# Patent

## Title
Inducing cellular immune responses to hepatitis B virus using peptide compositions

## Abstract

This invention uses our knowledge of the mechanisms by which antigen is recognized by T cells to develop epitope-based vaccines directed towards HBV. More specifically, this application communicates our discovery of pharmaceutical compositions and methods of use in the prevention and treatment of HBV infection.

## Background
CROSS-REFERENCES TO RELATED APPLICATIONS
This application is divisional of U.S. application Ser. No. 09/239,043, now U.S. Pat. No. 6,689,363 filed Jan. 27, 1999, which is herein incorporated by reference. This application is related to U.S. Ser. No. 08/820,360 filed Mar. 12, 1997 and now abandoned, which claims the benefit of U.S. Provisional Application No. 60/013,363 filed Mar. 13, 1996 and now abandoned. The present application is also related to U.S. Ser. No. 09/189,702 filed Nov. 10, 1998, which is a CIP of U.S. Ser. No. 08/205,713 filed Mar. 4, 1994 and now abandoned, which is a CIP of Ser. No. 08/159,184 filed Nov. 29, 1993 and now abandoned, which is a CIP of 08/073,205 filed Jun. 4, 1993 and now abandoned, which is a CIP of Ser. No. 08/027,146 filed Mar. 5, 1993 and now abandoned. The present application is also related to U.S. Ser. No. 08/197,484, now U.S. Pat. No. 6,419,931, abandoned U.S. Ser. No. 08/464,234, U.S. Ser. No. 08/464,496, now U.S. Pat. No. 6,322,789, abandoned U.S. Ser. No. 08/464,031, abandoned U.S. Ser. No. 08/464,433, and abandoned U.S. Ser. No. 08/461,603, which is a continuation of abandoned U.S. Ser. No. 07/935,811, which is a CIP of abandoned U.S. Ser. No. 07/874,491, which is a CIP of abandoned U.S. Ser. No. 07/827,682, which is a CIP of abandoned 07/749,568. The present application is also related to U.S. patent application Ser. No. entitled “Peptides and Methods for Creating Synthetic Peptides with Modulated Binding Affinity for HLA Molecules”, filed Jan. 6, 1999, which is a CIP of abandoned U.S. Ser. No. 08/815,396, which is a CIP of abandoned U.S. Ser. No. 60/013,113. Furthermore, the present application is related to abandoned U.S. Ser. No. 09/017,735, which is a CIP of abandoned U.S. Ser. No. 08/589,108; abandoned U.S. Ser. No. 08/753,622, abandoned U.S. Ser. No. 08/822,382, abandoned U.S. Ser. No. 60/013,980, abandoned U.S. Ser. No. 08/454,033, abandoned U.S. Ser. No. 09/116,424, abandoned U.S. Ser. No. 08/205,7 13, and abandoned U.S. Ser. No. 08/349,177, which is a CIP of abandoned U.S. Ser. No. 08/159,184, which is a CIP of abandoned U.S. Ser. No. 08/073,205, which is a CIP of abandoned U.S. Ser. No. 08/027,146. The present application is also related to abandoned U.S. Ser. No. 09/017,524, abandoned U.S. Ser. No. 08/821,739, abandoned U.S. Ser. No. 60/013,833, abandoned U.S. Ser. No. 08/758,409, abandoned U.S. Ser. No. 08/589,107, abandoned U.S. Ser. No. 08/451,913, U.S. Ser. No. 08/186,266, now U.S. Pat. No. 5,662,907, abandoned U.S. Ser. No. 09/116,061, and abandoned U.S. Ser. No. 08/347,610, which is a CIP of U.S. Ser. No. 08/159,339, now U.S. Pat. No. 6,037,135, which is a CIP of abandoned U.S. Ser. No. 08/103,396, which is a CIP of abandoned U.S. Ser. No. 08/027,746, which is a CIP of abandoned U.S. Ser. No. 07/926,666. The present application is also related to abandoned U.S. Ser. No. 09/017,743, abandoned U.S. Ser. No. 08/753,615; U.S. Ser. No. abandoned 08/590,298, abandoned U.S. Ser. No. 09/115,400, and abandoned U.S. Ser. No. 08/452,843, which is a CIP of abandoned U.S. Ser. No. 08/344,824, which is a CIP of abandoned U.S. Ser. No. 08/278,634. The present application is also related to provisional U.S. Ser. No. 60/087,192 and U.S. Ser. No. 09/009,953, now U.S. Pat. No. 6,413,517, which is a CIP of abandoned U.S. Ser. No. 60/036,713 and abandoned U.S. Ser. No. 60/037,432. In addition, the present application is related to abandoned U.S. Ser. No. 09/098,584 and to Provisional U.S. patent application entitled “Identification of Broadly Reactive HLA Restricted T Cell Epitopes”, filed of even date herewith. All of the above applications are incorporated herein by reference.


FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT
This invention was funded, in part, by the United States government under grants with the National Institutes of Health. The U.S. government has certain rights in this invention.


INDEX


    I. Background of the Invention
    II. Summary of the Invention
    III. Brief Description of the Figures
    IV. Detailed Description of the Invention
    
        A. Definitions
        B. Stimulation of CTL and HTL responses against HBV
        C. Immune Response Stimulating Peptides
        
            1. Binding Affinity of the Peptides for HLA Molecules
            2. Peptide Binding Motifs and Supermotifs
            
                a) HLA-A1 supermotif
                b) HLA-A2 supermotif
                c) HLA-A3 supermotif
                d) HLA-A24 supermotif
                e) HLA-B7 supermotif
                f) HLA-B27 supermotif
                g) HLA-B44 supermotif
                h) HLA-B58 supermotif
                i) HLA-B62 supermotif
                j) HLA-A1 motif
                k) HLA-A3 motif
                1) HLA-A11 motif
                m) HLA-A24 motif
                n) HLA-A2.1 motif
                o) HLA-DR-1-4-7 supermotif
                p) HLA-DR3 motifs
            
            
            3. Enhancing Population Coverage of the Vaccine
        
        
        D. Immune Response Stimulating Peptide Analogs
        E. Computer Screening of Protein Sequences from Disease-Related Antigens for Supermotif or Motif Containing Peptides
        F. Assays to Detect T-Cell Responses
        G. Preparation of Peptides
        H. Use of Peptide Epitopes for Evaluating Immune Responses
        I. Vaccine Compositions
        
            1. Minigene Vaccines
            2. Combinations with Helper Peptides
        
        
        J. Administration of Vaccines for Therapeutic or Prophylactic Purposes
        K. Kits
    
    
    V. Examples


I. BACKGROUND OF THE INVENTION
Chronic infection by hepatitis B virus (HBV) affects at least 5% of the world's population and is a major cause of cirrhosis and hepatocellular carcinoma (Hoofnagle, J., N. Engl. J. Med. 323:337, 1990; Fields, B. and Knipe, D., In: Fields Virology 2:2137, 1990). The World Health Organization lists hepatitis B as a leading cause of death worldwide, close behind chronic pulmonary disease, and more prevalent than AIDS. Chronic HBV infection can range from an asymptomatic carrier state to continuous hepatocellular necrosis and inflammation, and can lead to hepatocellular carcinoma.
The immune response to HBV is believed to play an important role in controlling hepatitis B infection. A variety of humoral and cellular responses to different regions of the HBV nucleocapsid core and surface antigens have been identified. T cell mediated immunity, particularly involving class I human leukocyte antigen-restricted cytotoxic T lymphocytes (CTL), is believed to be crucial in combatting established HBV infection.
Class I human leukocyte antigen (HLA) molecules are expressed on the surface of almost all nucleated cells. CTL recognize peptide fragments, derived from intracellular processing of various antigens, in the form of a complex with class I HLA molecules. This recognition event then results in the destruction of the cell bearing the HLA-peptide complex directly or the activation of non-destructive mechanisms e.g., the production of interferon, that inhibit viral replication.
Several studies have emphasized the association between self-limiting acute hepatitis and multispecific CTL responses (Penna, A. et al., J. Exp. Med. 174:1565, 1991; Nayersina, R. et al., J. Immunol. 150:4659, 1993). Spontaneous and interferon-related clearance of chronic HBV infection is also associated with the resurgence of a vigorous CTL response (Guidotti, L. G. et al., Proc. Natl. Acad. Sci. USA 91:3764, 1994). In all such cases the CTL responses are polyclonal, and specific for multiple viral proteins including the HBV envelope, core and polymerase antigens. By contrast, in patients with chronic hepatitis, the CTL activity is usually absent or weak, and antigenically restricted.
The crucial role of CTL in resolution of HBV infection has been further underscored by studies using HBV transgenic mice. Adoptive transfer of HBV-specific CTL into mice transgenic for the HBV genome resulted in suppression of virus replication. This effect was primarily mediated by a non-lytic, lymphokine-based mechanism (Guidotti, L. G. et al., Proc. Natl. Acad. Sci. USA 91:3764, 1994; Guidotti, L. G., Guilhot, S., and Chisari, F. V. J. Virol. 68:1265, 1994; Guidotti, L. G. et al., J. Virol. 69:6158, 1995; Gilles, P. N., Fey, G., and Chisari, F. V., J. Virol. 66:3955, 1992).
As is the case for HLA class I restricted responses, HLA class II restricted T cell responses are usually detected in patients with acute hepatitis, and are absent or weak in patients with chronic infection (Chisari, F. V. and Ferrari, C., Annu. Rev. Immunol. 1′:29, 1995). HLA Class II responses are tied to activation of helper T cells (IT Ls) Helper T lymphocytes, which recognize Class II HLA molecules, may directly contribute to the clearance of HBV infection through the secretion of cytokines which suppress viral replication (Franco, A. et al., J. Immunol. 159:2001, 1997). However, their primary role in disease resolution is believed to be mediated by inducing activation and expansion of virus-specific CTL and B cells.
In view of the heterogeneous immune response observed with HBV infection, induction of a multi-specific cellular immune response directed simultaneously against multiple epitopes appears to be important for the development of an efficacious vaccine against HBV. There is a need to establish vaccine embodiments that elicit immune responses that correspond to responses seen in patients that clear HBV infection. Epitope-based vaccines appear useful.
Upon development of appropriate technology, the use of epitope-based vaccines has several advantages over current vaccines. The epitopes for inclusion in such a vaccine are to be selected from conserved regions of viral or tumor-associated antigens, in order to reduce the likelihood of escape mutants. The advantage of an epitope-based approach over the use of whole antigens is that there is evidence that the immune response to whole antigens is directed largely toward variable regions of the antigen, allowing for immune escape due to mutations. Furthermore, immunosuppressive epitopes that may be present in whole antigens can be avoided with the use of epitope-based vaccines.
Additionally, with an epitope-based vaccine approach, there is an ability to combine selected epitopes (CTL and HTL) and additionally to modify the composition of the epitopes, achieving, for example, enhanced immunogenicity. Accordingly, the immune response can be modulated, as appropriate, for the target disease. Similar engineering of the response is not possible with traditional approaches.
Another major benefit of epitope-based immune-stimulating vaccines is their safety. The possible pathological side effects caused by infectious agents or whole protein antigens, which might have their own intrinsic biological activity, is eliminated.
An epitope-based vaccine also provides the ability to direct and focus an immune response to multiple selected antigens from the same pathogen. Thus, patient-by-patient variability in the immune response to a particular pathogen may be alleviated by inclusion of epitopes from multiple antigens from that pathogen in a vaccine composition. A “pathogen” may be an infectious agent or a tumor associated molecule.
However, one of the most formidable obstacles to the development of broadly efficacious epitope-based immunotherapeutics has been the extreme polymorphism of HLA molecules. To date, effective non-genetically biased coverage of a population has been a task of considerable complexity; such coverage has required that epitopes be used specific for HLA molecules corresponding to each individual HLA allele, therefore, impractically large numbers of epitopes would have to be used in order to cover ethnically diverse populations. There has existed a need to develop peptide epitopes that are bound by multiple HLA antigen molecules for use in epitope-based vaccines. The greater the number of HLA antigen molecules bound, the greater the breadth of population coverage by the vaccine.
Furthermore, as described herein in greater detail, a need has existed to modulate peptide binding properties, for example so that peptides that are able to bind to multiple HLA antigens do so with an affinity that will stimulate an immune response. Identification of epitopes restricted by more than one HLA allele at an affinity that correlates with immunogenicity is important to provide thorough population coverage, and to allow the elicitation of responses of sufficient vigor whereby the natural immune responses noted in self-limiting acute hepatitis, or of spontaneous clearance of chronic HBV infection is induced in a diverse segment of the population. Such a response can also target a broad array of epitopes. The technology disclosed herein provides for such favored immune responses.
The information provided in this section is intended to disclose the presently understood state of the art as of the filing date of the present application. Information is included in this section which was generated subsequent to the priority date of this application. Accordingly, background in this section is not intended, in any way, to delineate the priority date for the invention.
II. SUMMARY OF THE INVENTION
This invention applies our knowledge of the mechanisms by which antigen is recognized by T cells, for example, to develop epitope-based vaccines directed towards HBV. More specifically, this application communicates our discovery of specific epitope pharmaceutical compositions and methods of use in the prevention and treatment of HBV infection.
An embodiment of the present invention includes a peptide composition of less than 100 amino acid residues comprising a peptide epitope useful for inducing an immune response against hepatitis B virus (HBV) said epitope (a) having an amino acid sequence of about 8 to about 13 amino acid residues that have at least 65% identity with a native amino acid sequence for HBV, and, (b) binding to at least one MHC class I HLA allele with a dissociation constant of less than about 500 nM. Further, the peptide composition may comprise an amino acid sequence of at least 77% identity, or at least 100% identity with a native HBV amino acid sequence. In a preferred embodiment, the peptide is one of the peptides designated as being from the envelope, polymerase, protein X, or nucleocapsid core regions of HBV. Preferred peptides are described in Tables VI through XVII or XXI.
An additional embodiment of the present invention comprises a composition of less than 100 amino acid residues comprising a peptide epitope useful for inducing an immune response against hepatitis B virus (HBV) said peptide (a) having an amino acid sequence of about 8 to about 13 amino acid residues and (b) bearing one of the HLA supernotifs or motifs set out in Tables I and II. Furthermore, the composition may comprise a peptide wherein the peptide is one of those described in Tables VI through XVII or Table XXI which bear an HLA A1, A2, A3, A24, B7, B27, B44, B58, or B62 supermotif; or an HLA A1, A3, A11, A24, or A2.1 motif or an HLA A*3301, A*3101, A*6801, B*0702, B*3501, B51, B*5301, B*5401 motif.
In one embodiment of a peptide comprising an HLA A2.1 motif, the peptide does not bear an L or M at position 2 and V at the C-terminal position 9 of a 9 amino acid peptide.
An alternative embodiment of the invention comprises an analog of an HBV peptide of less than 100 amino acid residues in length that bears an HLA binding motif, the analog bearing the same HLA binding motif as the peptide but comprising at least one anchor residue that is different from that of the peptide. In a preferred embodiment, said peptide is an analog of a peptide described in Table VI through Table XVII bearing an HLA A1, A2, A3, A24, B7, B27, B44, B58, or B62 supermotif; or an HLA A1, A3, A11, A24, or A2.1 motif or A3301, A3101, A6801, B0702, B3501, B51, B5301, B5401 motif.
Embodiments of the invention further include a composition of less than 100 amino acid residues comprising a peptide epitope useful for inducing an immune response against hepatitis B virus (HBV) said peptide (a) having an amino acid sequence of about 9 to about 25 amino acid residues that have at least 65% identity with a native amino acid sequence for HBV and (b) binding to at least one MHC class II HLA allele with a dissociation constant of less than about 1000 nM. In a preferred embodiment, the composition comprises a peptide that has at least 77%, or, 100% identity with a native HBV amino acid sequence. Further, the composition may comprise a peptide wherein said peptide is one of those peptides described in Table XVIII or Table XIX.
The invention also includes a peptide composition of less than 100 amino acid residues, said composition comprising an epitope useful for inducing an immune response against hepatitis B virus (HBV) said epitope (a) having an amino acid sequence of about 10 to about 20 amino acid residues and (b) bearing one of the class II HLA motifs set out in Table III. In a preferred embodiment, said peptide is one of those peptides described in Table XVIII or XIX.
Additional embodiments of the invention include a composition that comprises an isolated nucleic acid sequence that encodes one of the peptides set out in Tables VI through XIX or XXI or XXIII.
Alternatively, an embodiment of the invention comprises a composition that comprises at least two peptides, at least one of said at least two peptides selected from Tables VI-XIX or XXI or XXIII. In a preferred embodiment, two or more of the at least two peptides are depicted in Tables VI-XIX or XXI or XXIII. The composition may further comprise at least one nucleic acid sequence. In a preferred embodiment each of said at least two peptides are encoded by a nucleic acid sequence, wherein each of the nucleic acid sequences are located on a single vector.
Embodiments of the invention additionally include a peptide composition of less than 100 amino acid residues, said composition comprising an epitope useful for inducing an immune response against HBV, said epitope having at least one of the amino acid sequences set out in Table XXIII.
An alternative modality for defining the peptides in accordance with the invention is to recite the physical properties, such as length; primary, secondary and/or tertiary structure; or charge, which are correlated with binding to a particular allele-specific HLA molecule or group of allele-specific HLA molecules. A further modality for defining peptides is to recite the physical properties of an HLA binding pocket, or properties shared by several allele-specific HLA binding pockets (e.g. pocket configuration and charge distribution) and reciting that the peptide fits and binds to said pocket or pockets.
An additional embodiment of the invention comprises a method for inducing a cytotoxic T cell response to HBV in a mammal comprising administering to said mammal at least one peptide from Tables VI to XIX or Table XXI.
Further embodiments of the invention include a vaccine for treating HBV infection that induces a protective immune response, wherein said vaccine comprises at least one peptide selected from Tables VI to Table XIX or Table XXI in a pharmaceutically acceptable carrier.
Also included as an embodiment of the invention is a vaccine for preventing HBV infection that induces a protective immune response, wherein said vaccine comprises at least one peptide selected from Tables VI to XIX or Table XXI in a pharmaceutically acceptable carrier.
The invention further includes an embodiment comprising a method for inducing a cytotoxic T cell response to HBV in a mammal, comprising administering to said mammal a nucleic acid sequence encoding a peptide selected from Tables VI to XIX or Table XXI.
A further embodiment of the invention comprises a kit for a vaccine for treating or preventing HBV infection, wherein the vaccine induces a protective immune response, said vaccine comprising at least one peptide selected from Tables VI to XIX or Table XXI in a pharmaceutically acceptable carrier and instructions for administration to a patient.
Lastly, the invention includes an embodiment comprising a method for monitoring immunogenic activity of a vaccine for HBV in a patient having a known HLA-type, the method comprising incubating a T lymphocyte sample from the patient with a peptide selected from Tables VI to XIX or Table XXI which binds the product of at least one HLA allele present in said patient, and detecting for the presence of a T lymphocyte that binds to the peptide. In a preferred embodiment, the peptide comprises a tetrameric complex.
As will be apparent from the discussion below, other methods and embodiments are also contemplated. Further, novel synthetic peptides produced by any of the methods described herein are also part of the invention.



III. BRIEF DESCRIPTION OF THE FIGURES
FIG. 1: FIG. 1 Illustrates the Position of Peptide Epitopes in Experimental Model Minigene Constructs



IV. DETAILED DESCRIPTION OF THE INVENTION
The peptides and corresponding nucleic acid compositions of the present invention are useful for stimulating an immune response to HBV either by stimulating the production of CTL or HTL responses. The peptides, which are derived directly or indirectly from native HBV amino acid sequences, are able to bind to HLA molecules and stimulate an immune response to HBV. The complete polyprotein sequence from HBV and its variants can be obtained from Genbank. Peptides can also be readily determined from sequence information that may subsequently be discovered for heretofore unknown variants of HBV as will be clear from the disclosure provided below.
The peptides of the invention have been identified in a number of ways, as will be discussed below. Further, analog peptides have been derived and the binding activity for HLA molecules modulated by modifying specific amino acid residues to create peptide analogs exhibiting altered immunogenicity. Further, the present invention provides compositions and combinations of compositions that enable epitope-based vaccines that are capable of interacting with multiple HLA antigens to provide broader population coverage than prior vaccines.
The invention can be better understood with reference to the following definitions:
IV.A. Definitions
“Cross-reactive binding” indicates that a peptide is bound by more than one HLA molecule; a synonym is degenerate binding.
A “cryptic epitope” elicits a response by immunization with an isolated peptide, but the response is not cross-reactive in vitro when intact whole protein which comprises the epitope is used as an antigen.
A “dominant epitope” is an epitope that induces an immune response upon immunization with a whole native antigen. (See, e.g., Sercarz, et al., Annu. Rev. Immunol. 11:729766 (1993)) Such a response is cross-reactive in vitro with an isolated peptide epitope.
With regard to a particular amino acid sequence, an “epitope” is a set of amino acid residues which is involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by T cell receptor proteins and/or Major Histocompatibility Complex (MHC) receptors. In an immune system setting, in vivo or in vitro, an epitope is the collective features of a molecule, such as primary, secondary and tertiary peptide structure, and charge, that together form a site recognized by an immunoglobulin, T cell receptor or HLA molecule.
As used herein, “high affinity” with respect to HLA class I molecules is defined as binding with an IC50 (or KD) of less than 50 nM. “Intermediate affinity” is binding with an IC50 (or KD) of between about 50 and about 500 nM. “High affinity” with respect to binding to HLA class II molecules is defined as binding with an KD of less than 100 nM. “Intermediate affinity” is binding with a KD of between about 100 and about 1000 nM. Assays for determining binding are described in detail in PCT publications WO 94/20127 and WO 94/03205. Alternatively, binding is expressed relative to a reference peptide. As a particular assay becomes more, or less, sensitive, the IC50's of the peptides tested may change somewhat. However, the binding relative to the reference peptide will not significantly change. For example, in an assay run under conditions such that the IC50 of the reference peptide increases 10-fold, the IC50 values of the test peptides will also shift approximately 10-fold. Therefore, to avoid ambiguities, the assessment of whether a peptide is a good, intermediate, weak, or negative binder is generally based on its IC50, relative to the IC50 of a standard peptide.
“Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif. (1994).
An “HLA supertype or family”, as used herein, describes sets of HLA molecules grouped on the basis of shared peptide-binding specificities. HLA class I molecules that share somewhat similar binding affinity for peptides bearing certain amino acid motifs We grouped into HLA supertypes. The terms HLA superfamily, HLA supertype family, and HLA xx-like supertype molecules (where xx denotes a particular HLA type) are synonyms.
Throughout this disclosure, results are expressed in terms of “IC50's.” IC50 is the concentration of peptide in a binding assay at which 50% inhibition of binding of a reference peptide is observed. Given the conditions in which the assays are run (i.e., limiting HLA proteins and labeled peptide concentrations), these values approximate KD values. It should be noted that IC50 values can change, often dramatically, if the assay conditions are varied, and depending on the particular reagents used (e.g., HLA preparation, etc.). For example, excessive concentrations of HLA molecules will increase the apparent measured IC50 of a given ligand.
The terms “identical” or percent “identity,” in the context of two or more peptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithms or by manual alignment and visual inspection.
An “immunogenic peptide” or “peptide epitope” is a peptide which comprises an allele-specific motif or supermotif such that the peptide will bind an HLA molecule and induce a CTL and/or HTL response. Thus, immunogenic peptides of the invention are capable of binding to an appropriate HLA molecule and thereafter inducing a cytotoxic T cell response, or a helper T cell response, to the antigen from which the immunogenic peptide is derived.
The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.
“Major Histocompatibility Complex” or “MHC” is a cluster of genes that plays a role in control of the cellular interactions responsible for physiologic immune responses. In humans, the MHC complex is also known as the HLA complex. For a detailed description of the MHC and HLA complexes, see, Paul, FUNDAMENTAL IMMUNOLOGY, 3RD ED., Raven Press, N.Y., 1993.
The term “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.
A “negative binding residue” is an amino acid which if present at certain positions (typically not primary anchor positions) of peptide epitope results in decreased binding affinity of the peptide for the peptide's corresponding HLA molecule.
The term “peptide” is used interchangeably with “oligopeptide” in the present specification to designate a series of residues, typically L-amino acids, connected one to the other, typically by peptide bonds between the a-amino and carboxyl groups of adjacent amino acids. The preferred CTL-inducing oligopeptides of the invention are fewer than 25 residues in length, or less than 15 residues in length or 13 residues or less in length and usually consist of between about 8 and about 11 residues, preferably 9 or 10 residues. The preferred HTL-inducing oligopeptides are less than about 50 residues in length and usually consist of between about 6 and about 30 residues, more usually between about 12 and 25, and often between about 15 and 20 residues.
“Pharmaceutically acceptable” refers to a non-toxic, inert, and physiologically compatible composition.
A “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding grooves of an HLA molecule, with their side chains buried in specific pockets of the binding grooves themselves. In one embodiment, the primary anchor residues are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 9 residue peptide in accordance with the invention. The primary anchor positions for each motif and supermotif are set forth in Table I. For example, analog peptides can be created by altering the presence or absence of particular residues in these primary anchor positions. Such analogs are used to finely modulate the binding affinity of a peptide comprising a particular motif or supermotif.
“Promiscuous binding” is where a distinct peptide is recognized by the same T cell clone in the context of various HLA molecules.
A “protective immune response” refers to a CTL and/or an HTL response to an antigen from an infectious agent or a tumor antigen from which an immunogenic peptide is derived, and thereby preventing or at least partially arresting disease symptoms or progression. The immune response may also include an antibody response which has been facilitated by the stimulation of helper T cells.
The term “residue” refers to an amino acid or amino acid mimetic incorporated into an oligopeptide by an amide bond or amide bond mimetic.
A “secondary anchor residue” is an amino acid at a position other than a primary anchor position in a peptide which may influence peptide binding. A secondary anchor residue occurs at a significantly higher frequency amongst bound peptides than would be expected by random distribution of amino acids at one position. The secondary anchor residues are said to occur at “secondary anchor positions.” A secondary anchor residue can be identified as a residue which is present at a higher frequency among high affinity binding peptides, or a residue otherwise associated with high affinity binding. For example, analog peptides can be created by altering the presence or absence of particular residues in these secondary anchor positions. Such analogs are used to finely modulate the binding affinity of a peptide comprising a particular motif or supermotif.
A “subdominant epitope” is an epitope which evokes little or no response upon immunization with whole antigens which comprise the epitope, but for which a response can be obtained by immunization with an isolated peptide, and this response (unlike the case of cryptic epitopes) is detected when whole protein is used to recall the response in vitro or in vivo.
A “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Thus, a preferably is recognized with high or intermediate affinity (as defined herein) by two or more HLA antigens.
“Synthetic peptide” refers to a peptide that is not naturally occurring, but is man-made using such methods as chemical synthesis or recombinant DNA technology.
The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) and the carboxyl group to the right (the C-terminus) of each amino acid residue. When amino acid residue positions are referred to in a peptide epitope they are numbered in an amino to carboxyl direction with position one being the position closest to the amino terminal. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three letter or single letter designations. The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form for those amino acids having D-forms is represented by a lower case single letter or a lower case three letter symbol. Glycine has no asymmetric carbon atom and is simply referred to as “Gly” or G. Symbols for the amino acids are shown below.















Single Letter Symbol
Three Letter Symbol
Amino Acids









A
Ala
Alanine



C
Cys
Cysteine



D
Asp
Aspartic Acid



E
Glu
Glutamic Acid



F
Phe
Phenylalanine



G
Gly
Glycine



H
His
Histidine



I
Ile
Isoleucine



K
Lys
Lysine



L
Leu
Leucine



M
Met
Methionine



N
Asn
Asparagine



P
Pro
Proline



Q
Gln
Glutamine



R
Arg
Arginine



S
Ser
Serine



T
Thr
Threonine



V
Val
Valine



W
Trp
Tryptophan



Y
Tyr
Tyrosine










IV.B. Stimulation of CTL and HTL Responses Against HBV

The mechanism by which T cells recognize antigens has been delineated during the past ten years. Based on our new understanding of the immune system we have generated efficacious peptide epitope vaccine compositions that can induce a therapeutic or prophylactic immune response to HBV infection in a broad population. For an understanding of the value and efficacy of the claimed compositions, a brief review of the technology is provided.
A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A., and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are described here and set forth in Tables I, II, and III (see also, e.g., Sette, A. and Grey, H. M, Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J., Curr. Biol. 6:52, 1994; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994). Furthermore, x-ray crystallographic analysis of HLA-peptide complexes has revealed pockets within the peptide binding cleft of HLA molecules which accommodate allele-specific residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present (Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991).
Accordingly, the definition of class I and class II allele-specific HLA binding motifs or class I supermotifs allows identification of regions within a protein that have the potential of binding particular HLA antigens (see also e.g., Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J., Curr. Biol. 6:52, 1994; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994Kast, W. M. et al., J. Immunol., 152:3904, 1994).
Furthermore, a variety of assays to detect and quantify the affinity of interaction between peptide and HLA have also been established (Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J., Curr. Biol. 6:52, 1994; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994).
We have found that the correlation of binding affinity with immunogenicity is an important factor to be considered when evaluating candidate peptides. Thus, by a combination of motif searches and HLA-peptide binding assays, candidates for epitope-based vaccines have been identified. After determining their binding affinity, additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with desired characteristics in terms of antigenicity and immunogenicity. Various strategies can be utilized to evaluate immunogenicity, including:
1) Primary T cell cultures from normal individuals (Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998); This procedure involves the stimulation of PBL from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using a 51Cr-release assay involving peptide sensitized target cells.
2) Immunization of HLA transgenic mice (Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997); In this method, peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using a 51Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.
3) Demonstration of recall T cell responses from immune individuals who have recovered from infection, and/or from chronically infected patients (Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). In applying this strategy, recall responses were detected by culturing PBL from subjects that had been naturally exposed to the antigen, for instance through infection, and thus had generated an immune response “naturally”. PBL from subjects were cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” Tcells. At the end of the culture period, T cell activity is detected using assays for T cell activity including 51Cr release involving peptide-sensitized targets, T cell proliferation or lymphokine release.
The following describes the peptide epitopes and corresponding nucleic acids of the invention.
IV.C. Immune Response Stimulating Peptides
As indicated herein, the large degree of HLA polymorphism is an important factor to be taken into account with the epitope-based approach to vaccine development. To address this factor, epitope selection encompassing identification of peptides capable of binding at high or intermediate affinity to multiple HLA molecules is preferably utilized, most preferably these epitopes bind at high or intermediate affinity to two or more allele specific HLA molecules.
IV.C.1. Binding Affinity of the Peptides for HLA Molecules
CTL-inducing peptides of interest for vaccine compositions preferably include those that have a binding affinity for class I HLA molecules of less than 500 nM. HTL-inducing peptides preferably include those that have a binding affinity for class II HLA molecules of less than 1000 nM. For example, peptide binding is assessed by testing the capacity of a candidate peptide to bind to a purified HLA molecule in vitro. Peptides exhibiting high or intermediate affinity are then considered for further analysis. Selected peptides are tested on other members of the supertype family. In preferred embodiments, peptides that exhibit cross-reactive binding preferably are then used in cellular screening analyses. A peptide is considered to be an epitope if it possesses the molecular features that form the binding site for a particular immunoglobulin or T cell receptor protein.
As disclosed herein, high HLA binding affinity is correlated with greater immunogenicity. Greater immunogenicity can be manifested in several different ways. Immunogenicity corresponds to whether an immune response is elicited at all, and to the vigor of any particular response. For example, a peptide might elicit an immune response in a diverse array of the population, yet in no instance produce a vigorous response. In accordance with these principles, close to 90% of high binding peptides have been found to be immunogenic, as contrasted with about 50% of the peptides which bind with intermediate affinity. Moreover, higher binding affinity peptides leads to more vigorous immunogenic responses. As a result, less peptide is required to elicit a similar biological effect if a high affinity binding peptide is used. Thus, in preferred embodiments of the invention, high binding epitopes are particularly desired.
The relationship between binding affinity for HLA class I molecules and immunogenicity of discrete peptide epitopes on bound antigens has been determined for the first time in the art by the present inventors. The correlation between binding affinity and immunogenicity was analyzed in two different experimental approaches (Sette, et al., J. Immunol. 153:5586-5592, 1994). In the first approach, the immunogenicity of potential epitopes ranging in HLA binding affinity over a 10,000-fold range was analyzed in HLA-A*0201 transgenic mice. In the second approach, the antigenicity of approximately 100 different hepatitis B virus (HBV)-derived potential epitopes, all carrying A*0201 binding motifs, was assessed by using PBL (peripheral blood lymphocytes) of acute hepatitis patients. Pursuant to these approaches, it was determined that an affinity threshold of approximately 500 nM (preferably 500 nM or less) determines the capacity of a peptide epitope to elicit a CTL response. These data are true for class I binding affinity measurements for naturally processed peptides and for synthesized T cell epitopes. These data also indicate the important role of determinant selection in the shaping of T cell responses.
An affinity threshold associated with immunogenicity in the context of HLA class II DR molecules has also been delineated (Southwood et al. J. Immunology 160:3363-3373,1998, and U.S. Ser. No. 60/087,192 filed May 29, 1998). In order to define a biologically significant threshold of DR binding affinity, a database of the binding affinities of 32 DR-restricted epitopes for their restricting element was compiled. In approximately half of the cases (15 of 32 epitopes), DR restriction was associated with high binding affinities, i.e. binding affinities of less than 100 nM. In the other half of the cases (16 of 32), DR restriction was associated with intermediate affinity (binding affinities in the 100-1000 nM range). In only one of 32 cases was DR restriction associated with an IC50 of 1000 nM or greater. Thus, 1000 nM can be defined as an affinity threshold associated with immunogenicity in the context of DR molecules.
The binding affinity of peptides for HLA molecules can be determined as described in Example 1, below.
IV.C.2. Peptide Binding Motifs and Supermotifs
In the past few years evidence has accumulated to demonstrate that a large fraction of HLA class I, and possibly class II molecules can be classified into a relatively few supertypes characterized by largely overlapping peptide binding repertoires, and consensus structures of the main peptide binding pockets. Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues required for allele-specific binding to HLA molecules have been identified. These motifs are relevant since they indicate peptides that have binding affinity for HLA molecules.
For HLA molecule pocket analyses, the residues comprising the B and F pockets of HLA class I molecules as described in crystallographic studies (Guo, H. C. et al., Nature 360:364, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991; Madden, D. R., Garboczi, D. N. and Wiley, D. C., Cell 75:693, 1993), have been compiled from the database of Parham, et al. (Parham, P., Adams, E. J., and Arnett, K. L., Immunol. Rev. 143:141, 1995). In these analyses, residues 9, 45, 63, 66, 67, 70, and 99 were considered to make up the B pocket, and to determine the specificity for the residue in the second position of peptide ligands. Similarly, residues 77, 80, 81, and 116 were considered to determine the specificity of the F pocket, and to determine the specificity for the C-terminal residue of a peptide ligand bound by the HLA molecule.
Peptides of the present invention may also include epitopes that bind to MHC class II DR molecules. A significant difference between class I and class II HLA molecules is that, although a stringent size restriction exists for peptide binding to class I molecules, a greater degree of heterogeneity in both sizes and binding frame positions of the motif, relative to the N and C termini of the peptide, can be demonstrated for class II peptide ligands. This increased heterogeneity is due to the structure of the class II-binding groove which, unlike its class I counterpart, is open at both ends. Crystallographic analysis of DRB*0101-peptide complexes (see, e.g., Madden, D. R. Ann. Rev. Immunol. 13:587 (1995)) showed that the residues occupying position 1 and position 6 of peptides complexed with DRB*0101 engage two complementary pockets on the DRBa*0101 molecules, with the P1 position corresponding to the most crucial anchor residue and the deepest hydrophobic pocket. Other studies have also pointed to the P6 position as a crucial anchor residue for binding to various other DR molecules.
Thus, peptides of the present invention are identified by any one of several HLA-specific amino acid motifs. If the presence of the motif corresponds to the ability to bind several allele-specific LLA antigens it is referred to as a supermotif. The allele-specific HLA molecules that bind to peptides that possess a particular amino acid supermotif are collectively referred to as an HLA “supertype.”
The peptide motifs and supermotifs described below provide guidance for the identification and use of peptides in accordance with the invention. Examples of peptide epitopes bearing the respective supermotif or motif are included in Tables as designated in the description of each motif or supermotif. The Tables include a binding affinity ratio listing for some of the peptide epitopes. The ratio may be converted to IC50 by using the following formula: IC50 of the standard peptide/ratio=IC50 of the test peptide (i.e. the peptide epitope). The IC50 values of standard peptides used to determine binding affinities for Class I peptides are shown in Table IV. The IC50 values of standard peptides used to determine binding affinities for Class II peptides are shown in Table V. The peptides used as standards for the binding assay are examples of standards; alternative standard peptides can also be used when performing such an analysis.
To obtain the peptide epitope sequences listed in each Table, protein sequence data from twenty HBV strains (HPBADR, HPBADR1CG, HPBADRA, HPBADRC, HPBADRCG, HPBCGADR, HPBVADRM, HPBADW, HPBADW1, HPBADW2, HPBADW3, HPBADWZ, HPBHEPB, HPBVADW2, HPBAYR, HPBV, HPBVAYWC, HPBVAYWCI, NAD HPBVAYWE) were evaluated for the presence of the designated supermotif or motif. Peptide epitopes were also selected on the basis of their conservancy. A criterion for conservancy requires that the entire sequence of a peptide be totally conserved in 75% of the sequences available for a specific protein. The percent conservancy of the selected peptide epitopes is indicated on the Tables. The frequency, i.e. the number of strains of the 20 strains in which the peptide sequence was identified, is also shown. The “1st position” column in the Tables designates the amino acid position of the HBV polyprotein that corresponds to the first amino acid residue of the epitope. Preferred peptides are designated by an asterisk.
HLA Class I Motifs Indicative of CTL Inducing Peptide Epitopes:
IV.C.2.a) HLA-A1 Supermotif
The HLA-A1 supermotif is characterized by peptides having a general motif of small (T or S) and hydrophobic (L, I, V, M, or F) primary anchor residues in position 2, and aromatic (Y, F, or W) primary anchor residues at the C-terminal position The corresponding family of HLA molecules that bind to the A1 supermotif (the HLA-A1 supertype) includes A*0101, A*2601, A*2602, A*2501, and A*3201. (DiBrino, M. et al., J. Immunol. 151:5930, 1993; DiBrino, M. et al., J. Immunol. 152:620, 1994; Kondo, A. et al., Immunogenetics 45:249, 1997; Dumrese et al., submitted). Peptides binding to each of the individual HLA proteins can be modulated by substitutions at primary anchor positions.
Representative peptide epitopes that contain the A1 supermotif are set forth on the attached Table VI.
IV.C.2.b) HLA-A2 Supermotif
The HLA-A2 supermotif is characterized by the presence in peptide ligands of small or aliphatic amino acids (L, I, V, M, A, T, or Q) at position 2 and L, I, V, M, A, or T at the C-terminal position. These positions ate referred to as primary anchors. The corresponding family of HLA molecules (the HLA-A2 supertype that binds these peptides) is comprised of at least nine HLA-A proteins: A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. As explained in detail below, binding to each of the individual allele-specific HLA molecules can be modulated by substitutions at the primary anchor and/or secondary anchor positions.
Representative peptide epitopes that contain the A2 supermotif are set forth on the attached Table VII.
IV.C.2.c) HLA-A3 Supermotif
The HLA-A3 supermotif is characterized by peptide ligands having primary anchor residues: A, L, I, V, M, S, or, T at position 2, and positively charged residues, such as R or K at the C-terminal position (in position 9 of 9-mers). Exemplary members of the corresponding HLA family of HLA molecules (the HLA-A3 superfamily) that bind the A3 supermotif include: A3 (A*0301), A11 (A*1101), A31 (A*3101), A*3301, and A*6801. Other allele-encoded HLA molecules predicted to be members of the A3 superfamily include A34, A66, and A*7401. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions of amino acids at the primary and/or secondary anchor positions of the peptide.
Representative peptide epitopes that contain the A3 supermotif are set forth on the attached Table VIII.
IV.C.2.d) HLA-A24 Supermotif
The HLA-A24 supermotif is characterized by the presence in peptide ligands of an aromatic (F, W, or Y) residue as a primary anchor in position 2 and a hydrophobic (Y, F, L, I, V, or M) residue as primary anchor at the C-terminal position. The corresponding family of HLA molecules that bind to the A24 supermotif (the A24 supertype) includes A*2402, A*3001, and A*2301. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary anchor positions.
Representative peptide epitopes that contain the A24 supermotif are set forth on the attached Table IX.
IV.C.2.e) HLA-B7 Supermotif
The HLA-B7 supermotif is characterized by peptides bearing proline in position 2 as a primary anchor and hydrophobic or aliphatic amino acids (L, I, V, M, A, F, W, or Y) as the primary anchor at the C-terminal position. The corresponding family of HLA molecules that bind the B7 supermotif (the HLA-B7 supertype) is comprised of at least a dozen HLA-B proteins including B7, B*3501-1, B*3502-2, B*3501-3, B51, B*5301, B*5401, B*5501, B*5401, B*5501, B*5502, B*5601, B*6701, and B*7801 (See, e.g., Sidney, et al., J. Immunol. 154:247 (1995); Barber, et al., Curr. Biol. 5:179 (1995); Hill, et al., Nature 360:434 (1992); Rammensee, et al., Immunogenetics 41:178 (1995)). As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions at the primary and/or secondary anchor positions of the peptide.
Representative peptide epitopes that contain the B7 supermotif are set forth on the attached Table X.
IV.C.2.f) HLA-B27 Supermotif
The HLA-B27 supermnotif is characterized by the presence in peptide ligands of positively charged (R, H, or K) residues as primary anchors at position 2 and hydrophobic (A, L, I, V, M, Y, F, or W) residues as primary anchors at the C-terminal. Exemplary members of the corresponding HLA molecules that bind to the B27 supermotif (the B27 supertype) include B*14, B*1509, B*38, B*3901, B*3902, B*73, and various B27 subtypes. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary anchor positions.
Representative peptide epitopes that contain the B27 supermotif are set forth on the attached Table XI.
IV.C.2.g) HLA-B44 Supermotif
The HLA-B44 supermotif is characterized by the presence in peptide ligands of negatively charged (D or E) residues as a primary anchor in position 2, and hydrophobic residues (F, W, Y, L, I, M V, or A) as a primary anchor at the C-terminal. Exemplary members of the corresponding family of HLA molecules that bind to the B44 supermnotif (the B44 supertype) include B*3701, B*4402, B*4403, B60, and B61. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary anchor positions.
Representative peptide epitopes that contain the B44 supermotif are set forth on the attached Table XII.
IV.C.2.h) HLA-B58 Supermotif
The HLA-B58 supermotif is characterized by the presence in peptide ligands of small aliphatic residues (A, S, or T) as primary anchor residues at position 2 and aromatic or hydrophobic residues (F, W, Y, L, I, or V) as primary anchor residues at the C-terminal. Exemplary members of the corresponding HLA molecules that bind to the B58 supermotif (the B58 supertype) include B*1516, B*1517, B*5701, B*5702, and B*58. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary anchor positions.
Representative peptide epitopes that contain the B58 supermotif are set forth on the attached Table XIII.
IV.C.2.i) HLA-B62 Supermotif
The HLA-B62 supermotif is characterized by the presence in peptide ligands of the polar aliphatic residue Q or the hydrophobic aliphatic residues (L, V, M, or I) as a primary anchor in position 2 and hydrophobic residues (F, W, Y, M, I, or V) as a primary anchor at the C-terminal position. Exemplary members of the corresponding HLA molecules that a bind to the B62 supermotif (the B62 supertype) include B46, B52, B62, B75, and B77. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary anchor positions.
Representative peptide epitopes that contain the B62 supermotif are set forth on the attached Table XIV.
IV.C.2.j) HLA-A1 Motif
The allele-specific HLA-A1 motif is characterized by the presence in peptide ligands of T, S, or M as a primary anchor residue at position 2 and the presence of Y as a primary anchor residue at the C-terminal position. Alternatively, a primary anchor residue may be present at position 3 rather than position 2. This motif is characterized by the presence of D, E, A, or S as a primary anchor residue in position 3 and a Y as a primary anchor residue at the C-terminus. Peptide binding to HLA A1 can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptide epitopes that contain the A1 motif are set forth on the attached Table XV.
IV.C.2.k) HLA-A3 Motif
The allele-specific HLA-A3 motif is characterized by the presence in peptide ligands of L, M, V, I, S, A, T, F, C, G, or D as a primary anchor residue at position 2 and the presence of K, Y, R, H, F, or A as the primary anchor residue at the C-terminal position. Peptide binding to HLA-A3 can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptide epitopes that contain the A3 motif are set forth on the attached Table XVI.
IV.C.2.1) HLA-A11 Motif
The allele-specific HLA-A11 motif is characterized by the presence in peptide ligands of V, T, M, L, I, S, A, G, N, C, D, or F as a primary anchor residue in position 2 and K, R, Y, or H as a primary anchor residue at the C-terminal position. Peptide binding to HLA-A 11 can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptide epitopes that contain the A11 motif are set forth on the attached Table XVI; peptides bearing the A3 allele-specific motif are also present in Table XVII. The A11 and A3 motifs have a number of anchor residues in common, separate tables would provide a number of redundant entries.
IV.C.2.m) HLA-A24 Motif
The allele-specific HLA-A24 motif is characterized by the presence in peptide ligands of Y, F, W, or M as a primary anchor residue in position 2 and F, L, I, or W as a primary anchor residue at the C-terminal position. Peptide binding to HLA-A24 molecules can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptide epitopes that contain the A24 motif are set forth on the attached Table XVII.
IV.C.2.n) HLA-A2.1 Motif
The allele-specific HLA-A2.1 motif was first determined to be characterized by the presence in peptide ligands of L, M, V, I, A or T as a primary anchor residue in position 2 and, L, V, I, A, or T as a primary anchor residue at the C-terminal position. The preferred and tolerated residues that characterize the primary anchor positions of the HLA-A2.1 motif are identical to the preferred residue of the A2 supermotif. Secondary anchor residues that characterize the A2.1 motif have additionally been defined as disclosed herein. These are disclosed in Table II. Peptide binding to HLA-A2.1 molecules can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptide epitopes that contain the A2.1 motif are set forth on the attached Table VII. These peptides, which bear the HLA-A2 supermotif, also contain secondary anchor residues that are characteristic of the HLA-A2.1 motif. In one embodiment, the peptide epitope does not bear an L or M at position 2 and V at the C-terminal position 9 of a 9-amino acid peptide.
The primary anchor residues of the HLA class I peptide epitope supermotifs and motifs delineated above are summarized in Table I. Primary and secondary anchor positions are summarized in Table II.
Motifs Indicative of Class II HTL Inducing Peptide Epitopes
IV.C.2.o) HLA DR-1-4-7 Supermotif
Motifs have also been identified for peptides that bind to three common HLA class II types, HLA DRB1*0401, DRB1*0101, and DRB1*0701. Peptides binding to these DR molecules carry a motif characterized by a large aromatic or hydrophobic residue in position 1 (Y, F, W, L, I, V, or M) and a small, non-charged residue in position 6 (S, T, C, AP, V, I, L, or M). Allele specific secondary effects and secondary anchors for each of these HLA types have also been identified. These are set forth in Table III. Peptide binding to HLA-DR4, DR1, and DR7 can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptides are set forth in Table XVIII.
IV.C.2.p) HLA DR3 Motifs
Two alternative motifs characterize peptides that bind to HLA-DR3 molecules. In the first motif, a large, hydrophobic residue (I, L, V, M, Y, or F) is present in anchor position 1 and D is present as an anchor at position 4, which is defined as being 3 positions from anchor position 1 towards the carboxyl terminus regardless of the location of anchor position 1 in the peptide. Lack of either the large, hydrophobic residue at anchor position 1, or of the negatively charged or amide-like anchor residue at position 4 may be compensated for by the presence of a positive charge at position 6 (which is defined as being 5 positions from anchor position 1 towards the carboxyl terminus). Thus for the second, alternative motif I, L, V, M, Y, F, or A is present at anchor position 1; D, N, Q, E, S, or T is present at anchor position 4; and K, R, or H is present at anchor position 6. Peptide binding to HLA-DR3 can be modulated by substitutions at primary and/or secondary anchor positions.
Representative peptides are set forth in Table IXX.
IV.C.3. Enhancing Population Coverage of the Vaccine
Vaccines that have broad population coverage are preferred because they are more commercially viable and generally applicable to the most people. Broad population coverage can be obtained using the peptides of the invention (and nucleic acid compositions that encode such peptides) through selecting peptide epitopes that bind to HLA alleles which, when considered in total, are present in most of the population. Table XX lists the overall frequencies of the A2-, A3-, and B7-supertypes in various ethnicities. Coverage in excess of 80% is achieved with these motifs. These results suggest that effective and non-ethnically biased population coverage is achieved upon use of a limited number of cross-reactive peptides. Although the population coverage reached with these three main peptide specificities is high, coverage can be expanded to reach 95% population coverage and above, and more easily achieve truly multispecific responses upon use of additional supermotif or allele-specific motif bearing peptides.
Table XX summarizes the HLA supertypes that have been identified, and indicates an estimate of their combined prevalence in major ethnic groups. The B44-, A1-, and A24-supertypes are present, on average, in over 25% of the world's major ethnic populations. While less prevalent overall, the B27-, B58-, and B62 supertypes are each present with a frequency >25% in at least one major ethnic group. The Table indicates the population coverage achieved by the A2-, A3-, and B7-supertypes, and the incremental coverage obtained by the addition of A1-, A24-, and B44-supertypes, or all of the supertypes described herein. As shown, by including epitopes from the six most frequent supertypes, an average population coverage of 99% is obtained for five major ethnic groups.
The data presented herein, together with the previous definition of the A2-, A3-, and B7-supertypes, indicates that all antigens, with the possible exception of A29, B8, and B46, can be classified into a total of nine HLA supertypes. Focusing on the six most common supertypes affords population coverage greater than 98% for all major ethnic populations.
IV.D. Immune Response Stimulating Peptide Analogs
Although peptides with suitable cross-reactivity among all alleles of a superfamily are identified by the screening procedures described above, cross-reactivity is not always complete and in such cases procedures to further increase cross-reactivity of peptides can be useful; such procedures can also be used to modify other properties of the peptides. Having established the general rules that govern cross-reactivity of peptides for HLA alleles within a given motif or supermotif, modification (i.e., analoging) of the structure of peptides of particular interest in order to achieve broader (or otherwise modified) HLA binding capacity can be performed. More specifically, peptides which exhibit the broadest cross-reactivity patterns, (both amongst the known T cell epitopes, as well as the more extended set of peptides that contain the appropriate supermotifs), can be produced in accordance with the teachings herein.
The strategy employed utilizes the motifs or supermotifs which correlate with binding to certain HLA molecules. The motifs or supermotifs are defined by having primary anchors, though secondary anchors can also be modified. Analog peptides can be created by substituting amino acids residues at primary anchor, secondary anchor, or at primary and secondary anchor positions. Generally, analogs are made for peptides that already bear a motif or supermotif. Preferred secondary anchor residues of supermotifs and motifs that have been defined for HLA class I and class II binding peptides are shown in Tables II and III, respectively.
For a number of the motifs or supermotifs in accordance with the invention, residues are defined which are deleterious to binding to allele-specific HLA molecules or members of HLA supertypes that bind to the respective motif or supermotif (Tables II and III). Accordingly, removal of residues that are detrimental to binding can be performed in accordance with the present invention. For example, in the case of the A3 supertype, when all peptides that have such deleterious residues are removed from the population of analyzed peptides, the incidence of cross-reactivity increases from 22% to 37% (see, e.g., Sidney, J. et al., Hu. Immunol. 45:79, 1996). Thus, one strategy to improve the cross-reactivity of peptides within a given supermotif is simply to delete one or more of the deleterious residues present within a peptide and substitute a small “neutral” residue such as Ala (that may not influence T cell recognition of the peptide). An enhanced likelihood of cross-reactivity is expected if, together with elimination of detrimental residues within a peptide, residues associated with high affinity binding to multiple alleles within a superfamily are inserted.
To ensure that changes in the native or original epitope recognized by T cells do not lead to a failure of killing antigen presenting cells presenting the unaltered “wild type” peptide (or, in the case of class II epitopes, a failure to elicit helper T cells that cross-react with the wild type peptides), the variant peptide may be used to immunize T cells in vitro from individuals of the appropriate HLA allele, and the cells' capacity to induce lysis of wild type peptide sensitized target cells is evaluated. In both class I and class II systems it will be desirable to use as targets, cells that have been either infected or transfected with the appropriate genes to establish whether endogenously produced antigen is also recognized by the relevant T cells.
Another embodiment of the invention to ensure adequate numbers of cross-reactive cellular binders is to create analogs of weak binding peptides. Class I peptides exhibiting binding affinities of 500-50000 nM, and carrying an acceptable but suboptimal primary anchor residue at one or both positions can be “fixed” by substituting preferred anchor residues in accordance with the respective supertype. The analog peptides can then be tested for crossbinding activity.
Another embodiment for generating effective peptide analogs involves the substitution of residues that have an adverse impact on peptide stability or solubility in a liquid environment. This substitution may occur at any position of the peptide epitope. For example, a cysteine (C) can be substituted out in favor of α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substituting α-amino butyric acid for C not only alleviates this problem, but actually improves binding and crossbinding capability in certain instances (Review: A. Sette et al, In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, in press, 1998). Substitution of cysteine with α-amino butyric acid may occur at any residue of a peptide epitope, i.e. at either anchor or non-anchor positions.
In general, CTL and HTL responses are not directed against all possible epitopes. Rather, they are restricted to a few immunodominant determinants (Zinkemagel, et al., Adv. Immunol. 27:5159, 1979; Bennink, et al., J. Exp. Med. 168:19351939, 1988; Rawle, et al., J. Immunol. 146:3977-3984, 1991). It has been recognized that immunodominance (Benacerraf, et al., Science 175:273-279, 1972) could be explained by either the ability of a given epitope to selectively bind a particular HLA protein (determinant selection theory) (Vitiello, et al., J. Immunol. 131:1635, 1983); Rosenthal, et al., Nature 267:156-158, 1977), or being selectively recognized by the existing TCR (T cell receptor) specificity (repertoire theory) (Klein, J., IMMUNOLOGY, THE SCIENCE OF SELFNONSELF DISCRIMINATION, John Wiley & Sons, N.Y., pp. 270-310, 1982). It has been demonstrated that additional factors, mostly linked to processing events, can also play a key role in dictating, beyond strict immunogenicity, which of the many potential determinants will be presented as immunodominant (Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993).
The concept of dominance and subdominance is relevant to immunotherapy of both infectious diseases and cancer. For example, in the course of chronic viral disease, recruitment of subdominant epitopes can be important for successful clearance of the infection, especially if dominant CTL or HTL specificities have been inactivated by functional tolerance, suppression, mutation of viruses and other mechanisms (Franco, et al., Curr. Opin. Immunol. 7:524-531, (1995)). In the case of cancer and tumor antigens, CTLs recognizing at least some of the highest binding affinity peptides might be functionally inactivated. Lower binding affinity peptides are preferentially recognized at these times.
In particular, it has been noted that a significant number of epitopes derived from known non-viral tumor associated antigens (TAA) bind HLA class I with intermediate affinity (IC50 in the 50-500 nM range). For example, it has been found that 8 of 15 known TAA peptides recognized by tumor infiltrating lymphocytes (TIL) or CTL bound in the 50-500 nM range. (These data are in contrast with estimates that 90% of known viral antigens that were recognized as peptides bound HLA with IC50 of 50 nM or less, while only approximately 10% bound in the 50-500 nM range (Sette, et al., J. Immunol., 153:558-5592 (1994)). In the cancer setting this phenomenon is probably due to elimination, or functional inhibition of the CTL recognizing several of the highest binding peptides, presumably because of T cell tolerization events.
Without intending to be bound by theory, it is believed that because T cells to dominant epitopes may have been clonally deleted, selecting subdominant epitopes may allow extant T cells to be recruited, which will then lead to a therapeutic response. However, the binding of HLA molecules to subdominant epitopes is often less vigorous than to dominant ones. Accordingly, there is a need to be able to modulate the binding affinity of particular immunogenic epitopes for one or more BLA molecules, and thereby to modulate the immune response elicited by the peptide. Thus a need exists to prepare analog peptides which elicit a more vigorous response. This ability would greatly enhance the usefulness of peptide-based vaccines and therapeutic agents.
Representative analog peptides are set forth in Table XXI. The Table indicates the length and sequence of the analog peptide as well as the motif or supermotif, if appropriate. The information in the “Fixed Nomenclature” column indicates the residues substituted at the indicated position numbers for the respective analog.
IV.E. Computer Screening of Protein Sequences from Disease-Related Antigens for Supermotif or Motif Containing Peptides
Computer programs that allow the rapid screening of protein sequences for the occurrence of the subject supermotifs or motifs are encompassed by the present invention; as are programs that permit the generation of analog peptides. These programs are implemented to analyze any identified amino acid sequence or operate on an unknown sequence and simultaneously determine the sequence and identify motif-bearing epitopes thereof; analogs can be simultaneously determined as well. Generally, the identified sequences will be from a pathogenic organism or a tumor-associated peptide. For example, the target molecules considered herein include all of the HBV proteins (e.g. surface, core, polymerase, and X).
In cases where the sequence of multiple variants of the same target protein are available, peptides are also selected on the basis of their conservancy. A presently preferred criterion for conservancy defines that the entire sequence of a peptide be totally conserved in 75% of the sequences evaluated for a specific protein; this definition of conservancy has been employed herein.
It is important that the selection criteria utilized for prediction of peptide binding are as accurate as possible, to correlate most efficiently with actual binding. Prediction of peptides that bind, for example, to HLA-A*0201, on the basis of the presence of the appropriate primary anchors, is positive at about a 30% rate (Ruppert, J. et al. Cell 74:929, 1993). However, by analyzing an extensive peptide-HLA binding database, the present inventors have developed a number of allele specific polynomial algorithms that dramatically increase the predictive value over identification on the basis of the presence of primary anchor residues alone. These algorithms take into account not only the presence or absence of the correct primary anchors, but also consider the positive or deleterious presence of secondary anchor residues (to account for the impact of different amino acids at different positions). The algorithms are essentially based on the premise that the overall affinity (or AG) of peptide-HLA interactions can be approximated as a linear polynomial function of the type:

