PEPTIDES AND COMBINATIONS OF PEPTIDES FOR USE IN IMMUNOTHERAPY AGAINST AN INFECTION BY SARS-COV-2 (COVID-19)

Abstract
SARS-CoV2-associated T-cell peptide epitopes as active pharmaceutical ingredients of vaccine compositions to stimulate anti-SARS-CoV2 immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides of SARS-CoV2-associated T-cell peptide epitopes bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.
Description
FIELD OF THE INVENTION

The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of an infection by SARS-CoV-2 (COVID-19). The present invention furthermore relates to SARS-CoV2-associated T-cell peptide epitopes that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-SARS-CoV2 immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.


The present invention relates to several novel peptide sequences and their variants that can be used in vaccine compositions for eliciting anti-SARS-CoV2 immune responses, or as targets for the development of pharmaceutically/immunologically active compounds and cells.


The present invention relates to the field of molecular biology, more particular to the field of molecular immunology.


BACKGROUND OF THE INVENTION

The novel coronavirus SARS-CoV-2 is responsible for the COVID-19 lung disease, which especially in elderly, weakened and immunocompromised patients, shows severe and fatal courses. In the meantime, SARS-CoV-2 has spread to a worldwide pandemic with yet incalculable health, economic and socio-political consequences. So far, there are no established therapies and a vaccine is not yet available.


T-cell immunity plays an essential role in the control of viral infections. In particular, CD4+ T helper (Th) cells are essential for the regulation and maintenance of immune responses as well as for the production of anti-viral cytokines while cytotoxic CD8+ T cells (CTL) are responsible for the elimination of virus-infected cells. For the activation and function of T cells the recognition of viral antigens represented by short peptides presented by human leukocyte antigens (HLA) is indispensable. To decipher protective T-cell immune responses in the human population, an extensive identification and characterization of such viral-derived T-cell epitopes is therefore essential, followed by a detailed functional study of CD4+ and CD8+-specific T cells. Such knowledge is not only essential for the understanding of host immune defense and mechanisms of long-term protection upon virus rechallenge, but is also a prerequisite for developing new and more efficient immunotherapies.


It is, therefore, an object underlying the invention to provide SARS-CoV-2-derived T-cell epitopes which can be used to develop medicaments and therapeutic methods for the prophylaxis and treatment of an infection by SARS-CoV-2 (COVID-19) and which may allow a better understanding of the biology of SARS-CoV-2 and its transmission.


The present invention satisfies these and other needs.


SUMMARY OF THE INVENTION

The present invention provides a peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variant binds to molecule(s) of the major histocompatibility complex (MHC) and/or induces T cells cross-reacting with said variant peptide; and a pharmaceutical acceptable salt thereof, wherein said peptide is not a full-length polypeptide.


The inventors were able to predict 110 SARS-CoV-2-derived T-cell epitopes based on the established algorithms NetMHCpan and SYFPEITHI (www.syfpeithi.de). A total of 100 HLA class I and 10 HLA class II peptides from the ten described SARS-CoV-2 proteins are predicted, including ten peptides for each of the ten most common HLA class I and II allotypes. This will allow covering at least one HLA allotype for 91.7% of the world population and therefore will provide broadly applicable T-cell epitopes.


The term “peptide” is used herein to designate a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of the adjacent amino acids. The peptides are preferably between 7 and 12 amino acids in length, further preferably between 8 and 11, but can be as long as 5, 6, 7, 8, 9, 10, 11, 12 or longer.


Furthermore, the term “peptide” shall include salts of a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of the adjacent amino acids. Preferably, the salts are pharmaceutical acceptable salts of the peptides, such as, for example, the chloride or acetate (trifluoroacetate) salts. It has to be noted that the salts of the peptides according to the present invention differ substantially from the peptides in their state(s) in vivo, as the peptides are not salts in vivo.


The term “peptide” shall also include “oligopeptide”. The term “oligopeptide” is used herein to designate a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of the adjacent amino acids. The length of the oligopeptide is not critical to the invention, as long as the correct epitope or epitopes are maintained therein. The oligopeptides are typically less than about 30 amino acid residues in length, and greater than about 15 amino acids in length.


