 22. Primer set PCR-primer identification Gene used for PCR amplification Corresponding position of the crene fragment on 49 HAMJ490-HAMJ471 Variant New43 N-terminal 50 HAMJ564-HAMJ556 Variant New43 C-terminal 51 HAMJ4 89-HAMJ359 Variant New40 N-terminal 52 HAMJ559-HAMJ557 Variant New40 C-terminal 53 HAMJ610-HAMJ471 Variant New43S N-terminal 5 Table 24. List of PCR oligonucleotide primers designed for the generation of the chimeric genes encoding the polypeptides listed in Table'22. Primer SEQ ID NO Sequence 5' - 3' Restriction site HAMJ490 259 ccgaattccatatgcaaattaccta cactgatgatg Ndel HAMJ471 168 atatgggcccctgtataggagccgg ttgactttc Apal HAMJ564 327 atatgggccccaaattacctacact gatgatgagattcagg Apal HAMJ556 328 ataagaatgcggccgcctactgtat aggagccggttgactttc Not I HAMJ4B9 329 ccgaattccatatgcaaattgggca accgactc Ndel HAMJ359 173 tcccgggccccgctatgaaatcaga taaattc Apal HAMJ559 330 atatgggccccaaattgggcaaccg actc Apal HAMJ354 65 cgccaagcttctgtataggagccgg ttgac HindiII HAMJ610 268 cttgatcgacatatgttggcaggca agtacacaacag Ndel HAMJ557 331 ataagaatgcggccgcttacgctat. gaaatcagataaattc Not I HAMJ279 35 cgccaagcttcgctatgaaatcaga taaattc HindiII We claim: 1. An isolated polynucleotide chosen from: (a) an isolated polynucleotide encoding a polypeptide consisting of an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:258 (NEW43), which polypeptide is chosen from table E, wherein the polypeptide is capable of inducing an immune response to Streptococcus pneumoniae; (b) an isolated polynucleotide encoding a polypeptide consisting of the amino acid sequence set forth in SEQ ID NO:258 (NEW 43), which polypeptide is chosen from Table E; and (c) an isolated polynucleotide encoding a polypeptide consisting of an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:21 (10D7.5 epitope), SEQ ID NO:22 (10G9.3 epitope, B11B.2 epitope, and 10A2 epitope), or SEQ ID NO:23 (11B8.4 epitope), which polypeptide is chosen from Table F, wherein the polypeptide is capable of inducing an immune response to Streptococcus pneumoniae; (d) an isolated polynucleotide encoding a polypeptide consisting of the amino acid sequence set forth in SEQ ID NO:21 (10D7.5 epitope), SEQ ID NO:22 (10G9.3 epitope, B11B.2 epitope, and 10A2 epitope), or SEQ ID NO:23 (11B8.4 epitope), which polypeptide is chosen from Table F; and (e) an isolated polynucleotide complementary to the polynucleotide of(a)rfb), (c),or(d). 2. The isolated polynucleotide as claimed in claim 1 wherein said polynucleotide is (a). The isolated polynucleotide as claimed in claim 1 wherein said polynucleotide is (b). The isolated polynucleotide as claimed in claim 1 wherein said polynucleotide is (c). The isolated polynucleotide as claimed in claim 1 wherein said polynucleotide is (d). The isolated polynucleotide as claimed in claim 1 wherein said polynucleotide is (e). The polynucleotide as claimed in any one of claims 1-6, wherein said polynucleotide is DNA. The polynucleotide as claimed in any one of claims 1-6, wherein said polynucleotide is RNA. An expression vector comprising the polynucleotide as claimed in claim 7, wherein said DNA is operably linked to an expression control region. A process for producing a polypeptide comprising culturing a host cell transformed with a vector as claimed in claim 9, under conditions suitable for expression of said polypeptide. An isolated polypeptide chosen from: (a) an isolated polypeptide consisting of an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:258 (NEW43), which polypeptide is chosen from Table E, wherein the polypeptide is capable of inducing an immune response to Streptococcus pneumoniae; (b) an isolated polypeptide consisting of the amino acid sequence set forth in SEQ ID NO:258 (NEW 43), which polypeptide is chosen from Table E; (c) an isolated polypeptide consisting of the amino acid sequence set forth in SEQ ID NO:21 (10D7.5 epitope), SEQ ID NO:22 (10G9.3 epitope, B11B.2 epitope, and 10A2 epitope), or SEQ ID NO:23 (11B8.4 epitope), which polypeptide is chosen from Table F; and (d) an isolated polypeptide consisting of an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:21 (10D7.5 epitope), SEQ ID NO:22 (10G9.3 epitope, B11B.2 epitope, and 10A2 epitope), or SEQ ID NO:23 (11B8.4 epitope), which polypeptide is chosen from Table F, wherein the polypeptide is capable of inducing an immune response to Streptococcus pneumoniae. 12. The polypeptide as claimed in claim 14 wherein said polypeptide is the polypeptide of (a). 13. The polypeptide as claimed in claim 14 wherein said polypeptide is the polypeptide of (b). 14. The polypeptide as claimed in claim 14 wherein said polypeptide is the polypeptide of (c). 15. The polypeptide as claimed in claim 14 wherein said polypeptide is the polypeptide of (d). 16. A chimeric polypeptide comprising two or more polypeptides chosen from table E; provided that the two or more polypeptides are linked to form the chimeric polypeptide. Dated this 24th day of December, 2002 (RANJNA MEHTA DUTT) OF REMFRY AND SAGAR ATTORNEY FOR THE APPLICANTS

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