ΔG=a1i×a2i×a3i . . . ×ani 

    
    
        where aij is a coefficient that represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. An important assumption of this method is that the effects at each position are essentially independent of each other. This assumption is justified by studies that demonstrated that peptides are bound to HLA molecules and recognized by T cells in essentially an extended conformation. Derivation of specific algorithm coefficients has been described in Gulukota et al. (Gulukota, K. et al., J. Mol. Biol. 267:1258, 1997).
    
    


Additional methods to identify preferred peptide sequences, which also make use of specific motifs, include the use of neural networks and molecular modeling programs (Gulukota, K. et al., J. Mol. Biol. 267:1258, 1997; Milik et al., Nature Biotechnology 16:753, 1998; Altuvia et al., Hum. Immunol. 58:1, 1997; Altuvia et al, J. Mol. Biol. 249:244, 1995).
For example, it has been shown that in sets of A*0201 motif peptides, 69% of the peptides containing at least one preferred secondary anchor residue while avoiding the presence of any deleterious secondary anchor residues, will bind A*0201 with an IC50 less than 500 nM (Ruppert, J. et al. Cell 74:929, 1993). These algorithms are also flexible in that cut-off scores may be adjusted to select sets of peptides with greater or lower predicted binding properties, as desired.
In utilizing computer screening to identify peptide epitopes, all protein sequence or translated sequence may be analyzed using software developed to search for motifs, for example the “FINDPATTERNS” program (Devereux, et al. Nucl. Acids Res. 12:387-395, 1984) or MotifSearch 1.4 software program (D. Brown, San Diego, Calif.) to identify potential peptide sequences containing appropriate HLA binding motifs. As appreciated by one of ordinary skill in the art a large array of software and hardware options are available which can be employed to implement the motifs of the invention relative to known or unknown peptide sequences. The identified peptides will then be scored using customized polynomial algorithms to predict their capacity to bind specific HLA class I or class II alleles.
In accordance with the procedures described above, HBV peptides and analogs thereof that are able to bind HLA supertype groups or allele-specific BLA molecules have been identified (Tables VI-XIX; Table XI).
IV.F. Assays to Detect T-Cell Responses
Once HLA binding peptides are identified, they can be tested for the ability to elicit a T-cell response. The preparation and evaluation of motif-bearing peptides are described in PCT publications WO 94/20127 and WO 94/03205. Briefly, peptides comprising epitopes from a particular antigen are synthesized and tested for their ability to bind to the appropriate HLA proteins in assays using, for example, purified HLA class I molecules and radioiodonated peptides and/or cells expressing empty class I molecules (which lack peptide in their receptor) by, for instance, immunofluorescent staining and flow microfluorimetry, peptide-dependent class I assembly assays, and inhibition of CTL recognition by peptide competition. Those peptides that bind to the class I molecule are further evaluated for their ability to serve as targets for CTLs derived from infected or immunized individuals, as well as for their capacity to induce primary in vitro or in vivo CTL responses that can give rise to CTL populations capable of reacting with selected target cells associated with a disease. Corresponding assays are used for evaluation of HLA class II binding peptides.
Conventional assays utilized to detect CTL responses include proliferation assays, lymphokine secretion assays, direct cytotoxicity assays, and limiting dilution assays. For example, antigen-presenting cells that have been incubated with a peptide can be assayed for the ability to induce CTL responses in responder cell populations. Antigen-presenting cells can be normal cells such as peripheral blood mononuclear cells or dendritic cells. Alternatively, mutant mammalian cell lines that are deficient in their ability to load class I molecules with internally processed peptides and that have been transfected with the appropriate human class I gene may be used to test for the capacity of the peptide to induce in vitro primary CTL responses.
Peripheral blood lymphocytes may be used as the responder cell source of CTL precursors. The appropriate antigen-presenting cells are incubated with peptide and the peptide-loaded antigen-presenting cells are then incubated with the responder cell population under optimized culture conditions. Positive CTL activation can be determined by assaying the culture for the presence of CTLs that kill radio-labeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed forms of the HBV antigen from which the peptide sequence was derived.
More recently, a method has also been devised which allows direct quantification of antigen-specific T cells by staining with Fluorescein-labelled HLA tetrameric complexes (Altman, J. D. et al., Proc. Natl. Acad. Sci. USA 90:10330, 1993; Altman, J. D. et al., Science 274:94, 1996). Other relatively recent technical developments include staining for intracellular lymphokines, and interferon release assays or ELISPOT assays. Tetramer staining, intracellular lymphokine staining and ELISPOT assays all appear to be at least 10-fold more sensitive than more conventional assays (Lalvani, A. et al., J. Exp. Med. 186:859, 1997; Dunbar, P. R. et al., Curr. Biol. 8:413, 1998; Murali-Krishna, K. et al., Immunity 8:177, 1998).
HTL activation may also be assessed using such techniques as T cell proliferation and secretion of lymphokines, e.g. IL-2.
Alternatively, immunization of HLA transgenic mice can be used to determine immunogenicity of peptide epitopes. Several transgenic mouse models including mice with human A2.1, A11, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed. Additional transgenic mouse models with other HLA alleles may be generated as necessary. Mice may be immunized with peptides emulsified in Incomplete Freund's Adjuvant and the resulting T cells tested for their capacity to recognize peptide-pulsed target cells and target cells transfected with appropriate genes. CTL responses may be analyzed using cytotoxicity assays described above. Similarly, HTL responses may be analyzed using such assays as T cell proliferation or secretion of lymphokines.
IV.G. Preparation of Peptides
Peptides in accordance with the invention can be prepared synthetically, by recombinant DNA technology, or from natural sources such as native tumors or pathogenic organisms. Peptide epitopes may be synthesized individually or as polyepitopic peptides. Although the peptide will preferably be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments the peptides may be synthetically conjugated to native fragments or particles.
The peptides in accordance with the invention can be a variety of lengths, and either in their neutral (uncharged) forms or in forms which are salts. Peptides may be synthesized The peptides in accordance with the invention are either free of modifications such as glycosylation, side chain oxidation, or phosphorylation; or they contain these modifications, subject to the condition that modifications do not destroy the biological activity of the peptides as described herein.
Desirably, the peptide will be as small as possible while still maintaining substantially all of the biological activity of the large peptide. When possible, it may be desirable to optimize HLA class I binding peptides of the invention to a length of about 8 to about 13 amino acid residues, preferably 9 to 10. HLA class II binding peptides may be optimized to a length of about 6 to about 25 amino acids in length, preferably to between about 13 and about 20 residues. Preferably, the peptides are commensurate in size with endogenously processed pathogen-derived peptides or tumor cell peptides that are bound to the relevant HLA molecules. Moreover, the identification and preparation of peptides of other lengths can be carried out using the techniques described herein (e.g., the disclosures regarding primary and secondary anchor positions). However, it is also preferred to identify a larger region of a native peptide that encompasses one and preferably two or more epitopes in accordance with the invention. This sequence is selected on the basis that it contains the greatest number of epitopes per amino acid length. It is to be appreciated that epitopes can be present in a frame-shifted manner, e.g. a 10 amino acid long peptide could contain two 9 amino acid long epitopes and one 10 amino acid long epitope; each epitope can be exposed and bound by an HLA molecule upon administration of a plurality of such peptides. This larger, preferably multi-epitopic, peptide can then be generated synthetically, recombinantly, or via cleavage from the native source.
The peptides of the invention can be prepared in a wide variety of ways. For the preferred relatively short size, the peptides can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, for example, Stewart & Young, SOLID PHASE PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co. (1984). Further, individual peptides may be joined using chemical ligation to produce larger peptides.
Alternatively, recombinant DNA technology may be employed wherein a nucleotide sequence which encodes an immunogenic peptide of interest is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, as described generally in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). Thus, recombinant polypeptides which comprise one or more peptide sequences of the invention can be used to present the appropriate T cell epitope.
As the nucleotide coding sequence for peptides of the preferred lengths contemplated herein can be synthesized by chemical techniques, for example, the phosphotriester method of Matteucci, et al., J. Am. Chem. Soc. 103:3185 (1981) modification can be made simply by substituting the appropriate and desired nucleic acid base(s) for those that encode the native peptide sequence. The coding sequence can then be provided with appropriate linkers and ligated into expression vectors commonly available in the art, and the vectors used to transform suitable hosts to produce the desired fusion protein. A number of such vectors and suitable host systems are now available. For expression of the fusion proteins, the coding sequence will be provided with operably linked start and stop codons, promoter and terminator regions and usually a replication system to provide an expression vector for expression in the desired cellular host. For example, promoter sequences compatible with bacterial hosts are provided in plasmids containing convenient restriction sites for insertion of the desired coding sequence. The resulting expression vectors are transformed into suitable bacterial hosts. Of course, yeast, insect or mammalian cell hosts may also be used, employing suitable vectors and control sequences.
IV.H. Peptide Epitope Reagents to Evaluate Immune Responses.
HLA class I and class II binding peptides as described herein can be used, in one embodiment of the invention, as reagents to evaluate an immune response. The immune response to be evaluated may be induced by using as an immunogen any agent that would potentially result in the production of antigen-specific CTLs or HTLs to the peptide epitope(s) to be employed as the reagent. The peptide reagent is not used as the immunogen.
For example, a peptide of the invention may be used in a tetramer staining assay to assess peripheral blood mononuclear cells for the presence of antigen-specific CTLs following exposure to a pathogen or immunogen. The HLA-tetrameric complex is used to directly visualize antigen-specific CTLs (see, e.g., Ogg et al. Science 279:2103-2106, 1998; and Altman et al. Science 174:94-96, 1996) and determine the frequency of the antigen-specific CTL population in a sample of peripheral blood mononuclear cells. A tetramer reagent using a peptide of the invention may be generated as follows: A peptide that binds to an allele-specific HLA molecules, or supertype molecules, is refolded in the presence of the corresponding HLA heavy chain and β2-microglobulin to generate a trimolecular complex. The complex is biotinylated at the carboxyl terminal end of the heavy chain at a site that was previously engineered into the protein. Tetramer formation is then induced by the addition of streptavidin. By means of fluorescently labeled streptavidin, the tetramer can be used to stain antigen-specific cells. The cells may then be identified, for example, by flow cytometry. Such an analysis may be used for diagnostic or prognostic purposes.
Peptides of the invention may also be used as reagents to evaluate immune recall responses. (see, e.g., Bertoni et al. J. Clin. Invest. 100:503-513, 1997 and Penna et al. J. Exp. Med. 174:1565-1570, 1991.) For example, patient PBC samples from individuals with acute hepatitis B or who have recently recovered from acute hepatitis B may be analyzed for the presence of HBV antigen-specific CTLs using HBV-specific peptides. A blood sample containing mononuclear cells may be evaluated by cultivating the PBCs and stimulating the cells with a peptide of the invention. After an appropriate cultivation period, the expanded cell population may be analyzed for cytotoxic activity.
The peptides may also be used as reagents to evaluate the efficacy of a vaccine. PBMCs obtained from a patient vaccinated with an immunogen may be analyzed using, for example, either of the methods described above. A patient is HLA typed, and appropriate peptide reagents that recognize allele-specific molecules present in that patient may be selected for the analysis. The immunogenicity of the vaccine will be indicated by the presence of HBV epitope-specific CTLs in the PBMC sample.
IV.I. Vaccine Compositions
Vaccines that contain as an active ingredient an immunogenically effective amount of one or more peptides as described herein are a further embodiment of the invention. Once appropriately immunogenic epitopes have been defined, they can be sorted and delivered by various means, herein referred to as “vaccine” compositions. Such vaccine compositions can include, for example, lipopeptides (Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptides compositions encapsulated in poly(DL-lactide-co-glycolide) (PLG) microspheres (see, e.g., Eldridge, et al. Molec. Immunol. 28:287-294, 1991: Alonso et al. Vaccine 12:299-306, 1994; Jones et al. Vaccine 13:675-681, 1995), peptide compositions encapsulated in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al. Nature 344:873-875, 1990; Hu et al. Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M. -P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted, also know as receptor mediated targeting, delivery technologies also may be used such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.).
Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptide(s) that can be introduced into a host, including humans, linked to its own carrier, or as a homopolymer or heteropolymer of active peptide units., Such a polymer has the advantage of increased immunological reaction and, where different peptides are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targetted for an immune response.
Furthermore, useful carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, hepatitis B virus recombinant vaccine and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine P3CSS).
As disclosed in greater detail herein, upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs specific for the desired antigen, and the host becomes at least partially immune to later infection, or at least partially resistant to developing an ongoing chronic infection.
In some instances it may be desirable to combine the class I peptide vaccines of the invention with vaccines which induce or facilitate neutralizing antibody responses to the target antigen of interest, particularly to viral envelope antigens. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a PADRE®(Epimmune, San Diego, Calif.) molecule (described in the related U.S. Ser. No. 08/485,218, which is a CIP of U.S. Ser. No. 08/305,871, now U.S. Pat. No. 5,736,142, which is a CIP of abandoned application U.S. Ser. No. 08/121,101.) Furthermore, any of these embodiments can be administered as a nucleic acid mediated modality.
For therapeutic or immunization purposes, the peptides of the invention can also be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into an acutely or chronically infected host or into a non-infected host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL and/or HTL response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover, et al. Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.
Antigenic peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat chronic infections, or tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular pathogen (infectious agent or tumor antigen) are induced by incubating in tissue culture the patient's CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated, mature and expand into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (an infected cell or a tumor cell).
Transfected dendritic cells may also be used as antigen presenting cells. Alternatively, dendritic cells are transfected, e.g., with a minigene construct in accordance with the invention, in order to elicit immune responses. Minigenes will be discussed in greater detail in a following section.
DNA or RNA encoding one or more of the peptides of the invention can also be administered to a patient. This approach is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720; and in more detail below. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) delivery.
Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition, or for selecting epitopes to be included in a vaccine composition and/or to be encoded by a minigene. It is preferred that each of the following principles are balanced in order to make the selection.
1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with HBV clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of HBV. In other words, it has been observed that in patients who spontaneously clear HBV, that they had generated an immune response to at least 3 epitopes on at least one HBV antigen. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one HBV antigen (see e.g., Rosenberg et al. Science 278:1447-1450).
2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 nM or less.
3.) Sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess population coverage.
4.) When selecting epitopes from cancer-related antigens it is often preferred to select analogs. When selecting epitopes for infectious disease-related antigens it is often preferable to select native epitopes. Therefore, of particular relevance for infectious disease vaccines (but for cancer-related vaccines as well), are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.
When providing nested epitopes, it is preferable to provide a sequence that has the greatest number of epitopes per provided sequence. A limitation on this principle is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, it is important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.
5.) When creating a minigene, as disclosed in greater detail in the following section, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Thus, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis. Junctional epitopes are to be avoided because the recipient may generate an immune response to that epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.
IV.I.1. Minigene Vaccines
A growing body of experimental evidence demonstrates that a number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines above. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding one or multiple epitopes of the invention. The use of multi-epitope minigenes is described below and in, e.g. An, L. and Whitton, J. L., .1 J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding nine dominant HLA-A*0201- and A11-restricted epitopes derived from the polymerase, envelope, and core proteins of HBV and HIV, the PADRE® universal helper T cell (HTL) epitope, and an ER-translocating signal sequence was engineered. Immunization of HLA transgenic mice with this plasmid construct resulted in strong CTL induction responses against the nine epitopes tested, similar to those observed with a lipopeptide of known immunogenicity in humans, and significantly greater than immunization in oil-based adjuvants. Moreover, the immunogenicity of DNA-encoded epitopes in vivo correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid.
For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that could be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, a ubiquitination signal sequence, a leader sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes.
The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.
Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.
Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.
Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.
In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.
In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF) or costimulatory molecules. Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving CTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases).
Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.
Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids can also be used in the formulation (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, glycolipids, fusogenic liposomes, peptides and compounds referred to collectively as protective, interactive, non-condensing (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.
Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes, respectively. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (51Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by 51Cr release, indicates production of HLA presentation of minigene-encoded CTL epitopes.
In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, IP for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for 1 week in the presence of peptides encoding each epitope being tested. For CTL effector cells, assays are conducted for cytolysis of peptide-loaded, chromium-51 labeled target cells using standard techniques. Lysis of target cells sensitized by HLA loading of peptides corresponding to minigene-encoded epitopes demonstrates DNA vaccine function for in vivo induction of CTLs.
Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.
IV.I.2. Combinations with Helper Pepides
The peptides of the present invention, or analogs thereof, which have immunostimulatory activity may be modified to provide desired attributes, such as improved serum half life, or to enhance immunogenicity.
For instance, the ability of the peptides to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Particularly preferred immunogenic peptides/T helper conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues. Alternatively, the CTL peptide may be linked to the T helper peptide without a spacer.
The immunogenic peptide may be linked to the T helper peptide either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated. The T helper peptides used in the invention can be modified in the same manner as CTL peptides. For instance, they may be modified to include D-amino acids or be conjugated to other molecules such as lipids, proteins, sugars and the like. Exemplary T helper peptides include tetanus toxoid 830-843, influenza 307-319, and malarial circumsporozoite 382-398 and 378-389.
In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in the majority of the population. This can be accomplished by selecting amino acid sequences that bind to many, most, or all of the HLA class II molecules. These are known as “loosely HLA-restricted” or “promiscuous” T helper sequences. Examples of amino acid sequences that are promiscuous include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO:2572), Plasmodium falciparum CS protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 2573), and Streptococcus 18kD protein at positions 116 (GAVDSILGGVATYGAA; SEQ ID NO:2574). Other examples include peptides bearing a DR 1-4-7 supermotif.
Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE® Epimmune, Inc., San Diego, Calif.) are designed on the basis of their binding activity to most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVWANTLKAAa, where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine (SEQ ID NO:2575), has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type.
T helper epitopes can also be modified to alter their biological properties. For example, peptides presenting T helper epitopes can contain D-amino acids to increase their resistance to proteases and thus extend their serum half-life. Also, the epitope peptides of the invention can be conjugated to other molecules such as lipids, proteins or sugars, or any other synthetic compounds, to increase their biological activity. Specifically, the T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.
In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes cytotoxic T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo against viral antigens. For example, palmitic acid residues can be attached to the ε-and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.
As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide. See, Deres, et al., Nature 342:561 (1989). Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to specifically prime a CTL response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses to infection.
In addition, additional amino acids can be added to the termini of a peptide to provide for ease of linking peptides one to another, for coupling to a carrier support, or larger peptide, for modifying the physical or chemical properties of the peptide or oligopeptide, or the like. Amino acids such as tyrosine, cysteine, lysine, glutamic or aspartic acid, or the like, can be introduced at the C- or N-terminus of the peptide or oligopeptide, particularly class I peptides. However, it is to be noted that modification at the carboxyl terminus may, in some cases, alter binding characteristics of the peptide. In addition, the peptide or oligopeptide sequences can differ from the natural sequence by being modified by terminal-NH2 acylation, e.g., by alkanoyl (C1-C20) or thioglycolyl acetylation, terminal-carboxylamidation, e.g., ammonia, methylamine, etc. In some instances these modifications may provide sites for linking to a support or other molecule.
IV.J. Administration of Vaccines for Therapeutic or Prophylactic Purposes
The peptides of the present invention and pharmaceutical and vaccine compositions of the invention are useful for administration to mammals, particularly humans, to treat and/or prevent HBV infection. Vaccine compositions containing the peptides of the invention are administered to a patient susceptible to or otherwise at risk for HBV infection to elicit an immune response against HBV antigens and thus enhance the patient's own immune response capabilities. In therapeutic applications, compositions are administered to a patient in an amount sufficient to elicit an effective CTL response to the virus or tumor antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician. Generally the dosage range for an initial immunization (i.e., therapeutic or prophylactic administration) is between about 1.0 μg to about 5000 μg of peptide, typically between about 10 μg to about 1000 μg, for a 70 kg patient, followed by boosting dosages of between about 1.0 μg to about 5000 μg of peptide pursuant to a boosting regimen over weeks to months depending upon the patient's response and condition as determined by measuring specific CTL activity in the patient's blood. The peptides and compositions of the present invention may be employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.
As noted above, the “CTL” peptides of the invention induce immune responses when contacted with a CTL specific to an epitope comprised by the peptide. The manner in which the peptide is contacted with the CTL is not critical to the invention. For instance, the peptide can be contacted with the CTL either in vivo or in vitro. If the contacting occurs in vivo, the peptide itself can be administered to the patient, or other vehicles, e.g., DNA vectors encoding one or more peptides, vital vectors encoding the peptide(s), liposomes and the like, can be used, as described herein.
For pharmaceutical compositions, the immunogenic peptides, or DNA encoding them, are generally administered to an individual already infected with HBV. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Those in the incubation phase or the acute phase of infection can be treated with the immunogenic peptides separately or in conjunction with other treatments, as appropriate.
For therapeutic use, administration should generally begin at the first diagnosis of HBV infection. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. In chronic infection, loading doses followed by boosting doses may be required.
Treatment of an infected individual with the compositions of the invention may hasten resolution of the infection in acutely infected individuals. For those individuals susceptible (or predisposed) to developing chronic infection, the compositions are particularly useful in methods for preventing the evolution from acute to chronic infection. Where susceptible individuals are identified prior to or during infection, the composition can be targeted to them, minimizing need for administration to a larger population.
The peptide or other compositions as used for the treatment of chronic HBV infection and to stimulate the immune system to eliminate pathogen-infected cells in, e.g., persons who have not manifested symptoms of disease but who act as a disease vector. In this context, it is generally important to provide an amount of immuno-potentiating peptide in a formulation and mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention. Thus, for treatment of chronic infection, a representative dose is in the range of about 1.0 μg to about 5000 μg, preferably about 10 μg to 1000 μg, per 70 kg patient weight per dose. Immunizing doses followed by boosting doses at established intervals, e.g., from four weeks to six months, may be required, possibly for a prolonged period of time to effectively immunize an individual. In the case of chronic infection, administration should continue until at least clinical symptoms or laboratory tests indicate that the viral infection has been eliminated or substantially abated and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.
The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, intrathecal, or local administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, ie., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.
The peptides of the invention may also be administered via liposomes, which serve to target the peptides to a particular tissue, such as lymphoid tissue, or targeted selectively to infected cells, as well as increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g., a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), U.S. Pat. Nos. 4,235,871, 4,501,728,4,837,028, and 5,019,369.
For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.
For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.
For aerosol administration, the immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.
The vaccine compositions of the invention may also be used purely as prophylactic agents. Vaccine compositions containing the peptide epitopes of the invention are administered to a patient susceptible to, or otherwise at risk for, HBV infection to elicit an immune response against HBV antigens and thus enhance the patient's own immune response capabilities following exposure to HBV. Generally the dosage range for an initial prophylactic immunization is between about 1.0 μg to about 5000 μg of peptide, typically between about 10 μg to about 1000 μg, for a 70 kg patient. This is followed by boosting dosages of between about 1.0 μg to about 5000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine may be assessed by measuring specific CTL activity in the patient's blood.
IV.K. Kits
The peptide and nucleic acid compositions of this invention can be provided in kit form together with instructions for vaccine administration. Typically the kit would include desired peptide compositions in a container, preferably in unit dosage form and instructions for administration. An alternative kit would include a minigene construct with desired nucleic acids of the invention in a container, preferably in unit dosage form together with instruction for administration. Lymphokines such as IL-2 or IL-12 may also be included in the kit. Other kit components that may also be desirable include, for example, a sterile syringe, booster dosages, and other desired excipients.
The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of non-critical parameters that can be changed or modified to yield alternative embodiments in accordance with the invention.
V. EXAMPLES
Example 1
HLA Class I Binding Assays
The following example of peptide binding to HLA-A3 supertype molecules demonstrates quantification of binding affinities of HLA class I peptides. Analogous binding assays can be performed for other peptides that bind class I or class II HLA molecules. Furthermore, binding assays can be performed with peptides that are not motif-bearing.
For example, the affinity of peptides bearing an HLA-A3 supermotif was determined as follows. Epstein-Barr virus (EBV)-transformed homozygous cell lines were used as sources of class I molecules. Cell lines include, e.g., GM3107 (A3, B7; Human Genetic Mutant Repository); BVR (A11, B35.3, Cw4; Human Genetic Mutant Repository); SPACH (A31, B62, Cw1/3; ASHI Repository Collection); LWAGS (A*3301, B14, and Cw8; ASHI Repository Collection) (Bodmer, et al., Hum. Immunol. 43:149, 1995), and a C1R transfectant characterized by Dr. Walter Storkus (University of Pittsburgh) for the isolation of A*6801. Cell lines were maintained as previously described (Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)).
Cell lysates were prepared and HLA class I molecules purified in accordance with disclosed protocols (Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, cells were lysed at a concentration of 108 cells/ml in 50 mM Tris-HCl, pH 8.5, containing 1% Nonidet P-40 (Fluka Biochemika, Buchs, Switzerland), 150 mM NaCl, 5 mM EDTA, and 2 mM PMSF. The lysates were passed through 0.45 μM filters and cleared of nuclei and debris by centrifugation at 10,000 g for 20 minutes. HILA proteins were then purified by affinity chromatography. Columns of inactivated Sepharose CL 4B and Protein A Sepharose were used as precolumns. The cell lysate was depleted of HLA-B and HLA-C proteins by repeated passage over Protein A Sepharose beads conjugated with the anti-HLA(B,C) antibody B1.23.2 (Rebai, et al., Tissue Antigens 22:107 (1983)). Typically two to four passages were required for effective depletion. Subsequently, the anti HLA(A,B,C) antibody W6/32 (Barnstable, et al., Cell 14:9 (1978)) was used to capture HLA-A molecules. Protein purity, concentration, and effectiveness of depletion steps were monitored by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).
Binding Assays
Quantitative assays for the binding of peptides to soluble class I molecules on the basis of the inhibition of binding of a radiolabeled standard probe peptide to detergent solubilized HLA molecules were performed as described in the literature (Kubo, et al., J. Immunol. 152:3913 (1994); Kast, et al., J. Immunol. 152:3904 (1994); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994); Ruppert, et al., Cell 74:929 (1993)). Briefly, 1-10 nM of radiolabeled probe peptide, iodinated by the Chloramine-T method (Greenwood, et al., Biochem. J. 89:114 (1963)), was co-incubated at room temperature with various amounts of HLA in the presence of 1 μM human β2-microglobulin (Scripps Laboratories, San Diego, Calif., USA) and a cocktail of protease inhibitors. At the end of a two day incubation period, the percent of HLA-bound radioactivity was determined by size exclusion gel filtration chromatography on a TSK 2000 column.
The A3CON1 peptide (sequence KVFPYALINK; SEQ ID NO:2576) (Kubo, et al., J. Immunol. 152:3913 (1994)) was used as the radiolabeled probe for the A3, A11, A31, and A*6801 assays. A T7Y analogue of HBVc 141-151 (sequence STLPETYVVRRL; SEQ ID No:2577) (Missale, et al., J. Exp. Med. 177:751 (1993)) was used as the radiolabeled probe for the A*3301 assay. In the case of competitive assays, the concentration of peptide yielding 50% inhibition of the binding of the radiolabeled probe peptide (IC50) was calculated. Peptides were usually tested at one or two high doses, and the IC50 of peptides yielding positive inhibition were determined in subsequent experiments, in which two to six further dilutions were tested, as necessary. To achieve a suitable signal, HLA concentrations yielding approximately 15% binding of the radiolabled probe peptide were used for all competitive inhibition assays. Under these conditions the concentration of the labeled peptide is less than the concentration of the HLA molecule and the IC50 is less than the concentration of the HLA molecule, therefore the measured IC50s are reasonable approximations of the true KD values. Each competitor peptide was tested in two to four completely independent experiments. As a positive control, in each experiment, the unlabeled version of the relevant radiolabeled probe was tested and its IC50 measured. The average IC50 of A3CON1 for the A3, A11, A31, and A*6801 assays were 11, 6, 18, and 8 nM, respectively. The average IC50 of the HBVc 141-151 peptide in the A*3301 assay was 29 nM.
Example 2
Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Peptides by Creating Analogs
HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in preparing highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged, or “fixed”, to confer upon a peptide certain characteristics, e.g., greater cross-reactivity within the group of HLA molecules that make-up the supertype, and/or greater binding affinity for some or all of those HLA molecules Examples of analog peptides that exhibit modulated binding affinity are provided.
Analogs representing primary anchor single amino acid residues substituted with I residues at the C-terminus of two different B7-like peptides (HBV env 313 and HBV pol 541) were synthesized and tested for their B7-supertype binding capacity. It was found that the I substitution had an overall positive effect on binding affinity and/or cross-reactivity in both cases. In the case of HBV env 313 the 19 (I at C-terminal position 9) replacement was effective in increasing cross-reactivity from 4 to 5 alleles bound by virtue of an almost 400-fold increase B*5401 binding affinity. In the case of HBV pol 541, increased cross-reactivity was similarly achieved by a substantial increase in B*5401 binding. Also, significant gains in binding affinity for B*0702, B51, and B*5301 were observed with the HBV pol 541 I9 analog.
Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides by identifying particular residues at secondary anchor positions that are associated with such cross-reactive properties. Demonstrating this, the capacity of a second set of peptides representing discreet single amino acid substitutions at positions one and three of five different B7-supertype binding peptides were synthesized and tested for their B-7 supertype binding capacity. In 4/4 cases the effect of replacing the native residue at position 1 with the aromatic residue F (an “F1” substitution) resulted in an increase in cross-reactivity, compared to the parent peptide, and, in most instances, binding affinity was increased three-fold or better (Table XXII). More specifically, for HBV env 313, MAGE2 170, and HCV core 168 complete supertype cross-reactivity was achieved with the F1 substitution analogs. These gains were achieved by dramatically increasing B*5401 binding affinity. Also, gains in affinity were noted for other alleles in the cases of HCV core 168((B*3501 and B*5301) and MAGE2 170((B*3501, B51 and B*5301). Finally, in the case of MAGE3 196, the F1 replacement was effective in increasing cross-reactivity because of gains in B*0702 binding. An almost 70-fold increase in B51 binding capacity was also noted.
Two analogs were also made using the supermotif positive F substitution at position three (an “F3” substitution). In both instances increases in binding affinity and cross-reactivity were achieved. Specifically, in the case of HBV pol 541, the F3 substitution was effective in increasing cross-reactivity by virtue of its effect on B*5401 binding. In the case of MAGE3 196, complete supertype cross-reactivity was achieved by increasing B*0702 and B*3501 binding capacity. Also, in the case of MAGE3 196, it is notable that increases in binding capacity between 40- and 5000-fold were obtained for B*3501, B51, B*5301, and B*5401.
In conclusion, these data demonstrate that by the use of even single amino acid substitutions, it is possible to increase the binding affinity and/or cross-reactivity of peptide ligands for HLA supertype molecules.
Example 3
Induction Of HLA-Restricted CTL By Subcutaneous Priming With HBV Peptide In Incomplete Freund's Adjuvant (IFA)
The immunogenicity of HLA class I binding peptides can be assessed in vivo as described in, e.g., Sette et al. J. Immunol. 153:5586-5592 (1994). This example illustrates such a procedure, whereby subcutaneous injection of HBV peptide in Incomplete Freund's Adjuvant (IFA) can be used to induce HBV-specific CTL in mice that are transgenic for a human HLA allele such as the human HLA-A11 allele.
Priming and In Vitro Restimulation: Mice that are transgenic for HLA-A11, (e.g. HLA-A11/Kb strain) are injected with 100 microliters of an emulsion of purified HBV peptide in IFA. The purified peptide comprises an A11 motif, and is selected from the preferred peptides listed in Table XVI or, alternatively, may be an analog peptide. The peptide epitope (50 μg/mouse) and equimolar amounts of the helper epitope HBV core 128-140 (140 μg/mouse) are dissolved in PBS/5% DMSO, emulsified in IFA, and injected subcutaneously at the base of the tail of the transgenic mice. Eleven days after priming, splenocytes (5×106 cells/well in a 24-well plate) obtained from these animals are restimulated with syngeneic irradiated LPS blasts (2×106/well) coated with peptide.
LPS blasts from unprimed HLA-A11 transgenic mice are prepared 72 hours before use by suspending splenocytes in medium containing LPS (25 μg/ml) and dextran sulfate (7 μg/ml). Coating is achieved by incubating 50 μg of peptide with 1.2×106 LPS blasts in a volume of 0.4 ml of RPMI medium supplemented with 10% FCS for 1 hour at 37° C. The cells are washed once and then co-cultured with splenocytes. After six days, effector cells are assayed, as outlined for example in Example 5, for cytotoxicity against 51Cr-labeled 3A4-721.221-A11Kb target cells in the presence of the peptide.
The effector cells (2×106 cells/well) are re-stimulated at weekly intervals. For the first re-stimulation, peptide-coated LPS blasts are used, followed by peptide-coated A11/Kb cells. Six days afater re-stimulation, effector cells are assayed for cytotoxicity as above.
Example 4
Recognition of Generation of Endogenous Processed Antigens After Priming
This example determines that CTL induced by in vivo priming with peptide (as disclosed in Example 3) recognize endogenously synthesized antigens.
Effector cells from the procedure disclosed in Example 3 are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled 3A4-721.221-A11/Kb target cells, in the absence or presence of peptide, and also tested on 51Cr labeled target cells bearing the endogenously synthesized antigen.
The result will demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized HBV antigen.
Example 5
Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice
This example illustrates the induction of CTLs in transgenic mice by use of an HBV CTL/HTL peptide conjugate. An analagous study may be found in Oseroff et al. Vaccine 16:823-833 (1998). The peptide composition can comprise multiple CTL and/o HTL epitopes. Such a peptide composition can comprise a lipidated HTL epitope conjugated to a preferred CTL epitope containing, for example, an A11 motif or an analog of that epitope.
Lipopeptides are prepared by coupling the appropriate fatty acid to the amino terminus of the resin bound peptide. A typical procedure is as follows: A dichloromethane solution of a four-fold excess of a pre-formed symmetrical anhydride of the appropriate fatty acid is added to the resin and the mixture is allowed to react for two hours. The resin is washed with dichloromethane and dried. The resin is then treated with trifluoroacetic acid in the presence of appropriate scavengers [e.g. 5% (v/v) water] for 60 minutes at 20° C. After evaporation of excess trifluoroacetic acid, the crude peptide is washed with diethyl ether, dissolved in methanol and precipitated by the addition of water. The peptide is collected by filtration and dried.
Preparation of peptides for immunization: Peptide compositions are typically resuspended in DMSO at a concentration of 20 mg/ml. Before use, peptides are prepared at the required concentration by dilution in saline or the appropriate medium.
Immunization procedures: A11/Kb mice, which are transgenic for the human HLA A11 allele, are primed subcutaneously (base of the tail) with 0.1 ml of peptide conjugate formulated in saline, or DMSO/saline. Seven days after priming, splenocytes obtained from these animals are restimulated with syngeneic irradiated LPS-activated lymphoblasts coated with peptide.
Media:
a. RPMI-1640 supplemented with 10% fetal calf serum (FCS) 2 mM Glutamine, 50 μg/ml Gentamicin and 5×10−5 M 2-mercaptoethanol serves as culture medium
b. RPMI-1640 containing 25 mM HEPES buffer and supplemented with 2% (FCS) is used as cell washing medium.
Cell lines: The 3A4-721.221-A11/Kb cell line is used as target cells. This cell line is an EBV transformed cell line that was mutagenized and selected to be Class I negative which was transfected with an HLA-A11/Kb gene.
LPS-activated lymphoblasts: Splenocytes obtained from transgenic mice are resuspended at a concentration of 1-1.5×106/ml in culture medium supplemented with 25 μg/ml LPS and 7 μg/ml dextran sulfate in 75 cm tissue culture flasks. After 72 hours at 37° C., the lymphoblasts are collected for use by centrifugation.
Peptide coating of lymphoblasts: Peptide coating of the LPS activated lymphoblasts is achieved by incubating 30×106 irradiated (3000 rads) lymphoblasts with 100 μg of peptide in 1 ml of R10 medium for 1 hr at 37° C. Cells are then washed once and resuspended in culture medium at the desired concentration.
In vitro CTL activation: One week after priming, spleen cells (30×106 cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×106 cells/flask) in 10 ml of culture medium/T25 flask. After six days, the effector cells are harvested and assayed for cytotoxic activity.
Assay for cytotoxic activity: Target cells (1.0-1.5×106) are incubated at 37° C. in the presence of 200 μl of sodium 51Cr chromate. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 104 51Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a 6 hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % 51Cr release data is expressed as lytic units/106 cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a 6 hour SiCr release assay. To obtain specific lytic units/106, the lytic units/106 obtained in the absence of peptide is subtracted from the lytic units/106 obtained in the presence of peptide. For example, if 30% 51Cr release is obtained at the E:T of 50:1 (i.e., 5×105 effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×104 effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: (1×106(5×104)−(1×106(5×105)=18 LU/106.
The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation. Analyses similar to this may be performed to evaluate the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures it is found that CTL and HTL responses are induced.
Example 7
Induction Of Specific CTL Response In Humans
A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes is set up as an IND Phase I, dose escalation study (5, 50 and 500 μg) and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows:
A total of about 27 subjects are enrolled and divided into 3 groups:
Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;
Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;
Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.
After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.
The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.
Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.
Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.
Thus, the vaccine is found to be both safe and efficacious.
Example 8
Phase II Trials in Patients Infected with HBV
Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients (male and female) having chronic HBV infection. A main objective of the trials is to determine an effective dose and regimen for inducing CTLs in chronically infected HBV patients, to establish the safety of inducing a CTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of chronically infected CTL patients, as manifested by a transient flare in alanine aminotransferase (ALT), normalization of ALT, and reduction in HBV DNA. Such a study is designed, for example, as follows:
The studies are performed in multiple centers in the U.S. and Canada. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects are recorded.
There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65 and include both males and females. The patients represent diverse ethnic backgrounds. All of them are infected with HBV for over five years and are HIV, HCV and HDV negative, but have positive levels of HBe antigen and HBs antigen.
The magnitude and incidence of ALT flares and the levels of HBV DNA in the blood are monitored to assess the effects of administering the peptide compositions. The levels of HBV DNA in the blood are an indirect indication of the progress of treatment. The vaccine composition is found to be both safe and efficacious in the treatment of chronic HBV infection.
Example 9
Selection of CTL and HTL Epitopes for Inclusion in an HBV-specific Vaccine
This example illustrates the procedure for the selection of peptide epitopes for vaccine compositions of the invention.
The following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition, or for selecting epitopes to be included in a vaccine composition and/or to be encoded by a minigene. Each of the following principles are balanced in order to make the selection.
1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with HBV clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of HBV. In other words, it has been observed that in patients who spontaneously clear HBV, that they had generated an immune response to at least 3 epitopes on at least one HBV antigen. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one HBV antigen.
2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 nM or less.
3.) Sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. For example, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, is employed to assess population coverage.
4.) When selecting epitopes for HBV antigens it is often preferable to select native epitopes. Therefore, of particular relevance for infectious disease vaccines, are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.
When providing nested epitopes, a sequence that has the greatest number of epitopes per provided sequence is provided. A limitation on this principle is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, the sequence is screened in order to insure that it does not have pathological or other deleterious biological properties.
5.) When creating a minigene, as disclosed in greater detail in the Example 10, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Thus, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis. Junctional epitopes are to be avoided because the recipient may generate an immune response to that epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.
Peptide epitopes for inclusion in vaccine compositions are, for example, selected from those lsited in Table XXIII. A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude of an immune response that clears an acute HBV infection.
Example 10
Construction of Minigene Multi-Epitope DNA Pslasmids
Expression plasmids have been constructed and evaluated as described, for example, in U.S. Ser. No. 60/085,751 filed May 15, 1998 and U.S. Ser. No. 09/078,904 filed May 13, 1998. The binding peptide epitopes and their positions for some of the plasmids described therein are shown in FIG. 1 as example of the orientation of peptide epitopes in minigene constructs. Such a plasmid may, for example, also include multiple CTL and HTL peptide epitopes. In the present example, HLA-A11 motif-bearing peptides are used in conjunction with DR supermotif-bearing peptides. Preferred A11 epitopes are identified, for example, in Table XVI or Table XXI and peptide epitopes recognized by HLA DR molecules (Tables XVIII and XIX). Four class I A11 motif-bearing peptide epitopes or analogs of those peptide epitopes derived from the same HBV antigen, e.g. the envelope protein, are selected as CTL epitopes. Four class II motif-bearing peptide epitopes derived from the same antigen, e.g., the envelope protein, are selected as HTL epitopes. These epitopes are then incorporated into a minigene for expression in an expression vector.
This example illustrates the methods to be used for construction of such a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.
A pMin minigene DNA plasmid is constructed from an early generation DNA plasmid designated as pMin.0. This plasmid contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by a string of CTL and HTL epitopes selected in accordance with principles disclosed herein. The pMIN sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.
Overlapping oligonucleotides, for example eight oligonucleotides, averaging approximately 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.
For the first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: Oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)2SO4, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO4, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product for 25 additional cycles. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.
Example 11
The Plasmid Construct and the Degree to which it Induces Immunogenicity
The degree to which the plasmid construct prepared using the methodology outlined in Example 10 is able to induce immunogenicity is evaluated through in vivo injections into mice and in vitro CTL culture and cytotoxicity assays as detailed e.g., in U.S. Ser. No. 60/085,751 filed May 15, 1998. To assess the capacity of the pMin minigene construct to induce CTLs in vivo, HLA-A11/Kb transgenic mice are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide.
Splenocytes from immunized animals are stimulated twice with each of the peptide epitopes encoded in the minigene, then assayed for peptide-specific cytotoxic activity in a 51Cr release assay. The results indicate the magnitude of the CTL response directed against each of its A11-restricted epitopes, thus indicating the in vivo immunogenicity of the minigene vaccine. It is, therefore, found that the minigene elicits immune responses directed toward A11-restricted epitopes.
Example 12
Peptide Composition for Prophylactic Uses
Vaccine compositions of the present invention are used to prevent HBV infection in persons who are at risk. For example, a polyepitopic peptide epitope composition containing multiple CTL and HTL epitopes such as those selected in Examples 9 and/or 10, which are also selected to target greater than 80% of the population, is administered to individuals at risk for HBV infection. The composition is provided as a single lipidated polypeptide that encompasses multiple epitopes. The vaccine is administered in an aqueous carrier comprised of Freunds Incomplete Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 5,000 μg for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against HBV infection.
Alternatively, the polyepitopic peptide composition can be administered as a nucleic acid in accordance with methodologies known in the art and disclosed herein.
Example 13
Polyepitopic Vaccine Compositions Derived from Native HBV Sequences
A native HBV polyprotein sequence is screened, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes. This relatively short sequence that contains multiple distinct, even overlapping, epitopes is selected and used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence. As noted herein, epitope motifs may be overlapping (i.e., frame shifted relative to one another) with frame shifted overlapping epitopes, e.g. two 9-mer epitopes can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.
The vaccine composition will preferably include, for example, three CTL epitopes and at least one HTL epitope from the source antigen. Junctional sequences will be analyzed to avoid sequences containing a potentially immunodominant epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence.
The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment directs the immune response to sequences that are present in native HBV antigens. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions.
Related to this embodiment, computer programs can be derived which identify, in a target sequence, the greatest number of epitopes per sequence length.
Example 14
Polyepitotpic Vaccine Compositions Directed to Multiple Diseases
The HBV peptide epitopes of the present invention are used in conjunction with peptide epitopes from target antigens related to one or more other diseases, to create a vaccine composition that is useful for the prevention or treatment of HBV as well as another disease. Examples of other diseases include, but are not limited to, HIV, HCV, and HPV.
For example, a polyepitopic peptide composition comprising multiple CTL and HTL epitopes that target greater than 98% of the population may be created for administration to individuals at risk for both HBV and HIV infection. The composition can be provided as a single polypeptide that incorporates the multiple epitopes from the various disease-associated sources.
Example 15
Use of Peptides to Evaluate an Immune Response
Peptides of the invention may be used to analyze an immune response for the presence of specific CTL populations corresponding to HBV. Such an analysis may be performed as described by Ogg et al., Science 279:2103-2106, 1998. In the following example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.
In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) may be used for a cross-sectional analysis of, for example, HBV Env-specific CTL frequencies from untreated HLA A*0201-positive indiviuals at different stages of infection using an HBV Env peptide containing an A2.1 extended motif. Tetrameric complexes are synethesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A2.1 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.
Approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 ul of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixaation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive uninfected donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the stage of infection with HBV or the status of exposure to HBV or to a vaccine that elicits a protective response.
Example 16
Use of Peptide Epitopes to Evaluate Recall Responses
The peptide epitopes of the invention are used as reagents to evaluate T cell responses such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from infection or who are chronically infected with HBV or who have been vaccinated with an HBV vaccine.
For example, the class I restricted CTL response of persons at risk for HBV infection who have been vaccinated may be analyzed. The vaccine may be any HBV vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide reagents that, are highly conserved and, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members are then used for analysis of samples derived from individuals who bear that HLA type.
PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. Synthetic peptide is added at 10 μg/ml to each well and recombinant HBc Ag is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.
In the microculture format, 4×105 PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 ml of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimualted with peptide, rIL-2 and 105 irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific 51Cr release, based on comparison with uninfected control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).
Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).
Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with synthetic peptide at 10 μM and labeled with 100 μCi of 51Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS. Cytolytic activity is determined in a standard 4-h, split well 51Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at E/T ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100 x [(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100® Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.
The results of such an analysis will indicate to what extent HLA-restricted CTL populations have been stimulated with the vaccine. Of course, this protocol can also be used to monitor prior HBV exposure.
The above examples are provided to illustrate the invention but not to limit its scope. For example, the human terminology for the Major Histocompatibility Complex, namely HLA, is used throughout this document. It is to be appreciated that these principles can be extended to other species as well. Moreover, peptide epitopes have been disclosed in the related application U.S. Ser. No. 08/820,360, which was previously incorporated by reference. Thus, other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, patents, and patent application cited herein are hereby incorporated by reference for all purposes.