The term “peptide” shall also include “polypeptide”. The term “polypeptide” designates a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of the adjacent amino acids. The length of the polypeptide is not critical to the invention as long as the correct epitopes are maintained. In contrast to the terms peptide or oligopeptide, the term polypeptide is meant to refer to molecules containing more than about 30 amino acid residues.


By a “variant” of the given amino acid sequence the inventors mean that the side chains of, for example, one or two of the amino acid residues are altered (for example by replacing them with the side chain of another naturally occurring amino acid residue or some other side chain) such that the peptide is still able to bind to an MHC molecule in substantially the same way as a peptide consisting of the given amino acid sequence in consisting of SEQ ID NO: 1 to SEQ ID NO: 110. For example, a peptide may be modified so that it at least maintains, if not improves, the ability to interact with and bind to the binding groove of a suitable MHC molecule, such as HLA-A*02, and in that way, it at least maintains, if not improves, the ability to bind to the TCR of activated T cells.


A person skilled in the art will be able to assess, whether T cells induced by a variant of a specific peptide will be able to cross-react with the peptide itself (Appay et al., 2006; Colombetti et al., 2006; Fong et al., 2001; Zaremba et al., 1997).


These T cells can subsequently cross-react with cells and kill cells that express a polypeptide that contains the natural amino acid sequence of the cognate peptide as defined in the aspects of the invention. As can be derived from the scientific literature and databases (Rammensee et al., 1999; Godkin et al., 1997), certain positions of HLA binding peptides are typically anchor residues forming a core sequence fitting to the binding motif of the HLA receptor, which is defined by polar, electrophysical, hydrophobic and spatial properties of the polypeptide chains constituting the binding groove. Thus, one skilled in the art would be able to modify the amino acid sequences set forth in SEQ ID NO: 1 to SEQ ID NO: 110, by maintaining the known anchor residues, and would be able to determine whether such variants maintain the ability to bind MHC class I or II molecules. The variants of the present invention retain the ability to bind to the TCR of activated T cells, which can subsequently cross-react with and kill cells that express a polypeptide containing the natural amino acid sequence of the cognate peptide as defined in the aspects of the invention.


In the present invention, the term “homologous” refers to the degree of identity between sequences of two amino acid sequences, i.e. peptide or polypeptide sequences. The aforementioned “homology” is determined by comparing two sequences aligned under optimal conditions over the sequences to be compared. Such a sequence homology can be calculated by creating an alignment using, for example, the ClustalW algorithm. Commonly available sequence analysis software, more specifically, Vector NTI, GENETYX or other tools are provided by public databases.


“Percent identity” or “percent identical” in turn, when referring to a sequence, means that a sequence is compared to a claimed or described sequence after alignment of the sequence to be compared (the “Compared Sequence”) with the described or claimed sequence (the “Reference Sequence”). The percent identity is then determined according to the following formula: percent identity =100 [1 -(C/R)]

    • wherein C is the number of differences between the Reference Sequence and the Compared Sequence over the length of alignment between the Reference Sequence and the Compared Sequence, wherein
    • (i) each base or amino acid in the Reference Sequence that does not have a corresponding aligned base or amino acid in the Compared Sequence and
    • (ii) each gap in the Reference Sequence and
    • (iii) each aligned base or amino acid in the Reference Sequence that is different from an aligned base or amino acid in the Compared Sequence, constitutes a difference and (iiii) the alignment has to start at position 1 of the aligned sequences;
    • and R is the number of bases or amino acids in the Reference Sequence over the length of the alignment with the Compared Sequence with any gap created in the Reference Sequence also being counted as a base or amino acid.


If an alignment exists between the Compared Sequence and the Reference Sequence for which the percent identity as calculated above is about equal to or greater than a specified minimum Percent Identity then the Compared Sequence has the specified minimum percent identity to the Reference Sequence even though alignments may exist in which the herein above calculated percent identity is less than the specified percent identity.


According to the invention “full-length polypeptide” refers to the source proteins from which the peptides are derived, e.g. SARS-CoV-2 encoded proteins, such as the 7096 amino acid (aa) long ORF1ab polyprotein (replicase complex), the 1273 aa long surface glycoprotein (S for spikes), the 75 aa long envelope protein (E), the 222 aa long membrane glycoprotein (M), the 419 aa long nucleocapsid phosphoprotein (N) and another five proteins (ORF3a, ORF6, ORF7a, ORF8 and ORF10).