TABLE I







POSITION
POSITION



POSITION
3 (Primary
C Terminus



2 (Primary Anchor)
Anchor)
(Primary Anchor)







SUPERMOTIF





A1
T,I,L,V,M,S

F,W,Y


A2
L,I,V,M,A,T,Q

I,V,M,A,T,L


A3
V,S,M,A,T,L,I

R,K


A24
Y,F,W,I,V,L,M,T

F,I,Y,W,L,M


B7
P

V,I,L,F,M,W,Y,A


B27
R,H,K

F,Y,L,W,M,I


B44
E,D

F,W,Y,L,I,M,V,A


B58
A,T,S

F,W,Y,L,I,V


B62
Q,L,I,V,M,P

F,W,Y,M,I,V


MOTIF





A1
T,S,M

Y


A1

D,E,A,S
Y


A2.1
L,M,V,O,I,A,T

V,L,I,M,A,T


A3
L,M,V,I,S,A,T,F,C,G,D

K,Y,R,H,F,A


A11
V,T,M,L,I,S,A,G,N,C,D,F

K,R,Y,H


A24
Y,F,W,M

F,L,I,W


A*3101
M,V,T,A,L,I,S

R,K


A*3301
M,V,A,L,F,I,S,T

R,K


A*6801
A,V,T,M,S,L,I

R,K


B*0702
P

L,M,F,W,Y,A,I,V


B*3501
P

L,M,F,W,Y,I,V,A


B51
P

L,I,V,F,W,Y,A,M


B*5301
P

I,M,F,W,Y,A,L,V


B*5401
P

A,T,I,V,L,M,F,W,Y





Bold residues are preferred, italicized residues are less preferred. A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.















TABLE II









POSITION


















SUPER-













MOTIFS
1
2
3
4
5
6
7
8
C-terminus





A1






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    T
    ,
    I
    ,
    L
    ,
    V
    ,
    M
    ,
    S
  













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    W
    ,
    Y
  






 


A2






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    I
    ,
    V
    ,
    M
    ,
    A
    ,
    T
    ,
    Q
  














  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    I
    ,
    V
    ,
    M
    ,
    A
    ,
    T
  






A3
preferred





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    V
    ,
    S
    ,
    M
    ,
    A
    ,
    T
    ,
    L
    ,
    I
  




Y,F,W (4/5)

Y,F,W (3/5)
Y,F,W (4/5)
P (4/5)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    R
    ,
    K
  






 



deleterious
D,E (3/5);

D,E (4/5)




P (5/5)


 


A24






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    Y
    ,
    F
    ,
    W
    ,
    I
    ,
    V
    ,
    L
    ,
    M
    ,
    T
  













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    I
    ,
    Y
    ,
    W
    ,
    L
    ,
    M
  






 


B7
preferred
F,W,Y (5/5) L,I,V,M (3/5)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




F,W,Y (4/5)



F,W,Y (3/5)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    V
    ,
    I
    ,
    L
    ,
    F
    ,
    M
    ,
    W
    ,
    Y
    ,
    A
  






 



deleterious
D,E (3/5);


D,E (3/5)
G (4/5)
Q,N (4/5)
D,E (4/5)




P (5/5);




G (4/5);




A (3/5);




Q,N (3/5)


B27






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    R
    ,
    H
    ,
    K
  













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    Y
    ,
    L
    ,
    W
    ,
    M
    ,
    I
  






 


B44






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    E
    ,
    D
  













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    W
    ,
    Y
    ,
    L
    ,
    I
    ,
    M
    ,
    V
    ,
    A
  






 


B58






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    A
    ,
    T
    ,
    S
  













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    W
    ,
    Y
    ,
    L
    ,
    I
    ,
    V
  






 


B62






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    Q
    ,
    L
    ,
    I
    ,
    V
    ,
    M
    ,
    P
  













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    W
    ,
    Y
    ,
    M
    ,
    I
    ,
    V
  






 


MOTIFS


A1 9-mer
preferred
G,F,Y,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    S
    ,
    T
    ,
    M
  




D,E,A
Y,F,W

P
D,E,Q,N
Y,F,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
D,E

R,H,K,L,I,V,M
A
H
A






P


 


A1 9-mer
preferred
G,R,H,K
A,S,T,C,L,I,V, M




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    D
    ,
    E
    ,
    A
    ,
    S
  




G,S,T,C

A,S,T,C
L,I,V,M
D,E




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
A
R,H,K,D,E,P,Y

D,E
P,Q,N
R,H,K
P,G
G,P





F,W












POSITION




























9












or


POSITION:
1
2
3
4
5
6
7
8
C-terminus
C-terminus





A1 9-mer
preferred
Y,F,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    S
    ,
    T
    ,
    M
  




D,E,A,Q,N
A
Y,F,W,Q,N

P,A,S,T,C
G,D,E
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
G,P

R,H,K,G,L,I,V
D,E
R,H,K
Q,N,A
R,H,K, Y,F,W
R,H,K
A






M


 


A1 10-mer
preferred
Y,F,W
S,T,C,L,I,V,M




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    D
    ,
    E
    ,
    A
    ,
    S
  




A
Y,F,W

P,G
G
Y,F,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
R,H,K
R,H,K,D,E,P,Y


P
G

P,R,H,K
Q,N





F,W


A2.1 9-mer
preferred
Y,F,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    M
    ,
    I
    ,
    V
    ,
    Q
    ,
    A
    ,
    T
  




Y,F,W
S,T,C
Y,F,W

A
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    V
    ,
    L
    ,
    I
    ,
    M
    ,
    A
    ,
    T
  






 



deleterious
D,E,P

D,E,R,K,H


R,K,H
D,E,R,K,H


 


A2.1 10-mer
preferred
A,Y,F,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    M
    ,
    I
    ,
    V
    ,
    Q
    ,
    A
    ,
    T
  




L,V,I,M
G

G

F,Y,W,L, V,I,M





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    V
    ,
    L
    ,
    I
    ,
    M
    ,
    A
    ,
    T
  






 



deleterious
D,E,P

D,E
R,K,H,A
P

R,K,H
D,E,R, K,L,H
R,K,H


 


A3
preferred
R,H,K




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    M
    ,
    V
    ,
    I
    ,
    S
    ,
    A
    ,
    T
    ,
    F
    ,
    C
    ,
    G
    ,
    D
  




Y,F,W
P,R,H,K,K, Y,F,W
A
Y,F,W

P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    K
    ,
    Y
    ,
    R
    ,
    H
    ,
    F
    ,
    A
  






 



deleterious
D,E,P

D,E


 


A11
preferred
A




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    V
    ,
    T
    ,
    L
    ,
    M
    ,
    I
    ,
    S
    ,
    A
    ,
    G
    ,
    N
    ,
    C
    ,
    D
    ,
    F
  




Y,F,W
Y,F,W
A
Y,F,W
Y,F,W
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    K
    ,
    R
    ,
    Y
    ,
    H
  






 



deleterious
D,E,P





A
G


 


A24 9-mer
preferred
Y,F,W,R,H,K




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    Y
    ,
    F
    ,
    W
    ,
    M
  





S,T,C


Y,F,W
Y,F,W




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    L
    ,
    I
    ,
    W
  






 



deleterious
D,E,G

D,E
G
Q,N,P
D,E,R,H
G
A,Q,N









K


 


A24 10-mer
preferred





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    Y
    ,
    F
    ,
    W
    ,
    M
  





P
YFWP

P






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    F
    ,
    L
    ,
    I
    ,
    W
  






 



deleterious


G,D,E
Q,N
R,H,K
D,E
A
Q,N
D,E,A


 


A3101
preferred
R,H,K




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    M
    ,
    V
    ,
    T
    ,
    A
    ,
    L
    ,
    I
    ,
    S
  




Y,F,W
P

Y,F,W
Y,F,W
A,P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    R
    ,
    K
  






 



deleterious
D,E,P

D,E

A,D,E
D,E
D,E
D,E


 


A3301
preferred





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    M
    ,
    V
    ,
    A
    ,
    L
    ,
    F
    ,
    I
    ,
    S
    ,
    T
  




Y,F,W



A,Y,F,W





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    R
    ,
    K
  






 



deleterious
G,P

D,E


A6801
preferred
Y,F,W,S,T,C




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    A
    ,
    V
    ,
    T
    ,
    M
    ,
    S
    ,
    L
    ,
    I
  






Y,F,W,L,I,V, M

Y,F,W
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    R
    ,
    K
  






 



deleterious
G,P

D,E,G

R,H,K


A


B0702
preferred
R,H,K,F,W, Y




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




R,H,K

R,H,K
R,H,K
R,H,K
P,A




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    M
    ,
    F
    ,
    W
    ,
    Y
    ,
    A
    ,
    I
    ,
    V
  






 



deleterious
D,E,Q,N,P

D,E,P
D,E
D,E
G,D,E
Q,N
D,E


 


B3501
preferred
F,W,Y,L,I,V, M




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P







F,W,Y





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    M
    ,
    F
    ,
    W
    ,
    Y
    ,
    I
    ,
    V
    ,
    A
  






 



deleterious
A,G,P



G
G


 


B51
preferred
L,I,V,M,F,W, Y




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




F,W,Y
S,T,C
F,W,Y

G
F,W,Y




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    L
    ,
    I
    ,
    V
    ,
    F
    ,
    W
    ,
    Y
    ,
    A
    ,
    M
  






 



deleterious
A,G,P,D,E,R, H,K,S,T,C



D,E
G
D,E,Q,N
G,D,E


 


B5301
preferred
L,I,V,M,F,W, Y




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




F,W,Y
S,T,C
F,W,Y

L,I,V,M, F,W,Y
F,W,Y




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    I
    ,
    M
    ,
    F
    ,
    W
    ,
    Y
    ,
    A
    ,
    L
    ,
    V
  






 



deleterious
A,G,P,Q,N




G
R,H,K,Q,N
D,E


 


B5401
preferred
F,W,Y




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




F,W,Y,L, I,V,M

L,I,V,M

A,L,I,V,M
F,W,Y,A,P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  
    A
    ,
    T
    ,
    I
    ,
    V
    ,
    L
    ,
    M
    ,
    F
    ,
    W
    ,
    Y
  






 



deleterious
G,P,Q,N,D,E

G,D,E,S, T,C

R,H,K,D,E
D,E
Q,N,D,G,E
D,E





Italicized residues indicate less preferred or “tolerated” residues.


The information in this Table II specific for 9-mers unless otherwise specified.















TABLE III









POSITION
















MOTIFS
























































DR4
preferred
F,M,Y,L,I,V,W
M
T

I
V,S,T,C,P,
M,H

M,H









A,L,I,M



deleterious



W


R

W,D,E


DR1
preferred
M,F,L,I,V,W,Y


P,A,M,Q

V,M,A,T,
M

A,V,M



deleterious

C
C,H
F,D
C,W,D
S,P,L,I,C
G,D,E
D


DR7
preferred
M,F,L,I,V,W,Y
M
W
A

I,V,M,S,A,
M

I,V









C,T,P,L



deleterious

C

G


G,R,D
N
G


DR
Supermotif
M,F,L,I,V,W,Y




V,M,S,T,A,









C,P,L,I


















DR3 MOTIFS































motif a
L,I,V,M,F,Y


D





preferred



motif b
L,I,V,M,F,A,Y


D,N,Q,E,S,T
K,R,H



preferred







Italicized residues indicate less preferred or “tolerated” residues.














TABLE IV







HLA Class I Standard Peptide Binding Affinity.
















STANDARD







BINDING
SEQ



STANDARD

AFFINITY
ID


ALLELE
PEPTIDE
SEQUENCE
(nM)
NO:















A*0101
944.02
YLEPAIAKY
25
2486



 


A*0201
941.01
FLPSDYFPSV
5.0
2487


 


A*0202
941.01
FLPSDYFPSV
4.3
2487


 


A*0203
941.01
FLPSDYFPSV
10
2487


 


A*0206
941.01
FLPSDYFPSV
3.7
2487


 


A*0207
941.01
FLPSDYFPSV
23
2487


 


A*6802
1141.02
FTQAGYPAL
40
2488


 


A*0301
941.12
KVFPYALINK
11
2489


 


A*1101
940.06
AVDLYHFLK
6.0
2490


 


A*3101
941.12
KVFPYALINK
18
2489


 


A*3301
1083.02
STLPETYVVRR
29
2491


 


A*6801
941.12
KVFPYALINK
8.0
2489


 


A*2401
979.02
AYIDNYNKF
12
2492


 


B*0702
1075.23
APRTLVYLL
5.5
2493


 


B*3501
1021.05
FPFKYAAAF
7.2
2494


 


B51
1021.05
FPFKYAAAF
5.5
2494


 


B*5301
1021.05
FPFKYAAAF
9.3
2494


 


B*5401
1021.05
FPFKYAAAF
10
2494
















TABLE V







HLA Class II Standard Peptide Binding Affinity.


 
















Binding




Nomen-
Standard

Affinity



Allele
clature
Peptide
Sequence
(nM)
SEQ ID NO:















DRB1*0101
DR1
515.01
PKYVKQNTLKLAT
5.0
2495


 


DRB1*0301
DR3
829.02
YKTIAFDEEARR
300
2496


 


DRB1*0401
DR4w4
515.01
PKYVKQNTLKLAT
45
2495


 


DRB1*0404
DR4w14
717.01
YARFQSQTTLKQKT
50
2497


 


DRB1*0405
DR4w15
717.01
YARFQSQTTLKQKT
38
2497


 


DRB1*0701
DR7
553.01
QYIKANSKFIGITE
25
2498


 


DRB1*0802
DR8w2
553.01
QYIKANSKFIGITE
49
2498


 


DRB1*0803
DR8w3
553.01
QYIKANSKFIGITE
1600
2498


 


DRB1*0901
DR9
553.01
QYIKANSKFIGITE
75
2498


 


DRB1*1101
DR5w11
553.01
QYIKANSKFIGITE
20
2498


 


DRB1*1201
DR5w12
1200.05
EALIHQLKINPYVLS
298
2499


 


DRB1*1302
DR6w19
650.22
QYIKANAKFIGITE
3.5
2500


 


DRB1*1501
DR2w2β1
507.02
GRTQDENPVVHFFK
9.1
2501


 





NIVTPRTPPP


 


DRB3*0101
DR52a
511
NGQIGNDPNRDIL
470
2502


 


DRB4*0101
DRw53
717.01
YARFQSQTTLKQKT
58
2503


 


DRB5*0101
DR2w2β2
553.01
QYIKANSKFIGITE
20
2504





The “Nomenclature” column lists the allelic designations used in Table XVIII.













TABLE VI







HBV A01 SUPER MOTIF (With binding information)


 
















Conservancy
Freq.
Protein
Position
Sequence
String
Peptide
Filed
A*0101
SEQ ID NO:



















95
19
POL
521
AICSVVRRAF
XIXXXXXXXF



1


 


95
19
NUC
54
ALRQAILCW
XLXXXXXXW



2


 


80
16
ENV
108
AMQWNSTTF
XMXXXXXXF



3


 


100
20
POL
166
ASFCGSPY
XSXXXXXY
26.0026
*

4


 


100
20
POL
166
ASFCGSPYSW
XSXXXXXXXW



5


 


90
18
NUC
19
ASKLCLGW
XSXXXXXW



6


 


85
17
NUC
19
ASKLCLGWLW
XSXXXXXXXW



7


 


80
16
POL
822
ASPLHVAW
XSXXXXXW



8


 


100
20
ENV
312
CIPIPSSW
XIXXXXXW



9


 


100
20
ENV
312
CIPIPSSWAF
XIXXXXXXXF



10


 


95
19
ENV
253
CLIFLLVLLDY
XLXXXXXXXXY
26.0548


11


 


95
19
ENV
239
CLRRFIIF
XLXXXXXF



12


 


75
15
ENV
239
CLRRFIIFLF
XLXXXXXXXF



13


 


95
19
POL
523
CSVVRRAF
XSXXXXXF



14


 


100
20
ENV
310
CTCIPIPSSW
XTXXXXXXXW



15


 


90
18
NUC
31
DIDPYKEF
XIXXXXXF



16


 


85
17
NUC
29
DLLDTASALY
XLXXXXXXXY
1.0519
*
11.1000
17


 


95
19
ENV
196
DSWWTSLNF
XSXXXXXXF
20.0120


18


 


95
19
NUC
43
ELLSFLPSDF
XLXXXXXXXF



19


 


95
19
NUC
43
ELLSFLPSDFF
XLXXXXXXXXF



20


 


95
19
POL
374
ESRLVVDF
XSXXXXXF



21


 


95
19
POL
374
ESRLVVDFSQF
XSXXXXXXXXF



22


 


80
16
ENV
248
FILLLCLIF
XIXXXXXXF



23


 


80
16
ENV
246
FLFILLLCLIF
XLXXXXXXXXF



24


 


95
19
ENV
256
FLLVLLDY
XLXXXXXY
26.0027


25


 


95
19
POL
658
FSPTYKAF
XSXXXXXF



26


 


90
18
X
63
FSSAGPCALRF
XSXXXXXXXXF



27


 


100
20
ENV
333
FSWLSLLVPF
XSXXXXXXXF
20.0263


28


 


95
19
POL
656
FTFSPTYKAF
XTXXXXXXXF
20.0262


29


 


95
19
ENV
346
FVGLSPTVW
XVXXXXXXW



30


 


95
19
POL
627
GLLGFAAPF
XLXXXXXXF
20.0124


31


 


95
19
POL
509
GLSPFLLAQF
XLXXXXXXXF



32


 


85
17
NUC
29
GMDIDPYKEF
XMXXXXXXXF
26.0372


33


 


95
19
NUC
123
GVWIRTPPAY
XVXXXXXXXY
1.0525

0.0017
34


 


75
15
POL
569
HLNPNKTKRW
XLXXXXXXXW



35


 


80
16
POL
491
HLYSHPIILGF
XLXXXXXXXXF



36


 


85
17
POL
715
HTAELLAACF
XTXXXXXXXF



37


 


95
19
NUC
52
HTALRQAILCW
XTXXXXXXXXW



38


 


100
20
POL
149
HTLWKAGILY
XTXXXXXXXY
1.0542
*
0.0300
39


 


100
20
ENV
249
ILLLCLIF
XLXXXXXF



40


 


80
16
POL
760
ILRGTSFVY
XLXXXXXXY
1.0205
*
0.0017
41


 


90
18
ENV
188
ILTIPQSLDSW
XLXXXXXXXXW



42


 


90
18
POL
625
IVGLLGFAAPF
XVXXXXXXXXF



43


 


80
16
POL
503
KIPMGVGLSPF
XIXXXXXXXXF



44


 


85
17
NUC
21
KLCLGWLW
XLXXXXXW



45


 


75
15
POL
108
KLIMPARF
XLXXXXXF



46


 


75
15
POL
108
KLIMPARFY
XLXXXXXXY
1.0171

0.0017
47


 


80
16
POL
610
KLPVNRPIDW
XLXXXXXXXW



48


 


85
17
POL
574
KTKRWGYSLNF
XTXXXXXXXXF



49


 


95
19
POL
55
KVGNFTGLY
XVXXXXXXY
1.0166
*
0.0680
50


 


95
19
ENV
254
LIFLLVLLDY
XIXXXXXXXY
1.0899
*
0.0084
51


 


100
20
POL
109
LIMPARFY
XIXXXXXY
26.0028


52


 


85
17
NUC
30
LLDTASALY
XLXXXXXXY
1.0155
*
25.0000
53


 


80
16
POL
752
LLGCAANW
XLXXXXXW



54


 


95
19
POL
628
LLGFAAPF
XLXXXXXF



55


 


100
20
ENV
378
LLPIFFCLW
XLXXXXXXW



56


 


100
20
ENV
378
LLPIFFCLWVY
XLXXXXXXXXY
26.0549
*

57


 


95
19
NUC
44
LLSFLPSDF
XLXXXXXXF



58


 


95
19
NUC
44
LLSFLPSDFF
XLXXXXXXXF



59


 


90
18
POL
407
LLSSNLSW
XLXXXXXW



60


 


95
19
ENV
175
LLVLQAGF
XLXXXXXF



61


 


95
19
ENV
175
LLVLQAGFF
XLXXXXXXF
20.0121


62


 


100
20
ENV
338
LLVPFVQW
XLXXXXXW



63


 


100
20
ENV
338
LLVPFVQWF
XLXXXXXXF



64


 


85
17
NUC
100
LLWFHISCLTF
XLXXXXXXXXF



65


 


95
19
NUC
45
LSFLPSDF
XSXXXXXF



66


 


95
19
NUC
45
LSFLPSDFF
XSXXXXXXF
20.0123


67


 


95
19
POL
415
LSLDVSAAF
XSXXXXXXF



68


 


95
19
POL
415
LSLDVSAAFY
XSXXXXXXXY
2.0239
*
4.2000
69


 


100
20
ENV
336
LSLLVPFVQW
XSXXXXXXXW



70


 


100
20
ENV
336
LSLLVPFVQWF
XSXXXXXXXXF



71


 


95
19
X
53
LSLRGLPVCAF
XSXXXXXXXXF



72


 


95
19
POL
510
LSPFLLAQF
XSXXXXXXF



73


 


75
15
ENV
349
LSPTVWLSVIW
XSXXXXXXXXW



74


 


85
17
POL
742
LSRKYTSF
XSXXXXXF



75


 


85
17
POL
742
LSRKYTSFPW
XSXXXXXXXW



76


 


75
15
ENV
16
LSVPNPLGF
XSXXXXXXF



77


 


75
15
NUC
137
LTFGRETVLEY
XTXXXXXXXXY



78


 


90
18
ENV
189
LTIPQSLDSW
XTXXXXXXXW



79


 


90
18
ENV
189
LTIPQSLDSWW
XTXXXXXXXXW



80


 


90
18
POL
404
LTNLLSSNLSW
XTXXXXXXXXW



81


 


95
19
ENV
176
LVLQAGFF
XVXXXXXF



82


 


100
20
ENV
339
LVPFVQWF
XVXXXXXF



83


 


100
20
POL
377
LWDFSQF
XVXXXXXF



84


 


85
17
ENV
360
MMWYWGPSLY
XMXXXXXXXY
1039.01
*
0.0810
85


 


75
15
X
103
MSTTDLEAY
XSXXXXXXY
2.0126
*
0.8500
86


 


75
15
X
103
MSTTDLEAYF
XSXXXXXXXF



87


 


95
19
POL
42
NLGNLNVSIPW
XLXXXXXXXXW



88


 


90
18
POL
406
NLLSSNLSW
XLXXXXXXW



89


 


95
19
POL
45
NLNVSIPW
XLXXXXXW



90


 


75
15
ENV
15
NLSVPNPLGF
XLXXXXXXXF



91


 


90
18
POL
738
NSVVLSRKY
XSXXXXXXY
2.0123

0.0005
92


 


100
20
ENV
380
PIFFCLWVY
XIXXXXXXY
1.0843

0.0078
93


 


100
20
ENV
314
PIPSSWAF
XIXXXXXF



94


 


100
20
POL
124
PLDKGIKPY
XLXXXXXXY
1.0174
*
0.0190
95


 


100
20
POL
124
PLDKGIKPYY
XLXXXXXXXY
1.0541
*
0.1600
96


 


100
20
ENV
377
PLLPIFFCLW
XLXXXXXXXW



97


 


95
19
ENV
174
PLLVLQAGF
XLXXXXXXF



98


 


95
19
ENV
174
PLLVLQAGFF
XLXXXXXXXF



99


 


80
16
POL
505
PMGVGLSPF
XMXXXXXXF



100


 


85
17
POL
797
PTTGRTSLY
XTXXXXXXY
1.0208
*
0.7700
101


 


75
15
ENV
351
PTVWLSVIW
XTXXXXXXW



102


 


85
17
POL
612
PVNRPIDW
XVXXXXXW



103


 


95
19
POL
685
QVFADATPTG
XVXXXXXXXXW



104


 


90
18
POL
624
RIVGLLGF
XIXXXXXF



105


 


75
15
POL
106
RLKLIMPARF
XLXXXXXXXF



106


 


75
15
POL
106
RLKLIMPARFY
XLXXXXXXXXY



107


 


95
19
POL
376
RLVVDFSQF
XLXXXXXXF
20.0122


108


 


90
18
POL
353
RTPARVTGGVF
XTXXXXXXXXF



109


 


100
20
POL
49
SIPWTHKVGNF
XIXXXXXXXXF



110


 


95
19
ENV
194
SLDSWWTSLNF
XLXXXXXXXXF



111


 


95
19
POL
416
SLDVSAAF
XLXXXXXF



112


 


95
19
POL
416
SLDVSAAFY
XLXXXXXXY
1.0186
*
17.2000
113


 


100
20
ENV
337
SLLVPFVQW
XLXXXXXXW



114


 


100
20
ENV
337
SLLVPFVQWF
XLXXXXXXXF



115


 


95
19
X
54
SLRGLPVCAF
XLXXXXXXXF
20.0259


116


 


90
18
X
64
SSAGPCALRF
XSXXXXXXXF
26.0374


117


 


75
15
X
104
STTDLEAY
XTXXXXXY



118


 


75
15
X
104
STTDLEAYF
XTXXXXXXF



119


 


75
15
ENV
17
SVPNPLGF
XVXXXXXF



120


 


90
18
POL
739
SVVLSRKY
XVXXXXXY
26.0029


121


 


85
17
POL
739
SVVLSRKYTSF
XVXXXXXXXXF



122


 


90
18
ENV
190
TIPQSLDSW
XIXXXXXXW



123


 


90
18
ENV
190
TIPQSLDSWW
XIXXXXXXXW



124


 


100
20
POL
150
TLWKAGILY
XLXXXXXXY
1.0177
*
0.0017
125


 


75
15
X
105
TTDLEAYF
XTXXXXXF



126


 


85
17
POL
798
TTGRTSLY
XTXXXXXY
26.0030


127


 


80
16
NUC
16
TVQASKLCLGW
XVXXXXXXXXW



128


 


75
15
ENV
352
TVWLSVIW
XVXXXXXW



129


 


85
17
POL
741
VLSRKYTSF
XLXXXXXXF



130


 


85
17
POL
741
VLSRKYTSFPW
XLXXXXXXXXW



131


 


85
17
POL
740
VVLSRKYTSF
XVXXXXXXXF
20.0261


132


 


80
16
POL
759
WILRGTSF
XIXXXXXF



133


 


80
16
POL
759
WILRGTSFVY
XIXXXXXXXY
1.0572

0.0023
134


 


95
19
NUC
125
WIRTPPAY
XIXXXXXY
26.0031


135


 


80
16
POL
751
WLLGCAANW
XLXXXXXXW



136


 


95
19
POL
414
WLSLDVSAAF
XLXXXXXXXF



137


 


95
19
POL
414
WLSLDVSAAFY
XLXXXXXXXXY
26.0551


138


 


100
20
ENV
335
WLSLLVPF
XLXXXXXF



139


 


100
20
ENV
335
WLSLLVPFVQW
XLXXXXXXXXW



140


 


85
17
NUC
26
WLWGMDIDPY
XLXXXXXXXY
1.0774
*
0.0810
141


 


95
19
ENV
237
WMCLRRFIIF
XMXXXXXXXF
20.0266


142


 


85
17
ENV
359
WMMWYWGPS
XMXXXXXXXXY
26.0552
*

143


 


100
20
POL
52
WTHKVGNF
XTXXXXXF



144


 


100
20
POL
122
YLPLDKGIKPY
XLXXXXXXXXY
26.0553


145


 


90
18
NUC
118
YLVSFGVW
XLXXXXXW



146


 


80
16
POL
493
YSHPIILGF
XSXXXXXXF



147


 


85
17
POL
580
YSLNFMGY
XSXXXXXY
26.0032


148
















TABLE VII







HBV A02 SUPER MOTIF (With binding information)


 






















Conser-
Fre-




C-











vancy
quency
Protein
Position
Sequence
P2
term
Peptide
AA
Filed
A*0201
A*0202
A*0203
A*0206
A*6802
SEQ ID NO:

























85
17
POL
721
AACFARSRSGA
A
A

11






149


 


85
17
POL
431
AAMPHLLV
A
V

8






150


 


80
16
POL
756
AANWILRGT
A
T

9






151


 


95
19
POL
632
AAPFTQCGYPA
A
A

11






152


 


95
19
POL
521
AICSVVRRA
I
A
5.0025
9

0.0001




153


 


90
18
NUC
58
AILCWGEL
I
L

8






154


 


90
18
NUC
58
AILCWGELM
I
M

9






155


 


95
19
POL
642
ALMPLYACI
L
I
927.15
9
*
0.5000
0.0340
3.3000
0.2500
0.0470
156


 


80
16
ENV
108
AMQWNSTT
M
T

8






157


 


75
15
X
102
AMSTTDLEA
M
A
3.0051
9

0.0013




158


 


95
19
POL
690
ATPTGWGL
T
L

8






159


 


80
16
POL
690
ATPTGWGLA
T
A

9






160


 


75
15
POL
690
ATPTGWGLAI
T
I

10






161


 


95
19
POL
397
AVPNLQSL
V
L

8






162


 


95
19
POL
397
AVPNLQSLT
V
T
5.0026
9

0.0001




163


 


95
19
POL
397
AVPNLQSLTNL
V
L

11






164


 


80
16
POL
755
CAANWILRGT
A
T

10






165


 


95
19
X
61
CAFSSAGPCA
A
A
5.0090
10

0.0001




166


 


95
19
X
61
CAFSSAGPCAL
A
L

11






167


 


90
18
X
69
CALRFTSA
A
A

8






168


 


100
20
ENV
312
CIPIPSSWA
I
A
5.0007
9

0.0010




169


 


80
16
ENV
312
CIPIPSSWAFA
I
A

11






170


 


90
18
POL
533
CLAFSYMDDV
L
V
1.0559
10

0.0008




171


 


90
18
POL
533
CLAFSYMDDW
L
V

11






172


 


85
17
NUC
23
CLGWLWGM
L
M

8






173


 


85
17
NUC
23
CLGWLWGMDI
L
I
3.0210
10

0.0093




174


 


100
20
ENV
253
CLIFLLVL
L
L
Chisari
8

0.0002




175









4.011



 


100
20
ENV
253
CLIFLLVLL
L
L
1.0836
9

0.0006




176


 


95
19
ENV
239
CLRRFIIFL
L
L
1.0829
9

0.0002




177


 


75
15
ENV
239
CLRRFIIFLFI
L
I
Chisari
11

0.0004




178









4.055



 


90
18
NUC
107
CLTFGRET
L
T

8






179


 


90
18
NUC
107
CLTFGRETV
L
V
1.0160
9

0.0001




180


 


100
20
ENV
310
CTCIPIPSSWA
T
A

11






181


 


95
19
POL
689
DATPTGWGL
A
L
5.0027
9

0.0001




182


 


80
16
POL
689
DATPTGWGLA
A
A

10






183


 


75
15
POL
689
DATPTGWGLAI
A
I

11






184


 


90
18
NUC
31
DIDPYKEFGA
I
A

10






185


 


85
17
NUC
29
DLLDTASA
L
A

8






186


 


85
17
NUC
29
DLLDTASAL
L
L
1.0154
9

0.0001




187


 


95
19
POL
40
DLNLGNLNV
L
V
927.30
9

0.0004




188


 


95
19
POL
40
DLNLGNLNVSI
L
I

11






189


 


80
16
NUC
32
DTASALYREA
T
A

10






190


 


80
16
NUC
32
DTASALYREAL
T
L

11






191


 


95
19
X
14
DVLCLRPV
V
V

8






192


 


95
19
X
14
DVLCLRPVGA
V
A
5.0091
10

0.0001




193


 


90
18
POL
541
DVVLGAKSV
V
V
1.0190
9

0.0003




194


 


100
20
POL
17
EAGPLEEEL
A
L
5.0028
9

0.0001




195


 


80
16
X
122
ELGEEFL
L
L

8






196


 


90
18
POL
718
ELLAACFA
L
A

8






197


 


75
15
NUC
142
ETVLEYLV
T
V

8






198


 


95
19
POL
687
FADATPTGWGL
A
L

11






199


 


85
17
POL
724
FARSRSGA
A
A

8






200


 


80
16
POL
821
FASPLHVA
A
A

8






201


 


95
19
POL
396
FAVPNLQSL
A
L

9






202


 


95
19
POL
396
FAVPNLQSLT
A
T
5.0083
10

0.0003




203


 


80
16
ENV
243
FIIFLFIL
I
L
Chisari
8

0.0006




204









4.047



 


80
16
ENV
243
FIIFLFILL
I
L
1.0830
9

0.0002




205


 


80
16
ENV
243
FIIFLFILLL
I
L
1.0894
10

0.0012




206


 


80
16
ENV
248
FILLLCLI
I
I
Chisari
8

0.0003




207









4.048



 


80
16
ENV
248
FILLLCLIFL
I
L
1.0895
10
*
0.0280




208


 


80
16
ENV
248
FILLLCLIFLL
I
L
Chisari
11

0.0010




209









4.049



 


80
16
ENV
246
FLFILLLCL
L
L
1.0832
9

0.0002




210


 


80
16
ENV
246
FLFILLLCLI
L
I
3.0206
10

0.0013




211


 


75
15
ENV
171
FLGPLLVL
L
L

8






212


 


75
15
ENV
171
FLGPLLVLQA
L
A
3.0205
10
*
0.0190




213


 


95
19
POL
513
FLLAQFTSA
L
A
1069.07
9
*
0.2400




214


 


95
19
POL
513
FLLAQFTSAI
L
I
1147.13
10
*
0.2100
0.0320
7.0000
0.1100
0.0880
215


 


95
19
POL
562
FLLSLGIHL
L
L
927.11
9
*
0.6500
0.0010
0.0100
0.1100
0.0035
216


 


80
16
ENV
183
FLLTRILT
L
T

8






217


 


80
16
ENV
183
FLLTRILTI
L
I
777.03
9
*
0.5100
0.0430
8.0000
0.2000
0.0010
218


 


95
19
ENV
256
FLLVLLDYQGM
L
M

11






219


 


100
20
POL
363
FLVDKNPHNT
L
T
5.0084
10

0.0012




220


 


95
19
POL
656
FTFSPTYKA
T
A
1147.15
9
*
0.0056
0.0150
0.0031
0.8000
7.3000
221


 


95
19
POL
656
FTFSPTYKAFL
T
L

11






222


 


95
19
POL
59
FTGLYSST
T
T

8






223


 


90
18
POL
59
FTGLYSSTV
T
V
20.0118
9

0.0005




224


 


95
19
POL
635
FTQCGYPA
T
A

8






225


 


95
19
POL
635
FTQCGYPAL
T
L
5.0031
9

0.0009




226


 


95
19
POL
635
FTQCGYPALM
T
M
5.0085
10

0.0024




227


 


95
19
POL
518
FTSAICSV
T
V

8






228


 


95
19
POL
518
FTSAICSVV
T
V
5.0032
9

0.0090




229


 


95
19
ENV
346
FVGLSPTV
V
V

8






230


 


95
19
ENV
346
FVGLSPTVWL
V
L
1.0931
10

0.0008




231


 


90
18
X
132
FVLGGCRHKL
V
L
Chisari
10

0.0030




232









4.114



 


90
18
X
132
FVLGGCRHKLV
V
V

11






233


 


95
19
ENV
342
FVQWFVGL
V
L

8






234


 


95
19
ENV
342
FVQWFVGLSPT
V
T

11






235


 


90
18
POL
766
FVYVPSAL
V
L

8






236


 


90
18
POL
766
FVYVPSALNPA
V
A

11






237


 


95
19
X
50
GAHLSLRGL
A
L
5.0040
9

0.0001




238


 


90
18
X
50
GAHLSLRGLPV
A
V

11






239


 


85
17
POL
545
GAKSVQHL
A
L

8






240


 


85
17
POL
545
GAKSVQHLESL
A
L

11






241


 


75
15
POL
567
GIHLNPNKT
I
T

9






242


 


90
18
POL
155
GILYKRET
I
T

8






243


 


90
18
POL
155
GILYKRETT
I
T

9






244


 


85
17
POL
682
GLCQVFADA
L
A
1142.04
9
*
0.0024




245


 


85
17
POL
682
GLCQVFADAT
L
T

10






246


 


95
19
POL
627
GLLGFAAPFT
L
T
5.0086
10

0.0049




247


 


85
17
ENV
62
GLLGWSPQA
L
A
1142.07
9
*
0.4000
0.0003
0.0350
0.2800
0.0005
248


 


95
19
X
57
GLPVCAFSSA
L
A
5.0092
10

0.0008




249


 


95
19
POL
509
GLSPFLLA
L
A

8






250


 


95
19
POL
509
GLSPFLLAQFT
L
T

11






251


 


100
20
ENV
348
GLSPTVWL
L
L
Chisari
8

0.0036




252









4.012



 


75
15
ENV
348
GLSPTVWLSV
L
V
1.0518
10
*
0.2800




253


 


75
15
ENV
348
GLSPTVWLSVI
L
I
Chisari
11

0.0036




254









4.031



 


90
18
ENV
265
GMLPVCPL
M
L

8






255


 


90
18
POL
735
GTDNSVVL
T
L

8






256


 


75
15
ENV
13
GTNLSVPNPL
T
L

10






257


 


80
16
POL
763
GTSFVYVPSA
T
A

10






258


 


80
16
POL
763
GTSFVYVPSAL
T
L

11






259


 


80
16
POL
507
GVGLSPFL
V
L

8






260


 


80
16
POL
507
GVGLSPFLL
V
L
Chisari
9

0.0002




261









4.082



 


80
16
POL
507
GVGLSPFLLA
V
A

10






262


 


95
19
NUC
123
GVWIRTPPA
V
A
3.0040
9

0.0030




263


 


90
18
NUC
104
HISCLTFGRET
I
T

11






264


 


80
16
POL
435
HLLVGSSGL
L
L
927.43
9

0.0031




265


 


90
18
X
52
HLSLRGLPV
L
V
927.02
9

0.0014




266


 


90
18
X
52
HLSLRGLPVCA
L
A

11






267


 


80
16
POL
491
HLYSHPII
L
I
17.0256
8






268


 


80
16
POL
491
HLYSHPIIL
L
L
927.47
9
*
0.2200
0.0003
0.9300
0.1700
0.0530
269


 


85
17
POL
715
HTAELLAA
T
A

8






270


 


85
17
POL
715
HTAELLAACFA
T
A

11






271


 


100
20
NUC
52
HTALRQAI
T
I

8






272


 


95
19
NUC
52
HTALRQAIL
T
L
5.0021
9

0.0001




273


 


100
20
POL
149
HTLWKAGI
T
I

8






274


 


100
20
POL
149
HTLWKAGIL
T
L
5.0033
9

0.0001




275


 


80
16
ENV
244
IIFLFILL
I
L
Chisari
8

0.0004




276









4.051



 


80
16
ENV
244
IIFLFILLL
I
L
1.0831
9

0.0002




277


 


80
16
ENV
244
IIFLFILLLCL
I
L
Chisari
11

0.0002




278









4.052



 


80
16
POL
497
IILGFRKI
I
I

8






279


 


80
16
POL
497
IILGFRKIPM
I
M

10






280


 


90
18
NUC
59
ILCWGELM
L
M

8






281


 


80
16
POL
498
ILGFRKIPM
L
M
3.0016
9

0.0002




282


 


100
20
ENV
249
ILLLCLIFL
L
L
1137.04
9
*
0.0015




283


 


100
20
ENV
249
ILLLCLIFLL
L
L
1069.08
10
*
0.0190
0.0001
0.0002
0.1300
0.0015
284


 


100
20
ENV
249
ILLLCLIFLLV
L
V
Chisari
11

0.0056




285









4.013



 


80
16
POL
760
ILRGTSFV
L
V

8






286


 


80
16
POL
760
ILRGTSFVYV
L
V
1.0573
10
*
0.0160




287


 


100
20
NUC
139
ILSTLPET
L
T

8






288


 


100
20
NUC
139
ILSTLPETT
L
T
5.0022
9

0.0001




289


 


100
20
NUC
139
ILSTLPETTV
L
V
1069.14
10
*
0.0210
0.0085
0.0770
0.3100
0.0067
290


 


100
20
NUC
139
ILSTLPETTVV
L
V

11






291


 


95
19
ENV
188
ILTIPQSL
L
L

8






292


 


90
18
POL
156
ILYKRETT
L
T

8






293


 


90
18
POL
625
IVGLLGFA
V
A

8






294


 


90
18
POL
625
IVGLLGFAA
V
A
3.0041
9

0.0009




295


 


90
18
POL
153
KAGILYKRET
A
T

10






296


 


90
18
POL
153
KAGILYKRETT
A
T

11






297


 


80
16
POL
503
KIPMGVGL
I
L

8






298


 


85
17
NUC
21
KLCLGWLWGM
L
M
1142.02
10
*
0.0001




299


 


95
19
POL
489
KLHLYSHPI
L
I
927.46
9
*
0.0690
0.0340
2.7000
0.5900
0.0015
300


 


80
16
POL
489
KLHLYSHPII
L
I

10






301


 


80
16
POL
489
KLHLYSHPIIL
L
L

11






302


 


80
16
POL
610
KLPVNRPI
L
I

8






303


 


95
19
POL
574
KTKRWGYSL
T
L
5.0034
9

0.0001




304


 


85
17
POL
620
KVCQRIVGL
V
L
1.0198
9

0.0003




305


 


85
17
POL
620
KVCQRIVGLL
V
L
1.0567
10

0.0001




306


 


95
19
POL
55
KVGNFTGL
V
L
17.0116
8






307


 


85
17
X
91
KVLHKRTL
V
L

8






308


 


85
17
X
91
KVLHKRTLGL
V
L
Chisari
10

0.0004




309









4.115



 


90
18
POL
534
LAFSYMDDV
A
V
20.0119
9

0.0002




310


 


90
18
POL
534
LAFSYMDDVV
A
V
20.0257
10

0.0003




311


 


90
18
POL
534
LAFSYMDDVVL
A
L

11






312


 


95
19
POL
515
LAQFTSAI
A
I

8






313


 


95
19
POL
515
LAQFTSAICSV
A
V

11






314


 


100
20
ENV
254
LIFLLVLL
I
L
Chisari
8

0.0025




315









4.014



 


95
19
POL
514
LLAQFTSA
L
A

8






316


 


95
19
POL
514
LLAQFTSAI
L
I
1069.05
9
*
0.1000
0.2700
3.7000
0.2600
0.7900
317


 


100
20
ENV
251
LLCLIFLL
L
L
Chisari
8

0.0004




318









4.015



 


100
20
ENV
251
LLCLIFLLV
L
V
1137.03
9
*
0.0048




319


 


100
20
ENV
251
LLCLIFLLVL
L
L
1.0898
10

0.0075




320


 


100
20
ENV
251
LLCLIFLLVLL
L
L
Chisari
11

0.0013




321









4.016



 


85
17
NUC
30
LLDTASAL
L
L

8






322


 


95
19
ENV
260
LLDYQGML
L
L
Chisari
8

0.0004




323









4.021



 


90
18
ENV
260
LLDYQGMLPV
L
V
1137.02
10
*
0.0980
0.0001
0.0200
0.6700
0.0009
324


 


80
16
POL
752
LLGCAANWI
L
I
927.22
9

0.0011




325


 


80
16
POL
752
LLGCAANWIL
L
L
1.0912
10
*
0.0140




326


 


95
19
POL
628
LLGFAAPFT
L
T
5.0035
9

0.0008




327


 


85
17
ENV
63
LLGWSPQA
L
A

8






328


 


75
15
ENV
63
LLGWSPQAQGI
L
I

11






329


 


100
20
ENV
250
LLLCLIFL
L
L
Chisari
8

0.0006




330









4.017



 


100
20
ENV
250
LLLCLIFLL
L
L
1090.05
9
*
0.0065




331


 


100
20
ENV
250
LLLCLIFLLV
L
V
1137.01
10
*
0.0036




332


 


100
20
ENV
250
LLLCLIFLLVL
L
L
ChisaRi
11

0.0005




333









4.018



 


100
20
ENV
378
LLPIFFCL
L
L
Chisari
8

0.0055




334









4.019



 


100
20
ENV
378
LLPIFFCLWV
L
V
1069.10
10
*
0.0320
0.0008
0.0150
0.8000
0.0005
335


 


95
19
POL
563
LLSLGIHL
L
L

8






336


 


90
18
POL
407
LLSSNLSWL
L
L
927.41
9
*
0.0110
0.0780
3.9000
0.2700
0.0100
337


 


90
18
POL
407
LLSSNLSWLSL
L
L

11






338


 


80
16
ENV
184
LLTRILTI
L
I
Chisari
8

0.0026




339









4.053



 


80
16
POL
436
LLVGSSGL
L
L

8






340


 


95
19
ENV
257
LLVLLDYQGM
L
M
3.0207
10

0.0050




341


 


95
19
ENV
257
LLVLLDYQGML
L
L

11






342


 


90
18
ENV
175
LLVLQAGFFL
L
L
1090.06
10
*
0.0310
0.0037
0.0045
0.1500
0.0110
343


 


90
18
ENV
175
LLVLQAGFFLL
L
L
Chisari
11

0.0074




344









4.028



 


95
19
ENV
338
LLVPFVQWFV
L
V
1069.06
10
*
0.6700
0.3800
1.7000
0.2900
0.1400
345


 


90
18
NUC
100
LLWFHISCL
L
L
1142.01
9
*
0.0130
0.0002
0.0420
0.3100
0.0098
346


 


85
17
NUC
100
LLWFHISCLT
L
T

10






347


 


95
19
POL
643
LMPLYACI
M
I
17.0130
8






348


 


95
19
NUC
108
LTFGRETV
T
V

8






349


 


75
15
NUC
137
LTFGRETVL
T
L

9






350


 


90
18
POL
404
LTNLLSSNL
T
L

9






351


 


80
16
ENV
185
LTRILTIPQSL
T
L

11






352


 


85
17
POL
99
LTVNEKRRL
T
L

9






353


 


100
20
POL
364
LVDKNPHNT
V
T
5.0036
9

0.0001




354


 


95
19
ENV
258
LVLLDYQGM
V
M
3.0034
9

0.0001




355


 


95
19
ENV
258
LVLLDYQGML
V
L
1.0515
10

0.0001




356


 


90
18
ENV
176
LVLQAGFFL
V
L
1.0827
9

0.0096




357


 


90
18
ENV
176
LVLQAGFFLL
V
L
1132.17
10
*
0.0022




358


 


90
18
ENV
176
LVLQAGFFLLT
V
T

11






359


 


95
19
ENV
339
LVPFVQWFV
V
V
1132.01
9
*
0.0420
0.0150
0.0048
0.7900
2.8000
360


 


95
19
ENV
339
LVPFVQWFVGL
V
L

11






361


 


90
18
NUC
119
LVSFGVWI
V
I
Chisari
8

0.0004




362









4.078



 


90
18
NUC
119
LVSFGVWIRT
V
T

10






363


 


85
17
ENV
360
MMWYWGPSL
M
L
1039.03
9
*
0.6400




364


 


100
20
NUC
136
NAPILSTL
A
L

8






365


 


100
20
NUC
136
NAPILSTLPET
A
T

11






366


 


95
19
POL
42
NLGNLNVSI
L
I
3.0008
9

0.0047




367


 


90
18
POL
406
NLLSSNLSWL
L
L
1.0549
10

0.0016




368


 


95
19
POL
45
NLNVSIPWT
L
T
5.0037
9

0.0005




369


 


100
20
POL
400
NLQSLTNL
L
L

8






370


 


100
20
POL
400
NLQSLTNLL
L
L
927.40
9

0.0047




371


 


75
15
ENV
15
NLSVPNPL
L
L

8






372


 


90
18
POL
411
NLSWLSLDV
L
V
927.42
9
*
0.0650
0.0051
0.6400
0.1600
0.0990
373


 


90
18
POL
411
NLSWLSLDVSA
L
A

11






374


 


100
20
POL
47
NVSIPWTHKV
V
V
1.0532
10

0.0001




375


 


100
20
POL
430
PAAMPHLL
A
L

8






376


 


85
17
POL
430
PAAMPHLLV
A
V

9






377


 


90
18
POL
775
PADDPSRGRL
A
L

10






378


 


90
18
ENV
131
PAGGSSSGT
A
T

9






379


 


90
18
ENV
131
PAGGSSSGTV
A
V

10






380


 


95
19
POL
641
PALMPLYA
A
A

8






381


 


95
19
POL
641
PALMPLYACI
A
I
5.0087
10

0.0001




382


 


75
15
X
145
PAPCNFFT
A
T

8






383


 


75
15
X
145
PAPCNFFTSA
A
A

10






384


 


80
16
X
11
PARDVLCL
A
L

8






385


 


75
15
X
11
PARDVLCLRPV
A
V

11






386


 


90
18
POL
355
PARVTGGV
A
V

8






387


 


90
18
POL
355
PARVTGGVFL
A
L

10






388


 


90
18
POL
355
PARVTGGVFLV
A
V

11






389


 


95
19
NUC
130
PAYRPPNA
A
A

8






390


 


95
19
NUC
130
PAYRPPNAPI
A
I
5.0081
10

0.0001




391


 


95
19
NUC
130
PAYRPPNAPIL
A
L

11






392


 


85
17
POL
616
PIDWKVCQRI
I
I
Chisari
10

0.0001




393









4.091



 


85
17
POL
616
PIDWKVCQRIV
I
V

11






394


 


100
20
ENV
380
PIFFCLWV
I
V

8






395


 


100
20
ENV
380
PIFFCLWVYI
I
I
Chisari
10

0.0004




396









3.074



 


85
17
POL
713
PIHTAELL
I
L

8






397


 


85
17
POL
713
PIHTAELLA
I
A

9






398


 


85
17
POL
713
PIHTAELLAA
I
A

10






399


 


80
16
POL
496
PIILGFRKI
I
I
927.48
9

0.0001




400


 


80
16
POL
496
PIILGFRKIPM
I
M

11






401


 


100
20
NUC
138
PILSTLPET
I
T
5.0023
9
0.0001




402


 


100
20
NUC
138
PILSTLPETT
I
T
5.0082
10

0.0001




403


 


100
20
NUC
138
PILSTLPETTV
I
V
Chisari
11

0.0001




404









5.125



 


80
16
ENV
314
PIPSSWAFA
I
A

9






405


 


95
19
POL
20
PLEEELPRL
L
L
927.29
9

0.0003




406


 


90
18
POL
20
PLEEELPRLA
L
A
3.0225
10

0.0001




407


 


95
19
ENV
10
PLGFFPDHQL
L
L
1.0511
10

0.0002




408


 


100
20
POL
427
PLHPAAMPHL
L
L
1.0550
10

0.0001




409


 


100
20
POL
427
PLHPAAMPHLL
L
L

11






410


 


100
20
ENV
377
PLLPIFFCL
L
L
1069.13
9
*
0.0650
0.0001
0.0018
0.1100
0.0047
411


 


100
20
ENV
377
PLLPIFFCLWV
L
V

11






412


 


90
18
ENV
174
PLLVLQAGFFL
L
L
Chisari
11

0.0008




413









4.029



 


80
16
POL
711
PLPIHTAEL
L
L
927.19
9

0.0004




414


 


80
16
POL
711
PLPIHTAELL
L
L
1.0569
10

0.0001




415


 


80
16
POL
711
PLPIHTAELLA
L
A

11






416


 


75
15
POL
2
PLSYQHFRKL
L
L
1.0527
10

0.0001




417


 


75
15
POL
2
PLSYQHFRKLL
L
L

11






418


 


85
17
POL
98
PLTVNEKRRL
L
L
1.0536
10

0.0001




419


 


80
16
POL
505
PMGVGLSPFL
M
L
1.0557
10

0.0001




420


 


80
16
POL
505
PMGVGLSPFLL
M
L

11






421


 


75
15
POL
692
PTGWGLAI
T
I

8






422


 


80
16
ENV
219
PTSNHSPT
T
T

8






423


 


85
17
POL
797
PTTGRTSL
T
L

8






424


 


85
17
POL
797
PTTGRTSLYA
T
A

10






425


 


80
16
NUC
15
PTVQASKL
T
L

8






426


 


80
16
NUC
15
PTVQASKLCL
T
L

10






427


 


75
15
ENV
351
PTVWLSVI
T
I

8






428


 


75
15
ENV
351
PTVWLSVIWM
T
M

10






429


 


95
19
X
59
PVCAFSSA
V
A

8






430


 


85
17
POL
612
PVNRPIDWKV
V
V
1.0566
10

0.0002




431


 


95
19
POL
654
QAFTFSPT
A
T

8






432


 


95
19
POL
654
QAFTFSPTYKA
A
A

11






433


 


95
19
ENV
179
QAGFFLLT
A
T

8






434


 


80
16
ENV
179
QAGFFLLTRI
A
I

10






435


 


80
16
ENV
179
QAGFFLLTRIL
A
L

11






436


 


90
18
NUC
57
QAILCWGEL
A
L

9






437


 


90
18
NUC
57
QAILCWGELM
A
M

10






438


 


95
19
ENV
107
QAMQWNST
A
T

8






439


 


80
16
ENV
107
QAMQWNSTT
A
T

9






440


 


80
16
NUC
18
QASKLCLGWL
A
L

10






441


 


80
16
X
8
QLDPARDV
L
V
Chisari
8

0.0001




442









4.116



 


80
16
X
8
QLDPARDVL
L
L
927.01
9

0.0001




443


 


80
16
X
8
QLDPARDVLCL
L
L
Chisari
11

0.0001




444









4.073



 


90
18
NUC
99
QLLWFHISCL
L
L
1142.03
10
*
0.0060




445


 


85
17
NUC
99
QLLWFHISCLT
L
T

11






446


 


95
19
POL
685
QVFADATPT
V
T
5.0038
9

0.0001




447


 


95
19
POL
528
RAFPHCLA
A
A

8






448


 


80
16
ENV
187
RILTIPQSL
I
L
Chisari
9

0.0010




449









4.054



 


90
16
POL
624
RIVGLLGFA
I
A

9






450


 


90
18
POL
624
RIVGLLGFAA
I
A

10






451


 


75
15
POL
106
RLKLIMPA
L
A

8






452


 


90
18
POL
353
RTPARVTGGV
T
V

10






453


 


95
19
NUC
127
RTPPAYRPPNA
T
A

11






454


 


95
19
POL
36
RVAEDLNL
V
L

8






455


 


90
18
POL
36
RVAEDLNLGNL
V
L

11






456


 


80
16
POL
818
RVHFASPL
V
L

8






457


 


75
15
POL
818
RVHFASPLHV
V
V
1.0576
10

0.0001




458


 


75
15
POL
818
RVHFASPLHVA
V
A

11






459


 


100
20
POL
357
RVTGGVFL
V
L

8






460


 


100
20
POL
357
RVTGGVFLV
V
V
1.0181
9

0.0041




461


 


90
18
X
65
SAGPCALRFT
A
T

10






462


 


95
19
POL
520
SAICSVVRRA
A
A
5.0088
10

0.0001




463


 


90
18
NUC
35
SALYREAL
A
L

8






464


 


100
20
POL
49
SIPWTHKV
I
V

8






465


 


95
19
ENV
194
SLDSWWTSL
L
L
F126.64
9






466


 


75
15
POL
565
SLGIHLNPNKT
L
T

11






467


 


95
19
ENV
337
SLLVPFVQWFV
L
V

11






468


 


75
15
POL
581
SLNFMGYV
L
V

8






469


 


75
15
POL
581
SLNFMGYVI
L
I
927.12
9

0.0038




470


 


95
19
X
54
SLRGLPVCA
L
A
3.0030
9

0.0007




471


 


90
18
POL
403
SLTNLLSSNL
L
L
1.0548
10

0.0014




472


 


75
15
ENV
280
STGPCKTCT
T
T

9






473


 


100
20
NUC
141
STLPETTV
T
V

8






474


 


100
20
NUC
141
STLPETTVV
T
V
5.0024
9

0.0019




475


 


80
16
ENV
85
STNRQSGRQPT
T
T

11






476


 


85
17
POL
548
SVQHLESL
V
L

8






477


 


80
16
ENV
330
SVRFSWLSL
V
L
Chisari
9

0.0001




478









4.025



 


80
16
ENV
330
SVRFSWLSLL
V
L
Chisari
10

0.0004




479









4.026



 


80
16
ENV
330
SVRFSWLSLLV
V
V

11






480


 


90
18
POL
739
SVVLSRKYT
V
T

9






481


 


95
19
POL
524
SVVRRAFPHCL
V
L

11






482


 


85
17
POL
716
TAELLAACFA
A
A

10






483


 


95
19
NUC
53
TALRQAIL
A
L

8






484


 


80
16
NUC
33
TASALYREA
A
A

9






485


 


80
16
NUC
33
TASALYREAL
A
L

10






486


 


90
18
ENV
190
TIPQSLDSWWT
I
T

11






487


 


100
20
NUC
142
TLPETTVV
L
V

8






488


 


100
20
POL
150
TLWKAGIL
L
L

8






489


 


85
17
POL
798
TTGRTSLYA
T
A

9






490


 


75
15
ENV
278
TTSTGPCKT
T
T

9






491


 


75
15
ENV
278
TTSTGPCKTCT
T
T

11






492


 


85
17
POL
100
TVNEKRRL
V
L

8






493


 


80
18
NUC
16
TVQASKLCL
V
L
1.0365
9

0.0002




494


 


75
15
ENV
352
TVWLSVIWM
V
M
3.0035
9

0.0002




495


 


95
19
POL
37
VAEDLNLGNL
A
L
5.0089
10

0.0001




496


 


95
19
X
15
VLCLRPVGA
L
A
3.0028
9

0.0014




497


 


85
17
POL
543
VLGAKSVCHL
L
L
1.0560
10

0.0001




498


 


90
18
X
133
VLGGCRHKL
L
L
927.08
9

0.0009




499


 


90
18
X
133
VLGGCRHKLV
L
V
1.0589
10

0.0001




500


 


85
17
X
92
VLHKRTLGL
L
L
927.03
9

0.0012




501


 


95
19
ENV
259
VLLDYQGM
L
M
17.0107
8






502


 


95
19
ENV
259
VLLDYQGML
L
L
1069.09
9
*
0.0440
0.0001
0.0210
0.9000
0.0002
503


 


90
18
ENV
259
VLLDYQGMLPV
L
V
1147.14
11
*
0.5800
0.2200
4.9000
0.3400
0.0170
504


 


95
19
ENV
177
VLQAGFFL
L
L
Chisari
8

0.0019




505









4.027



 


95
19
ENV
177
VLQAGFFLL
L
L
1013.14
9
*
0.0660




506


 


95
19
ENV
177
VLQAGFFLLT
L
T
5.0066
10

0.0011




507


 


100
20
POL
358
VTGGVFLV
T
V

8






508


 


90
18
POL
542
VVLGAKSV
V
V

8






509


 


80
16
POL
542
VVLGAKSVQHL
V
L

11






510


 


90
18
POL
740
VVLSRKYT
V
T

8






511


 


95
19
POL
525
VVRRAFPHCL
V
L
2.0217
10

0.0003




512


 


95
19
POL
525
VVRRAFPHCLA
V
A

11






513


 


80
16
POL
759
WILRGTSFV
I
V
927.24
9
*
0.0270




514


 


80
16
POL
759
WILRGTSFVYV
I
V

11






515


 


80
16
POL
751
WLLGCAANWI
L
I
Chisari
10

0.0053




516









4.101



 


80
16
POL
751
WLLGCAANWIL
L
L

11






517


 


100
20
POL
414
WLSLDVSA
L
A

8






518


 


95
19
POL
414
WLSLDVSAA
L
A
3.0023
9

0.0059




519


 


100
20
ENV
335
WLSLLVPFV
L
V
1013.0102
9
*
1.1000
0.0380
7.2000
0.3600
0.0310
520


 


95
19
ENV
237
WMCLRRFI
M
I

8






521


 


95
19
ENV
237
WMCLRRFII
M
I
1147.10
9
*
0.0005




522


 


95
19
ENV
237
WMCLRRFIIFL
M
L
Chisari
11

0.0019




523









4.024



 


85
17
ENV
359
WMMWYWGPSL
M
L
1137.05
10
*
0.0009




524


 


100
20
POL
52
WTHKVGNFT
T
T
5.0039
9

0.0001




525


 


95
19
POL
52
WTHKVGNFTGL
T
L

11






526


 


100
20
POL
147
YLHTLWKA
L
A

8






527


 


100
20
POL
147
YLHTLWKAGI
L
I
1069.11
10
*
0.0160
0.0005
0.5600
0.1000
0.0320
528


 


100
20
POL
147
YLHTLWKAGIL
L
L

11






529


 


100
20
POL
122
YLPLDKGI
L
I

8






530


 


90
18
NUC
118
YLVSFGVWI
L
I
1090.12
9
*
0.3800




531


 


90
18
NUC
118
YLVSFGVWIRT
L
T

11






532


 


90
18
POL
538
YMDDVVLGA
M
A
1090.14
9
*
0.0250
0.0001
0.0024
0.1000
0.0002
533


 


85
17
POL
746
YTSFPWLL
T
L

8






534


 


75
15
POL
746
YTSFPWLLGCA
T
A

11






535


 


90
18
POL
768
YVPSALNPA
V
A
3.0042
9

0.0039




536


 






388
















TABLE VIII







HBV A03 SUPER MOTIF (With binding information)


 




























C-










Conservancy
Frequency
Protein
Position
Sequence
P2
term
Peptide
AA
Filed
A*0301
A*1101
A*3101
A*3301
A*6801
SEQ ID NO:

























85
17
POL
721
AACFARSR
A
R
26.0003
8

0.0004
0.0003
0.0056
0.0035
0.0014
537


 


95
19
POL
521
AICSVVRR
I
R
26.0004
8

−0.0002
0.0003
0.0014
−0.0009
0.0006
538


 


90
18
POL
772
ALNPADDPSR
L
R
1.1090
10

0.0003
0.0001



539


 


85
17
X
70
ALRFTSAR
L
R
26.0005
8

0.0047
0.0009
0.0450
0.0230
0.0004
540


 


80
16
POL
822
ASPLHVAWR
S
R

9






541


 


75
15
ENV
84
ASTNRQSGR
S
R
1150.60
9

0.0009
0.0002
0.0088
0.0008
0.0001
542


 


80
16
POL
755
CAANWILR
A
R

8






543


 


85
17
X
69
CALRFTSAR
A
R
26.0149
9
*
0.0034
0.0230
1.5000
8.0000
0.7300
544


 


90
16
X
17
CLRPVGAESR
L
R
1.1093
10

0.0011
0.0001



545


 


100
20
NUC
48
CSPHHTALR
S
R
5.0055
9
*
0.0029
0.0001
0.0520
0.0250
0.0440
546


 


85
17
NUC
29
DLLDTASALYR
L
R
26.0530
11

0.0042
−0.0003
−0.0012
3.7000
0.0410
547


 


85
17
NUC
32
DTASALYR
T
R
26.0006
8

0.0004
−0.0002
−0.0009
0.0018
0.0009
548


 


95
19
POL
17
EAGPLEEELPR
A
R
26.0531
11

−0.0009
−0.0003
−0.0012
0.0015
0.0110
549


 


90
18
POL
718
ELLAACFAR
L
R
1.0988
9

0.0002
0.0004



550


 


85
17
POL
718
ELLAACFARSR
L
R
26.0532
11

0.0062
0.0016
0.0200
0.2000
0.1600
551


 


95
19
NUC
174
ETTVVRRR
T
R
26.0007
8

0.0003
−0.0002
−0.0009
0.1400
0.0027
552


 


80
16
NUC
174
ETTVVRRRGR
T
R
1.1073
10

0.0003
0.0001



553


 


80
16
POL
821
FASPLHVAWR
A
R

10






554


 


90
18
X
83
FSSAGPCALR
S
R

10






555


 


95
19
POL
856
FTFSPTYK
T
K
1147.19
8
*
0.0100
0.0100
0.0023
0.2100
0.0590
556


 


95
19
POL
518
FTSAICSVVR
T
R
1.1085
10

0.0003
0.0003



557


 


95
19
POL
518
FTSAICSVVRR
T
R
26.0533
11

0.0065
0.0092
0.0170
0.0350
1.5000
558


 


90
18
X
132
FVLGGCRHK
V
K
1090.03
9
*
0.0430
0.0090



559


 


75
15
POL
567
GIHLNPNK
I
K

8






560


 


75
15
POL
567
GIHLNPNKTK
I
K
1.0563
10

0.0025
0.0011
0.0009
0.0009
0.0003
561


 


75
15
POL
567
GIHLNPNKTKR
I
R

11






562


 


85
17
NUC
29
GMDIDPYK
M
K
26.0009
8

0.0006
0.0004
−0.0009
−0.0009
0.0001
563


 


90
16
POL
735
GTDNSVVLSR
T
R
1090.04
10
*
0.0010
0.0420
0.0030
0.0019
0.0008
564


 


90
16
POL
735
GTDNSVVLSRK
T
K
1147.17
11
*
0.0140
0.5600
−0.0002
−0.0006
0.0001
565


 


95
19
NUC
123
GVWIRTPPAYR
V
R
26.0535
11
*
0.1900
0.1700
6.8000
0.7300
0.6600
566


 


90
18
NUC
104
HISCLTFGR
I
R
1069.16
9
*
0.0160
0.0065



567


 


75
15
POL
569
HLNPNKTK
L
K

8






568


 


75
15
POL
569
HLNPNKTKR
L
R
1.0983
9

0.0025
0.0001



569


 


100
20
POL
149
HTLWKAGILYK
T
K
1147.16
11
*
0.5400
0.4400
0.0370
0.0720
0.1900
570


 


90
18
NUC
105
ISCLTFGR
S
R
26.0010
8

0.0004
0.0002
0.0017
−0.0009
0.0017
571


 


100
20
POL
153
KAGILYKR
A
R
26.0011
8

0.0002
−0.0002
0.0015
−0.0009
0.0001
572


 


80
16
POL
610
KLPVNRPIDWK
L
K

11






573


 


75
15
X
130
KVFVLGGCR
V
R
1.0993
9
*
0.0420
0.0820
0.6000
0.0710
0.0030
574


 


85
17
POL
720
LAACFARSR
A
R
20.0129
9

0.0058
0.0065



575


 


90
18
POL
719
LLAACFAR
L
R
26.0012
8

0.0024
0.0003
0.0015
0.0029
0.0064
576


 


85
17
POL
719
LLAACFARSR
L
R

10






577


 


85
17
NUC
30
LLDTASALYR
L
R
1.1070
10

0.0050
0.0002



578


 


80
16
POL
752
LLGCAANWILR
L
R

11






579


 


75
15
POL
564
LSLGIHLNPNK
S
K

11






580


 


95
19
NUC
169
LSTLPETTVVR
S
R
26.0537
11

−0.0009
0.0008
−0.0012
−0.0023
0.0078
581


 


75
15
POL
3
LSYQHFRK
S
K

8






582


 


85
17
POL
99
LTVNEKRR
T
R
26.0013
8

−0.0002
−0.0002
−0.0009
−0.0009
0.0001
583


 


90
18
NUC
119
LVSFGVWIR
V
R
1090.08
9
*
0.0028
0.0120



584


 


100
20
POL
377
LVVDFSQFSR
V
R
1069.20
10
*
0.0016
0.3600
0.0260
0.2300
0.4900
585


 


75
15
X
103
MSTTDLEAYFK
S
K

11






586


 


90
18
NUC
75
NLEDPASR
L
R
26.0014
8

−0.0002
−0.0002
−0.0009
−0.0009
0.0001
587


 


95
19
POL
45
NLNVSIPWTHK
L
K
26.0538
11

−0.0009
0.0005
−0.0012
−0.0023
0.0019
588


 


90
18
POL
738
NSVVLSRK
S
K
26.0015
8

0.0006
0.0010
−0.0009
−0.0009
0.0007
589


 


100
20
POL
47
NVSIPWTHK
V
K
1069.16
9
*
0.0620
0.0570
0.0002
0.0100
0.0320
590


 


90
18
POL
775
PADDPSRGR
A
R
1150.35
9

0.0008
0.0002
0.0004
0.0015
0.0002
591


 


80
16
X
11
PARDVLCLR
A
R
1150.36
9

0.0002
0.0002
0.0100
0.0180
0.0002
592


 


75
15
ENV
83
PASTNRQSGR
A
R

10






593


 


90
18
POL
616
PIDWKVCQR
I
R
1.0985
9

0.0002
0.0005



594


 


80
16
POL
496
PIILGFRK
I
K

8






595


 


95
19
POL
20
PLEEELPR
L
R
26.0016
8

0.0002
−0.0002
−0.0009
−0.0009
0.0001
596


 


100
20
POL
2
PLSYQHFR
L
R
26.0017
8

−0.0002
−0.0002
−0.0009
−0.0009
0.0001
597


 


75
15
POL
2
PLSYQHFRK
L
K
1.0161
9

0.0011
0.0031
0.0006
0.0008
0.0002
598


 


85
17
POL
98
PLTVNEKR
L
R
26.0018
8

0.0002
−0.0002
−0.0009
−0.0009
0.0001
599


 


85
17
POL
98
PLTVNEKRR
L
R
1.0974
9

0.0008
0.0005
0.0004
0.0027
0.0002
600


 


90
18
X
20
PVGAESRGR
V
R
1.0990
9

0.0002
0.0005
0.0004
0.0043
0.0002
601


 


85
17
POL
612
PVNRPIDVVK
V
K
1142.06
9
*
0.0310
0.1400
0.0002
0.0006
0.0009
602


 


95
19
POL
654
QAFTFSPTYK
A
K
1090.10
10
*
0.0450
0.5400
0.0010
0.0057
1.2000
603


 


80
16
ENV
179
QAGFFLLTR
A
R

9






604


 


75
15
NUC
169
QSPRRRRSQSR
S
R
28.0839
11






605


 


80
16
POL
189
QSSGILSR
S
R

8






606


 


75
15
POL
106
RLKLIMPAR
L
R
1.0975
9
*
0.0950
0.0002
3.1000
0.0490
0.0002
607


 


75
15
X
128
RLKVFVLGGCR
L
R

11






608


 


95
19
POL
376
RLVVDFSQFSR
L
R
26.0539
11
*
0.2800
3.8000
2.6000
1.2000
6.1000
609


 


95
19
NUC
183
RSPRRRTPSPR
S
R
26.0540
11

−0.0007
−0.0003
0.0190
−0.0023
0.0003
610


 


75
15
NUC
167
RSQSPRRR
S
R

8






611


 


75
15
NUC
167
RSQSPRRRR
S
R

9






612


 


95
19
NUC
188
RTPSPRRR
T
R
26.0019
8

−0.0002
−0.0002
0.0033
0.0014
0.0002
613


 


95
19
NUC
188
RTPSPRRRR
T
R
1.0971
9
*
0.0054
0.0005
0.2000
0.0016
0.0003
614


 


100
20
POL
357
RVTGGVFLVDK
V
K
1147.18
11
*
0.0190
0.0290
−0.0002
−0.0003
0.0001
615


 


90
18
X
65
SAGPCALR
A
R
26.0020
8

−0.0002
0.0020
0.0029
0.0024
0.0360
616


 


95
19
POL
520
SAICSVVR
A
R
26.0021
8

−0.0002
0.0071
0.0280
0.0081
0.0690
617


 


95
19
POL
520
SAICSVVRR
A
R
1090.11
9
*
0.0058
0.2100
0.0150
0.0650
0.3800
618


 


90
18
POL
771
SALNPADDPSR
A
R
26.0542
11

−0.0004
−0.0003
−0.0012
−0.0023
0.0003
619


 


75
15
POL
565
SLGIHLNPNK
L
K
28.0758
10
*





620


 


90
18
X
64
SSAGPCALR
S
R
26.0153
9
*
0.0080
0.1400
0.3300
0.1600
0.7500
621


 


95
19
NUC
170
STLPETTVVR
T
R
1069.21
10
*
0.0007
0.0600
0.0080
0.0240
0.0250
622


 


95
19
NUC
170
STLPETTVVRR
T
R
1083.01
11

0.0150
1.4000
0.1000
0.1600
0.3100
623


 


80
16
ENV
85
STNRQSGR
T
R

8






624


 


75
15
X
104
STTDLEAYFK
T
K
1.0584
10
*
0.0066
2.7000



625


 


85
17
POL
716
TAELLAACFAR
A
R
26.0544
11

0.0006
0.0023
0.0066
0.1600
0.0590
626


 


95
19
NUC
171
TLPETTVVR
L
R
1.0969
9

0.0008
0.0002
0.0009
0.0024
0.0180
627


 


95
19
NUC
171
TLPETTVVRR
L
R
1069.22
10
*
0.0007
0.0230
0.0006
0.0120
0.0440
628


 


95
19
NUC
171
TLPETTVVRRR
L
R
26.0545
11
*
0.0005
0.0160
0.0061
0.0710
0.6400
629


 


100
20
POL
150
TLWKAGILYK
L
K
1069.15
10
*
5.3000
0.3600
0.0051
0.0010
0.0130
630


 


100
20
POL
150
TLWKAGILYKR
L
R
26.0546
11

0.0082
0.0095
0.1000
0.1100
0.0640
631


 


95
19
POL
519
TSAICSVVR
S
R
5.0057
9

0.0005
0.0008
0.0600
0.0200
0.0820
632


 


95
19
POL
519
TSAICSVVRR
S
R
1142.08
10
*
0.0018
0.0006
0.0030
0.0066
0.0048
633


 


75
15
X
105
TTDLEAYFK
T
K
1.0215
9
*
0.0006
0.9200
0.0006
0.0012
0.0170
634


 


75
15
ENV
278
TTSTGPCK
T
K

8






635


 


80
16
NUC
175
TTVVRRRGR
T
R
1.0970
9

0.0008
0.0005
0.2500
0.1400
0.0095
636


 


80
16
NUC
176
TVVRRRGR
V
R
3.0324
8

0.0003
0.0001



637


 


80
18
NUC
176
TVVRRRGRSPR
V
R
28.0837
11






638


 


90
18
X
133
VLGGCRHK
L
K
26.0022
8

0.0150
0.0002
−0.0005
−0.0009
0.0001
639


 


80
16
ENV
177
VLQAGFFLLTR
L
R

11






640


 


90
18
NUC
120
VSFGVWIR
S
R
26.0023
8
*
0.0040
0.0290
0.0750
0.0270
0.0360
641


 


100
20
POL
48
VSIPWTHK
S
K
26.0024
8
*
0.0130
0.0170
0.0031
0.0013
0.0004
642


 


100
20
POL
358
VTGGVFLVDK
T
K
1069.17
10
*
0.0390
0.0920
0.0002
0.0006
0.0022
643


 


100
20
POL
378
VVDFSQFSR
V
R
1069.19
9
*
0.0015
0.0750
0.0013
0.0170
0.0330
644


 


80
16
NUC
177
VVRRRGRSPR
V
R
1.1074
10

0.0027
0.0001



645


 


80
16
NUC
177
VVRRRGRSPRR
V
R
28.0838
11






646


 


95
19
NUC
125
WIRTPPAYR
I
R
1.0968
9

0.0008
0.0005



647


 


90
18
POL
314
WLQFRNSK
L
K
26.0025
8

−0.0002
0.0005
0.0020
0.0052
0.0001
648


 


85
17
NUC
26
WLWGMDIDPYK
L
K
26.0547
11

0.0030
0.0013
−0.0003
0.0039
0.0490
649


 


100
20
POL
122
YLPLDKGIK
L
K
1.0173
9

0.0001
0.0001
0.0006
0.0008
0.0002
650


 


90
18
NUC
118
YLVSFGVWIR
L
R
1090.13
10
*
0.0005
0.0002



651


 


90
18
POL
538
YMDDVVLGAK
M
K
1090.15
10
*
0.0330
0.0043
0.0002
0.0008
0.0001
652


 


80
16
POL
493
YSHPIILGFR
S
R

10






653


 


80
16
POL
493
YSHPIILGFRK
S
K

11






654






118
















TABLE IX







HBV A24 SUPER MOTIF (With binding information)


 
















Conservancy
Freq
Protein
Position
Sequence
String
Peptide
Filed
A*2401
SEQ ID NO:



















95
19
POL
529
AFPHCLAF
XFXXXXXF



655


 


95
19
POL
529
AFPHCLAFSY
XFXXXXXXXY



656


 


95
19
POL
529
AFPHCLAFSYM
XFXXXXXXXXM



657


 


95
19
X
62
AFSSAGPCAL
XFXXXXXXXL
5.0118

0.0012
658


 


90
18
POL
535
AFSYMDDVVL
XFXXXXXXXL
13.0130

0.0009
659


 


95
19
POL
655
AFTFSPTY
XFXXXXXY



660


 


95
19
POL
655
AFTFSPTYKAF
XFXXXXXXXXF



661


 


95
19
POL
521
AICSVVRRAF
XIXXXXXXXF



662


 


90
18
NUC
58
AILCWGEL
XIXXXXXL



663


 


90
18
NUC
58
AILCWGELM
XIXXXXXXM



664


 


95
19
POL
642
ALMPLYACI
XLXXXXXXI
3.0012
*

665


 


95
19
NUC
54
ALRQAILCW
XLXXXXXXW



666


 


80
16
ENV
108
AMQWNSTTF
XMXXXXXXF



667


 


95
19
POL
690
ATPTGWGL
XTXXXXXL



668


 


75
15
POL
690
ATPTGWGLAI
XTXXXXXXXI



669


 


95
19
POL
397
AVPNLQSL
XVXXXXXL



670


 


95
19
POL
397
AVPNLQSLTNL
XVXXXXXXXXL



671


 


100
20
NUC
131
AYRPPNAPI
XYXXXXXXI
5.0062
*
0.0260
672


 


100
20
NUC
131
AYRPPNAPIL
XYXXXXXXXL
2.0172
*
0.0220
673


 


75
15
POL
607
CFRKLPVNRPI
XFXXXXXXXXI



674


 


100
20
ENV
312
CIPIPSSW
XIXXXXXW



675


 


100
20
ENV
312
CIPIPSSWAF
XIXXXXXXXF



676


 


85
17
NUC
23
CLGWLWGM
XLXXXXXM



677


 


85
17
NUC
23
CLGWLWGMDI
XLXXXXXXXI
2.0229


678


 


100
20
ENV
253
CLIFLLVL
XLXXXXXL
17.0248


679


 


100
20
ENV
253
CLIFLLVLL
XLXXXXXXL
1.0836


680


 


95
19
ENV
253
CLIFLLVLLDY
XLXXXXXXXXY
26.0548


681


 


95
19
ENV
239
CLRRFIIF
XLXXXXXF



682


 


95
19
ENV
239
CLRRFIIFL
XLXXXXXXL
1.0829


683


 


75
15
ENV
239
CLRRFIIFLF
XLXXXXXXXF



684


 


75
15
ENV
239
CLRRFIIFLFI
XLXXXXXXXXI
Chisari


685








4.055



 


100
20
ENV
310
CTCIPIPSSW
XTXXXXXXXW



686


 


90
18
NUC
31
DIDPYKEF
XIXXXXXF



687


 


85
17
NUC
29
DLLDTASAL
XLXXXXXXL
1.0154


688


 


85
17
NUC
29
DLLDTASALY
XLXXXXXXXY
1.0519
*

689


 


95
19
POL
40
DLNLGNLNVSI
XLXXXXXXXXI



690


 


80
16
NUC
32
DTASALYREAL
XTXXXXXXXXL



691


 