The problem underlying the invention is herewith completely solved.


In an embodiment of the invention said peptide has the ability to bind to an MHC class-I or -II molecule, and wherein said peptide, when bound to said MHC, is capable of being recognized by CD4 and/or CD8 T cells.


This measure has the advantage that the capability of the peptide according to the invention to induce an immune response, in particular a T-cell response, is ensured.


In another embodiment of the invention the amino acid sequence thereof comprises a continuous stretch of amino acids according to any one of SEQ ID NO: 1 to SEQ ID NO: 110.


This measure has the advantage that the peptide according to the invention comprises all amino acids which are predicted as being involved in the induction of an immune response. The therapeutic efficacy is herewith further improved.


Another subject-matter of the present invention relates to an antibody, in particular a soluble or membrane-bound antibody, preferably a monoclonal antibody or fragment thereof, that specifically recognizes the peptide or variant thereof according to the invention, preferably when bound to an MHC molecule.


The term “antibody” or “antibodies” is used herein in a broad sense and includes both polyclonal and monoclonal antibodies. In addition to intact or “full” immunoglobulin molecules, also included in the term “antibodies” are fragments (e.g. CDRs, Fv, Fab and Fc fragments) or polymers of those immunoglobulin molecules and humanized versions of immunoglobulin molecules, as long as they exhibit any of the desired properties, i.e. specifically recognize the peptide or variant thereof according to the invention. Whenever possible, the antibodies of the invention may be purchased from commercial sources. The antibodies of the invention may also be generated using well-known methods.


The features, characteristics, advantages and embodiments disclosed for the peptide according to the invention apply to the antibody and fragment thereof correspondingly.


Another subject-matter of the invention relates to a T-cell receptor, preferably soluble or membrane-bound, or a fragment thereof, that is reactive with an HLA ligand, wherein said ligand is the peptide or variant thereof according to the invention, preferably when bound to an MHC molecule.


The term “T-cell receptor” (abbreviated TCR) according to the invention refers to a heterodimeric molecule comprising an alpha polypeptide chain (alpha chain) and a beta polypeptide chain (beta chain), wherein the heterodimeric receptor is capable of binding to a peptide antigen presented by an HLA molecule. The term also includes so-called gamma/delta TCRs.


The features, characteristics, advantages and embodiments disclosed for the peptide and antibody or fragment thereof according to the invention apply to the T-cell receptor correspondingly.


A still further subject-matter according to the invention relates to a nucleic acid, encoding for a peptide or variant thereof according to the invention, an antibody or fragment thereof according to the invention, a T-cell receptor or fragment thereof according to the invention, optionally linked to a heterologous promoter sequence, or an expression vector expressing said nucleic acid.


The nucleic acid coding for a particular peptide, oligopeptide, or polypeptide may be naturally occurring or they may be synthetically constructed. The nucleic acid (for example a polynucleotide) may be, for example, DNA, cDNA, PNA, RNA or combinations thereof, either single- and/or double- stranded, or native or stabilized forms of polynucleotides, such as, for example, polynucleotides with a phosphorothioate backbone and it may or may not contain introns so long as it codes for the peptide. Of course, only peptides that contain naturally occurring amino acid residues joined by naturally occurring peptide bonds are encodable by a polynucleotide. A still further aspect of the invention provides an expression vector capable of expressing a polypeptide according to the invention. As used herein the term “nucleic acid coding for (or encoding) a peptide” refers to a nucleotide sequence coding for the peptide including artificial (man-made) start and stop codons compatible for the biological system the sequence is to be expressed by, for example, a dendritic cell or another cell system useful for the production of TCRs. The term “promoter” means a region of DNA involved in binding of RNA polymerase to initiate transcription.


The features, characteristics, advantages and embodiments disclosed for the peptide according to the invention apply to the nucleic acid and expression vector correspondingly.


Another subject-matter of the invention relates to a recombinant host cell comprising the peptide according to the invention, the antibody or fragment thereof according to the invention, the T-cell receptor or fragment thereof according to the invention or the nucleic acid or the expression vector according to the invention, wherein said host cell preferably is selected from an antigen presenting cell, such as a dendritic cell, a T cell or an NK cell.