85
17
POL
618
DWKVCQRI
XWXXXXXI



692


 


85
17
POL
618
DWKVCQRIVGL
XWXXXXXXXXL



693


 


90
18
ENV
262
DYQGMLPVCPL
XYXXXXXXXXL
3.0441

0.0002
694


 


80
16
X
122
ELGEEIRL
XLXXXXXL



695


 


95
19
NUC
43
ELLSFLPSDF
XLXXXXXXXF



696


 


95
19
NUC
43
ELLSFLPSDFF
XLXXXXXXXXF



697


 


90
18
NUC
117
EYLVSFGVW
XYXXXXXXW
26.0150


698


 


90
18
NUC
117
EYLVSFGVWI
XYXXXXXXXI
13.0129
*
0.0340
699


 


100
20
ENV
382
FFCLWVYI
XFXXXXXI



700


 


80
16
ENV
182
FFLLTRIL
XFXXXXXL



701


 


80
16
ENV
182
FFLLTRILTI
XFXXXXXXXI



702


 


85
17
ENV
13
FFPDHQLDPAF
XFXXXXXXXXF



703


 


80
16
ENV
243
FIIFLFIL
XIXXXXXL
17.0246


704


 


80
16
ENV
243
FIIFLFILL
XIXXXXXXL
1.0830


705


 


80
16
ENV
243
FIIFLFILLL
XIXXXXXXXL
1.0894


706


 


80
16
ENV
248
FILLLCLI
XIXXXXXI
Chisari


707








4.048



 


80
16
ENV
248
FILLLCLIF
XIXXXXXXF



708


 


80
16
ENV
248
FILLLCLIFL
XIXXXXXXXL
1.0895


709


 


80
16
ENV
248
FILLLCLIFLL
XIXXXXXXXXL
Chisari


710








4.049



 


80
16
ENV
246
FLFILLLCL
XLXXXXXXL
1.0832


711


 


80
16
ENV
246
FLFILLLCLI
XLXXXXXXXI
3.0206


712


 


80
16
ENV
246
FLFILLLCLIF
XLXXXXXXXXF



713


 


75
15
ENV
171
FLGPLLVL
XLXXXXXL



714


 


95
19
POL
513
FLLAQFTSAI
XLXXXXXXXI
1147.13
*

715


 


95
19
POL
562
FLLSLGIHL
XLXXXXXXL
1.0851
*

716


 


80
16
ENV
183
FLLTRILTI
XLXXXXXXI
3.0005
*

717


 


95
19
ENV
256
FLLVLLDY
XLXXXXXY
26.0027


718


 


95
19
ENV
256
FLLVLLDYQGM
XLXXXXXXXXM



719


 


95
19
POL
656
FTFSPTYKAF
XTXXXXXXXF
20.0262


720


 


95
19
POL
656
FTFSPTYKAFL
XTXXXXXXXXL



721


 


95
19
POL
635
FTQCGYPAL
XTXXXXXXL
5.0031


722


 


95
19
POL
635
FTQCGYPALM
XTXXXXXXXM
5.0085


723


 


95
19
ENV
346
FVGLSPTVW
XVXXXXXXXW



724


 


95
19
ENV
346
FVGLSPTVWL
XVXXXXXXXL
1.0931


725


 


90
18
X
132
FVLGGCRHKL
XVXXXXXXXL
1.0588


726


 


95
19
ENV
342
FVQWFVGL
XVXXXXXL
17.0109
*

727


 


90
18
POL
766
FVYVPSAL
XVXXXXXL
17.0260
*

728


 


95
19
POL
630
GFAAPFTQCGY
XFXXXXXXXXY



729


 


80
16
ENV
181
GFFLLTRI
XFXXXXXI



730


 


80
16
ENV
181
GFFLLTRIL
XFXXXXXXL



731


 


80
16
ENV
181
GFFLLTRILTI
XFXXXXXXXXI



732


 


95
19
ENV
12
GFFPDHQL
XFXXXXXL



733


 


75
15
ENV
170
GFLGPLLVL
XFXXXXXXL



734


 


80
16
POL
500
GFRKIPMGVGL
XFXXXXXXXXL



735


 


95
19
POL
627
GLLGFAAPF
XLXXXXXXF
20.0124


736


 


95
19
POL
509
GLSPFLLPAQF
XLXXXXXXXF



737


 


100
20
ENV
348
GLSPTVWL
XLXXXXXL
Chisari


738








4.012



 


75
15
ENV
348
GLSPTVWLSVI
XLXXXXXXXXI
Chisari


739








4.031



 


85
17
NUC
29
GMDIDPYKEF
XMXXXXXXXF
26.0372


740


 


90
18
ENV
265
GMLPVCPL
XMXXXXXL



741


 


90
18
POL
735
GTDNSVVL
XTXXXXXL



742


 


75
15
ENV
13
GTNLSVPNPL
XTXXXXXXXL



743


 


80
16
POL
763
GTSFVYVPSAL
XTXXXXXXXXL



744


 


80
16
POL
507
GVGLSPFL
XVXXXXXL



745


 


80
16
POL
507
GVGLSPFLL
XVXXXXXXL
1.0850


746


 


95
19
NUC
123
GVWIRTPPAY
XVXXXXXXXV
1.0525


747


 


85
17
NUC
25
GWLWGMDI
XWXXXXXI



748


 


85
17
NUC
25
GWLWGMDIDPY
XWXXXXXXXXY



749


 


85
17
ENV
65
GWSPQAQGI
XWXXXXXXI
20.0134

0.0024
750


 


85
17
ENV
65
GWSPQAQGIL
XWXXXXXXXL
20.0268

0.0003
751


 


95
19
POL
639
GYPALMPL
XYXXXXXL



752


 


95
19
POL
639
GYPALMPLY
XYXXXXXXY
2.0060
*
0.0490
753


 


95
19
ENV
234
GYRWMCLRRF
XYXXXXXXXF
2.0171
*
0.0110
754


 


95
19
ENV
234
GYRWMCLRRFI
XYXXXXXXXXI



755


 


85
17
POL
579
GYSLNFMGY
XYXXXXXXY
2.0058

0.0002
756


 


75
15
POL
579
GYSLNFMGYVI
XYXXXXXXXXI



757


 


80
16
POL
820
HFASPLHVAW
XFXXXXXXXW



758


 


75
15
POL
7
HFRKLLLL
XFXXXXXL



759


 


80
16
POL
435
HLLVGSSGL
XLXXXXXXL
1.0187


760


 


75
15
POL
569
HLNPNKTKRW
XLXXXXXXXW



761


 


80
16
POL
491
HLYSHPII
XLXXXXXI
17.0256


762


 


80
16
POL
491
HLYSHPIIL
XLXXXXXXL
1.0849
*

763


 


80
16
POL
491
HLYSHPIILGF
XLXXXXXXXXF



764


 


85
17
POL
715
HTAELLAACF
XTXXXXXXXF



765


 


100
20
NUC
52
HTALRQAI
XTXXXXXI



766


 


95
19
NUC
52
HTALRQAIL
XTXXXXXXL
5.0021


767


 


95
19
NUC
52
HTALRQAILCW
XTXXXXXXXXW



768


 


100
20
POL
149
HTLWKAGI
XTXXXXXI



769


 


100
20
POL
149
HTLWKAGIL
XTXXXXXXL
5.0033


770


 


100
20
POL
149
HTLWKAGILY
XTXXXXXXXY
1.0542
*

771


 


100
20
POL
146
HYLHTLWKAGI
XYXXXXXXXXI



772


 


100
20
ENV
381
IFFCLWVY
XFXXXXXY



773


 


100
20
ENV
381
IFFCLWVYI
XFXXXXXXI
5.0058

0.0087
774


 


80
16
ENV
245
IFLFILLL
XFXXXXXL



775


 


80
16
ENV
245
IFLFILLLCL
XFXXXXXXXL



776


 


80
16
ENV
245
IFLFILLLCLI
XFXXXXXXXXI



777


 


95
19
ENV
255
IFLLVLLDY
XFXXXXXXY



778


 


80
16
ENV
244
IIFLFILL
XIXXXXXL
17.0105


779


 


80
16
ENV
244
IIFLFILLL
XIXXXXXXL
1.0831


780


 


80
16
ENV
244
IIFLFILLLCL
XIXXXXXXXXL
Chisari


781








4.052



 


80
16
POL
497
IILGFRKI
XIXXXXXI
17.0124
*

782


 


80
16
POL
497
IILGFRKIPM
XIXXXXXXXM



783


 


90
18
NUC
59
ILCWGELM
XLXXXXXM



784


 


80
16
POL
498
ILGFRKIPM
XLXXXXXXM
3.0016


785


 


100
20
ENV
249
ILLLCLIF
XLXXXXXF



786


 


100
20
ENV
249
ILLLCLIFL
XLXXXXXXL
1.0833
*

787


 


100
20
ENV
249
ILLLCLIFLL
XLXXXXXXXL
1.0896
*

788


 


80
16
POL
760
ILRGTSFVY
XLXXXXXXY
1.0205
*

789


 


95
19
ENV
188
ILTIPQSL
XLXXXXXL



790


 


90
18
ENV
188
ILTIPQSLDSW
XLXXXXXXXXW



791


 


90
18
POL
625
IVGLLGFAAPF
XVXXXXXXXXF



792


 


85
17
ENV
358
IWMMWYWGPS
XWXXXXXXXXL
1039.07

0.0004
793


 


95
19
POL
395
KFAVPNLQSL
XFXXXXXL
5.0114

0.0020
794


 


80
16
POL
503
KIPMGVGL
XIXXXXXL



795


 


80
16
POL
503
KIPMGVGLSPF
XIXXXXXXXXF



796


 


85
17
NUC
21
KLCLGWLW
XLXXXXXW



797


 


85
17
NUC
21
KLCLGWLWGM
XLXXXXXXXM
3.0209
*

798


 


95
19
POL
489
KLHLYSHPI
XLXXXXXXI
3.0009
*

799


 


80
16
POL
489
KLHLYSHPII
XLXXXXXXXI



800


 


80
16
POL
489
KLHLYSHPIIL
XLXXXXXXXXL



801


 


75
15
POL
108
KLIMPARF
XLXXXXXF



802


 


75
15
POL
108
KLIMPARFY
XLXXXXXXY
1.0171


803


 


80
16
POL
610
KLPVNRPI
XLXXXXXI



804


 


80
16
POL
610
KLPVNRPIDW
XLXXXXXXXW



805


 


95
19
POL
574
KTKRWGYSL
XTXXXXXXL
5.0034


806


 


85
17
POL
574
KTKRWGYSLNF
XTXXXXXXXXF



807


 


85
17
POL
620
KVCQRIVGL
XVXXXXXXL
1.0198


808


 


85
17
POL
620
KVCQRIVGLL
XVXXXXXXXL
1.0567


809


 


95
19
POL
55
KVGNFTGL
XVXXXXXL
17.0116


810


 


95
19
POL
55
KVGNFTGLY
XVXXXXXXY
1.0166
*

811


 


85
17
X
91
KVLHKRTL
XVXXXXXL



812


 


85
17
X
91
KVLHKRTLGL
XVXXXXXXXL
1.0800


813


 


100
20
POL
121
KYLPLDKGI
XYXXXXXXI
5.0063
*
0.0028
814


 


85
17
POL
745
KYTSFPWL
XYXXXXXL
17.0132


815


 


85
17
POL
745
KYTSFPWLL
XYXXXXXXL
2.0061
*
3.6000
816


 


80
16
ENV
247
LFILLLCL
XFXXXXXL
17.0247


817


 


80
16
ENV
247
LFILLLCLI
XFXXXXXXI



818


 


80
16
ENV
247
LFILLLCLIF
XFXXXXXXXF



819


 


80
16
ENV
247
LFILLLCLIFL
XFXXXXXXXXL



820


 


100
20
ENV
254
LIFLLVLL
XIXXXXXL
Chisari


821








4.014



 


95
19
ENV
254
LIFLLVLLDY
XIXXXXXXXY
1.0899


822


 


100
20
POL
109
LIMPARFY
XIXXXXXY
26.0028


823


 


95
19
POL
514
LLAQFTSAI
XLXXXXXXI
3.0010
*

824


 


100
20
ENV
251
LLCLIFLL
XLXXXXXL
Chisari


825








4.015



 


100
20
ENV
251
LLCLIFLLVL
XLXXXXXXXL
1.0898


826


 


100
20
ENV
251
LLCLIFLLVLL
XLXXXXXXXXL
Chisari


827








4.016



 


85
17
NUC
30
LLDTASAL
XLXXXXXL



828


 


85
17
NUC
30
LLDTASALY
XLXXXXXXY
1.0155
*

829


 


95
19
ENV
260
LLDYQGML
XLXXXXXL
Chisari


830








4.021



 


80
16
POL
752
LLGCAANW
XLXXXXXW



831


 


80
16
POL
752
LLGCAANWI
XLXXXXXXI
3.0013


832


 


80
16
POL
752
LLGCAANWIL
XLXXXXXXXL
1.0912
*

833


 


95
19
POL
628
LLGFAAPF
XLXXXXXF



834


 


75
15
ENV
63
LLGWSPQAQGI
XLXXXXXXXXI



835


 


100
20
ENV
250
LLLCLIFL
XLXXXXXL
Chisari


836








4.017



 


100
20
ENV
250
LLLCLIFLL
XLXXXXXXL
1.0834
*

837


 


100
20
ENV
250
LLLCLIFLLVL
XLXXXXXXXXL
Chisari


838








4.018



 


100
20
ENV
378
LLPIFFCL
XLXXXXXL
17.0112


839


 


100
20
ENV
378
LLPIFFCLW
XLXXXXXXW



840


 


100
20
ENV
378
LLPIFFCLWVY
XLXXXXXXXXY
26.0549
*

841


 


95
19
NUC
44
LLSFLPSDF
XLXXXXXXF



842


 


95
19
NUC
44
LLSFLPSDFF
XLXXXXXXXF



843


 


95
19
POL
563
LLSLGIHL
XLXXXXXL



844


 


90
18
POL
407
LLSSNLSW
XLXXXXXW



845


 


90
18
POL
407
LLSSNLSWL
XLXXXXXXL
1.0184
*

846


 


90
18
POL
407
LLSSNLSWLSL
XLXXXXXXXXL



847


 


80
16
ENV
184
LLTRILTI
XLXXXXXI
Chisari


848








4.053



 


80
16
POL
436
LLVGSSGL
XLXXXXXL



849


 


95
19
ENV
257
LLVLLDYQGM
XLXXXXXXXM
3.0207


850


 


95
19
ENV
257
LLVLLDYQGML
XLXXXXXXXXL



851


 


95
19
ENV
175
LLVLQAGF
XLXXXXXF



852


 


95
19
ENV
175
LLVLQAGFF
XLXXXXXXF
20.0121


853


 


90
18
ENV
175
LLVLQAGFFL
XLXXXXXXXL
1.0892
*

854


 


90
18
ENV
175
LLVLQAGFFLL
XLXXXXXXXXL
Chisari


855








4.028



 


100
20
ENV
338
LLVPFVQW
XLXXXXXW



856


 


100
20
ENV
338
LLVPFVQWF
XLXXXXXXF



857


 


90
18
NUC
100
LLWFHISCL
XLXXXXXXL
1.0844
*

858


 


85
17
NUC
100
LLWFHISCLTF
XLXXXXXXXXF



859


 


95
19
POL
643
LMPLYACI
XMXXXXXI
17.0130


860


 


75
15
NUC
137
LTFGRETVL
XTXXXXXXL



861


 


75
15
NUC
137
LTFGRETVLEY
XTXXXXXXXXY



862


 


90
18
ENV
189
LTIPQSLDSW
XTXXXXXXXW



863


 


90
18
ENV
189
LTIPQSLDSWW
XTXXXXXXXXW



864


 


90
18
POL
404
LTNLLSSNL
XTXXXXXXL



865


 


90
18
POL
404
LTNLLSSNLSW
XTXXXXXXXXW



866


 


80
16
ENV
185
LTRILTIPQSL
XTXXXXXXXXL



867


 


85
17
POL
99
LTVNEKRRL
XTXXXXXXL



868


 


95
19
ENV
258
LVLLDYQGM
XVXXXXXXM
3.0034


869


 


95
19
ENV
258
LVLLDYQGML
XVXXXXXXXL
1.0515


870


 


95
19
ENV
176
LVLQAGFF
XVXXXXXF



871


 


90
16
ENV
176
LVLQAGFFL
XVXXXXXXL
1.0827


872


 


90
18
ENV
176
LVLQAGFFLL
XVXXXXXXXL
1.0893
*

873


 


100
20
ENV
339
LVPPVQWF
XVXXXXXF



874


 


95
19
ENV
339
LVPFVQWFVGL
XVXXXXXXXXL



875


 


90
18
NUC
119
LVSFGVWI
XVXXXXXI
Chisari


876








4.078



 


100
20
POL
377
LVVDFSQF
XVXXXXXF



877


 


90
18
NUC
101
LWFHISCL
XWXXXXXL



878


 


85
17
NUC
101
LWFHISCLTF
XWXXXXXXXF
26.0373


879


 


85
17
NUC
27
LWGMDIDPY
XWXXXXXXY



880


 


100
20
POL
151
LWKAGILY
XWXXXXXY



881


 


80
16
POL
492
LYSHPIIL
XYXXXXXL



882


 


80
16
POL
492
LYSHPIILGF
XYXXXXXXXF
2.0161
*
1.1000
883


 


85
17
ENV
360
MMWYWGPSL
XMXXXXXXL
1.0839
*
0.0012
884


 


85
17
ENV
360
MMWYWGPSLY
XMXXXXXXXY
1039.01
*
0.0001
885


 


85
17
ENV
361
MWYWGPSL
XWXXXXXL
17.0249


886


 


85
17
ENV
361
MWYWGPSLY
XWXXXXXXY
1039.02

0.0027
887


 


95
19
POL
561
NFLLSLGI
XFXXXXXI



888


 


95
19
POL
561
NFLLSLGIHL
XFXXXXXXXL
5.0115

0.0099
889


 


95
19
POL
42
NLGNLNVSI
XLXXXXXXI
3.0008


890


 


95
19
POL
42
NLGNLNVSIPW
XLXXXXXXXXW



891


 


90
18
POL
406
NLLSSNLSW
XLXXXXXXW



892


 


90
18
POL
406
NLLSSNLSWL
XLXXXXXXXL
1.0549


893


 


95
19
POL
45
NLNVSIPW
XLXXXXXW



894


 


100
20
POL
400
NLQSLTNL
XLXXXXXL



895


 


100
20
POL
400
NLQSLTNLL
XLXXXXXXL
1.0189


896


 


75
15
ENV
15
NLSVPNPL
XLXXXXXL



897


 


75
15
ENV
15
NLSVPNPLGF
XLXXXXXXXF



898


 


80
16
POL
758
NWILRGTSF
XWXXXXXXF



899


 


80
16
POL
758
NWILRGTSFVY
XWXXXXXXXXY



900


 


95
19
POL
512
PFLLAQFTSAI
XFXXXXXXXXI



901


 


95
19
POL
634
PFTQCGYPAL
XFXXXXXXXL
5.0116

0.0002
902


 


95
19
POL
634
PFTQCGYPALM
XFXXXXXXXXM



903


 


95
19
ENV
341
PFVQWFVGL
XFXXXXXXL
5.0059

0.0003
904


 


85
17
POL
616
PIDWKVCQRI
XIXXXXXXXI
Chisari


905








4.091



 


100
20
ENV
380
PIFFCLWVY
XIXXXXXXY
1.0843


906


 


100
20
ENV
380
PIFFCLWVYI
XIXXXXXXXI
20.0258


907


 


85
17
POL
713
PIHTAELL
XIXXXXXL



908


 


80
16
POL
496
PIILGFRKI
XIXXXXXXI
927.48


909


 


80
15
POL
496
PIILGFRKlPM
XIXXXXXXXXM



910


 


100
20
ENV
314
PIPSSWAF
XIXXXXXF



911


 


100
20
POL
124
PLDKGIKPY
XLXXXXXXY
1.0174
*

912


 


100
20
POL
124
PLDKGIKPYY
XLXXXXXXXY
1.0541
*

913


 


95
19
POL
20
PLEEELPRL
XLXXXXXXL
1.0163


914


 


95
19
ENV
10
PLGFFPDHQL
XLXXXXXXXL
1.0511


915


 


100
20
POL
427
PLHPAAMPHL
XLXXXXXXXL
1.0550


916


 


100
20
POL
427
PLHPAAMPHLL
XLXXXXXXXXL



917


 


100
20
ENV
377
PLLPIFFCL
XLXXXXXXL
1.0842
*

918


 


100
20
ENV
377
PLLPIFFCLW
XLXXXXXXXW



919


 


95
19
ENV
174
PLLVLQAGF
XLXXXXXXF



920


 


95
19
ENV
174
PLLVLQAGFF
XLXXXXXXXF



921


 


90
18
ENV
174
PLLVLQAGFFL
XLXXXXXXXXL
Chisari


922








4.029



 


80
16
POL
711
PLPIHTAEL
XLXXXXXXL
1.0201


923


 


80
18
POL
711
PLPIHTAELL
XLXXXXXXXL
1.0569


924


 


75
16
POL
2
PLSYQHFRKL
XLXXXXXXXL
1.0527


925


 


75
15
POL
2
PLSYQHFRKLL
XLXXXXXXXXL



926


 


85
17
POL
98
PLTVNEKRRL
XLXXXXXXXL
1.0536


927


 


80
16
POL
505
PMGVGLSPF
XMXXXXXXF



928


 


80
16
POL
505
PMGVGLSPFL
XMXXXXXXXL
1.0557


929


 


80
16
POL
505
PMGVGLSPFLL
XMXXXXXXXXL



930


 


75
15
POL
692
PTGWGLAI
XTXXXXXI



931


 


85
17
POL
797
PTTGRTSL
XTXXXXXL



932


 


85
17
POL
797
PTTGRTSLY
XTXXXXXXY
1.0208
*

933


 


80
16
NUC
15
PTVQASKL
XTXXXXXL



934


 


80
16
NUC
15
PTVQASKLCL
XTXXXXXXXL



935


 


75
15
ENV
361
PTVWLSVI
XTXXXXXI



936


 


75
15
ENV
351
PTVWLSVIW
XTXXXXXXW



937


 


75
15
ENV
351
PTVWLSVIWM
XTXXXXXXXM



938


 


85
17
POL
612
PVNRPIDW
XVXXXXXW



939


 


80
16
POL
750
PWLLGCAANW
XWXXXXXXXW



940


 


80
15
POL
750
PWLLGCAANWI
XWXXXXXXXXI



941


 


100
20
POL
51
PWTHKVGNF
XWXXXXXXF
20.0138
*
0.0280
942


 


80
16
X
8
QLDPARDVL
XLXXXXXXL
1.0210


943


 


80
16
X
8
QLDPARDVLCL
XLXXXXXXXXL
Chisari


944








4.073



 


90
18
NUC
99
QLLWFHISCL
XLXXXXXXXL
1.0908
*

945


 


95
19
POL
665
QVFADATPTGW
XVXXXXXXXXW



946


 


95
19
ENV
344
QWFVGLSPTVW
XWXXXXXXXX



947


 


75
15
ENV
242
RFIIFLFI
XFXXXXXI
17.0151


948


 


75
15
ENV
242
RFIIFLFIL
XFXXXXXXL



949


 


75
15
ENV
242
RFIIFLFILL
XFXXXXXXXL



950


 


75
15
ENV
242
RFIIFLFILLL
XFXXXXXXXXL



951


 


100
20
ENV
332
RFSWLSLL
XFXXXXXL



952


 


100
20
ENV
332
RFSWLSLLVPF
XFXXXXXXXXF



953


 


80
16
ENV
167
RILTIPQSL
XIXXXXXXL
1.0149


954


 


90
18
POL
524
RIVGLLGF
XIXXXXXF



955


 


75
15
POL
106
RLKLIMPARF
XLXXXXXXXF



956


 


75
15
POL
106
RLKLIMPARFY
XLXXXXXXXXY



957


 


95
19
POL
376
RLVVDFSQF
XLXXXXXXF
20.0122


958


 


90
18
POL
355
RTPARVTGGVF
XTXXXXXXXXF



959


 


95
19
POL
36
RVAEDLNL
XVXXXXXL



960


 


90
18
POL
36
RVAEDLNLGNL
XVXXXXXXXXL



961


 


80
16
POL
818
RVHFASPL
XVXXXXXL



962


 


100
20
POL
357
RVTGGVFL
XVXXXXXL



963


 


85
17
POL
577
RWGYSLNF
XWXXXXXF



964


 


85
17
POL
577
RWGYSLNFM
XWXXXXXXM



965


 


85
17
POL
577
RWGYSLNRMGY
XWXXXXXXXXY



966


 


95
19
ENV
238
RWMCLRRF
XWXXXXXF



967


 


95
19
ENV
236
RWMCLRRFI
XWXXXXXXI
20.0135
*
0.0710
968


 


95
19
ENV
236
RWMCLRRFII
XWXXXXXXXI
20.0269
*
1.1000
969


 


95
19
ENV
236
RWMCLRRRIF
XWXXXXXXXXF



970


 


100
20
POL
167
SFCGSPYSW
XFXXXXXXW
20.0139
*
0.0710
971


 


95
19
NUC
46
SFLPSDFF
XFXXXXXF



972


 


80
16
POL
765
SFVYVPSAL
XFXXXXXXL



973


 


100
20
POL
49
SIPWTHKVGNF
XIXXXXXXXXF



974


 


95
19
ENV
194
SLDSWWTSL
XLXXXXXXL
1.0150


975


 


95
19
ENV
194
SLDSWWTSLNF
XLXXXXXXXXF



976


 


95
19
POL
416
SLDVSAAF
XLXXXXXF



977


 


95
19
POL
416
SLDVSAAFY
XLXXXXXXY
1.0186
*

978


 


100
20
ENV
337
SLLVPFVQW
XLXXXXXXW



979


 


100
20
ENV
337
SLLVPFVQWF
XLXXXXXXXF



980


 


75
15
POL
581
SLNFMGYVI
XLXXXXXXI
3.0011


981


 


95
19
X
54
SLRGLPVCAF
XLXXXXXXXF
20.0259


982


 


90
18
POL
403
SLTNLLSSNL
XLXXXKXXXL
1.0548


983


 


75
15
X
104
STTDLEAY
XTXXXXXY



984


 


75
15
X
104
STTDLEAYF
XTXXXXXXF



985


 


75
15
ENV
17
SVPNPLGF
XVXXXXXF



986


 


85
17
POL
548
SVQHLESL
XVXXXXXL



987


 


80
16
ENV
330
SVRFSWLSL
XVXXXXXXL
1.0153


988


 


80
16
ENV
330
SVRFSWLSLL
XVXXXXXXXL
1.0517


989


 


90
18
POL
739
SVVLSRKY
XVXXXXXY
26.0029


990


 


85
17
POL
739
SVVLSRKYTSF
XVXXXXXXXXF



991


 


95
19
POL
524
SVVRRAFPHCL
XVXXXXXXXXL



992


 


95
19
POL
413
SWLSLDVSAAF
XWXXXXXXXXF



993


 


100
20
ENV
334
SWLSLLVPF
XWXXXXXXF
20.0136
*
0.3900
994


 


95
19
POL
392
SWPKFAVPNL
XWXXXXXXXL
20.0271
*
5.6000
995


 


100
20
ENV
197
SWWTSLNF
XWXXXXXF



996


 


95
19
ENV
197
SWWTSLNFL
XWXXXXXXL
20.0137
*
0.3800
997


 


90
18
POL
537
SYMDDVVL
XYXXXXXL



998


 


75
15
POL
4
SYQHFRKL
XYXXXXXL



999


 


75
15
POL
4
SYQHFRKLL
XYXXXXXXL
2.0042

0.0051
1000


 


75
15
POL
4
SVQHFRKLLL
XYXXXXXXXL
2.0173
*
0.0660
1001


 


75
15
POL
4
SYQHFRKLLLL
XYXXXXXXXXL



1002


 


75
15
NUC
138
TFGRETVL
XFXXXXXL



1003


 


75
15
NUC
138
TFGRETVLEY
XFXXXXXXXY



1004


 


75
15
NUC
138
TFGRETVLEYL
XFXXXXXXXXL



1005


 


95
19
POL
657
TFSPTYKAF
XFXXXXXXF
5.0064

0.0060
1006


 


95
19
POL
657
TFSPTYKAFL
XFXXXXXXKL
5.0117

0.0043
1007


 


90
18
ENV
190
TIPQSLDSW
XIXXXXXXW



1008


 


90
18
ENV
190
TIPQSLDSWW
XIXXXXXXXW



1009


 


100
20
POL
150
TLWKAGIL
XLXXXXXL



1010


 


100
20
POL
150
TLWKAGILY
XLXXXXXXY
1.0177
*

1011


 


75
15
X
105
TTDLEAYF
XTXXXXXF



1012


 


85
17
POL
798
TTGRTSLY
XTXXXXXY
26.0030


1013


 


85
17
POL
100
TVNEKRRL
XVXXXXXL



1014


 


80
16
NUC
16
TVQASKLCL
XVXXXXXXL
1.0365


1015


 


80
16
NUC
16
TVQASKLCLGW
XVXXXXXXXXW



1016


 


75
15
ENV
352
TVWLSVIW
XVXXXXXW



1017


 


75
15
ENV
352
TVWLSVIWM
XVXXXXXXM
3.0035


1018


 


95
19
POL
686
VFADATPTGW
XFXXXXXXXW
20.0272
*
0.0180
1019


 


75
15
X
131
VFVLGGCRHKL
XFXXXXXXXXL



1020


 


85
17
POL
543
VLGAKSVQHL
XLXXXXXXXL
1.0560


1021


 


90
18
X
133
VLGGCRHKL
XLXXXXXXL
1.0220


1022


 


85
17
X
92
VLHKRTLGL
XLXXXXXXL
1.0391


1023


 


95
19
ENV
259
VLLDYQGM
XLXXXXXM
17.0107


1024


 


95
19
ENV
259
VLLDYQGML
XLXXXXXXL
1.0151
*

1025


 


95
19
ENV
177
VLQAGFFL
XLXXXXXL
Chisari


1026








4.027



 


95
19
ENV
177
VLQAGFFLL
XLXXXXXXL
1.0828
*

1027


 


85
17
POL
741
VLSRKYTSF
XLXXXXXXF



1028


 


85
17
POL
741
VLSRKYTSFPW
XLXXXXXXXXW



1029


 


80
16
POL
542
VVLGAKSVQHL
XVXXXXXXXXL



1030


 


85
17
POL
740
VVLSRKYTSF
XVXXXXXXXXF
20.0261


1031


 


95
19
POL
525
VVRRAFPHCL
XVXXXXXXXL
1.0558


1032


 


95
19
NUC
124
VWIRTPPAY
XWXXXXXXY



1033


 


75
15
ENV
353
VWLSVIWM
XWXXXXXM



1034


 


90
18
NUC
102
WFHISCLTF
XFXXXXXXF
13.0073
*
0.0300
1035


 


95
19
ENV
345
WFVGLSPTVW
XFXXXXXXXW
20.0270
*
0.0120
1036


 


95
19
ENV
345
WFVGLSPTVWL
XFXXXXXXXXL



1037


 


80
16
POL
759
WILRGTSF
XIXXXXXF



1038


 


80
16
POL
759
WLRGTSFVY
XIXXXXXXXY
1.0572


1039


 


95
19
NUC
125
WIRTPPAY
XIXXXXXY
26.0031


1040


 


80
16
POL
751
WLLGCAANW
XLXXXXXXW



1041


 


80
16
POL
751
WLLGCAANWI
XLXXXXXXXI
Chisari


1042








4.104



 


80
16
POL
751
WLLGCAANWIL
XLXXXXXXXXL



1043


 


95
19
POL
414
WLSLDVSAAF
XLXXXXXXXF



1044


 


95
19
POL
414
WLSLDVSAAFY
XLXXXXXXXXY
26.0551


1045


 


100
20
ENV
335
WLSLLVPF
XLXXXXXF



1046


 


100
20
ENV
335
WLSLLVPFVQW
XLXXXXXXXXW



1047


 


85
17
NUC
26
WLWGMDIDPY
XLXXXXXXXY
1.0774
*

1048


 


95
19
ENV
237
WMCLRRFI
XMXXXXXI



1049


 


95
19
ENV
237
WMCLRRFII
XMXXXXXXI
3.0031
*
0.0230
1050


 


95
19
ENV
237
WMCLRRFIIF
XMXXXXXXXF
20.0266

0.0013
1051


 


95
19
ENV
237
WMCLRRFIIFL
XMXXXXXXXXL
Chisari


1052








4.024



 


85
17
ENV
359
WMMWYWGPSL
XMXXXXXXXL
1.0901
*
0.0005
1053


 


85
17
ENV
359
WMMWYWGPSL
XMXXXXXXXXY
26.0552
*

1054


 


100
20
POL
52
WTHKVGNF
XTXXXXXF



1055


 


95
19
POL
52
WTHKVGNFTGL
XTXXXXXXXXL



1056


 


95
19
ENV
198
WWTSLNFL
XWXXXXXL



1057


 


95
17
ENV
362
WYWGPSLY
XYXXXXXY
3.0362

0.0001
1058


 


100
20
POL
147
YLHTLWKAGI
XLXXXXXXXI
7.0066
*

1059


 


100
20
POL
147
YLHTLWKAGIL
XLXXXXXXXXL



1060


 


100
20
POL
122
YLPLDKGI
XLXXXXXI



1061


 


100
20
POL
122
YLPLDKGIKPY
XLXXXXXXXXY
26.0553


1062


 


90
18
NUC
118
YLVSFGVW
XLXXXXXW



1063


 


90
18
NUC
118
YLVSFGVWI
XLXXXXXI
3.0007
*

1064


 


85
17
POL
746
YTSFPWLL
XTXXXXXL



1065


 






411
















TABLE X







HBV B07 SUPER MOTIF (With binding information)


 




























C-










Conservancy
Frequency
Protein
Position
Sequence
P2
term
Peptide
AA
Filed
B*0702
B*3501
B*5101
B*5301
B*5401
SEQ ID NO:

























75
15
X
146
APCNFFTSA
P
A

9






1066


 


95
19
POL
633
APFTQCGY
P
Y
19.0013
8

0.0001
0.0012
0.0019
0.0002
0.0002
1067


 


95
19
POL
633
APFTQCGYPA
P
A
16.0180
10
*
0.0029
0.0001

0.0002
1.4000
1068


 


95
19
POL
633
APFTQCGYPAL
P
L
26.0554
11
*
0.2300
0.0010
0.0004
−0.0003
0.0093
1069


 


100
20
ENV
232
CPGYRWMCL
P
L
1308.21
9






1070


 


80
16
NUC
14
CPTVQASKL
P
L

9






1071


 


80
16
NUC
14
CPTVQASKLCL
P
L

11






1072


 


80
16
X
10
DPARDVLCL
P
L

9






1073


 


80
16
ENV
122
DPRVRGLY
P
L

8






1074


 


90
18
POL
778
DPSRGRLGL
P
L
1147.01
9
*
0.0120
0.0001
0.0001
0.0001
0.0001
1075


 


90
18
NUC
33
DPYKEFGA
P
A
19.0008
8

0.0001
0.0001
0.0019
0.0002
0.0019
1076


 


75
15
ENV
130
FPAGGSSSGTV
P
V

11






1077


 


90
18
ENV
14
FPDHQLDPA
P
A
1308.23
9
*





1078


 


85
17
ENV
14
FPDHQLDPAF
P
F
20.0274
10

0.0002
0.0016
0.0003
0.0011
0.0021
1079


 


95
19
POL
530
FPHCLAFSY
P
Y
1145.08
9
*
0.0001
0.5250
0.0665
0.5400
0.0199
1080


 


95
19
POL
530
FPHCLAFSYM
P
M
1147.05
10
*
0.0990
0.2200
0.0900
0.0790
0.0480
1081


 


75
15
POL
749
FPWLLGCA
P
A

8






1082


 


75
15
POL
749
FPWLLGCAA
P
A

9






1083


 


75
15
POL
749
FPWLLGCAANW
P
W

11






1084


 


90
18
X
67
GPCALRFTSA
P
A
16.0182
10
*
0.0900
0.0001
0.0001
0.0002
0.0035
1085


 


95
19
POL
19
GPLEEELPRL
P
L
15.0208
10

0.0001
0.0001
0.0002
0.0001
0.0002
1086


 


90
18
POL
19
GPLEEELPRLA
P
A
26.0555
11

−0.0002
0.0001
0.0001
−0.0003
0.0001
1087


 


95
19
ENV
173
GPLLVLQA
P
A
19.0003
8
*
0.0003
0.0001
0.0110
0.0002
0.0065
1088


 


95
19
ENV
173
GPLLVLQAGF
P
A
15.0212
10

0.0001
0.0001
0.0002
0.0001
0.0002
1089


 


95
19
ENV
173
GPLLVLQAGFF
P
F
26.0556
11

0.0011
0.0001
0.0001
0.0008
0.0009
1090


 


85
17
POL
97
GPLTVNEKRRL
P
L
26.0557
11

0.0031
0.0001
0.0001
−0.0003
0.0001
1091


 


100
20
POL
429
HPAAMPHL
P
L
19.0011
8
*
0.0650
0.0004
0.3100
0.0037
0.0160
1092


 


100
20
POL
429
HPAAMPHLL
P
L
1147.02
9
*
0.0980
0.0270
0.0110
0.0500
0.0120
1093


 


85
17
POL
429
HPAAMPHLLV
P
V
20.0273
10
*
0.0160
0.0020
0.0078
0.0140
0.0170
1094


 


80
16
POL
495
HPILGFRKI
P
I

10






1095


 


100
20
ENV
313
IPIPSSWA
P
A
19.0005
8
*
0.0004
0.0004
0.0019
0.0002
0.0600
1096


 


100
20
ENV
313
IPIPSSWAF
P
F
1145.04
9
*
0.1300
2.7679
2.3500
0.7450
0.0034
1097


 


80
16
ENV
313
IPIPSSWAFA
P
A
16.0177
10
*
0.0013
0.0024

0.0014
0.4500
1098


 


80
16
POL
504
IPMGVGLSPF
P
F

10






1099


 


80
16
POL
504
IPMGVGLSPFL
P
L

11






1100


 


90
18
ENV
191
IPQSLDSW
P
W
F126.65
8






1101


 


90
18
ENV
191
IPQSLDSWW
P
W
F126.60
9
*





1102


 


80
16
ENV
315
IPSSWAFA
P
A

8






1103


 


100
20
POL
50
IPWTHKVGNF
P
F
15.0209
10

0.0013
0.0001
0.0007
0.0001
0.0002
1104


 


100
20
ENV
379
LPIFFCLW
P
W
19.0007
8
*
0.0001
0.0001
0.0360
0.1400
0.0035
1105


 


100
20
ENV
379
LPIFFCLWV
P
V
1308.22
9
*





1106


 


100
20
ENV
379
LPIFFCLWVY
P
Y
15.0215
10

0.0002
0.0079
0.0002
0.0006
0.0002
1107


 


100
20
ENV
379
LPIFFCLWVYI
P
I
26.0558
11

0.0002
0.0001
0.0043
0.0139
0.0021
1108


 


85
17
POL
712
LPIHTAEL
P
L
17.0259
8






1109


 


85
17
POL
712
LPIHTAELL
P
L
20.0140
9
*
0.0040
0.0630
0.0052
0.3100
0.0005
1110


 


85
17
POL
712
LPIHTAELLA
P
A
16.0181
10
*
0.0018
0.0011

0.0016
0.3300
1111


 


85
17
POL
712
LPIHTAELLAA
P
A
26.0559
11

0.0090
0.0027
−0.0003
0.0120
2.7500
1112


 


80
16
X
89
LPKVLHKRTL
P
L

10






1113


 


100
20
POL
123
LPLDKGIKPY
P
Y
15.0210
10
*
0.0001
0.0290
0.0002
0.0003
0.0002
1114


 


100
20
POL
123
LPLDKGIKPYY
P
Y
26.0560
11

−0.0002
0.0009
0.0001
0.0007
0.0001
1115


 


95
19
X
58
LPVCAFSSA
P
A
1147.06
9
*
0.0480
0.0710
0.0110
0.0009
19.0000
1116


 


80
16
POL
611
LPVNRPIDW
P
W

9






1117


 


80
16
POL
611
LPVNRPIDWKV
P
V

11



 


80
16
POL
433
MPHLLVGSSGL
P
L

11



 


100
20
POL
1
MPLSYQHF
P
F
19.0010
8
*
0.0001
0.0097
0.0120
0.0370
0.0190


 


75
15
POL
1
MPLSYQHFRKL
P
L

11



 


90
18
POL
774
NPADDPSRGRL
P
L
26.0561
11
*
0.0120
0.0001
0.0001
−0.0003
0.0001


 


95
19
ENV
9
NPLGFFPDHQL
P
L
26.0562
11

0.0012
0.0021
0.0001
0.0028
0.0001


 


75
15
POL
571
NPNKTKRW
P
W

8



 


75
15
POL
571
NPNKTKRWGY
P
Y

10



 


95
19
NUC
129
PPAYRPPNA
P
A
16.0007
9

0.0001
0.0001
0.0001
0.0002
0.0003


 


95
19
NUC
129
PPAYRPPNAPI
P
I
26.0583
11

0.0003
0.0001
0.0001
−0.0003
0.0001


 


85
17
ENV
58
PPHGGLLGW
P
W
20.0141
9

0.0001
0.0002
0.0001
0.0003
0.0002


 


100
20
NUC
134
PPNAPILSTL
P
L
15.0211
10

0.0001
0.0001
0.0035
0.0001
0.0002


 


80
16
POL
615
RPIDWKVCQRI
P
I

11



 


100
20
NUC
133
RPPNAPIL
P
L
19.0009
8
*
0.0076
0.0001
0.0280
0.0002
0.0002


 


100
20
NUC
133
RPPNAPILSTL
P
L
26.0564
11
*
0.1300
0.0001
0.0018
−0.0003
0.0001


 


100
20
NUC
44
SPEHCSPHHTA
P
A
26.0565
11

−0.0002
0.0001
0.0001
−0.0003
0.0011


 


95
19
POL
511
SPFLLAQF
P
F
19.0012
8
*
0.5500
0.0009
0.0180
0.0009
0.0093


 


95
19
POL
511
SPFLLAQFTSA
P
A
26.0566
11
*
0.0820
0.0001
0.0001
−0.0003
12.0500


 


100
20
NUC
49
SPHHTALRQA
P
A
16.0178
10

0.0012
0.0001

0.0002
0.0035


 


100
20
NUC
49
SPHHTALRQAI
P
I
26.0567
11
*
0.5800
0.0001
0.0004
0.0005
0.0002


 


85
17
ENV
67
SPQAQGIL
P
L

8



 


85
17
POL
808
SPSVPSHL
P
L

8



 


75
15
ENV
350
SPTVWLSV
P
V

8



 


75
15
ENV
350
SPTVWLSVI
P
I
1308.16
9



 


75
15
ENV
350
SPTVWLSVIW
P
W
1308.17
10



 


75
15
ENV
350
SPTVWLSVIWM
P
M

11



 


95
19
POL
659
SPTYKAFL
P
L
19.0015
8
*
0.3900
0.0001
0.0019
0.0002
0.0002


 


90
18
POL
354
TPARVTGGV
P
V
1147.07
9
*
0.0078
0.0001
0.0013
0.0001
0.0015


 


90
18
POL
354
TPARVTGGVF
P
F
1147.04
10
*
0.3200
0.1000
0.0001
0.0099
0.0006


 


90
18
POL
354
TPARVTGGVFL
P
L
26.0568
11
*
0.0950
0.0001
0.0001
0.0005
0.0005


 


95
19
NUC
128
TPPAYRPPNA
P
A
16.0179
10
*
0.0001
0.0001

0.0002
0.0100


 


75
15
ENV
57
TPPHGGLL
P
L

8



 


75
15
ENV
57
TPPHGGLLGW
P
W
1308.04
10



 


80
16
POL
691
TPTGWGLA
P
A

8



 


75
15
POL
691
TPTGWGLAI
P
I

9



 


95
19
ENV
340
VPFVQWFV
P
V
19.0008
8
*
0.0010
0.0001
19.0000
0.0002
0.1100


 


95
19
ENV
340
VPFVQWFVGL
P
L
15.0213
10

0.0011
0.0001
0.0100
0.0001
0.0025


 


95
19
POL
398
VPNLQSLTNL
P
L
15.0216
10

0.0006
0.0001
0.0004
0.0001
0.0002


 


95
19
POL
398
VPNLQSLTNLL
P
L
26.0569
11

0.0004
0.0001
0.0001
−0.0003
0.0002


 


90
18
POL
769
VPSALNPA
P
A
19.0016
8
*
0.0011
0.0001
0.0070
0.0002
1.0000


 


95
19
POL
393
WPKFAVPNL
P
L
15.0035
9

0.0054
0.0002
0.0016
0.0001
0.0015


 


95
19
POL
640
YPALMPLY
P
Y
19.0014
8
*
0.0004
0.2600
0.4100
0.0450
0.0056


 


95
19
POL
640
YPALMPLYA
P
A
1147.08
9
*
0.0180
0.0480
0.0340
0.0140
16.0000


 


95
19
POL
640
YPALMPLYACI
P
I
26.0570
11

0.0040
0.0001
0.0470
0.0320
0.0700


 






96
















TABLE XI







HBV B27 SUPER MOTIF


 
























Super-


SEQ ID


Source
Conservancy
Freq
Protein
Position
Sequence
String
Motif
Peptide
Filed
NO:




















HBV
95
19
X
51
AHLSLRGL
XHXXXXXL
B27s


1162


 


HBV
85
17
POL
546
AKSVQHLESL
XKXXXXXXXL
B27s


1163


 


HBV
90
18
POL
356
ARVTGGVF
XRXXXXXF
B27s


1164


 


HBV
90
18
POL
356
ARVTGGVFL
XRXXXXXXL
B27s


1165


 


HBV
95
19
X
48
DHGAHLSL
XHXXXXXL
B27s


1166


 


HBV
95
19
X
48
DHGAHLSLRGL
XHXXXXXXXXL
B27s


1167


 


HBV
90
18
ENV
16
DHQLDPAF
XHXXXXXF
B27s


1168


 


HBV
100
20
POL
126
DKGIKPYY
XKXXXXXY
B27s


1169


 


HBV
100
20
NUC
46
EHCSPHHTAL
XHXXXXXXXL
B27s


1170


 


HBV
90
18
NUC
103
FHISCLTF
XHXXXXXF
B27s


1171


 


HBV
80
16
POL
501
FRKIPMGVGL
XRXXXXXXXL
B27s


1172


 


HBV
80
16
POL
608
FRKLPVNRPI
XRXXXXXXXI
B27s


1173


 


HBV
75
15
NUC
140
GRETVLEY
XRXXXXXY
B27s


1174


 


HBV
75
15
NUC
140
GRETVLEYL
XRXXXXXXL
B27s


1175


 


HBV
100
20
NUC
51
HHTALRQAI
XHXXXXXXI
B27s


1176


 


HBV
95
19
NUC
51
HHTALRQAIL
XHXXXXXXXL
B27s


1177


 


HBV
95
19
POL
54
HKVGNFTGL
XKXXXXXXL
B27s
17.0358

1178


 


HBV
95
19
POL
54
HKVGNFTGLY
XKXXXXXXXY
B27s


1179


 


HBV
75
15
POL
568
IHLNPNKTKRW
XHXXXXXXXXW
B27s


1180


 


HBV
85
17
POL
714
IHTAELLAACF
XHXXXXXXXXF
B27s


1181


 


HBV
85
17
POL
576
KRWGYSLNF
XRXXXXXF
B27s


1182


 


HBV
85
17
POL
576
KRWGYSLNFM
XRXXXXXXXM
B27s


1183


 


HBV
90
18
X
93
LHKRTLGL
XHXXXXXL
B27s


1184


 


HBV
95
19
POL
490
LHLYSHPI
XHXXXXXI
B27s


1185


 


HBV
80
16
POL
490
LHLYSHPII
XHXXXXXXI
B27s


1186


 


HBV
80
16
POL
490
LHLYSHPIIL
XHXXXXXXXL
B27s


1187


 


HBV
100
20
POL
428
LHPAAMPHL
XHXXXXXXL
B27s


1188


 


HBV
100
20
POL
428
LHPAAMPHLL
XHXXXXXXXL
B27s


1189


 


HBV
100
20
POL
148
LHTLWKAGI
XHXXXXXXI
B27s


1190


 


HBV
100
20
POL
148
LHTLWKAGIL
XHXXXXXXXL
B27s


1191


 


HBV
100
20
POL
148
LHTLWKAGILY
XHXXXXXXXXY
B27s


1192


 


HBV
75
15
POL
107
LKLIMPARF
XKXXXXXXF
B27s


1193


 


HBV
75
15
POL
107
LKLIMPARFY
XKXXXXXXXY
B27s


1194


 


HBV
95
19
X
55
LRGLPVCAF
XRXXXXXXF
B27s


1195


 


HBV
80
16
POL
761
LRGTSFVY
XRXXXXXY
B27s


1196


 


HBV
95
19
NUC
55
LRQAILCW
XRXXXXXW
B27s


1197


 


HBV
90
18
NUC
55
LRQAILCWGEL
XRXXXXXXXXL
B27s


1198


 


HBV
95
19
ENV
240
LRRFIIFL
XRXXXXXL
B27s


1199


 


HBV
75
15
ENV
240
LRRFIIFLF
XRXXXXXXF
B27s


1200


 


HBV
75
15
ENV
240
LRRFIIFLFI
XRXXXXXXXI
B27s


1201


 


HBV
75
15
ENV
240
LRRFIIFLFIL
XRXXXXXXXXL
B27s


1202


 


HBV
75
15
POL
573
NKTKRWGY
XKXXXXXY
B27s


1203


 


HBV
75
15
POL
573
NKTKRWGYSL
XKXXXXXXXL
B27s


1204


 


HBV
85
17
POL
34
NRRVAEDL
XRXXXXXL
B27s


1205


 


HBV
85
17
POL
34
NRRVAEDLNL
XRXXXXXXXL
B27s


1206


 


HBV
95
19
POL
531
PHCLAFSY
XHXXXXXY
B27s


1207


 


HBV
95
19
POL
531
PHCLAFSYM
XHXXXXXXM
B27s


1208


 


HBV
85
17
ENV
59
PHGGLLGW
XHXXXXXW
B27s


1209


 


HBV
100
20
NUC
50
PHHTALRQAI
XHXXXXXXXI
B27s


1210


 


HBV
95
19
NUC
50
PHHTALRQAIL
XHXXXXXXXXL
B27s


1211


 


HBV
80
16
POL
434
PHLLVGSSGL
XHXXXXXXXL
B27s


1212


 


HBV
95
19
POL
394
PKFAVPNL
XKXXXXXL
B27s


1213


 


HBV
95
19
POL
394
PKFAVPNLQSL
XKXXXXXXXXL
B27s


1214


 


HBV
85
17
X
90
PKVLHKRTL
XKXXXXXXL
B27s


1215


 


HBV
85
17
X
90
PKVLHKRTLGL
XKXXXXXXXXL
B27s


1216


 


HBV
75
15
POL
6
QHFRKLLL
XHXXXXXL
B27s


1217


 


HBV
75
15
POL
6
QHFRKLLLL
XHXXXXXXL
B27s


1218


 


HBV
90
18
POL
623
QRIVGLLGF
XRXXXXXXF
B27s


1219


 


HBV
100
20
POL
145
RHYLHTLW
XHXXXXXW
B27s


1220


 


HBV
80
16
POL
502
RKIPMGVGL
XKXXXXXXL
B27s


1221


 


HBV
80
16
POL
609
RKLPVNRPI
XKXXXXXXI
B27s


1222


 


HBV
80
16
POL
609
RKLPVNRPIDW
XKXXXXXXXXW
B27s


1223


 


HBV
85
17
POL
744
RKYTSFPW
XKXXXXXW
B27s


1224


 


HBV
85
17
POL
744
RKYTSFPWL
XKXXXXXXL
B27s


1225


 


HBV
85
17
POL
744
RKYTSFPWLL
XKXXXXXXXL
B27s


1226


 


HBV
95
19
POL
527
RRAFPHCL
XRXXXXXL
B27s


1227


 


HBV
95
19
POL
527
RRAFPHCLAF
XRXXXXXXXF
B27s


1228


 


HBV
75
15
ENV
241
RRFIIFLF
XRXXXXXF
B27s


1229


 


HBV
75
15
ENV
241
RRFIIFLFI
XRXXXXXXI
B27s


1230


 


HBV
75
15
ENV
241
RRFIIFLFIL
XRXXXXXXXL
B27s


1231


 


HBV
75
15
ENV
241
RRFIIFLFILL
XRXXXXXXXXL
B27s


1232


 


HBV
75
15
POL
105
RRLKLIMPARF
XRXXXXXXXXF
B27s


1233


 


HBV
90
16
POL
35
RRVAEDLNL
XRXXXXXXL
B27s


1234


 


HBV
80
16
POL
494
SHPIILGF
XHXXXXXF
B27s


1235


 


HBV
80
16
POL
494
SHPIILGFRKI
XHXXXXXXXXI
B27s


1236


 


HBV
90
18
NUC
20
SKLCLGWL
XKKXXXXL
B27s


1237


 


HBV
85
17
NUC
20
SKLCLGWLW
XKXXXXXXW
B27s


1238


 


HBV
85
17
NUC
20
SKLCLGWLWGM
XKXXXXXXXXM
B27s


1239


 


HBV
85
17
POL
743
SRKYTSFPW
XRXXXXXXW
B27s


1240


 


HBV
85
17
POL
743
SRKYTSFPWL
XRXXXXXXXL
B27s


1241


 


HBV
85
17
POL
743
SRKYTSFPWLL
XRXXXXXXXXL
B27s


1242


 


HBV
95
19
POL
375
SRLVVDFSQF
XRXXXXXXXF
B27s


1243


 


HBV
80
16
POL
472
SRNLYVSL
XRXXXXXL
B27s
17.0123

1244


 


HBV
95
19
POL
53
THKVGNFTGL
XHXXXXXXXL
B27s


1245


 


HBV
95
19
POL
53
THKVGNFTGLY
XHXXXXXXXXY
B27s


1246


 


HBV
95
19
POL
575
TKRWGYSL
XKXXXXXL
B27s


1247


 


HBV
85
17
POL
575
TKRWGYSLNF
XKXXXXXXXF
B27s


1248


 


HBV
85
17
POL
575
TKRWGYSLNFM
XKXXXXXXXXM
B27s


1249


 


HBV
100
20
POL
120
TKYLPLDKGI
XKXXXXXXXI
B27s


1250


 


HBV
100
20
POL
144
TRHYLHTL
XRXXXXXL
B27s


1251


 


HBV
100
20
POL
144
TRHYLHTLW
XRXXXXXXW
B27s


1252


 


HBV
80
16
ENV
186
TRILTIPQSL
XRXXXXXXXL
B27s


1253


 


HBV
80
16
POL
819
VHFASPLHVAW
XHXXXXXXXXW
B27s


1254


 


HBV
80
16
ENV
331
VRFSWLSL
XRXXXXXL
B27s


1255


 


HBV
80
16
ENV
331
VRFSWLSLL
XRXXXXXXL
B27s


1256


 


HBV
95
19
POL
526
VRRAFPHCL
XRXKXXXXL
B27s


1257


 


HBV
95
19
POL
526
VRRAFPHCLAF
XRXXXXXXXXF
B27s


1258


 


HBV
85
17
POL
619
WKVCQRIVGL
XKXXXXXXXL
B27s


1259


 


HBV
85
17
POL
619
WKVCQRIVGLL
XKXXXXXXXXL
B27s


1260


 


HBV
100
20
NUC
132
YRPPNAPI
XRXXXXXI
B27s


1261


 


HBV
100
20
NUC
132
YRPPNAPIL
XRXXXXXXL
B27s
17.0356

1262


 


HBV
95
19
ENV
235
YRWMCLRRF
XRXXXXXXF
B27s


1263


 


HBV
95
19
ENV
235
YRWMCLRRFI
XRXXXXXXXI
B27s


1264


 


HBV
95
19
ENV
235
YRWMCLRRFII
XRXXXXXXXXI
B27s


1265


 







104
















TABLE XII







HBV B44 SUPER MOTIF

















Source
Conservancy
Freq
Protein
Position
Sequence
String
Supermotif
Peptide
Filed
SEQ ID NO:




















HBV
95
19
POL
688
ADATPTGW
XDXXXXXW
B44


1266


 


HBV
95
19
POL
688
ADATPTGWGL
XDXXXXXXXL
B44


1267


 


HBV
80
16
POL
688
ADATPTGWGL
XDXXXXXXXXA
B44


1268


 


HBV
90
18
POL
776
ADDPSRGRL
XDXXXXXXL
B44


1269


 


HBV
90
18
POL
776
ADDPSRGRLGL
XDXXXXXXXXL
B44


1270


 


HBV
95
19
POL
38
AEDLNLGNL
XEXXXXXXL
B44
17.0357

1271


 


HBV
95
19
POL
38
AEDLNLGNLNV
XEXXXXXXXXV
B44


1272


 


HBV
85
17
POL
717
AELLAACF
XEXXXXXF
B44


1273


 


HBV
85
17
POL
717
AELLAACFA
XEXXXXXXA
B44


1274


 


HBV
90
18
POL
777
DDPSAGRL
XDXXXXXL
B44
17.0010

1275


 


HBV
90
18
POL
777
DDPSRGRLGL
XDXXXXXXXL
B44
17.0418

1276


 


HBV
90
18
POL
540
DDVVLGAKSV
XDXXXXXXXV
B44


1277


 


HBV
75
15
POL
18
DEAGPLEEEL
XEXXXXXXXL
B44


1278


 


HBV
95
19
POL
39
EDUNLGNL
XDXXXXXL
B44


1279


 


HBV
95
19
POL
39
EDUNLGNUNV
XDXXXXXXXV
B44


1280


 


HBV
90
18
POL
22
EEELPRLA
XEXXXXXA
B44


1281


 


HBV
80
16
X
121
EELGEEIRL
XEXXXXXXL
B44


1282


 


HBV
90
18
NUC
32
IDPYKEFGA
XDXXXXXXA
B44


1283


 


HBV
85
17
POL
617
IDWKVCORI
XDXXXXXXI
B44


1284


 


HBV
85
17
POL
617
IDWKVCORIV
XDXXXXXXXV
B44


1285


 


HBV
100
20
POL
125
LDKGIKPY
XDXXXXXY
B44


1286


 


HBV
100
20
POL
125
LDKGIKPYY
XDXXXXXXY
B44


1287


 


HBV
80
16
X
9
LDPARDVL
XDXXXXXL
B44
17.0012

1288


 


HBV
80
16
X
9
LDPARDVLCL
XDXXXXXXXL
B44
17.0419

1289


 


HBV
95
19
ENV
195
LDSWWTSL
XDXXXXXL
B44


1290


 


HBV
95
19
ENV
195
LDSWWTSLNF
XDXXXXXXXF
B44


1291


 


HBV
90
18
BW
195
LDSWWTSLNFL
XDXXXXXXXXL
B44


1292


 


HBV
85
17
NUC
31
LDTASALY
XDXXXXXY
B44


1293


 


HBV
80
16
NUC
31
LDTASALYREA
XDXXXXXXXXA
B44


1294


 


HBV
95
19
POL
417
LDVSAAFY
XDXXXXXY
B44


1295


 


HBV
90
18
ENV
261
LDYQGMLPV
XDXXXXXXV
B44


1296


 


HBV
95
19
POL
21
LEEELPRL
XEXXXXXL
B44


1297


 


HBV
90
18
POL
21
LEEELPRLA
XEXXXXXXA
B44


1298


 


HBV
90
18
POL
539
MDDVVLGA
XDXXXXXA
B44


1299


 


HBV
90
18
POL
539
MDDVVGAKSV
XDXXXXXXXXV
B44


1300


 


HBV
90
18
NUC
30
MDIDPYKEF
XDXXXXXXF
B44


1301


 


HBV
90
18
NUC
30
MDIDPYKEFGA
XDXXXXXXXXA
B44


1302


 


HBV
95
19
ENV
15
PDHQLDPA
XDXXXXXA
B44


1303


 


HBV
90
18
ENV
15
PDHQLDPAF
XDXXXXXXF
B44


1304


 


HBV
100
20
NUC
45
PEHCSPHHTA
XEXXXXXXXA
B44


1305


 


HBV
100
20
NUC
45
PEHCSPHHTAL
XEXXXXXXXXL
B44


1306


 


HBV
85
17
NUC
28
RDLLDTASA
XDXXXXXXA
B44


1307


 


HBV
85
17
NUC
28
RDLLDTASAL
XDXXXXXXXL
B44


1308


 


HBV
85
17
NUC
28
RDLLDTASALY
XDXXXXXXXXY
B44


1309


 


HBV
95
19
X
13
RDVLCLRPV
XDXXXXXXV
B44


1310


 


HBV
95
19
X
13
RDVLCLRPVGA
XDXXXXXXXXA
B44


1311


 


HBV
75
15
NUC
141
RETVLEYL
XEXXXXXL
B44


1312


 


HBV
75
15
NUC
141
RETVLEYLV
XEXXXXXXV
B44


1313


 


HBV
90
18
POL
736
TDNSVVLSRKY
XDXXXXXXXXY
B44


1314


 


HBV
95
19
NUC
42
VELLSFLPSDF
XEXXXXXXXXF
B44


1315


 


HBV
80
16
X
120
WEELGEEEI
XEXXXXXI
B44


1316


 


HBV
80
16
X
120
WEELGEEIRL
XEXXXXXXXL
B44


1317


 







52
















TABLE XIII







HBV B58 SUPER MOTIF

















Source
Convervancy
Freq
Protein
Position
Sequence
String
Supermotif
Peptide
Filed
SEQ ID NO:




















HBV
85
17
POL
431
AAMPHLLV
XAXXXXXV
B58


1318


 


HBV
95
19
POL
632
AAPFTQCGY
XAXXXXXXY
B58


1319


 


HBV
85
17
NUC
34
ASALYREAL
XSXXXXXXL
B58


1320


 


HBV
100
20
POL
166
ASFCGSPY
XSXXXXXY
B58
26.0026
*
1321


 


HBV
100
20
POL
166
ASFCGSPYSW
XSXXXXXXXW
B58


1322


 


HBV
90
18
NUC
19
ASKLCLGW
XSXXXXXW
B58


1323


 


HBV
90
18
NUC
19
ASKLCLGWL
XSXXXXXXL
B58


1324


 


HBV
85
17
NUC
19
ASKLCLGWLW
XSXXXXXXXW
B58


1325


 


HBV
80
16
POL
822
ASPLHVAW
XSXXXXXW
B58


1326


 


HBV
80
16
ENV
329
ASVRFSWL
XSXXXXXL
B58


1327


 


HBV
80
16
ENV
329
ASVRFSWLSL
XSXXXXXXXL
B58


1328


 


HBV
80
16
ENV
329
ASVRFSWLSLL
XSXXXXXXXXL
B58


1329


 


HBV
95
19
POL
690
ATPTGWGL
XTXXXXXL
B58


1330


 


HBV
75
15
POL
690
ATPTGWGLAI
XTXXXXXXXI
B58


1331


 


HBV
95
19
X
61
CAFSSAGPCAL
XAXXXXXXXXL
B58


1332


 


HBV
100
20
NUC
48
CSPHHTAL
XSXXXXXL
B58


1333


 


HBV
80
16
POL
471
CSRNLYVSL
XSXXXXXXL
B58


1334


 


HBV
95
19
POL
523
CSVVRRAF
XSXXXXXF
B58


1335


 


HBV
100
20
ENV
310
CTCIPIPSSW
XTXXXXXXXW
B58


1336


 


HBV
95
19
POL
689
DATPTGWGL
XAXXXXXXL
B58
5.0027

1337


 


HBV
75
15
POL
689
DATPTGWGLAI
XAXXXXXXXXI
B58


1338


 


HBV
95
19
ENV
196
DSWWTSLNF
XSXXXXXXF
B58
20.0120

1339


 


HBV
90
18
ENV
196
DSWWTSLNFL
XSXXXXXXXL
B58


1340


 


HBV
80
16
NUC
32
DTASALYREA
XTXXXXXXXXL
B58


1341


 


HBV
80
16
NUC
32
DTASALYREAL
XTXXXXXXXXL
B58


1342


 


HBV
100
20
POL
17
EAGPLEEEL
XAXXXXXXL
B58
5.0028

1343


 


HBV
95
19
POL
374
ESRLVVDF
XSXXXXXF
B58


1344


 


HBV
95
19
POL
374
ESRLVVDFSQF
XSXXXXXXXXF
B58


1345


 


HBV
75
15
NUC
142
ETVLEYLV
XTXXXXXV
B58


1346


 


HBV
95
19
POL
631
FAAPFTQCGY
XAXXXXXXXV
B58
20.0254
*
1347


 


HBV
95
19
POL
687
FADATPTGW
XAXXXXXXW
B58


1348


 


HBV
95
19
POL
687
FADATPTGWGL
XAXXXXXXXXL
B58


1349


 


HBV
80
16
POL
821
FASPLHVAW
XAXXXXXXW
B58


1350


 


HBV
95
19
POL
396
FAVPNLQSL
XAXXXXXXL
B58
5.0029
*
1351


 


HBV
95
19
POL
658
FSPTYKAF
XSXXXXXF
B58


1352


 


HBV
95
19
POL
658
FSPTYKAFL
XSXXXXXXL
B58


1353


 


HBV
95
19
X
63
FSSAGPCAL
XSXXXXXXL
B58


1354


 


HBV
90
18
X
63
FSSAGPCALRF
XSXXXXXXXXF
B58


1355


 


HBV
100
20
ENV
333
FSWLSLLV
XSXXXXXV
B58


1356


 


HBV
100
20
ENV
333
FSWLSLLVPF
XSXXXXXXXF
B58
20.0263

1357


 


HBV
100
20
ENV
333
FSWLSLLVPFV
XSXXXXXXXXV
B58


1358


 


HBV
90
18
POL
536
FSYMDDVV
XSXXXXXV
B58
17.0257

1359


 


HBV
90
18
POL
536
FSYMDDVVL
XSXXXXXXL
B58


1360


 


HBV
95
19
POL
656
FTFSPTYKAF
XTXXXXXXXF
B58
20.0262

1361


 


HBV
95
19
POL
656
FTFSPTYKAFL
XTXXXXXXXXL
B58


1362


 


HBV
90
18
POL
59
FTGLYSSTV
XTXXXXXXV
B58
20.0118

1363


 


HBV
95
19
POL
635
FTQCGYPAL
XTXXXXXXL
B58
5.0031

1364


 


HBV
95
19
POL
635
FTQCGYPALM
XTXXXXXXXM
B58
5.0085

1365


 


HBV
95
19
POL
518
FTSAICSV
XTXXXXXV
B58


1366


 


HBV
95
19
POL
518
FTSAICSVV
XTXXXXXXV
B58
5.0032

1367


 


HBV
95
19
X
50
GAHLSLRGL
XAXXXXXXL
B58
5.0040

1368


 


HBV
90
18
X
50
GAHLSLRGLPV
XAXXXXXXXXV
B58


1369


 


HBV
85
17
POL
545
GAKSVQHL
XAXXXXXL
B58


1370


 


HBV
85
17
POL
545
GAKSVQHLESL
XAXXXXXXXXL
B58


1371


 


HBV
75
15
ENV
134
GSSSGTVNPV
XSXXXXXXXV
B58


1372


 


HBV
90
18
POL
735
GTDNSVVL
XTXXXXXL
B58


1373


 


HBV
75
15
ENV
13
GTNLSVPNPL
XTXXXXXXXL
B58


1374


 


HBV
80
16
POL
763
GTSFVYVPSAL
XTXXXXXXXXL
B58


1375


 


HBV
85
17
POL
715
HTAELLAACF
XTXXXXXXXF
B58


1376


 


HBV
100
20
NUC
52
HTALRQAI
XTXXXXXI
B58


1377


 


HBV
95
19
NUC
52
HTALRQAIL
XTXXXXXXL
B58
5.0021

1378


 


HBV
95
19
NUC
52
HTALRQAILCW
XTXXXXXXXXW
B58


1379


 


HBV
100
20
POL
149
HTLWKAGI
XTXXXXXI
B58


1380


 


HBV
100
20
POL
149
HTLWKAGIL
XTXXXXXXL
B58
5.0033

1381


 


HBV
100
20
POL
149
HTLWKAGILY
XTXXXXXXXY
B58
1.0542
*
1382


 


HBV
90
18
NUC
105
ISCLTFGRETV
XSXXXXXXXXV
B58


1383


 


HBV
85
17
POL
547
KSVQHLESL
XSXXXXXXL
B58


1384


 


HBV
95
19
POL
574
KTKRWGYSL
XTXXXXXXL
B58
5.0034

1385


 


HBV
85
17
POL
574
KTKRWGYSLNF
XTXXXXXXXXF
B58


1386


 


HBV
90
18
POL
534
LAFSYMDDV
XAXXXXXXV
B58
20.0118

1387


 


HBV
90
18
POL
534
LAFSYMDDVV
XAXXXXXXXV
B58
20.0257

1388


 


HBV
90
18
POL
534
LAFSYMDDVVL
XAXXXXXXXXL
B58


1389


 


HBV
95
19
POL
515
LAQFTSAI
XAXXXXXI
B58


1390


 


HBV
95
19
POL
515
LAQFTSAICSV
XAXXXXXXXXV
B58


1391


 


HBV
95
19
NUC
45
LSFLPSDF
XSXXXXXF
B58


1392


 


HBV
95
19
NUC
45
LSFLPSDFF
XSXXXXXXF
B58
20.0123

1393


 


HBV
95
19
POL
415
LSLDVSAAF
XSXXXXXXF
B58


1394


 


HBV
95
19
POL
415
LSLDVSAAFY
XSXXXXXXXY
B58
2.0239
*
1395


 


HBV
100
20
ENV
336
LSLLVPFV
XSXXXXXV
B58


1396


 


HBV
100
20
ENV
336
LSLLVPFVQW
XSXXXXXXXW
B58


1397


 


HBV
100
20
ENV
336
LSLLVPFVQWF
XSXXXXXXXXF
B58


1398


 


HBV
95
19
X
53
LSLRGLPV
XSXXXXXV
B58


1399


 


HBV
95
19
X
53
LSLRGLPVCAF
XSXXXXXXXXF
B58


1400


 


HBV
95
19
POL
510
LSPFLLAQF
XSXXXXXXF
B58


1401


 


HBV
75
15
ENV
349
LSPTVWLSV
XSXXXXXXV
B58


1402


 


HBV
75
15
ENV
349
LSPTVWLSVI
XSXXXXXXXI
B58


1403


 


HBV
75
15
ENV
349
LSPTVWLSVIW
XSXXXXXXXXW
B58


1404


 


HBV
85
17
POL
742
LSRKYTSF
XSXXXXXF
B58


1405


 


HBV
85
17
POL
742
LSRKYTSFPW
XSXXXXXXXW
B58


1406


 


HBV
85
17
POL
742
LSRKYTSFPWL
XSXXXXXXXXL
B58


1407


 


HBV
90
18
POL
408
LSSNLSWL
XSXXXXXL
B58


1408


 


HBV
90
18
POL
408
LSSNLSWLSL
XSXXXXXXXL
B58


1409


 


HBV
100
20
NUC
140
LSTLPETTV
XSXXXXXXV
B58


1410


 


HBV
100
20
NUC
140
LSTLPETTVV
XSXXXXXXXV
B58


1411


 


HBV
75
15
ENV
16
LSVPNPLGF
XSXXXXXXF
B58


1412


 


HBV
100
20
POL
412
LSWLSLDV
XSXXXXXV
B58


1413


 


HBV
75
15
POL
3
LSYQHFRKL
XSXXXXXXL
B58


1414


 


HBV
75
15
POL
3
LSYQHFFRKLL
XSXXXXXXXL
B58


1415


 


HBV
75
15
POL
3
LSYQHFRKLLL
XSXXXXXXXXL
B58


1416


 


HBV
95
19
NUC
108
LTFGRETV
XTXXXXXV
B58


1417


 


HBV
75
15
NUC
137
LTFGRETVL
XTXXXXXXL
B58


1418


 


HBV
75
15
NUC
137
LTFGRETVLEY
XTXXXXXXXXY
B58


1419


 


HBV
90
18
ENV
189
LTIPQSLDSW
XTXXXXXXXW
B58


1420


 


HBV
90
18
ENV
189
LTIPQSLDSWW
XTXXXXXXXXW
B58


1421


 


HBV
90
18
POL
404
LTNLLSSNL
XTXXXXXXL
B58


1422


 


HBV
90
18
POL
404
LTNLLSSNLSW
XTXXXXXXXXW
B58


1423


 


HBV
80
16
ENV
185
LTRILTIPQSL
XTXXXXXXXXL
B58


1424


 


HBV
85
17
POL
99
LTVNEKRRL
XTXXXXXXL
B58


1425


 


HBV
75
15
X
103
MSTTDLEAY
XSXXXXXXY
B58
2.0126
*
1426


 


HBV
75
15
X
103
MSTTDLEAYF
XSXXXXXXXF
B58


1427


 


HBV
100
20
NUC
136
NAPILSTL
XAXXXXXL
B58


1428


 


HBV
90
18
POL
738
NSVVLSRKY
XSXXXXXXY
B58
2.0123

1429


 


HBV
100
20
POL
430
PAAMPHLL
XAXXXXXL
B58


1430


 


HBV
85
17
POL
430
PAAMPHLLV
XAXXXXXXV
B58


1431


 


HBV
90
18
POL
775
PADDPSRGRL
XAXXXXXXXL
B58


1432


 


HBV
90
18
ENV
131
PAGGSSSGTV
XAXXXXXXXV
B58


1433


 


HBV
95
19
POL
641
PALMPLYACI
XAXXXXXXXI
B58
5.0087

1434


 


HBV
80
16
X
11
PARDVLCL
XAXXXXXL
B58


1435


 


HBV
75
15
X
11
PARDVLCLRPV
XAXXXXXXXXV
B58


1436


 


HBV
90
18
POL
355
PARVTGGV
XAXXXXXV
B58


1437


 


HBV
90
18
POL
355
PARVTGGVF
XAXXXXXXF
B58


1438


 


HBV
90
18
POL
355
PARVTGGVFL
XAXXXXXXXL
B58


1439


 


HBV
90
18
POL
355
PARVTGGVFLV
XAXXXXXXXXV
B58


1440


 


HBV
95
19
NUC
130
PAYRPPNAPI
XAXXXXXXXI
B58
5.0081

1441


 


HBV
95
19
NUC
130
PAYRPPNAPIL
XAXXXXXXXXL
B58


1442


 


HBV
90
18
POL
779
PSRGRLGL
XSXXXXXL
B58


1443


 


HBV
75
15
POL
692
PTGWGLAI
XTXXXXXI
B58


1444


 


HBV
85
17
POL
797
PTTGRTSL
XTXXXXXL
B58


1445


 


HBV
85
17
POL
797
PTTGRTSLY
XTXXXXXXY
B58
1.0208
*
1446


 


HBV
80
16
NUC
15
PTVQASKL
XTXXXXXL
B58


1447


 


HBV
80
16
NUC
15
PTVQASKLCL
XTXXXXXXXL
B58


1448


 


HBV
75
15
ENV
351
PTVWLSVI
XTXXXXXI
B58


1449


 


HBV
75
15
ENV
351
PTVWLSVIW
XTXXXXXXW
B58


1450


 


HBV
150
30
ENV
351
PTVWLSVIWM
XTXXXXXXXM
B58


1451


 


HBV
95
19
POL
654
QAFTFSPTY
XAXXXXXXY
B58
20.0127

1452


 


HBV
80
16
ENV
179
QAGFFLLTRIL
XAXXXXXXXXL
B58


1453


 


HBV
90
18
NUC
57
QAILCWGEL
XAXXXXXXL
B58


1454


 


HBV
180
36
NUC
57
QAILCWGELM
XAXXXXXXXM
B58


1455


 


HBV
80
16
ENV
107
QAMQWNSTTF
XAXXXXXXXF
B58


1456


 


HBV
80
16
NUC
18
QASKLCLGW
XAXXXXXXW
B58


1457


 


HBV
80
16
NUC
18
QASKLCLGWL
XAXXXXXXXL
B58


1458


 


HBV
75
15
NUC
18
QASKLCLGWLW
XAXXXXXXXXW
B58


1459


 


HBV
90
18
ENV
193
QSLDSWWTSL
XSXXXXXXXL
B58
F126.63

1460


 


HBV
90
18
POL
402
QSLTNLLSSNL
XSXXXXXXXXL
B58


1461


 


HBV
95
19
POL
528
RAFPHCLAF
XAXXXXXXF
B58
20.0125

1462


 


HBV
95
19
POL
528
RAFPHCLAFSY
XAXXXXXXXXY
B58
26.0550
*
1463


 


HBV
90
18
POL
353
RTPARVTGGV
XTXXXXXXXV
B58


1464


 


HBV
90
18
POL
353
RTPARVTGGVF
XTXXXXXXXXF
B58


1465


 


HBV
90
18
X
65
SAGPCALRF
XAXXXXXXF
B58
26.0152

1466


 


HBV
95
19
POL
520
SAICSVVRRAF
XAXXXXXXXXF
B58


1467


 


HBV
90
18
NUC
35
SALYREAL
XAXXXXXL
B58


1468


 


HBV
100
20
POL
165
SASFCGSPY
XAXXXXXXY
B58
20.0117
*
1469


 


HBV
100
20
POL
165
SASFCGSPYSW
XAXXXXXXXXW
B58


1470


 


HBV
95
19
X
64
SSAGPCAL
XSXXXXXL
B58


1471


 


HBV
90
18
X
64
SSAGPCALRF
XSXXXXXXXF
B58
26.0374

1472


 


HBV
75
15
ENV
136
SSGTVNPV
XSXXXXXV
B58


1473


 


HBV
90
18
POL
409
SSNLSWLSL
XSXXXXXXL
B58


1474


 


HBV
90
18
POL
409
SSNLSWSLDV
XSXXXXXXXXV
B58


1475


 


HBV
75
15
ENV
135
SSSGTVNPV
XSXXXXXXV
B58


1476


 


HBV
100
20
NUC
141
STLPETTV
XTXXXXXV
B58


1477


 


HBV
100
20
NUC
141
STLPETTVV
XTXXXXXXV
B58
5.0024

1478


 


HBV
75
15
X
104
STTDLEAY
XTXXXXXY
B58


1479


 


HBV
75
15
X
104
STTDLEAYF
XTXXXXXXF
B58


1480


 


HBV
85
17
POL
716
TAELLAACF
XAXXXXXXF
B58


1481


 


HBV
95
19
NUC
53
TALRQAIL
XAXXXXXL
B58


1482


 


HBV
95
19
NUC
53
TALRQAILCW
XAXXXXXXXW
B58


1483


 


HBV
80
16
NUC
33
TASALYREAL
XAXXXXXXXL
B58


1484


 


HBV
95
19
POL
519
TSAICSVV
XSXXXXXV
B58


1485


 


HBV
80
16
POL
764
TSFVYVPSAL
XSXXXXXXXL
B58


1486


 


HBV
80
16
ENV
168
TSGFLGPL
XSXXXXXL
B58


1487


 


HBV
75
15
ENV
168
TSGFLGPLL
XSXXXXXXL
B58


1488


 


HBV
75
15
ENV
168
TSGFLGPLLV
XSXXXXXXXV
B58


1489


 


HBV
75
15
ENV
168
TSGFLGPLLVL
XSXXXXXXXXL
B58


1490


 


HBV
75
15
X
105
TTDLEAYF
XTXXXXXF
B58


1491


 


HBV
85
17
POL
798
TTGRTSLY
XTXXXXXY
B58
26.0030

1492


 


HBV
95
19
POL
37
VAEDLNLGNL
XAXXXXXXXL
B58
5.0089

1493


 


HBV
100
20
POL
48
VSIPWTHKV
XSXXXXXXV
B58


1494


 


HBV
95
19
POL
391
VSWPKFAV
XSXXXXXV
B58


1495


 


HBV
95
19
POL
391
VSWPKFAVPNL
XSXXXXXXXXL
B58


1496


 


HBV
100
20
POL
358
VTGGVFLV
XTXXXXXV
B58


1497


 


HBV
85
17
ENV
66
WSPQAQGI
XSXXXXXI
B58


1498


 


HBV
85
17
ENV
66
WSPQAQGIL
XSXXXXXXL
B58


1499


 


HBV
100
20
POL
52
WTHKVGNF
XTXXXXXF
B58


1500


 


HBV
95
19
POL
52
WTHKVGNFTGL
XTXXXXXXXXL
B58


1501


 


HBV
80
16
POL
493
YSHPIILGF
XSXXXXXXF
B58


1502


 


HBV
85
17
POL
580
YSLNFMGY
XSXXXXXY
B58
26.0032

1503


 


HBV
75
15
POL
580
YSLNFMGYV
XSXXXXXXV
B58


1504


 


HBV
75
15
POL
580
YSLNFMGYVI
XSXXXXXXXI
B58


1505


 


HBV
85
17
POL
746
YTSFPWLL
XTXXXXXL
B58


1506


 







189
















TABLE XIV







HBV B62 SUPER MOTIF

















Source
Conservancy
Freq
Protein
Position
Sequence
String
Supermotif
Peptide
Filed
SEQ ID NO:




















HBV
95
19
POL
521
AICSVVRRAF
XIXXXXXXXF
B62s


1507


 


HBV
90
18
NUC
58
ALLCWGELM
XIXXXXXXM
B62s


1508


 


HBV
95
19
POL
642
ALMPLYACI
XLXXXKXXI
B62s
3.0012
*
1509


 


HBV
95
19
NUC
54
ALRQAILCW
XLXXXXXXW
B62s


1510


 


HBV
80
16
ENV
108
AMQWNSTTF
XMXXXXXXF
B62s


1511


 


HBV
95
19
POL
633
APFTQCGY
XPXXXXXY
B62s
19.0013

1512


 


HBV
95
19
POL
516
AQFTSAICSV
XQXXXXXXXV
B62s


1513


 


HBV
95
19
POL
516
AQFTSAICSVV
XQXXXXXXXXV
B62s


1514


 


HBV
100
20
ENV
312
CIPIPSSW
XIXXXXXW
B62s


1515


 


HBV
100
20
ENV
312
CIPIPSSWAF
XIXXXXXXXF
B62s


1516


 


HBV
90
16
POL
533
CLAFSYMDDV
XLXXXXXXXV
B62s
1.0559

1517


 


HBV
90
18
POL
533
CLAFSYMDDVV
XLXXXXXXXXV
B62s


1518


 


HBV
85
17
NUC
23
CLGWLWGM
XLXXXXXM
B62s


1519


 


HBV
85
17
NUC
23
CLGWLWGMDI
XLXXXXXXXI
B62s
2.0229

1520


 


HBV
95
19
ENV
253
CLIFLLVLLDY
XLXXXXXXXY
B62s
26.0548

1521


 


HBV
95
19
ENV
239
CLRRFIIF
XLXXXXXF
B62s


1522


 


HBV
75
15
ENV
239
CLRRFIIFLF
XLXXXXXXXF
B62s


1523


 


HBV
75
15
ENV
239
CLRRFIIFLFI
XLXXXXXXXXI
B62s
Chisari

1524


 


HBV
90
15
NUC
107
CLTFGRETV
XLXXXXXXV
B62s
1.0160

1525


 


HBV
80
16
X
7
CQLDRADV
XQXXXXXXV
B62s


1526


 


HBV
85
17
POL
622
CQRIVGLLGF
XQXXXXXXXF
B62s


1527


 


HBV
90
18
NUC
31
DIDPYKEF
XIXXXXXF
B62s


1528


 


HBV
85
17
NUC
29
DLLDTASALY
XLXXXXXXXY
B62s
1.0519
*
1529


 


HBV
95
19
POL
40
DLNLGNLNV
XLXXXXXXV
B62s
1.0164

1530


 


HBV
95
19
POL
40
DLNLGNLNVSI
XLXXXXXXXXI
B62s


1531


 


HBV
80
16
ENV
122
DPRVRGLY
XPXXXXXY
B62s


1532


 


HBV
95
19
X
14
DVLCLRPV
XVXXXXXV
B62s


1533


 


HBV
90
18
POL
541
DVVLGAKSV
XVXXXXXXV
B62s
1.0190

1534


 


HBV
95
19
NUC
43
ELLSFLPSDF
XLXXXXXXXF
B62s


1535


 


HBV
95
19
NUC
43
ELLSFLPSDFF
XLXXXXXXXXF
B62s


1536


 


HBV
80
16
ENV
248
FILLLCLI
XIXXXXXI
B62s
Chisari

1537


 


HBV
80
16
ENV
248
FILLLCLIF
XIXXXXXXF
B62s


1538


 


HBV
80
16
ENV
246
FIFLLLLCLI
XLXXXXXXXI
B62s
3.0206

1539


 


HBV
80
16
ENV
246
FLFILLLCLIF
XLXXXXXXXXF
B62s


1540


 


HBV
95
19
POL
513
FLLAQFTSAI
XLXXXXXXXI
B62s
1147.13
*
1541


 


HBV
80
16
ENV
183
FLLTRILTI
XLXXXXXXI
B62s
3.0005
*
1542


 


HBV
95
19
ENV
256
FLLVLLDY
XLXXXXXY
B62s
26.0027

1543


 


HBV
95
19
ENV
256
FLLVLLDYQGM
XLXXXXXXXXM
B62s


1544


 


HBV
75
15
ENV
130
FPAGGSSSGTV
XPXXXXXXXXV
B62s


1545


 


HBV
85
17
ENV
14
FPDHQLDPAF
XPXXXXXXXF
B62s
20.0274

1546


 


HBV
95
19
POL
530
FPHCLAFSY
XPXXXXXXY
B62s
15.0037
*
1547


 


HBV
95
19
POL
530
FPHCLAFSYM
XPXXXXXXXM
B62s
15.0217
*
1548


 


HBV
75
15
POL
749
FPWLLGCAANW
XPXXXXXXXXW
B62s


1549


 


HBV
95
19
ENV
346
FVGLSPTV
XVXXXXXV
B62s


1550


 


HBV
95
19
ENV
346
FVGLSPTVW
XVXXXXXXW
B62s


1551


 


HBV
90
18
X
132
FVLGGCRHKLV
XVXXXXXXXXV
B62s


1552


 


HBV
95
19
POL
627
GLLGFAAPF
XLXXXXXXF
B62s
20.0124

1553


 


HBV
95
19
POL
509
GLSPFLLAQF
XLXXXXXXXF
B62s


1554


 


HBV
75
15
ENV
348
GLSPTVWLSV
XLXXXXXXXV
B62s
1.0518
*
1555


 


HBV
75
15
ENV
348
GLSPTVWLSVI
XLXXXXXXXXI
B62s
Chisari

1556


 


HBV
85
17
NUC
29
GMDIDPYKEF
XMXXXXXXXF
B62s
26.0372

1557


 


HBV
95
19
ENV
173
GPLLVLQAGF
XPXXXXXXXF
B62s
15.0212

1558


 


HBV
95
19
ENV
173
GPLLVLQAGFF
XPXXXXXXXXF
B62s
26.0556

1559


 


HBV
95
19
NUC
123
GVWIRTPPAY
XVXXXXXXXY
B62s
1.0525

1560


 


HBV
75
15
POL
569
HLNPNKTKRW
XLXXXXXXXW
B62s


1561


 


HBV
90
18
X
52
HLSLRGLPV
XLXXXXXXV
B62s
1.0212

1562


 


HBV
80
16
POL
491
HLYSHPII
XLXXXXXI
B62s
17.0256

1563


 


HBV
80
16
POL
491
HLYSHPIILGF
XLXXXXXXXXF
B62s


1564


 


HBV
85
17
POL
429
HPAAMPHLLV
XPXXXXXXXV
B62s
20.0273
*
1565


 


HBV
80
16
POL
495
HPIILGFRKI
XPXXXXXXXI
B62s


1566


 


HBV
80
16
POL
497
IILGFRKI
XIXXXXXI
B62s
17.0124
*
1567


 


HBV
80
16
POL
497
IILGFRKIPM
XIXXXXXXXM
B62s


1568


 


HBV
90
18
NUC
59
ILCQGELM
XLXXXXXM
B62s


1569


 


HBV
80
16
POL
498
ILGFRKIPM
XLXXXXXXM
B62s
3.0016

1570


 


HBV
100
20
ENV
249
ILLLCLIF
XLXXXXXF
B62s


1571


 


HBV
100
20
ENV
249
ILLLCLIFLLV
XLXXXXXXXXV
B62s
Chisari

1572


 


HBV
80
16
POL
760
ILRGTSFV
XLXXXXXV
B62s


1573


 


HBV
80
16
POL
760
ILRGTSFVY
XLXXXXXXY
B62s
1.0205
*
1574


 


HBV
80
16
POL
760
ILRGTSFVYV
XLXXXXXXXV
B62s
1.0573
*
1575


 


HBV
100
20
NUC
139
ILSTLPETTV
XLXXXXXXXV
B62
1.0526

1576


 


HBV
100
20
NUC
139
ILSTLPETTVV
XLXXXXXXXXV
B62s

*
1577


 


HBV
90
18
ENV
188
ILTIPQSLDSW
XLXXXXXXXXW
B62s


1578


 


HBV
100
20
ENV
313
IPIPSSWAF
XPXXXXXXF
B62s
15.0032
*
1579


 


HBV
80
16
POL
504
IPMGVGLSPF
XPXXXXXXXF
B62s


1580


 


HBV
90
18
ENV
191
IPQSLDSW
XPXXXXXW
B62s
19.0004

1581


 


HBV
90
18
ENV
191
IPQSLDSWW
XPXXXXXXW
B62s
15.0030
*
1582


 


HBV
100
20
POL
50
IPWTHKVGNF
XPXXXXXXXF
B62s
15.0209

1583


 


HBV
90
18
POL
625
IVGLLGFAAPF
XVXXXXXKXXF
B62s


1584


 


HBV
80
16
POL
503
KIPMGVGLSPF
XIXXXXXXXXF
B62s


1585


 


HBV
85
17
NUC
21
KLCLGWLW
XLXXXXXW
B62s


1586


 


HBV
85
17
NUC
21
KLCLGWLWGM
XLXXXXXXXM
B62s
3.0209
*
1587


 


HBV
95
19
POL
489
KLHLYSHPI
XLXXXXXXI
B62s
3.0009
*
1588


 


HBV
80
16
POL
489
KLHLYSHPII
XLXXXXXXXI
B62s


1589


 


HBV
75
15
POL
108
KLIMPARF
XLXXXXXF
B62s


1590


 


HBV
75
15
POL
108
KLIMPARFY
XLXXXXXXY
B62s
1.0171

1591


 


HBV
80
16
POL
610
KLPVNRPI
XLXXXXXI
B62s


1592


 


HBV
80
16
POL
610
KLPVNRPIDW
XLXXXXXXXW
B62s


1593


 


HBV
95
19
POL
653
KQAFTFSPTY
XQXXXXXXXY
B62s
20.0256

1594


 


HBV
95
19
POL
55
KVGNFTGLY
XVXXXXXXY
B62s
1.0166
*
1595


 


HBV
95
19
ENV
254
LIFLLVLLDY
XIXXXXXXXY
B62s
1.0899

1596


 


HBV
100
20
POL
109
LIMPARFY
XIXXXXXY
B62s
26.0028

1597


 


HBV
95
19
POL
514
LLAQFTSAI
XLXXXXXXI
B62s
3.0010
*
1598


 