The features, characteristics, advantages and embodiments disclosed for the peptide according to the invention apply to the host cell correspondingly.


A still further subject-matter of the invention relates to an in vitro method for producing activated T lymphocytes, the method comprising contacting in vitro T cells with antigen loaded human class I or II MHC molecules expressed on the surface of a suitable antigen-presenting cell or an artificial construct mimicking an antigen-presenting cell for a period of time sufficient to activate said T cells in an antigen specific manner, wherein said antigen is a peptide according to the invention.


The activated T cells that are directed against the peptides of the invention are useful in therapy. Thus, a further aspect of the invention provides activated T cells obtainable by the foregoing methods of the invention.


Activated T cells, which are produced by the above method, will selectively recognize a cell that aberrantly expresses a polypeptide that comprises an amino acid sequence of SEQ ID NO: 1 to SEQ ID NO: 110.


Another subject-matter according to the invention relates to a pharmaceutical composition comprising at least one active ingredient selected from the group consisting of the peptide according to the invention, the antibody or fragment thereof according to the invention, the T-cell receptor or fragment thereof according to the invention, the nucleic acid or the expression vector according to the invention, the recombinant host cell according to the invention, or the activated T lymphocyte according to the invention, or a conjugated or labelled active ingredient, and a pharmaceutically acceptable carrier, and optionally, pharmaceutically acceptable excipients and/or stabilizers.


A “pharmaceutical composition” is a composition suitable for administration to a human being in a medical setting. Preferably, a pharmaceutical composition is sterile and produced according to GMP guidelines.


The pharmaceutical compositions comprise the peptides either in the free form or in the form of a pharmaceutically acceptable salt (see also above). As used herein, “a pharmaceutically acceptable salt” refers to a derivative of the disclosed peptides wherein the peptide is modified by making acid or base salts of the agent. For example, acid salts are prepared from the free base (typically wherein the neutral form of the drug has a neutral -NH2 group) involving reaction with a suitable acid. Suitable acids for preparing acid salts include both organic acids, e.g., acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methane sulfonic acid, ethane sulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like, as well as inorganic acids, e.g., hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid phosphoric acid and the like. Conversely, preparation of basic salts of acid moieties which may be present on a peptide are prepared using a pharmaceutically acceptable base such as sodium hydroxide, potassium hydroxide, ammonium hydroxide, calcium hydroxide, trimethylamine or the like.


Preferably, the pharmaceutical composition of the present invention is an immunotherapeutic such as a vaccine. It may be administered directly into the patient, into the affected organ or systemically i.d., i.m., s.c., i.p. and i.v., or applied ex vivo to cells derived from the patient or a human cell line which are subsequently administered to the patient, or used in vitro to select a subpopulation of immune cells derived from the patient, which are then re-administered to the patient. If the nucleic acid is administered to cells in vitro, it may be useful for the cells to be transfected so as to co-express immune-stimulating cytokines, such as interleukin-2. The peptide may be substantially pure, or combined with an immune-stimulating adjuvant or used in combination with immune-stimulatory cytokines, or be administered with a suitable delivery system, for example liposomes. The peptide may also be conjugated to a suitable carrier such as keyhole limpet haemocyanin (KLH) or mannan (see WO 95/18145 and (Longenecker et al., 1993)). The peptide may also be tagged, may be a fusion protein, or may be a hybrid molecule. The peptides whose sequence is given in the present invention are expected to stimulate CD4 or CD8 T cells. However, stimulation of CD8 T cells is more efficient in the presence of help provided by CD4 T-helper cells. Thus, for MHC Class I epitopes that stimulate CD8 T cells the fusion partner or sections of a hybrid molecule suitably provide epitopes which stimulate CD4-positive T cells. CD4- and CD8-stimulating epitopes are well known in the art and include those identified in the present invention. In one aspect, the vaccine comprises at least one peptide having the amino acid sequence set forth SEQ ID NO: 1 to SEQ ID NO: 109, and at least one additional peptide, preferably two to 50, more preferably two to 25, even more preferably two to 20 and most preferably two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen or eighteen peptides. The peptide(s) may be derived from one or more specific TAAs and may bind to MHC class I molecules.