HBV
100
20
ENV
251
LLCLIFLLV
XLXXXXXXV
B62s
1.0835
*
1599


 


HBV
85
17
NUC
30
LLDTASALY
XLXXXXXXY
B62s
1.0155
*
1600


 


HBV
90
18
ENV
260
LLDYQGMLPV
XLXXXXXXXV
B62s
1.0516
*
1601


 


HBV
80
16
POL
752
LLGCAANW
XLXXXXXW
B62s


1602


 


HBV
80
16
POL
752
LLGCAANWI
XLXXXXXXI
B62s
3.0013

1603


 


HBV
95
19
POL
628
LLGFAAPF
XLXXXXXF
B62s


1604


 


HBV
75
15
ENV
63
LLGWSPQAQGI
XLXXXXXXXXI
B62s


1605


 


HBV
100
20
ENV
250
LLLCLIFLLV
XLXXXXXXXV
B62s
1.0897
*
1606


 


HBV
100
20
ENV
378
LLPIFFCLW
XLXXXXXXW
B62s

*
1607


 


HBV
100
20
ENV
378
LLPIFFCLWV
XLXXXXXXXV
B62s
1.0904
*
1608


 


HBV
100
20
ENV
378
LLPIFFCLWVY
XLXXXXXXXXY
B62s
26.0549
1609


 


HBV
95
19
NUC
44
LLSFLPSDF
XLXXXXXXF
B62s


1610


 


HBV
95
19
NUC
44
LLSFLPSDFF
XLXXXXXXXF
B62s


1611


 


HBV
90
18
POL
407
LLSSNLSW
XLXXXXXW
B62s


1612


 


HBV
80
16
ENV
184
LLTRILTI
XLXXXXXI
B62s
Chisari

1613


 


HBV
80
16
POL
436
LLVGSSGL
XLXXXXXL
b62S


1614


 


HBV
95
19
ENV
257
LLVLLDYQGM
XLXXXXXXXM
B62s
3.0207

1615


 


HBV
95
19
ENV
175
LLVLQAGF
XLXXXXXF
B62s


1616


 


HBV
95
19
ENV
175
LLVLQAGFF
XLXXXXXXF
B62s
20.0121

1617


 


HBV
100
20
ENV
338
LLVPFVQW
XLXXXXXW
B62s


1618


 


HBV
100
20
ENV
338
LLVPFVQWF
XLXXXXXXF
B62s


1619


 


HBV
95
19
ENV
338
LLVPFVQWFV
XLXXXXXXXV
B62s
1.0930
*
1620


 


HBV
85
17
NUC
100
LLWFHISCLTF
XLXXXXXXXXF
B62s


1621


 


HBV
95
19
POL
643
LMPLYACI
XMXXXXXI
B62s
17.0130

1622


 


HBV
100
20
ENV
379
LPIFFCLW
XPXXXXXW
B62s
19.0007

1623


 


HBV
100
20
ENV
379
LPIFFCLWV
XPXXXXXXV
B62s
15.0034

1624


 


HBV
100
20
ENV
379
LPIFFCLWVY
XPXXXXXXXY
B62s
15.0215

1625


 


HBV
100
20
ENV
379
LPIFFCLWVYI
XPXXXXXXXXI
B62s
26.0558

1626


 


HBV
100
20
POL
123
LPLDKGIKPY
XPXXXXXXXY
B62s
15.0210
*
1627


 


HBV
100
20
POL
123
LPLDKGIKPYY
XPXXXXXXXXY
B62s
26.0560

1628


 


HBV
80
16
POL
611
LPVNRPIDW
XPXXXXXXW
B62s


1629


 


HBV
80
16
POL
611
LPVNRPIDWKV
XPXXXXXXXXV
B62s


1630


 


HBV
80
16
ENV
178
LQAGFFLLTRI
XQXXXXXXXXI
B62s


1631


 


HBV
95
19
ENV
258
LVLLDYQGM
XVXXXXXXM
B62s
3.0034

1632


 


HBV
95
19
ENV
176
LVLQAGFF
XVXXXXXF
B62s


1633


 


HBV
100
20
ENV
339
LVPFVQWF
XVXXXXXF
B62s


1634


 


HBV
95
19
ENV
339
LVPFVQWFV
XVXXXXXXV
B62s
1.0877
*
1635


 


HBV
90
1 8
NUC
119
LVSFGVWI
XVXXXXXI
B62s
Chisari

1636


 


HBV
100
20
POL
377
LWDFSQF
XVXXXXXF
B62s


1637


 


HBV
85
17
ENV
360
MMWYWGPSLY
XMXXXXXXXY
B62s
1039.01
*
1638


 


HBV
100
20
POL
1
MPLSYQHF
XPXXXXXF
B62s
19.0010
*
1639


 


HBV
60
16
ENV
109
MQWNSTTF
XQXXXXXF
B62s


1640


 


HBV
95
19
POL
42
NLGNLNVSI
XLXXXXXXI
B62s
3.0008

1641


 


HBV
95
19
POL
42
NLGNLNVSIPW
XLXXXXXXXXW
B62s


1642


 


HBV
90
18
POL
406
NLLSSNLSW
XLXXXXXXW
B62s


1643


 


HBV
95
19
POL
45
NLNVSIPW
XLXXXXXW
B62s


1644


 


HBV
75
15
ENV
15
NLSVPNPLGF
XLXXXXXXXF
B62s


1645


 


HBV
90
18
POL
411
NLSWLSLDV
XLXXXXXXV
B62s
1.0185
*
1646


 


HBV
75
15
POL
571
NPNKTKRW
XPXXXXXW
B62s


1647


 


HBV
75
15
POL
571
NPNKTKRWGY
XPXXXXXXXY
B62s


1648


 


HBV
100
20
POL
47
NVSIPWTHKV
XVXXXXXXXV
B62s
1.0532

1649


 


HBV
85
17
POL
616
PIDWKVCQRI
XIXXXXXXXI
B62s
Chisari

1650


 


HBV
85
17
POL
616
PIDWKVCQRIV
XIXXXXXXXXV
B62s


1651


 


HBV
100
20
ENV
380
PIFFCLWV
XIXXXXXV
B62s


1652


 


HBV
100
20
ENV
380
PIFFCLWVY
XIXXXXXXY
B62s
1.0843

1653


 


HBV
100
20
ENV
380
PIFFCLWVYI
XIXXXXXXXI
B62s
20.0258

1654


 


HBV
80
16
POL
496
PIILGFRKI
XIXXXXXXI
B62s
927.48

1655


 


HBV
80
16
POL
496
PIILGFRKIPM
XIXXXXXXXXM
B62s


1656


 


HBV
100
20
NUC
138
PILSTLPETTV
XIXXXXXXXXV
B62s
Chisari

1657


 


HBV
100
20
ENV
314
PIPSSWAF
XIXXXXXF
B62s


1658


 


HBV
100
20
POL
124
PLDKGIKPY
XLXXXXXXY
B62s
1.0174
*
1659


 


HBV
100
20
POL
124
PLDKGIKPYY
XLXXXXXXXY
B62s
1.0541
*
1660


 


HBV
100
20
ENV
377
PLLPIFFCLW
XLXXXXXXXW
B62s


1661


 


HBV
100
20
ENV
377
PLLPIFFCLWV
XLXXXXXXXXV
B62s


1662


 


HBV
95
19
ENV
174
PLLVLQAGF
XLXXXXXXF
B62s


1663


 


HBV
95
19
ENV
174
PLLVLQAGFF
XLXXXXXXXF
B62s


1664


 


HBV
80
16
POL
505
PMGVGLSPF
XMXXXXXXF
B62s


1665


 


HBV
95
19
NUC
129
PPAYRPPNAPI
XPXXXXXXXXI
B62s
26.0563

1666


 


HBV
85
17
ENV
58
PPHGGLLGW
XPXXXXXXW
B62s
20.0141

1667


 


HBV
80
16
ENV
106
PQAMQWNSTT
XQXXXXXXXXF
B62s


1668


 


HBV
90
18
ENV
192
PQSLDSWW
XQXXXXXW
B62s


1669


 


HBV
85
17
POL
612
PVNRPIDW
XVXXXXXW
B62s


1670


 


HBV
85
17
POL
612
PVNRPIDWKV
XVXXXXXXXV
B62s
1.0566

1671


 


HBV
80
16
X
8
QLDPARDV
XLXXXXXV
B62s
Chisari

1672


 


HBV
95
19
POL
685
QVFADATPTGW
XVXXXXXXXXW
B62s


1673


 


HBV
90
18
POL
624
RIVGLLGF
XIXXXXXF
B62s


1674


 


HBV
75
15
POL
106
RLKLIMPARF
XLXXXXXXXF
B62s


1675


 


HBV
75
15
POL
106
RLKLIMPARFY
XLXXXXXXXXY
B62s


1676


 


HBV
95
19
POL
376
RLWDFSQF
XLXXXXXXF
B62s
20.0122

1677


 


HBV
80
16
POL
615
RPIDWKVCORI
XPXXXXXXXXI
B62s


1678


 


HBV
90
18
NUC
56
RQAILCWGELM
XQXXXXXXXXM
B62s


1679


 


HBV
90
18
NUC
98
RQLLWFHI
XQXXXXXI
B62s


1680


 


HBV
75
15
POL
818
RVHFASPLHV
XVXXXXXXXV
B62s
1.0576

1681


 


HBV
100
20
POL
357
RVTGGVFLV
XVXXXXXXV
B62s
1.0181

1682


 


HBV
100
20
POL
49
SIPWTHKV
XIXXXXXV
B62s


1683


 


HBV
100
20
POL
49
SIPWTHKVGNF
XIXXXXXXXXF
B62s


1684


 


HBV
95
19
ENV
194
SLDSWWTSLNF
XLXXXXXXXXF
B62s


1685


 


HBV
95
19
POL
416
SLDVSAAF
XLXXXXXF
B62s


1686


 


HBV
95
19
POL
416
SLDVSAAFY
XLXXXXXXY
B62s
1.0186
*
1687


 


HBV
100
20
ENV
337
SLLVPFVQW
XLXXXXXXW
B62s


1688


 


HBV
100
20
ENV
337
SLLVPFVQWF
XLXXXXXXXF
B62s


1689


 


HBV
95
19
ENV
337
SLLVPFVQWFV
XLXXXXXXXXV
B62s


1690


 


HBV
75
15
POL
581
SLNFMGYV
XLXXXXXV
B62s


1691


 


HBV
75
15
POL
581
SLNFMGYVI
XLXXXXXXI
B62s
3.0011

1692


 


HBV
95
19
X
54
SLRGLPVCAF
XLXXXXXXXF
B62s
20.0259

1693


 


HBV
95
19
POL
511
SPFILAQF
XPXXXXXF
B62s
19.0012
*
1694


 


HBV
100
20
NUC
49
SPHHTALRQAI
XPXXXXXXXXI
B62s
26.0567
*
1695


 


HBV
75
15
ENV
350
SPTVWLSV
XPXXXXXV
B62s


1696


 


HBV
75
15
ENV
350
SPTVWLSVI
XPXXXXXXI
B62s
1308.16

1697


 


HBV
75
15
ENV
350
SPTVWLSVIW
XPXXXXXXXW
B62s
1308.17

1698


 


HBV
75
15
ENV
350
SPTVWLSVIWM
XPXXXXXXXXM
B62s


1699


 


HBV
75
15
ENV
17
SVPNPLGF
XVXXXXXF
B62s


1700


 


HBV
80
16
ENV
330
SVRFSWLSLLV
XVXXXXXXXXV
B62s


1701


 


HBV
90
18
POL
739
SWLSRKY
XVXXXXXY
B62s
26.0029

1702


 


HBV
85
17
POL
739
SVVLSRKYTSF
XVXXXXXXXXF
B62s


1703


 


HBV
90
18
ENV
190
TIPQSLDSW
XIXXXXXXW
B62s


1704


 


HBV
90
18
ENV
190
TIPQSLDSWW
XIXXXXXXXW
B62s


1705


 


HBV
100
20
NUC
142
TLPETTVV
XLXXXXXV
B62s


1706


 


HBV
100
20
POL
150
TLWKAGILY
XLXXXXXXY
B62s
1.0177
*
1707


 


HBV
90
18
POL
354
TPARVTGGV
XPXXXXXXV
B62s
15.0033
*
1708


 


HBV
90
18
POL
35
TPARVTGGVF
XPXXXXXXXF
B62s
15.0214
*
1709


 


HBV
75
15
ENV
57
TPPHGGLLGW
XPXXXXXXXW
B62s
1308.04

1710


 


HBV
75
15
POL
691
TPTGWGLAI
XPXXXXXXI
B62s


1711


 


HBV
95
19
POL
636
TQCGVPALM
XQXXXXXXM
B62s


1712


 


HBV
80
16
NUC
16
TVQASKLCLGW
XVXXXXXXXXW
B62s


1713


 


HBV
75
15
ENV
352
TVWLSVIW
XVXXXXXW
B62s


1714


 


HBV
75
15
ENV
352
TVWLSVIWM
XVXXXXXXM
B62s
3.0035

1715


 


HBV
90
18
X
133
VLGGCRHKLV
XLXXXXXXXV
B62s
1.0589

1716


 


HBV
95
19
ENV
259
VLLDYQGM
XLXXXXXM
B62s
17.0107

1717


 


HBV
90
18
ENV
259
VLLDYQGMLPV
XLXXXXXXXXV
B62s
1147.14
*
1718


 


HBV
85
17
POL
741
VLSRKYTSF
XLXXXXXXF
B62s


1719


 


HBV
85
17
POL
741
VLSRKYTSFPW
XLXXXXXXXXW
B62s


1720


 


HBV
95
19
ENV
340
VPFVQWFV
XPXXXXXV
B62s
19.0006
*
1721


 


HBV
80
16
NUC
17
VQASKLCLGW
XQXXXXXXXW
B62s


1722


 


HBV
95
19
ENV
343
VQWFVGLSPTV
XQXXXXXXXXV
B62s


1723


 


HBV
90
18
POL
542
VVLGAKSV
XVXXXXXV
B62s


1724


 


HBV
80
16
POL
759
WILRGTSF
XIXXXXXF
B62s


1725


 


HBV
80
16
POL
759
WILRGTSFV
XIXXXXXXV
B62s
1.0204
*
1726


 


HBV
80
16
POL
759
WILRGTSFVY
XIXXXXXXXY
B62s
1.0572

1727


 


HBV
80
16
POL
759
WILRGTSFVYV
XIXXXXXXXXV
B62s


1728


 


HBV
95
19
NUC
125
WIRTPPAY
XIXXXXXY
B62s
26.0031

1729


 


HBV
80
16
POL
751
WLLGCAANW
XLXXXXXXW
B62s


1730


 


HBV
80
16
POL
751
WLLGCAANWI
XLXXXXXXXI
B62s
Chisari

1731


 


HBV
95
19
POL
414
WLSLDVSAAF
XLXXXXXXXF
B62s


1732


 


HBV
95
19
POL
414
WLSLDVSAAFY
XLXXXXXXXXY
B62s
26.0551

1733


 


HBV
100
20
ENV
335
WLSLLVPF
XLXXXXXF
B62s


1734


 


HBV
100
20
ENV
335
WLSLLVPFV
XLXXXXXXV
B62s
1.0838
*
1735


 


HBV
100
20
ENV
335
WLSLLVPFVQW
XLXXXXXXXXW
B62s


1736


 


HBV
85
17
NUC
26
WLWGMDIDPY
XLXXXXXXXY
B62s
1.0774
*
1737


 


HBV
95
19
ENV
237
WMCLRRFI
XMXXXXXI
B62s


1738


 


HBV
95
19
ENV
237
WMCLRRFII
XMXXXXXXI
B62s
3.0031
*
1739


 


HBV
95
19
ENV
237
WMCLRRFIIF
XMXXXXXXXF
B62s
20.0266

1740


 


HBV
85
17
ENV
359
WMMWyWGPSL
XMXXXXXXXXY
B62s
1.0901
*
1741


 


HBV
100
20
POL
147
YLHTLWKAGI
XLXXXXXXXI
B62s
7.0066

1742


 


HBV
100
20
POL
122
YLPLDKGI
XLXXXXXI
B62s


1743


 


HBV
100
20
POL
122
YLPLDKGIKPY
XLXXXXXXXXY
B62s
26.0553

1744


 


HBV
90
18
NUC
118
YLVSFGVW
XLXXXXXW
B62s


1745


 


HBV
90
16
NUC
118
YLVSFGVWI
XLXXXXXXI
B62s
3.0007
*
1746


 


HBV
95
19
POL
640
YPALMPLY
XPXXXXXY
B62s
19.0014
*
1747


 


HBV
95
19
POL
640
YPALMPLYACI
XPXXXXXXXXI
B62s
26.0570

1748


 







242
















TABLE XV







HBV A01 Motif (With Binding Information)




















1st


C-



SEQ ID


Conservancy
Frequency
Protein
Pos
Sequence
P2
term
Peptide
Filed
A*0101
NO:




















80
16
ENV
119
AMQWNSTTF
M
F



1749


 


90
16
POL
748
DNSVVLSRKY
N
Y
20.0255

0.0001
1750


 


95
19
POL
642
FAAPFTQCGY
A
Y
20.0254
*
0.0680
1751


 


85
17
POL
590
GYSLNFMGY
Y
Y
2.0058


1752


 


100
20
POL
149
HTLWKAGILY
T
Y
1069.04
*
0.1100
1753


 


95
19
POL
664
KQAFTFSPTY
Q
Y
20.0256

0.0001
1754


 


85
17
NUC
30
LLDTASALY
L
Y
1069.01
*
12.0000
1755


 


95
19
POL
415
LSLDVSAAFY
S
Y
1090.07
*
0.0150
1756


 


85
17
ENV
360
MMWYWGPSLY
M
Y
1039.01
*
0.0810
1757


 


75
15
X
103
MSTTDLEAY
S
Y
2.0126
*
0.8500
1758


 


90
18
POL
738
NSVVLSRKY
S
Y
2.0123

0.0005
1759


 


100
20
POL
124
PLDKGIKPY
L
Y
1147.12
*

1760


 


100
20
POL
124
PLDKGIKPYY
L
Y
1069.03
*
0.1700
1761


 


85
17
POL
797
PTTGRTSLY
T
Y
1090.09
*
0.2100
1762


 


100
20
POL
165
SASFCGSPY
A
Y



1763


 


95
19
POL
416
SLDVSAAFY
L
Y
1069.02
*
5.2000
1764






16
















TABLE XVI







HBV A03 and A11 Motif (With binding information)




















Conservancy
Frequency
Protein
1st Pos
Sequence
Motif
Super Motif
P2
C-term
Peptide
Filed
A*0301
A*1101
SEQ ID NO:























85
17
POL
721
AACFARSR
A03/A11
A03
A
R
26.0003

0.0004
0.0003
1765


 


95
19
POL
643
AAPFTQCGY
A03/A11
A03
A
Y




1766


 


95
19
POL
540
AFPHCLAFSY
A03/A11
A03
F
Y




1767


 


95
19
X
62
AFSSAGPCA
A03/A11
A03
F
A




1768


 


95
19
POL
866
AFTFSPTYK
A03/A11
A03
F
K
20.0130
*
0.2600
0.0400
1769


 


95
19
POL
666
AFTFSPTYKA
A03/A11
A03
F
A




1770


 


95
19
POL
18
AGFLEEFLPR
A03/A11
A03
G
R
20.0265

0.0004
0.0002
1771


 


95
19
POL
521
AICSVVRR
A03/A11
A03
I
R
26.0004

−0.0002
0.0003
1772


 


95
19
POL
532
AICSVVRRAF
A03/A11
A03
I
F




1773


 


90
18
POL
772
ALNPADDPSR
A03/A11
A03
L
R
1.1090

0.0003
0.0001
1774


 


85
17
X
70
ALRFTSAR
A03/A11
A03
L
R
26.0005

0.0047
0.0009
1775


 


80
16
ENV
119
AMQWNSTTF
A03/A11
A03
M
F




1776


 


80
16
ENV
119
AMQWNSTTF
A03/
A03
M
F




1777


 


80
16
ENV
119
AMQWNSTTFH
A03/A11
A03
M
H




1778


 


80
16
POL
822
ASPLHVAWR
A03/A11
A03
S
R




1779


 


75
15
ENV
84
ASTNRCSGR
A03/A11
A03
S
R
1150.60

0.0009
0.0002
1780


 


80
16
POL
755
CAANWILR
A03/A11
A03
A
R




1781


 


85
17
X
69
CALRFTSAR
A03/A11
A03
A
R
26.0149
*
0.0034
0.0230
1782


 


85
17
POL
734
CFARSRSGA
A03/A11
A03
F
A




1783


 


75
15
POL
618
CFRKLPVNR
A03/A11
A03
F
R




1784


 


95
19
POL
649
CGYPALMPLY
A03/A11
A03
G
Y




1785


 


100
20
EVN
323
CIPIPSSWAF
A03/A11
A03
I
F




1786


 


90
18
X
17
CLRPVGAESR
A03/A11
A03
L
R
1.1093

0.0011
0.0001
1787


 


75
15
ENV
239
CLRRHFIIFLF
A03/A11
A03
L
F




1788


 


100
20
NUC
48
CSPHHTALR
A03/A11
A03
S
R
5.0055
*
0.0029
0.0001
1789


 


95
19
POL
534
CSVVRRAFPH
A03/A11
A03
S
H




1790


 


85
17
NUC
58
DLLDTASALY
A03/A11
A03
L
Y
1.0519
*
0.0001
0.0001
1791


 


85
17
NUC
29
DLLDTASALYR
A03/A11
A03
L
R
26.0530

0.0042
−0.0003
1792


 


95
19
ENV
207
DSWWTSLNF
A03/A11
A03
S
F
20.0120

0.0006
0.0002
1793


 


85
17
NUC
32
DTASALYR
A03/A11
A03
T
R
26.0006

0.0004
−0.0002
1794


 


95
19
POL
17
EAGPLEEELPR
A03/A11
A03
A
R
26.0531

−0.0009
−0.0003
1795


 


90
18
POL
718
ELLAACFAR
A03/A11
A03
L
R
1.0988

0.0002
0.0004
1796


 


85
17
POL
718
ELLAACFARSR
A03/A11
A03
L
R
26.0532

0.0062
0.0016
1797


 


95
19
NUC
43
ELLSFLPSDF
A03/A11
A03
L
F




1798


 


95
19
NUC
72
ESPEHCSPH
A03/A11
A03
S
H




1799


 


95
19
NUC
72
ESPEHCSPHH
A03/A11
A03
S
H




1800


 


95
19
NUC
174
ETTVVRRR
A03/A11
A03
T
R
26.0007

0.0003
−0.0002
1801


 


80
16
NUC
174
ETTVVRRRGR
A03/A11
A03
T
R
1.1073

0.0003
0.0001
1802


 


95
19
POL
642
FAAPFTQCGY
A01/A03/
A03
A
Y
20.0254
*


1803


 


80
16
POL
821
FASPLHVAWR
A03/A11
A03
A
R




1804


 


90
18
ENV
24
FFPDHQLDPA
A03/A11
A03
F
A




1805


 


75
15
NUC
139
FGRETVLEY
A03/A11
A03
G
Y




1806


 


75
15
POL
255
FGVEPSGSGH
A03/A11
A03
G
H




1807


 


80
16
ENV
248
FILLLCLIF
A03/A11
A03
I
F




1808


 


90
18
X
63
FSSAGPCALR
A03/A11
A03
S
R




1809


 


100
20
ENV
344
FSWLSLLVPF
A03/A11
A03
S
F
20.0263

0.0004
0.0002
1810


 


95
19
POL
656
FTFSPTYK
A03/A11
A03
T
K
1147.19
*
0.0100
0.0100
1811


 


95
19
POL
867
FTFSPTYKAF
A03/A11
A03
T
F
20.0262

0.0004
0.0006
1812


 


95
19
POL
518
FTSAICSVVR
A03/A11
A03
T
R
1.1085

0.0003
0.0003
1813


 


95
19
POL
518
FTSAICSVVRR
A03/A11
A03
T
R
26.0533

0.0065
0.0092
1814


 


90
18
X
132
FVLGGCRHK
A03/A11
A03
V
K
1090.03
*
0.0430
0.0090
1815


 


80
16
POL
765
GCAANWILR
A03/A11
A03
C
R




1816


 


75
15
POL
587
GIHLNPNK
A03/A11
A03
I
K




1817


 


75
15
POL
567
GIHLNPNKTK
A03/A11
A03
I
K
1.0563

0.0025
0.0011
1818


 


76
15
POL
567
GIHLNPNKTKR
A03/A11
A03
I
R




1819


 


95
19
POL
638
GLLGFAAPF
A03/A11
A03
L
F
20.0124

0.0006
0.0002
1820


 


95
19
POL
520
GLSPFLLAQF
A03/A11
A03
L
F




1821


 


85
17
NUC
29
GMDIDPYK
A03/A11
A03
M
K
26.0009

0.0006
0.0004
1822


 


85
17
NUC
29
GMDIDPYKEF
A03/A24
A03
M
F
26.0372

−0.0003
−0.0002
1823


 


90
18
POL
735
GTDNSVVLSR
A03/A11
A03
T
R
1090.04
*
0.0010
0.0420
1824


 


90
18
POL
735
GTDNSVVLSRK
A03/A11
A03
T
K
1147.17
*
0.0140
0.5600
1825


 


80
16
POL
258
GVEPSGSGH
A03/A11
A03
V
H




1826


 


100
20
POL
372
GVFLVDKNPH
A03/A11
A03
V
H




1827


 


95
19
NUC
152
GVWIRTPPAY
A03/A11
A03
V
Y
1.0525

0.0047
0.0002
1828


 


95
19
NUC
123
GVVIRTPPAYR
A03/A11
A03
V
R
26.0535
*
0.1900
0.1700
1829


 


100
20
NUC
78
HCSPHHTALR
A03/A11
A03
C
R




1830


 


80
18
POL
831
HFASPLHVA
A03/A11
A03
F
A




1831


 


90
18
NUC
104
HISCLTFGR
A03/A11
A03
I
R
1069.18
*
0.0160
0.0065
1832


 


75
15
POL
569
HLNPNKTK
A03/A11
A03
L
K




1833


 


75
15
POL
569
HLNPNKTKR
A03/A11
A03
L
H
1.0983

0.0025
0.0001
1834


 


85
17
POL
728
HTAELLAACF
A03/A11
A03
T
F




1835


 


100
20
POL
149
HTLWKAGILYK
A03/A11
A03
T
K
1147.16
*
0.5400
0.4400
1836


 


95
19
POL
533
ICSVVRRAF
A03/A11
A03
C
F




1837


 


95
19
ENV
266
IFLLVLLDY
A03/A11
A03
F
Y




1838


 


80
16
POL
771
ILRGTSFVY
A03/A11
A03
L
Y
1.0205
*
0.0440
00002
1839


 


90
18
NUC
105
ISCLTFGR
A03/A11
A03
S
R
26.0010

0.0004
0.0002
1840


 


100
20
POL
153
KAGILYKR
A03/A11
A03
A
R
26.0011

0.0002
−0.0002
1841


 


75
15
POL
108
KLIMPARFY
A03/A11
A03
L
Y
1.0171



1842


 


80
16
POL
610
KLPVNRPIDWK
A03/A11
A03
L
K




1843


 


75
15
X
130
KVFVLGGCR
A03/A11
A03
V
R
1.0993
*
0.0420
0.0820
1844


 


75
15
X
130
KVFVLGGCRH
A03/A11
A03
V
H




1845


 


95
19
POL
55
KVGNFTGLY
A03/A11
A03
V
Y
1142.05
*
0.2100
0.0170
1846


 


85
17
POL
720
LAACFARSR
A03/A11
A03
A
R
20.0129

0.0058
0.0065
1847


 


100
20
POL
125
LDKGIKPYY
A03/A11
A03
D
Y




1848


 


95
19
ENV
206
LDSWWTSLNF
A03/A11
A03
D
F




1849


 


85
17
NUC
60
LDTASALYR
A03/A11
A03
D
R
26.0151

0.0004
−0.0002
1850


 


95
19
POL
428
LDVSAAFYH
A03/A11
A03
D
H




1851


 


80
16
EVN
247
LFILLLCLIF
A03/A11
A03
F
F




1852


 


80
16
ENV
247
LFILLLCLIF
A03/A24
A03
F
F




1853


 


80
16
POL
764
LGCAANWILR
A03/A11
A03
G
R




1854


 


75
15
POL
577
LGHLNPNK
A03/A11
A03
G
K




1855


 


95
19
ENV
265
LIFLLVLLDY
A03/A11
A03
I
Y
1.0899

0.0022
0.0004
1856


 


90
18
POL
719
LLAACFAR
A03/A11
A03
L
R
26.0012

0.0024
0.0003
1857


 


85
17
POL
719
LLAACFARSR
A03/A11
A03
L
R




1858


 


85
17
NUC
30
LLDTASALYR
A03/A11
A03
L
R
1.1070

0.0050
0.0002
1859


 


80
16
POL
752
LLGCAANWILR
A03/A11
A03
L
R




1860


 


95
19
NUC
44
LLSFLPSDF
A03/A11
A03
L
F




1861


 


95
19
NUC
44
LLSFLPSDFF
A03/A11
A03
L
F




1862


 


95
19
ENV
175
LLVLQAGFF
A03/A11
A03
L
F
20.0121

0.0006
0.0002
1863


 


100
20
ENV
349
LLVPFVQWF
A03/A11
A03
L
F




1864


 


95
19
NUC
45
LSFLPSDFF
A03/A11
A03
S
F
20.0123

0.0006
0.0002
1865


 


95
19
POL
426
LSLDVSAAF
A03/A11
A03
S
F




1866


 


75
15
POL
564
LSLGIHLNPNK
A03/A11
A03
S
K




1867


 


95
19
X
53
LSLRGLPVCA
A03/A11
A03
S
A




1868


 


95
19
POL
521
LSPFLLAQF
A03/A11
A03
S
F




1869


 


95
19
NUC
169
LSTLPETTVVR
A03/A11
A03
S
R
26.0537

−0.0009
0.0008
1870


 


75
15
ENV
18
LSVPNPLGF
A03/A11
A03
S
F




1871


 


100
20
POL
423
LSWLSLDVSA
A03/A11
A03
S
A
20.0260

0.0048
0.0035
1872


 


75
15
POL
3
LSYQHFRK
A03/A11
A03
S
K




1873


 


85
17
POL
99
LTVNEKRR
A03/A11
A03
T
R
26.0013

−0.0002
−0.0002
1874


 


90
18
NUC
119
LVSFGVWIR
A03/A11
A03
V
R
1090.08
*
0.0028
0.0120
1875


 


100
20
POL
377
LVVDFSQFSR
A03/A11
A03
V
R
1069.20
*
0.0016
0.3600
1876


 


95
19
ENV
249
MCLRRFIIF
A03/A11
A03
C
F




1877


 


90
18
POL
550
MDDVVLGAK
A03/A11
A03
D
K




1878


 


90
18
NUC
30
MDIDIPYKEF
A03/A11
A03
D
F




1879


 


85
17
ENV
360
MMWYWGPSLY
A01/A03/
A03
M
Y
1039.01
*
0.0500
0.0008
1880


 


75
15
X
103
MSTTDLEAYF
A03/A11
A03
S
F




1881


 


75
15
X
103
MSTTDLEAYFK
A03/A11
A03
S
K




1882


 


95
19
POL
572
NFLLSLGIH
A03/A11
A03
F
H




1883


 


90
18
NUC
75
NLEDPASR
A03/A11
A03
L
R
26.0014

−0.0002
−0.0002
1884


 


95
19
POL
45
NLNVSIPWTH
A03/A11
A03
L
H




1885


 


95
19
POL
45
NLNVSIPWTHK
A03/A11
A03
L
K
26.0538

−0.0009
0.0005
1886


 


75
15
ENV
15
NLSVPNPLGF
A03/A11
A03
L
F




1887


 


75
15
ENV
215
NSQSPTSNH
A03/A11
A03
S
H




1888


 


90
18
POL
738
NSVVLSRK
A03/A11
A03
S
K
26.0015

0.0006
0.0010
1889


 


100
20
POL
47
NVSIPWTHK
A03/A11
A03
V
K
1069.16
*
0.0820
0.0570
1890


 


90
18
POL
775
PADDPSAGR
A03/A11
A03
A
R
1150.35

0.0008
0.0002
1891


 


80
16
X
11
PARDVLCLR
A03/A11
A03
A
R
1150.36

0.0002
0.0002
1892


 


90
18
POL
385
PARVTGGVF
A03/A11
A03
A
F




1893


 


75
15
EVN
83
PASTNRQSGR
A03/A11
A03
A
R




1894


 


85
17
X
68
PCALRFTSAR
A03/A11
A03
C
R




1895


 


90
18
ENV
26
PDHQLDPAF
A03/A11
A03
D
F




1896


 


95
19
POL
523
PFLLAQFTSA
A03/A11
A03
F
A




1897


 


95
19
POL
645
PFTQCGYPA
A03/A11
A03
F
A




1898


 


100
20
ENV
244
PGYRWMCLR
A03/A11
A03
G
A
1.0964

0.0008
0.0005
1899


 


95
19
ENV
244
PGYRWMCLRR
A03/A11
A03
G
R
1.1068

0.0048
0.0001
1900


 


90
18
POL
616
PIDWKVCQR
A03/A11
A03
I
R
1.0985

0.0002
0.0005
1901


 


100
20
ENV
391
PIFFCLWVY
A03/A11
A03
I
Y
1.0843

0.0011
0.0002
1902


 


80
16
POL
496
PIILGFRK
A03/A11
A03
I
K




1903


 


95
19
POL
20
PLEEELPR
A03/A11
A03
L
R
26.0016

0.0002
−0.0002
1904


 


100
20
POL
438
PLHPAAMPH
A03/A11
A03
L
H
20.0128

0.0012
0.0002
1905


 


95
19
ENV
174
PLLYLQAGF
A03/A11
A03
L
F




1906


 


95
19
ENV
174
PLLVQAGFF
A03/A11
A03
L
F




1907


 


100
20
POL
2
PLSYQHFR
A03/A11
A03
L
R
26.0017

−0.0002
−0.0002
1908


 


75
15
POL
2
PLSYQHFRK
A03/A11
A03
L
K
1.0161

0.0011
0.0031
1909


 


85
17
POL
98
PLTVNEKR
A03/A11
A03
L
R
26.0018

0.0002
−0.0002
1910


 


85
17
POL
98
PLTVNEKRR
A03/A11
A03
L
R
1.0974

0.0008
0.0005
1911


 


80
16
POL
516
PMGVGLSPF
A03/A11
A03
M
F




1912


 


80
16
POL
516
PMGVGLSPF
A03/A24
A03
M
F




1913


 


90
18
X
20
PVGAESRGR
A03/A11
A03
V
R
1.0990

0.0002
0.0005
1914


 


85
17
POL
612
PVNRPIDWK
A03/A11
A03
V
K
1142.06
*
0.0310
0.1400
1915


 


95
19
POL
665
QAFTFSPTY
A03/A11
A03
A
V
20.0127

0.0030
0.0017
1916


 


95
19
POL
654
QAFTFSPTYK
A03/A11
A03
A
K
1090.10
*
0.0450
0.5400
1917


 


80
16
EVN
179
QAGFFLLTR
A03/A11
A03
A
R




1918


 


80
18
ENV
118
QAMQWNSTTF
A03/A11
A03
A
F




1919


 


75
15
NUC
169
QSPRFFFSQSR
A03/A11
A03
S
R
28.0839



1920


 


80
16
POL
189
QSSGILSR
A03/A11
A03
S
R




1921


 


95
19
POL
539
RAFPHCLAF
A03/A11
A03
A
F
20.0125

0.0015
0.0007
1922


 


75
15
POL
106
RLKLIMPAR
A03/A11
A03
L
R
1.0975
*
0.0950
0.0002
1923


 


75
15
POL
106
RLKLIMPARF
A03/A11
A03
L
F




1924


 


75
15
X
128
RLKVFVLGGCR
A03/A11
A03
L
R




1925


 


95
19
POL
387
RLVVDFSCF
A03/A11
A03
L
F
20.0122

0.0006
0.0002
1926


 


95
19
POL
376
RLWDPSQFSR
A03/A11
A03
L
R
26.0539
*
0.2800
3.8000
1927


 


95
19
NUC
183
RSPRRRTPSPR
A03/A11
A03
S
A
26.0540

−0.0007
−0.0003
1928


 


75
15
NUC
167
RSQSPRRR
A03/A11
A03
S
R




1929


 


75
15
NUC
187
RSQSPRRRR
A03/A11
A03
S
R




1930


 


95
19
NUC
188
RTPSPRRR
A03/A11
A03
T
R
26.0019

−0.0002
−0.0002
1931


 


95
19
NUC
188
RTPSPRRRR
A03/A11
A03
T
R
1.0971
*
0.0054
0.0005
1932


 


80
18
POL
829
RVHFASPLH
A03/A11
A03
V
H




1933


 


100
20
POL
357
RVTGGVFLVDK
A03/A11
A03
V
K
1147.18
*
0.0190
0.0290
1934


 


90
18
X
65
SAGPCALR
A03/A11
A03
A
R
26.0020

−0.0002
0.0020
1935


 


90
18
X
65
SAGPCALRF
A03/A11
A03
A
F
26.0152

−0.0003
0.0004
1936


 


95
19
POL
520
SAICSVVR
A03/A11
A03
A
R
26.0021

−0.0002
0.0071
1937


 


95
19
POL
520
SAICSVVRR
A03/A11
A03
A
R
1090.11
*
0.0058
0.2100
1938


 


90
18
POL
771
SALNPADDPSR
A03/A11
A03
A
R
26.0542

−0.0004
−0.0003
1939


 


100
20
POL
165
SASFCGSPY
A01/A03/
A03
A
Y

*


1940


 


75
15
POL
759
SFPWLLGCA
A03/A11
A03
F
A




1941


 


75
15
POL
769
SFPWLLGCAA
A03/A11
A03
F
A




1942


 


95
19
POL
427
SLDVSAAFYH
A03/A11
A03
L
H




1943


 


75
15
POL
565
SLGHLNPNK
A03/A11
A03
L
K
28.0758
*


1944


 


100
20
ENV
348
SLLVPFVQWF
A03/A11
A03
L
F




1945


 


95
19
X
54
SLRGLPVCAF
A03/A11
A03
L
F
20.0259

0.0004
0.0002
1946


 


90
18
X
64
SSAGPCALR
A03/A11
A03
S
R
26.0153
*
0.0080
0.1400
1947


 


90
18
X
64
SSAGPCALRF
A03/A11
A03
S
F
26.0374

−0.0003
−0.0002
1948


 


95
19
NUC
170
STLPETTVVR
A03/A11
A03
T
R
1069.21
*
0.0007
0.0600
1949


 


95
19
NUC
170
STLPETTVVRR
A03/A11
A03
T
R
1083.01

0.0150
1.4000
1950


 


80
16
ENV
85
STNRQSGR
A03/A11
A03
T
R




1951


 


75
15
X
104
STTDLEAYF
A03/A11
A03
T
F




1952


 


75
15
X
104
STTDLEAYFK
A03/A11
A03
T
K
1.0584
*
0.0066
2.7000
1953


 


95
19
POL
535
SVVRRAFPH
A03/A11
A03
V
H
20.0131
*
0.1100
0.6100
1954


 


85
17
POL
727
TAELLAACF
A03/A11
A03
A
F




1955


 


85
17
POL
716
TAELLAACFAR
A03/A11
A03
A
R
26.0544

0.0006
0.0023
1956


 


90
18
POL
747
TDNSVVLSR
A03/A11
A03
D
R




1957


 


90
18
POL
747
TDNSVVLSRK
A03/A11
A03
D
K
20.0264

0.0006
0.0017
1958


 


75
15
NUC
138
TFGRETVLEY
A03/A11
A03
F
Y




1959


 


95
19
POL
688
TFSPTYKAF
A03/A24
A03
F
F
5.0064



1960


 


100
20
POL
370
TGGVFLVDK
A03/A11
A03
G
K
20.0133

0.0007
0.0061
1961


 


95
19
NUC
171
TLPETTVVR
A03/A11
A03
L
R
1.0969

0.0008
0.0002
1962


 


95
19
NUC
171
TLPETTVVRR
A03/A11
A03
L
R
1069.22
*
0.0007
0.0230
1963


 


95
19
NUC
171
TLPETTVVRRR
A03/A11
A03
L
R
26.0545
*
0.0005
0.0160
1964


 


100
20
POL
150
TLWKAGILY
A03/A11
A03
L
Y
1099.03
*
0.1300
0.0008
1965


 


100
20
POL
150
TLWKAGILYK
A03/A11
A03
L
K
1069.15
*
5.3000
0.3600
1966


 


100
20
POL
150
TLWKAGILYKR
A03/A11
A03
L
R
26.0546

0.0082
0.0095
1967


 


95
19
POL
519
TSAICSVVR
A03/A11
A03
S
R
5.0057

0.0005
0.0008
1968


 


95
19
POL
519
TSAICSVVAR
A03/A11
A03
S
R
1142.08
*
0.0018
0.0006
1969


 


75
15
POL
756
TSFPWLLGCA
A03/A11
A03
S
A




1970


 


80
16
POL
775
TSFVYVPSA
A03/A11
A03
S
A




1971


 


75
15
X
105
TTDLEAYFK
A03/A11
A03
T
K
1.0215
*
0.0006
0.9200
1972


 


75
15
EVN
278
TTSTGPCK
A03/A11
A03
T
K




1973


 


80
16
NUC
175
TTVVRRRGR
A03/A11
A03
T
R
1.0970

0.0008
0.0005
1974


 


80
16
NUC
176
TVVRRRGR
A03/A11
A03
V
R
3.0324

0.0003
0.0001
1975


 


80
16
NUC
176
TVVRRRGRSPR
A03/A11
A03
V
R
28.0837



1976


 


100
20
POL
373
VFLVDKNPH
A03/A11
A03
F
H




1977


 


80
18
X
131
VFVLGGCRH
A03/A11
A03
F
H




1978


 


75
15
X
131
VFVLGGCRHK
A03/A11
A03
F
K




1979


 


95
19
POL
637
VGLLGFAAPF
A03/A11
A03
G
F




1980


 


85
17
POL
96
VGPLTVNEK
A03/A11
A03
G
K
20.0132

0.0007
0.0078
1981


 


85
17
POL
96
VGPLTVNEKR
A03/A11
A03
G
R




1982


 


95
19
POL
554
VLGAKSVQH
A03/A11
A03
L
H




1983


 


90
18
X
133
VGGCRHK
A03/A11
A03
L
K
26.0022

0.0150
0.0002
1984


 


80
16
ENV
177
VLQAGFFLLTR
A03/A11
A03
L
R




1985


 


85
17
POL
752
VLSRKYTSF
A03/A11
A03
L
F




1986


 


90
18
NUC
120
VSFGWWR
A03/A11
A03
S
R
26.0023
*
0.0040
0.0290
1987


 


100
20
POL
48
VSIPWTHK
A03/A11
A03
S
K
26.0024
*
0.0130
0.0170
1988


 


100
20
POL
358
VTGGVFLVDK
A03/A11
A03
T
K
1069.17
*
0.0390
0.0920
1989


 


100
20
POL
378
VVDFSQFSR
A03/A11
A03
V
R
1069.19
*
0.0015
0.0750
1990


 


90
18
POL
553
VVLGAKSVQH
A03/A11
A03
V
H




1991


 


85
17
POL
751
VVLSRKYTSF
A03/A11
A03
V
F
20.0261

0.0004
0.0002
1992


 


80
16
NUC
177
VVRRRGRSPR
A03/A11
A03
V
R
1.1074

0.0027
0.0001
1993


 


80
16
NUC
177
VVRRRGRSPRR
A03/A11
A03
V
R
28.0838



1994


 


90
18
NUC
131
WFHISCLTF
A03/A11
A03
F
F
13.0073
*


1995


 


90
18
NUC
131
WFHISCLTF
A03/A24
A03
F
F
13.0073
*


1996


 


85
17
NUC
28
WGMDIDPYK
A03/A11
A03
G
K
26.0154

−0.0003
0.0006
1997


 


85
17
POL
589
WGYSLNFMGY
A03/A11
A03
G
Y




1998


 


80
16
POL
770
WILRGTSFVY
A03/A11
A03
I
Y
1.0572

0.0076
0.0011
1999


 


95
19
NUC
125
WIRTPPAYR
A03/A11
A03
I
R
1.0968

0.0008
0.0005
2000


 


90
18
POL
314
WLQFRNSK
A03/A11
A03
L
K
26.0025

−0.0002
0.0005
2001


 


95
19
POL
425
WLSLDVSAAF
A03/A11
A03
L
F




2002


 


85
17
NUC
26
WLWGMDIDPY
A03/A11
A03
L
Y
1.0774
*
0.0002
0.0002
2003


 


85
17
NUC
26
WLWGMDIDPYK
A03/A11
A03
L
K
26.0547

0.0030
0.0013
2004


 


95
19
ENV
248
WMCLRRFIIF
A03/A11
A03
M
F
20.0266

0.0004
0.0011
2005


 


95
19
ENV
248
WMCLRRRIIF
A03/A24
A03
M
F
20.0266

0.0004
0.0011
2006


 


100
20
POL
122
YLPLDKGIK
A03/A11
A03
L
K
1.0173

0.0001
0.0001
2007


 


90
18
NUC
118
YLVSFGVWIR
A03/A11
A03
L
R
1090.13
*
0.0005
0.0002
2008


 


90
18
POL
538
YMDDVVLGAK
A03/A11
A03
M
K
1090.15
*
0.0330
0.0043
2009


 


80
16
POL
504
YSHPILGF
A03/A11
A03
S
F




2010


 


80
16
POL
493
YSHPILGFR
A03/A11
A03
S
R




2011


 


80
16
POL
493
YSHPIILGFRK
A03/A11
A03
S
K




2012


 






248
















TABLE XVII







HBV A24 Motif With Binding Information

















Conservancy
Frequency
Protein
Position
Sequence
P2
C-term
Peptide
Filed
A*2401
SEQ ID NO:




















95
19
X
62
AFSSAGPCAL
F
L
5.0118

0.0012
2013


 


90
18
POL
535
AFSYMDDVVL
F
L
13.0130

0.0009
2014


 


80
16
ENV
108
AMQWNSTTF
M
F



2015


 


100
20
NUC
131
AYRPPNAPI
Y
I
1090.02
*
0.0310
2016


 


100
20
NUC
131
AYRPPNAPIL
Y
L
1069.24
*
0.0042
2017


 


90
18
NUC
117
EYLVSFGVW
Y
W
26.0150


2018


 


90
18
NUC
117
EYLVSFGVWI
Y
I
17.0426
*

2019


 


80
16
ENV
182
FFLLTRILTI
F
I



2020


 


80
16
ENV
181
GFFLLTRIL
F
L



2021


 


75
15
ENV
170
GFLGPLLVL
F
L



2022


 


85
17
NUC
29
GMDIDPYKEF
M
F
26.0372


2023


 


85
17
ENV
65
GWSPQAQGI
W
I
20.0134

0.0024
2024


 


85
17
ENV
65
GWSPQAQGIL
W
L
20.0268

0.0003
2025


 


95
19
ENV
234
GYRWMCLRRF
Y
F
1069.25
*
0.0007
2026


 


80
16
POL
820
HFASPLHVAW
F
W



2027


 


100
20
ENV
381
IFFCLWVYI
F
I
5.0058

0.0087
2028


 


80
16
ENV
245
IFLFILLLCL
F
L



2029


 


95
19
POL
395
KFAVPNLQSL
F
L
5.0114

0.0020
2030


 


100
20
POL
121
KYLPLDKGI
Y
I



2031


 


85
17
POL
745
KYTSFPWLL
Y
L
1069.23
*
5.3000
2032


 


80
16
ENV
247
LFILLLCLI
F
I



2033


 


80
16
ENV
247
LFILLLCLIF
F
F



2034


 


85
17
NUC
101
LWFHISCLTF
W
F
26.0373


2035


 


80
16
POL
492
LYSHPIILGF
Y
F
2.0181
*
1.1000
2036


 


95
19
POL
561
NFLLSLGIHL
F
L
5.0115

0.0099
2037


 


80
16
POL
758
NWILRGTSF
W
F



2038


 


95
19
POL
634
PFTQCGYPAL
F
L
5.0116

0.0002
2039


 


95
19
ENV
341
PFVQWFVGL
F
L
5.0059

0.0003
2040


 


80
16
POL
505
PMGVGLSPF
M
F



2041


 


80
16
POL
750
PWLLGCAANW
W
W



2042


 


100
20
POL
51
PWTHKVGNF
W
F
20.0138
*
0.0290
2043


 


75
15
ENV
242
RFIIFLFIL
F
L



2044


 


75
15
ENV
242
RFIIFLFILL
F
L



2045


 


95
19
ENV
236
RWMCLRRFI
W
I
20.0135
*
0.0710
2046


 


95
19
ENV
236
RWMCLRRFII
W
I
20.0269
*
1.1000
2047


 


100
20
POL
167
SFCGSPYSW
F
W
20.0139
*
0.0710
2048


 


80
16
POL
765
SFVYVPSAL
F
L



2049


 


100
20
ENV
334
SWLSLLVPF
W
F
20.0136
*
0.3900
2050


 


95
19
POL
392
SWPKFAVPNL
W
L
20.0271
*
5.6000
2051


 


95
19
ENV
197
SWWTSLNFL
W
L
20.0137
*
0.3800
2052


 


75
15
POL
4
SYQHFFKLL
Y
L
2.0042

0.0051
2053


 


75
15
POL
4
SYQHFRKLLL
Y
L
2.0173
*
0.0660
2054


 


95
19
POL
657
TFSPTYKAF
F
F
5.0064

0.0060
2055


 


95
19
POL
657
TFSPTYKAFL
F
L
5.0117

0.0043
2056


 


95
19
POL
686
VFADATPTGW
F
W
20.0272
*
0.0180
2057


 


90
18
NUC
102
WFHISCLTF
F
F
13.0073
*
0.0300
2058


 


95
19
ENV
345
WFVGLSPTVW
F
W
20.0270
*
0.0120
2059


 


95
19
ENV
237
WMCLRRFIIF
M
F
20.0266

0.0013
2060


 






48
















TABLE XVIII







DR SUPER MOTIF (With binding information)






















SEQ ID NO:
Sequence
Peptide
DR1
DR2w2B1
DR2w2b1
DR3
DR4w4
DR4w15
DR5w11
DR5w12
DR6w19
DR7
DR8w2
DR9
DRW53

























2061
AANWILRGTSFVYVP
1298.07
0.0920
0.0240
0.0061
0.0023
0.0510
0.0250
0.0140
0.3700
0.0250
0.5800
0.2500
0.2700



 


2062
AEDLNLGNLNVSIPW
1186.01
0.0001

−0.0005

−0.0007

−0.0002


−0.0003


0.0170


 


2063
AELLAACFARSRSGA


 


2064
AFSYMDDVVLGAKSV
1186.02
0.0027

−0.0005
0.00130
2.9000

0.0006


−0.0003


−0.0005


 


2065
AGFFLLTRILTIPQS
1280.06
4.6000
0.0420
0.0190
0.0040
5.3000
0.1500
3.6000
0.0700
0.3700
3.1000
0.2600
1.3000


 


2066
AGPLEEELPRLADEG
35.0091



0.0022


 


2067
AKLIGTDNSVVLSRK


 


2068
ANWILRGTSFVYVPS


 


2069
ARDVLCLRPVGAESR


 


2070
ASALYREALESPEHC


 


2071
ASKLCLGWLWGMDID
1186.03
0.0002

−0.0005

0.0017

−0.0002


0.0013


0.0010


 


2072
CLIFLLVLLDYQGML


 


2073
CLTFGRETVLEYLVS


 


2074
CPGYRWMCLRRFIIF


 


2075
CPTVQASKLCLGWLW


 


2076
CQVGADATPTGWGLA


 


2077
CSVVRRAFPHCLAFS
1186.04
0.1000
0.1024
0.0770
0.0032
0.0016
−0.0022
0.0008
−0.0013
0.0540
0.0590
0.0250
1.2000
0.0460


 


2078
CTCIPIPSSWAFARF


 


2079
CWWLQFRNSKPCSDY


 


2080
DDVVLGAKSVCHLES


 


2081
DEGLNRRVAEDLNLG


 


2082
DLNLGNLNVSIPWTH
1280.07
0.0038



0.0240




0.0010


 


2083
DVVLGAKSVQHLESL


 


2084
DWKVCQRIVGLLGFA
1186.05
0.0120

−0.0026

0.0030

0.2500


0.0018


0.0130


 


2085
EIRLKVFVLGGCRHK


 


2086
ESRLVVDFSQFSRGN
35.0096
0.0007


2.6000


 


2087
FFLLTRILTIPQSLD
F064.01


 


2088
FGVWIRTPPAYRPPN


 


2089
FIIFLFILLLCLIFL


 


2090
FLFILLLCLIFLLVL


 


2091
FPWLLGCAANWILRG


 


2092
FRKLPVNRPIDWKVC


 


2093
FSWLSLLVPFVQWFV


 


2094
FSYMDDVVLGAKSVQ


 


2095
FVQWFVGLSPTVWLS
1186.06
0.4700
0.0035
0.0160
−0.0013
0.0130

0.0072
0.0021
0.0190
0.0690
0.0180
0.0410
0.0044


 


2096
GAHLSLRGLPVCAFS
1186.07
0.7800

0.0042
−0.0041
0.0011

0.0025


0.0077


0.0150


 


2097
GFFLLTRILTIPQSL
1280.08
0.4300
0.0150
0.0110

3.1000
0.4500
2.3000

0.0780
3.5000
1.6000
0.5500


 


2098
GIHLNPNKTKRWGYS


 


2099
GLPVCAFSSAGPCAL


 


2100
GLYFPAGGSSSGTVN


 


2101
GTNLSVPNPLGFFPD


 


2102
GTSFVYVPSALNPAD
1280.09
0.3500
0.0140
0.0500
−0.0006
0.3800
0.4100
0.0470
−0.0001
0.0001
0.2700
0.0610
0.3400


 


2103
GVFLVDKNPHNTTES


 


2104
GVGLSPFLLAQFTSA


 


2105
GVWIRTPPAYRPPNA
27.0280
0.3700
0.0420
7.2000
0.0120
3.4000
0.5700
0.4800
0.0140
−0.0004
0.2200
0.5300
0.0450


 


2106
HGGLLGWSPQAQGIL


 


2107
HLPLHPAAMPHLLVG


 


2108
HLSLRGLPVCAFSSA
1280.10
1.3000



0.0028




0.0130


 


2109
HTALRQAILCWGELM


 


2110
HTLWKAGILYKRETT


 


2111
IFLFILLLCLIFLLV
1280.11
0.0005



0.0041




0.0018


 


2112
IIFLFILLLCLIFLL
1280.12


 


2113
ILGFRKIPMGVGLSP


 


2114
ILLLCLIFLLVLLDY
F107.01
0.0026

0.0069

0.0320

0.0018


0.0047


 


2115
IRDLLDTASALYREA


 


2116
IRQLLWFHISCLTFG


 


2117
IVGLLGFAAPFTQCG
1186.09
0.0200

−0.0005

−0.0007

−0.0002


0.0009


0.0067


 


2118
IWMMWYWGPSLYNIL


 


2119
KFAVPNLQSLTNLLS
1280.13
0.0180
0.0005
−0.0003

0.1300

0.0043

0.0088
−0.0003

0.0056


 


2120
KIPMGVGLSPFLLAQ


 


2121
KLHLYSHPIILGFRK


 


2122
KQAFTFSPTYKAFLC
1298.06
0.5300
0.2400
0.1400
0.0090
1.1000
0.2200
0.2400
0.0024
0.0200
0.3300
0.1200
0.5400


 


2123
KQCFRKLPVNRPIDW
1298.04
1.5000
0.0022
0.0210
−0.0006
1.2000
0.8500
0.0130
0.0043
0.4000
0.0580
0.0250


 


2124
KRRLKLIMPARFYPN


 


2125
LAQFTSAICSVVRRA
1186.10
0.0120
0.0065
0.1500
−0.0009
0.0150
0.0280
0.0076
0.0091
0.0010
0.0280
0.0150
0.0880
0.0190


 


2126
LCLIFLLVLLDYQGM
F107.02
0.0016

0.0060

0.0230

0.0017


0.0044


 


2127
LCQVFADATPTGWGL
1280.14
0.0020



0.9600




0.0013


 


2128
LEYLVSFGVWIRTPP


 


2129
LFILLLCLIFLLVLL


 


2130
LGFFPDHQLDPAFGA


 


2131
LGNLNVSIPWTHKVG


 


2132
LGPLLVLQAGFFLLT


 


2133
LGWLWGMDIDPYKEF
1186.12
0.0004

0.0006
0.0200
0.0280

−0.0002


0.0004


0.0430


 


2134
LHLYSHPIILGFRKI
1280.15
0.0220
0.0340
0.0400
0.0040
0.6800
0.1600
0.0410
0.0310
0.0002
0.0006
0.0610
0.0490


 


2135
LHTLWKAGILYKRET


 


2136
LKVFVLGGCRHKLVC


 


2137
LLCLIFLLVLLDYQG


 


2138
LLDYQGMLPVCPLIP


 


2139
LLGFAAPFTQCGYPA


 


2140
LLWFHISCLTFGRET


 


2141
LPKVLHKRTLGLSAM


 


2142
LPLLPIFFCLWVYIZ


 


2143
LQSLTNLLSSNLSWL
F107.03
2.5000
0.4400
0.0200
−0.0013
4.8000
0.8100
0.0680
0.7500
0.0260
0.1500
0.0880
0.1100


 


2144
LSAMSTTDLEAYFKD


 


2145
LSTLPETTVVRRRGR


 


2146
LSWLSLDVSAAFYHI


 


2147
LTNLLSSNLSWLSLD
1186.14
0.0010

0.0083

0.0160

0.0013


0.0019


0.0200


 


2148
LVLLDYQGMLPVCPL
1280.17
0.0034



−0.0013




0.0011


 


2149
LVPFVQWFVGLSPTV
1186.15
0.0130
0.6900
0.0140
−0.0013
0.1500
1.4000
0.3800
0.6600
0.0018
0.0092
0.6600
2.5000
2.6000


 


2150
MQLFHLCLIISCSCP


 


2151
NAPILSTLPETTVVR
1186.16
0.0009

0.0009

−0.0007

−0.0002


0.0005


0.1600


 


2152
NLNVSIPWTHKVGNF
1186.17
0.0001

−0.0005
−0.0041
−0.0007

−0.0002


0.0005


0.0009


 


2153
NLSWLSLDVSAAFYH
1186.18
0.1400
0.0003
−0.0005
1.3000
0.2900

0.0033
0.0022
0.0330
0.0041
0.0150
0.0620
2.4000


 


2154
NRPIDWKVCQRIVGL


 


2155
PAAMPHLLVGSSGLS


 


2156
PDRVHFASPLHVAWR
1298.08
0.0510
0.0290
0.0008

0.0008
0.0054
0.0008

0.0190
0.0810
0.0035
0.2400


 


2157
PFLLAQFTSAICSVV
F107.04
0.1800
0.0270
0.0042
−0.0013
0.0800
0.1200
0.0120
0.0016
0.0800
0.0770
0.0580
0.0590


 


2158
PHCLAFSYMDDVVLG


 


2159
PIILGFRKIPMGVGL


 


2160
PLPIHTAELLAACFA
1280.18
0.0046



0.0490




−0.0003


 


2161
PPAYRPPNAPILSTL
1186.20
0.0056

−0.0005

0.0038

0.0022


0.0024


0.0015


 


2162
PQAMQWNSTTFHQTL
1298.01
0.0012



0.0300




0.1200


 


2163
PQSLDSWWTSLNFLG


 


2164
QCGYPALMPLYACIQ
1186.21
0.0062

0.0018

0.0068

0.0023


0.0006


 


2165
QLLWFHISCLTFGRE


 


2166
QQYVGPLTVNEKRRL


 


2167
QWFVGLSPTVWLSVI


 


2168
RDLLDTASALYREAL
1280.19
0.0001



0.0092




0.0770


 


2169
RDVLCLRPVGAESRG


 


2170
RFIIFLFILLLCLIF


 


2171
RFSWLSLLVPFVQWF
1186.22
0.0430

0.0009

−0.0007

0.0002


0.0005


0.0031


 


2172
RPGLCQVFADATPTG


 


2173
RQLLWFHISCLTFGR
1186.23
0.0002

0.0009

0.0140

0.0011


0.0061


0.0096


 


2174
RRAFPHCLAFSYMDD
F107.05
0.0010

0.0010

−0.0009

0.0010


0.0017


 


2175
RRFIIFLFILLLCLI


 


2176
RRSFGVEPSGSGHID


 


2177
RVSWPKFAVPNLQSL


 


2178
RWGYSLNFMGYVIGS


 


2179
SFGVWIRTPPAYRPP
1186.25
0.0094
0.0110
0.4300
−0.0009
0.0780
0.0630
0.0260
0.0071
0.0002
0.0240
0.2500
0.0800
0.0016


 


2180
SFPWLLGCAANWILR


 


2181
SFVYVPSALNPADDP


 


2182
SGFLGPLLVLQAGFF


 


2183
SPFLLAQFTSAICSV
1186.26
0.1200
0.0200
0.0085
−0.0013
0.0740
0.0190
−0.0002
−0.0013
0.0540
0.0330
0.0014
0.0380
0.2000


 


2184
SSNLSWLSLDVSAAF
1186.27
0.1400
0.0030
−0.0005
1.5000
0.2700

0.0046
0.0180
0.1000
0.0039
0.0460
0.0110
6.2000


 


2185
SVELLSFLPSDFFPS


 


2186
SVRFSWLSLLVPFVQ
1280.20
0.9000



0.0099




0.0037


 


2187
SVVLSRKYTSFPWLL
27.0282
0.0005

0.0057
0.2100
−0.0016

0.5300


0.0130


 


2188
TNFLLSLGIHLINPK
1298.03
3.5000
0.0410
0.1200

0.0220
0.0360
0.0053

0.0160
0.2200
0.0032
0.3800


 


2189
TNLLSSNLSWLSLDV
1186.26
0.0016

−0.0005

0.1300

0.0006


0.0019


0.0410


 


2190
TRILTIPQSLDSWWT


 


2191
TSFVYVPSALNPADD


 


2192
TSGFLGPLLVLQAGF


 


2193
VAPLPIHTAELLAAC


 


2194
VCAFSSAGPCALRFT
1186.29
0.2100

0.2600

0.0023

0.0003


0.0200


0.0150


 


2195
VELLSFLPSDFFPSI


 


2196
VGLLGFAAPFTQCGY
1280.21
0.0470
0.3100
0.0008

−0.0014

−0.0004

−0.0001
0.0014

0.5700


 


2197
VGNFTGLYSSTVPVF
1298.02
1.7000
0.0100
0.0016

0.0140
0.1700
0.0035

0.0580
0.5600
0.0044
0.3100


 


2198
VLCLRPVGAESRGRP


 


2199
VQWFVGLSPTVWLSV


 


2200
WASVRFSWLSLLVPF


 


2201
WLSLDVSAAFYHIPL


 


2202
WLSLLVPFVQWFVGL


 


2203
WMCLRRFIIFLFILL


 


2204
WPKFAVPNLQSLTNL
1186.30
0.0007

0.0013

0.0023

0.0002


0.0008


0.0180


 


2205
YPALMPLYACIQSKQ
1298.05
0.2400



0.0014




0.0011


 



145
















TABLE XIX







HBV DR3 MOTIF PEPTIDES WITH BINDING DATA
































Binding



Total

Core
Core
Pro-
Posi-

Core




Data



Conservancy
Total
Convervancy
Freq.
tein
tion
Core Sequence
SEQ ID NO:
Sequence
SEQ ID NO:
Peptide
Filed
DR3
Motif























90.00
18
90.00
18
POL
535
YMDDVVLGA
2228
AFSYMDDVVLGAKSV
2206
1186.02

0.0130
DR3


 


55.00
11
95.00
19
POL
655
FSPTYKAFL
2229
AFTFSPTYKAFLCKQ
2207
35.0099

0.0035
DR3


 


65.00
13
90.00
18
POL
18
LEEELPRLA
2230
AGPLEEELPRLADEG
2208
35.0091

0.0022
DR3


 


65.00
13
80.00
16
POL
731
IGTDNSVVL
2231
AKLIGTDNSVVLSRK
2209



DR3


 


85.00
17
85.00
17
NUC
34
LYREALESP
2232
ASALYREALESPEHC
2210



DR3


 


70.00
14
75.00
15
NUC
136
FGRETVLEY
2233
CLTFGRETVLEYLVS
2211



DR3


 


90.00
18
90.00
18
x
48
AHLSLRGLP
2234
DHGAHLSLRGLPVCA
2212



DR3


 


85.00
17
90.00
18
POL
737
VVLSRKYTS
2235
DNSVVLSRKYTSFPW
2213



DR3


 


45.00
9
100.00
20
POL
374
LVVDFSQFS
2236
ESRLVVDFSQFSRGN
2214
35.0096
*
2.6000
DR3


 


5.00
1
75.00
1
ENV
172
AVLDPRVRG
2237
FHQAVLDPRVRGLYL
2215



DR3


 


90.00
18
95.00
19
ENV
256
VLLDYQGML
2238
FLLVLLDYQGMLPVC
2216
35.009

0.0170
DR3


 


55.00
11
100.00
20
POL
360
FLVDKNPHN
2239
GGVFLVDKNPHNTTE
2217
35.0095

0.0790
DR3


 


95.00
19
95.00
19
POL
683
VFADATPTG
2240
LCQVFADATPTGWGL
2218
1280.14

0.0000
DR3


 


35.00
7
95.00
19
X
18
VGAESRGRP
2241
LRPVGAESRGRPVSG
2219
35.0101

−0.0017
DR3


 


55.00
11
95.00
19
POL
412
LSLDVSAAF
2242
LSWLSLDVSAAFYHI
2220



DR3


 


45.00
9
85.00
17
NUC
27
MDIDPYKEF
2243
LWGMDIDPYKEFGAS
2221



DR3


 


85.00
17
100.00
20
POL
34
VAEDLNLGN
2244
NRRVAEDLNLGNLNV
2222
35.0092

0.1400
DR3


 


100.00
20
100.00
20
POL
47
IPWTHKVGN
2245
NVSIPWTHKVGNFTG
2223



DR3


 


45.00
9
95.00
19
ENV
10
FFPDHQLDP
2246
PLGFFPDHQLDPAFG
2224



DR3


 


30.00
6
75.00
15
POL
241
FGVEPSGSG
2247
RRSFGVEPSGSGHID
2225



DR3


 


100.00
20
100.00
20
POL
120
LPLDKGIKP
2248
TKYLPLDKGIKPYYP
2226
35.0094

−0.0017
DR3


 


60.00
12
85.00
17
POL
96
LTVNEKRRL
2249
VGPLTVNEKRRLKLI
2227
35.0093
*
2.2000
DR3


 








22

22
















TABLE XX







Population coverage with combined HLA Supertypes









PHENOTYPIC FREQUENCY













HLA-SUPERTYPES
Caucasian
N.A. Black
Japanese
Chinese
Hispanic
Average
















A2, A3, B7
83.0
86.1
87.5
88.4
86.3
86.2


A2, A3, B7, A24,
99.5
98.1
100.0
99.5
99.4
99.3


B44, A1


A2, A3, B7, A24,
99.9
99.6
100.0
99.8
99.9
99.8


B44, A1, B27, B62,


B58
















TABLE XXI







HBV ANALOGS





















A2
A3

B7
1°







A1
Super
Super
A24
Super
Anchor




AA
Sequence
Fixed Nomen.
Motif
Motif
Motif
Motif
Motif
Fixer
Analog
SEQ ID NO:





















ALFKDWEEL








2250


 


9
ALMPLYACV
L2.IV9
N
Y
N
N
N
1
A
2251


 



ALMPLYASI








2252


 


9
ALMPLYAXI

N
Y
N
N
N

A
2253


 


10
ALPSDFFPSV

N
Y
N
N
N
No
A
2254


 



ALPSDFFPSV-NH2








2255


 



ALSLIVNLL








2256


 


9
AMTFSPTYK

N
N
Y
N
N

A
2257


 



ATVELLSFLPSDFFPSV-NH2








2258


 


10
CILLLCLIFL

N
Y
N
N
N
No
A
2259


 


11
CILLLCLIFLL

N
Y
N
N
N
No
A
2260


 


9
DPFRGRLGL

N
N
N
N
Y

A
2261


 


9
DPSRGRLGI

N
N
N
N
Y

A
2262


 



ELLSFLPSDFFPSV-NH2








2263


 


10
FAPSDFFPSV
LA2.V10
N
Y
N
N
N
Rev
A
2264


 


10
FILLLXLIFL

N
Y
N
N
N

A
2265


 


10
FLASDFFPSV

N
Y
N
N
N
No
A
2266


 


10
FLGLSPTVWV
VL2.LV1
N
Y
N
N
N
1
A
2267


 


10
FLKSDFFPSV

N
Y
N
N
N
No
A
2268


 


10
FLLAQFTSAV
L2.IV10
N
Y
N
N
N
1
A
2269


 


9
FLLAQFTSV
L2.AV9
N
Y
N
N
N
1
A
2270


 


9
FLLPIFFCL

N
Y
N
N
N
No
A
2271


 


9
FLLSLGIHV
L2.LV9
N
Y
N
N
N
1
A
2272


 


9
FLLTRILTV
L2.IV9
N
Y
N
N
N
1
A
2273


 


9
FLLTRILYI

N
Y
N
N
N

A
2274


 


9
FLLTYILTI

N
Y
N
N
N

A
2275


 


10
FLMSDYFPSV

N
Y
N
N
N
No
A
2276


 


9
FLMSYFPSV

N
Y
N
N
N
No
A
2277


 


10
FLPADFFPSI
L2.SA4
N
Y
N
N
N
Rev
A
2278


 


10
FLPADFFPSV

N
Y
N
N
N
No
A
2279


 


10
FLPDDFFPSA
L2.SD4
N
Y
N
N
N
Rev
A
2280


 


10
FLPDDFFPSV

N
Y
N
N
N
No
A
2281


 


10
FLPNDFFPSA
L2.SN4
N
Y
N
N
N
Rev
A
2282


 


10
FLPNDFFPSV

N
Y
N
N
N
No
A
2283


 


10
FLPS(X)YFPSV

N
N
N
N
N

A
2284


 


10
FLPSAFFPSV

N
Y
N
N
N
No
A
2285


 


10
FLPSD(X)FPSV

N
N
N
N
N

A
2286


 


10
FLPSDAFPSV

N
Y
N
N
N
No
A
2287


 


10
FLPSDFAPSV

N
Y
N
N
N
No
A
2288


 



FLPSDFF-NH2








2289


 


10
FLPSDFFASV

N
Y
N
N
N
No
A
2290


 


10
FLPSDFFKSV

N
Y
N
N
N
No
A
2291


 


8
FLPSDFFP

N
N
N
N
N

A
2292


 



FLPSDFFP-NH2








2293


 


10
FLPSDFFPAV

N
Y
N
N
N
No
A
2294


 


10
FLPSDFFPKV

N
Y
N
N
N
No
A
2295


 


9
FLPSDFFPS

N
N
N
N
N

A
2296


 



FLPSDFFPS-NH2








2297


 


10
FLPSDFFPSA
LV.VA10
N
Y
N
N
N
Rev
A
2298


 


10
FLPSDFFPSI
LV.VI10
N
Y
N
N
N
Rev
A
2299


 



FLPSDFFPSV(CONH2)








2300


 



FLPSDFFPSV-NH2








2301


 


11
FLPSDFFPSVR

N
N
Y
N
N

A
2302


 



FLPSDFFPSVR-NH2








2303


 


12
FLPSDFFPSVRD

N
N
N
N
N

A
2304


 


10
FLPSDFYPSV

N
Y
N
N
N
No
A
2305


 


11
FLPSDLLPSVR

N
N
Y
N
N

A
2306


 


10
FLPSDYFPSV

N
Y
N
N
N
No
A
2307


 


10
FLPSEFFPSV

N
Y
N
N
N
No
A
2308


 


9
FLPSYFPSA
L2.FY5.
N
Y
N
N
N
Rev3
A
2309


 


9
FLPSYFPSV
L2.FY5.
N
Y
N
N
N
3
A
2310


 


10
FLPSZFFPSV

N
Y
N
N
N
No
A
2311


 


10
FLPSZFFPSV

N
Y
N
N
N
No
A
2312


 


10
FLPVDFFPSI
L2.SV4.
N
Y
N
N
N
Rev
A
2313


 


10
FLPVDFFPSV

N
Y
N
N
N
No
A
2314


 



FLSKQYLNL








2315


 


9
FLYTRILTI

N
Y
N
N
N

A
2316


 


8
FMFSPTYK

N
N
Y
N
N

A
2317


 


10
FMLLLCLIFL
IM2.L10
N
Y
N
N
N
1
A
2318


 


10
FMPSDFFPSV
LM2.V1
N
Y
N
N
N
1
A
2319


 


8
FPAAMPHL

N
N
N
N
Y

A
2320


 


9
FPAAMPHLL

N
N
N
N
Y

A
2321


 


10
FPAAMPHLLV

N
N
N
N
Y

A
2322


 


9
FPALMPLYA

N
N
N
N
Y

A
2323


 


10
FPARVTGGVF

N
N
N
N
Y

A
2324


 


10
FPCALRFTSA

N
N
N
N
Y

A
2325


 


9
FPFCLAFSY

N
N
N
N
Y

A
2326


 


10
FPFCLAFSYM

N
N
N
N
Y

A
2327


 


9
FPHCLAFAL

N
N
N
N
Y

A
2328


 


9
FPHCLAFAY

N
N
N
N
Y

A
2329


 


9
FPHCLAFSA

N
N
N
N
Y

A
2330


 


9
FPHCLAFSI

N
N
N
N
Y

A
2331


 


9
FPHCLAFSL

N
N
N
N
Y

A
2332


 


10
FPHCLAFSYI

N
N
N
N
Y

A
2333


 


10
FPHXLAFSYM

N
N
N
N
Y

A
2334


 


9
FPIPSSWAF

N
N
N
N
Y

A
2335


 


9
FPSRGRLGL

N
N
N
N
Y

A
2336


 


9
FPVCAFSSA

N
N
N
N
Y

A
2337


 


9
FPVCLAFSY

N
N
N
N
Y

A
2338


 


10
FQPSDYFPSV

N
N
N
N
Y
Rev
A
2339


 


8
FVFSPTYK

N
N
Y
N
N

A
2340


 


9
FVLGGXRHK

N
N
Y
N
N

A
2341


 


9
GLCQVGADV
L2.AV9
N
Y
N
N
N
1
A
2342


 


9
GLLGWSPQV
L2.AV9
N
Y
N
N
N
1
A
2343


 


9
GLWIRTIPPV
VL2.AV9
N
Y
N
N
N
1
A
2344


 


9
GLXQFADA

N
Y
N
N
N

A
2345


 


10
GMDNSVVLSR

N
N
Y
N
N

A
2346


 


11
GMDNSVVLSRK

N
N
Y
N
N

A
2347


 


10
GPCALRFTSI

N
N
N
N
Y

A
2348


 


10
GPFALRFTSA

N
N
N
N
Y

A
2349


 


10
GPXALRFTSA

N
N
N
N
Y

A
2350


 


10
GTFNSVVLSR

N
N
Y
N
N

A
2351


 


11
GTFNSVVLSRK

N
N
Y
N
N

A
2352


 


10
GVDNSVVLSR

N
N
Y
N
N

A
2353


 


11
GVDNSVVLSRK

N
N
Y
N
N

A
2354


 


10
GYRWMXLRRF

N
N
N
Y
N

A
2355


 


9
HISXLTFGR

N
N
Y
N
N

A
2356


 


10
HMLWKAGILY

Y
N
Y
N
N

A
2357


 


11
HMLWKAGILYK

N
N
Y
N
N

A
2358


 


8
HPAAMPHI

N
N
N
N
Y

A
2359


 


9
HPAAMPHLI

N
N
N
N
Y

A
2360


 


10
HPAAMPHLLI

N
N
N
N
Y

A
2361


 


8
HPFAMPHL

N
N
N
N
Y

A
2362


 


9
HPFAMPHLL

N
N
N
N
Y

A
2363


 


10
HPFAMPHLLV

N
N
N
N
Y

A
2364


 


10
HTLWKAGILK

N
N
Y
N
N

A
2365


 


10
HTLWKAGILR

N
N
Y
N
N

A
2366


 


10
HVLWKAGILY

N
N
Y
N
N

A
2367


 


11
HVLWKAGILYK

N
N
Y
N
N

A
2368


 



IIKKSEQFV








2369


 


9
ILGLLGFAV
VL2.AV9
N
Y
N
N
N
1
A
2370


 


10
ILLLCLIFLV
L2.LV10
N
Y
N
N
N
1
A
2371


 


9
ILLLXLIFL

N
Y
N
N
N

A
2372


 


10
ILLLXLIFLL

N
Y
N
N
N

A
2373


 


9
IPFPSSWAF

N
N
N
N
Y

A
2374


 


9
IPILSSWAF

N
N
N
N
Y

A
2375


 


9
IPIPMSWAF

N
N
N
N
Y

A
2376


 


9
IPIPSSWAI

N
N
N
N
Y

A
2377


 


9
IPITSSWAF

N
N
N
N
Y

A
2378


 



KIKESFRKL

N
N
N
N
Y

A
2379


 


9
KLFLYSHPI

N
Y
N
N
N
No
A
2380


 


9
KLHLYSHPV
L2.IV9
N
Y
N
N
N
1
A
2381


 


9
KVGNFTGLK

N
N
Y
N
N

A
2382


 


9
KVGNFTGLR

N
N
Y
N
N

A
2383


 


9
LLAQFTSAV
L2.IV9
N
Y
N
N
N
1
A
2384


 


10
LLFYQGMLPV

N
Y
N
N
N
No
A
2385


 



LLGSAANWI








2386


 


10
LLGXAANWIL

N
Y
N
N
N

A
2387


 


9
LLLXLIFLL

N
Y
N
N
N

A
2388


 


10
LLLXLIFLLV

N
Y
N
N
N

A
2389


 


10
LLLYQGMLPV

N
Y
N
N
N
No
A
2390


 


9
LLPFVQWFV
VL2.V9
N
Y
N
N
N
1
A
2391


 


10
LLPIFFXLWV

N
Y
N
N
N

A
2392


 



LLSFLPSDFFPSV-NH2








2393


 


9
LLSSNLSWV
L2.LV9
N
Y
N
N
N
1
A
2394


 


10
LLVLQAGFFV
L2.LV10
N
Y
N
N
N
1
A
2395


 


9
LLXLIFLLV

N
Y
N
N
N

A
2396


 


10
LMLLDYQGMV
VM2.LV
N
Y
N
N
N
1
A
2397


 


10
LMLQAGFFLV
VM2.LV
N
Y
N
N
N
1
A
2398


 


9
LMPFVQWFV
VM2.V9
N
Y
N
N
N
1
A
2399


 


9
LPFCAFSSA

N
N
N
N
Y

A
2400


 


8
LPIFFCLI

N
N
N
N
Y

A
2401


 


9
LPIFFCLWI

N
N
N
N
Y

A
2402


 


9
LPIHTAELI

N
N
N
N
Y

A
2403


 


11
LPIHTAELLAI

N
N
N
N
Y

A
2404


 



LPSDFFPSV-NH2








2405


 


9
LPVCAFSSI

N
N
N
N
Y

A
2406


 


9
LPVXAFSSA

N
N
N
N
Y

A
2407


 


12
LSFLPSDFFPSV

N
N
N
N
N

A
2408


 



LSFLPSDFFPSV-NH2








2409


 


10
MMWYWGPSLK

N
N
Y
N
N

A
2410


 


10
MMWYWGPSLR

N
N
Y
N
N

A
2411


 


9
MMWYWGPSV
M2.LV9
N
Y
N
N
N
1
A
2412


 


8
MPLSYCHI

N
N
N
N
Y

A
2413


 


9
NLGNLNVSV
L2.IV9
N
Y
N
N
Y
1
A
2414


 



NLNNLNVSI








2415


 


9
NMGLKYRQL

N
Y
N
Y
N
No
A
2416


 


11
NPLGFFPDHQI

N
N
N
N
Y

A
2417


 


9
PLLPIFFCV
L2.LV9
N
Y
N
N
N
1
A
2418


 


9
PLLPIFFXL

N
Y
N
N
N

A
2419


 


8
PSDFFPSV

N
N
N
N
N

A
2420


 



PSDFFPSV-NH2








2421


 


10
QLLWFHSXL

N
Y
N
N
N

A
2422


 


10
QMFTFSPTYK

N
N
Y
N
N

A
2423


 


10
QVFTFSPTYK

N
N
Y
N
N

A
2424


 



RIPRTPRSV








2425


 


9
RLSWPKFAV
VL2.V9
N
Y
N
N
N
1
A
2426


 


9
RLTGGVFLV
VL2.V9
N
Y
N
N
N
1
A
2427


 


9
RMLTIPQSV
IM2.LV9
N
Y
N
N
N
1
A
2428


 


9
RMTGGVFLV
VM2.V9
N
Y
N
N
N
1
A
2429


 


9
RMYLHTLWK

N
N
Y
N
N

A
2430


 


9
RVYLHTLWK

N
N
Y
N
N

A
2431


 


9
SAIXSVVRR

N
N
Y
N
N

A
2432


 


11
SFLPSDFFPSV

N
N
N
N
N

A
2433


 



SFLPSDFFPV-NH2








2434


 


9
SLDSWWTSV
L2.LV9
N
Y
N
N
N
1
A
2435


 



SLNFLGGTTV(NH2)
L2.LV9
N
Y
N
N
N
1
A
2436


 


9
SMICSVVRR

N
N
Y
N
Y

A
2437


 


10
SMLPETTVVR

N
N
Y
N
N

A
2438


 


11
SMLPETTVVRR

N
N
Y
N
N

A
2439


 


10
SMLSPFLPLY
IM2.LV1
N
Y
N
N
N
1
A
2440


 


8
SPFLLAQI

N
N
N
N
Y

A
2441


 


11
STLPETYVVRR

N
N
Y
N
N

A
2442


 


9
SVICSVVRR

N
N
Y
N
N

A
2443


 


10
SVLPETTVVR

N
N
Y
N
N

A
2444


 


11
SVLPETTVVRR

N
N
Y
N
N

A
2445


 


9
SVNRPIDWK

N
N
Y
N
N

A
2446


 


9
SVVRRAFPK

N
N
Y
N
N

A
2447


 


9
SVVRRAFPR

N
N
Y
N
N

A
2448


 


9
TLWKAGILK

N
N
Y
N
N

A
2449


 


9
TLWKAGILR

N
N
Y
N
N

A
2450


 


10
TMPETTVVRR

N
N
Y
N
N

A
2451


 


9
TMWKAGILY

Y
N
Y
N
N

A
2452


 


10
TMWKAGILYK

N
N
Y
N
N

A
2453


 


10
TPARVTGGVI

N
N
N
N
Y

A
2454


 


10
TPFRVTGGVF

N
N
N
N
Y

A
2455


 


10
TSAIXSVVRR

N
N
Y
N
N

A
2456


 



TVELLSFLPSDFFPSV-NH2








2457


 


10
TVPETTVVRR

N
N
Y
N
N

A
2458


 


9
TVWKAGILY

N
N
Y
N
N

A
2459


 


10
TVWKAGILYK

N
N
Y
N
N

A
2460


 



VELLSFLPSDFFPSV-NH2








2461


 



VLEYLVSFGV(NH2)








2462


 



VLGGSRHKL








2463


 


9
VLLDYQGMV
L2.LV9
N
Y
N
N
N
1
A
2464


 


9
VLQAGFFLV
L2.LV9
N
Y
N
N
N
1
A
2465


 


10
VMGGVFLVDK

N
N
Y
N
N

A
2466


 


10
VPFVQWFVGI

N
N
N
N
Y

A
2467


 


8
VPSALNPI

N
N
N
N
Y

A
2468


 


9
VVFFSQFSR

N
N
Y
N
N

A
2469


 


10
VVGGVFLVDK

N
N
Y
N
N

A
2470


 


9
WLLRGTSFV
IL2.V9
N
Y
N
N
N
1
A
2471


 


10
YLFTLWKAGI

N
Y
N
N
N
No
A
2472


 


10
YLHTLWKAGV
L2.IV10
N
Y
N
N
N
1
A
2473


 


10
YLLTLWKAGI

N
Y
N
N
N
No
A
2474


 


9
YLLTRILTI

N
Y
N
N
N

A
2475


 


9
YLPSALNPV
VL2.AV9
N
Y
N
N
N
1
A
2476


 


10
YLPSDFFPSV

N
Y
N
N
N
No
A
2477


 


9
YMDDVVLGV
M2.AV9
N
Y
N
N
N
1
A
2478


 


9
YMFDVVLGA

N
Y
N
N
N
No
A
2479


 


10
YMFDVVLGAK

N
N
Y
N
N

A
2480


 


10
YNMGLKFRQL

N
N
N
N
N

A
2481


 


8
YPALMPLI

N
N
N
N
N

A
2482


 


9
YPALMPLYI

N
N
N
N
Y

A
2483


 


9
YPFLMPLYA

N
N
N
N
Y

A
2484


 


12
YSFLPSDFFPSV

N
N
N
N
N

A
2485


 



237
















TABLE XXII







Discreet substitutions improve the B7 supertype binding capacity and


degeneracy of peptide ligands.









Binding (IC50 nM)























Source
1
2
3
4
5
6
7
8
9
B*0701
B*3501
B*5101
B*5301
B*5401
x-rxn
SEQ ID NO:


























HBV ENV
I
P
I
P
S
S

A
F
42
2.6
2.3
12
2970
4
2505


313



F
P
I
P
S
S

A
F
24
1.2
305
1.7
105
5
2506



I
P
I
P
S
S

A
I
31
54
15
24
7.7
5
2507


HBV POL 541
F
P
H
C
L
A
F
S
Y
—
14
83
17
503
3
2508



F
P
H
C
L
A
F
A
L
25
2.7
28
5.0
24
5
2509



F
P
H
C
L
A
F
S
L
74
2.4
4.5
15
7.7
5
2510



F
P
F
C
L
A
F
S
Y
—
6.5
27
4.8
5.1
4
2511



F
P
H
C
L
A
F
S
I
675
29
6.3
3.8
1.0
4
2512



F
P
H
C
L
A
F
S
A
3667
6.5
250
137
0.6
4
2513


HCV Core 168
L
P
G
C
S
F
S
I
F
28
90
100
114
6897
4
2514



F
P
G
C
S
F
S
I
F
19
1.6
132
3.2
67
5
2515


MAGE2 170
V
P
I
S
H
L
Y
I
L
22
171
96
238
3175
4
2516



F
P
I
S
H
L
Y
I
L
16
7.3
6.4
7.0
28
5
2517


MAGE3 196

P
K
A
G
L
L
I
I
940
5039
393
90
248
3
2518



F
P
K
A
G
L
L
I
I
162
1303
5.8
60
150
4
2519




P
F
A
G
L
L
I
I
229
1.0
0.9
2.3
0.27
5
2520
















TABLE XXIII







Sets of preferred epitopes restricted by class


I and class II molecules can be selected for


inclusion in an HBV-specific vaccine.


Table XXIII lists as a matter of example one


such set of epitopes.















SEQ





restric-
ID


Peptide
Sequence
Protein
tion
NO:










A) Class I restricted epitopes











924.07
FLPSDFFPSV
core 18
A2
2521


 


777.03
FLLTRILTI
env 183
A2
2522


 


927.15
ALMPLYACI
pol 642
A2
2523


 


1013.01
WLSLLVPFV
env 335
A2
2524


 


1090.14
YMDDVVLGA
pol 538
A2/A1
2525


 


1168.02
GLSRYVARL
pol 455
A2
2526


 


927.11
FLLSLGIHL
pol 562
A2
2527


 


1069.10
LLPIFFCLWV
env 378
A2
2528


 


1069.06
LLVPFVQWFV
env 338
A2
2529


 


1147.16
HTLWKAGILYK
pol 149
A3/A1
2530


 


1083.01
STLPETTVVRR
core 141
A3
2531


 


1069.16
NVSIPWTHK
pol 47
A3
2532


 


1069.20
LVVDFSQFSR
pol 388
A3
2533


 


1090.10
QAFTFSPTYK
pol 665
A3
2534


 


1090.11
SAICSVVRR
pol 531
A3
2535


 


1142.05
KVGNFTGLY
pol 629
A3/A1
2536


 


1147.05
FPHCLAFSYM
pol 530
B7
2537


 


988.05
LPSDFFPSV
core 19
B7
2538


 


1145.04
IPIPSSWAF
env 313
B7
2539


 


1147.02
HPAAMPHLL
pol 429
B7
2540


 


26.0570
YPALMPLYACI
pol 640
B7
2541


 


1147.04
TPARVTGGVF
pol 354
B7
2542


 


1.0519
DLLDTASALY
core 419
A1
2543


 


2.0239
LSLDVSAAFY
pol 1000
A1
2544


 


1039.06
WMMWYWGPSLY
env 359
A1
2545


 


20.0269
RWMCLRRFII
env 236
A24
2546


 


20.0136
SWLSLLVPF
env 334
A24
2547


 


20.0137
SWWTSLNFL
env 197
A24
2548


 


13.0129
EYLVSFGVWI
core 117
A24
2549


 


1090.02
AYRPPNAPI
core 131
A24
2550


 


13.0073
WFHISCLTF
core 102
A24
2551


 


20.0271
SWPKFAVPNL
pol 392
A24
2552


 


1069.23
KYTSFPWLL
pol 745
A24
2553


 


2.0181
LYSHPIILGF
pol 492
A24
2554


 







B) Glass II restricted epitopes











F107.03
LQSLTNLLSSNLSWL
pol 412
DR
2555





super-





motif


 


1298.06
KQAFTFSPTYKAFLC
pol 664

2556


 


1280.06
AGFFLLTRILTIPQS
env 180

2557


 


1280.09
GTSFVYVPSALNPAD
pol 774

2558


 


CF-08
VSFGVWIRTPPAYRPP-
core 120

2559



NAPI


 


 27.0281
RHYLHTLWKAGILYK
pol 145

2560


 


1186.15
LVPFVQWFVGLSPTV
env 339

2561


 


1280.15
LHLYSHPIILGFRKI
pol 501

2562


 


F107.04
PFLLAQFTSAICSVV
pol 523

2563


 


1298.04
KQCFRKLPVNRPIDW
pol 618

2564


 


1298.07
AANWILRGTSFVYVP
pol 767

2565


 


857.02
PHHTALRQAILCWGEL-
core 50

2566



MTLA


 


1280.14
LCQVFADATPTGWGL
pol 694
DR3
2567





motif


 


35.0096
ESRLVVDFSQFSRGN
pol 385

2568


 


35.0093
VGPLTVNEKRRLKLI
pol 96

2569


 


1186.27
SSNLSWLSLDVSAAF
pol 420

2570


 


1186.18
NLSWLSLDVSAAFYH
pol 442

2571

## Claims

1. An isolated peptide consisting of the oligopeptide LWFHISCLTF (SEQ ID NO:879).

2. A composition comprising the peptide of claim 1 and a carrier.

3. A composition comprising the peptide of claim 1 and a pharmaceutically acceptable carrier.

4. A composition comprising the peptide of claim 1 and a liposome.

5. A composition comprising the peptide of claim 1, wherein the peptide is admixed with at least one other peptide comprising a helper T lymphocyte (HTL) epitope or is joined to at least one other peptide consisting of an HTL epitope.