In an embodiment of the pharmaceutical composition according to the invention it comprises at least 5, preferably at least 6, further preferably at least 7, further preferably at least 8, further preferably at least 9, and highly preferably at least 10 different peptides, each peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variant binds to molecule(s) of the major histocompatibility complex (MHC) and/or induces T cells cross-reacting with said variant peptide; and a pharmaceutical acceptable salt thereof, wherein said peptide is not a full-length polypeptide.


The inventors have realized that a pharmaceutical composition, such as a vaccine, has a good immunogenic effect if at least 5 peptides or amino acid sequences out of the SEQ ID NOS. 1 to 110 are contained therein. When using 10 peptides or amino acid sequences 91.7% of the human world population may be covered. Preferably the vaccine comprises at peptides 1 to 9 peptides comprising amino acid sequences out of the SEQ ID NOS. 1 to 100, and 1 to 9 peptides comprising amino acid sequences out of the SEQ ID NOS. 101 to 110. “1 to 9” in this context means 1, 2, 3, 4, 5, 6, 7, 8, or 9.


In this context it is an preferred embodiment of the pharmaceutical composition if the at least 1 peptide or amino acid sequence is selected out of each of the following ‘groups of ten’: SEQ ID NOs: 1 to 10; SEQ ID NOs: 11 to 20; SEQ ID NOs: 21 to 30; SEQ ID NOs: 31 to 40; SEQ ID NOs: 41 to 50; SEQ ID NOs: 51 to 60; SEQ ID NOs: 61 to 70; SEQ ID NOs: 71 to 80; SEQ ID NOs: 81 to 90; SEQ ID NOs: 91 to 100 SEQ ID NOs: 101 to 110. “At least 1” means 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. This ensures a coverage of 91.7% of the world population.


Another subject-matter of the invention relates to the peptide according to the invention, the antibody or fragment thereof according to the invention, the T-cell receptor or fragment thereof according to the invention, the nucleic acid or the expression vector according to the invention, the recombinant host cell according to the invention, or the activated T lymphocyte according to the invention for use in medicine, preferably for use against an infection by SARS-CoV-2 (COVID-19), such as a vaccine.


A still further subject-matter according to the invention relates to a kit comprising:

    • (a) a container comprising a pharmaceutical composition containing the peptide(s) or the variant according to the invention, the antibody or fragment thereof according to the invention, the T-cell receptor or fragment thereof according to the invention, the nucleic acid or the expression vector according to the invention, the recombinant host cell according to the invention, or the activated T lymphocyte according to the invention, in solution or in lyophilized form;
    • (b) optionally, a second container containing a diluent or reconstituting solution for the lyophilized formulation;
    • (c) optionally, at least one more peptide selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 110, and
    • (d) optionally, instructions for (i) use of the solution or (ii) reconstitution and/or use of the lyophilized formulation.


The kit may further comprise one or more of (iii) a buffer, (iv) a diluent, (v) a filter, (vi) a needle, or (v) a syringe. The container is preferably a bottle, a vial, a syringe or test tube; and it may be a multi-use container. The pharmaceutical composition is preferably lyophilized.


Kits of the present invention preferably comprise a lyophilized formulation of the present invention in a suitable container and instructions for its reconstitution and/or use. Suitable containers include, for example, bottles, vials (e.g. dual chamber vials), syringes (such as dual chamber syringes) and test tubes. The container may be formed from a variety of materials such as glass or plastic. Preferably the kit and/or container contain/s instructions on or associated with the container that indicates directions for reconstitution and/or use. For example, the label may indicate that the lyophilized formulation is to be reconstituted to peptide concentrations as described above. The label may further indicate that the formulation is useful or intended for subcutaneous administration.


It is to be understood that the before-mentioned features and those to be mentioned in the following cannot only be used in the combination indicated in the respective case, but also in other combinations or in an isolated manner without departing from the scope of the invention.


The invention is now further explained by means of embodiments resulting in additional features, characteristics and advantages of the invention. The embodiments are of pure illustrative nature and do not limit the scope or range of the invention. The features mentioned in the specific embodiments are features of the invention and may be seen as general features which are not applicable in the specific embodiment but also in an isolated manner in the context of any embodiment of the invention.


The invention is now further described and explained in further detail by referring to the following non-limiting examples and figure.





BRIEF DESCRIPTION OF THE DRAWING


FIG. 1 (A) Summary of predicted SARS-CoV-2 T-cell epitopes. The grey-scaled bars show the number of peptides predicted per allotype for the different SARS-Cov-2 proteins. (B) HLA class I allotype population coverage for the predicted SARS-CoV-2 peptide compared to the world population (calculated by the IEDB population coverage tool, www.iedb.org). The frequencies of individuals within the world population carrying up to six HLA allotypes (x-axis) of the ten allotypes used to predicted SARS-CoV-2 T-cell epitopes are indicated as grey bars on the left y-axis. The cumulative percentage of population coverage is depicted as black dots on the right y-axis.





DESCRIPTION OF PREFERRED EMBODIMENTS
1. General

The novel coronavirus SARS-CoV-2 is responsible for the COVID-19 lung disease, which especially in elderly, weakened and immunocompromised patients, shows severe and fatal courses. In the meantime, SARS-CoV-2 has spread to a worldwide pandemic with yet incalculable health, economic and socio-political consequences. So far, there are no established therapies and a vaccine is not yet available. Furthermore, it is not known whether and when T cell-mediated immunity against the novel SARS-CoV-2 virus is induced, let alone what the immunogenic epitopes of the virus are. Knowledge and experiences from two other zoonotic coronaviruses—SARS-CoV-1 and MERS-CoV—confirmed that T-cell immunity plays an important role in the recovery from coronavirus infections, with the detection of CoV-specific CD8+ and long-lasting memory CD4+ T-cell responses in convalescent individuals. Several CD4+ and CD8+ T-cell epitopes have been described for SARS-CoV-1 and MERS-CoV, which suggest due to the sequence homology of the two corona viruses potential cross reactivity between the two viruses and might also represent potential T-cell epitopes for the novel SARS-CoV-2 virus. However, most of the SARS-CoV-1 and MERS-CoV T-cell epitopes are so far limited to the spike protein and single HLA allotypes in particular HLA-A*02. Therefore, the objective of the invention is the first-time characterization of SARS-CoV-2-specific CD4+ and CD8+ T-cell epitopes from all different proteins of the virus covering a wide range of the most common HLA allotypes. This approach will allow to i) gain more detailed knowledge about the interaction of SARS-CoV-2 with the immune system, ii) provide novel diagnostic tools, beside the detection of SARS-CoV-2-specific antibodies, which, from today's perspective, show a high cross-reactivity, to identify people with SARS-Cov-2 immunity and monitor T-cell immunity-based long-term protection, and furthermore iii) define possible target structures for the development of virus-specific immunotherapies for the treatment of the COVID-19 disease. Such therapeutic approaches include, for example, vaccination strategies and the adoptive transfer of virus-specific T cells or T-cell receptors (TCRs).


2. Data Retrieval

The complete proteome sequence of SARS-CoV-2 isolate Wuhan-Hu-1 containing ten different open reading frames (ORFs) was retrieved from the NCBI database with the accession number MN908947.


3. Prediction of SARS-CoV-2-Derived HLA class I-Binding Peptides

The protein sequences of all ten ORFs were split into 9-12 amino acid long peptides covering the complete proteome of the virus. The prediction algorithms NetMHCpan 4.0 and SYFPEITHI 1.0 were used to predict the binding of the peptides to HLA A*01:01, A*02:01, A*03:01, A*11:01, A*24:02, B*07:02, B*08:01, B*15:01, B*40:01, and C*07:02. Only peptides predicted by both algorithms as HLA binding peptides (SYFPEITHI score ≥60% NetMHCpan rank ≤2) for the respective allotype were further examined. Furthermore, peptides containing cysteines were excluded. The inventors ranked the peptides for each allotype and ORF separately according to their SYFPEITHI and NetMHCpan score, respectively. The final selection and ranking of the peptides was then based on the calculation of the average rank therefore combining NetMHCpan and SYFPEITHI-derived prediction scores in a single rank. The inventors then selected one peptide for each ORF and allotype aiming to receive 10 peptides in total for each allotype. From peptides with the same average rank, the inventors selected those with the higher SYFPEITHI score. For some allotypes not every ORF gave rise to an appropriate HLA-binding peptide. In those cases, the inventors filled up the remaining slots with additional peptides from the nucleocapsid protein, the spike protein, and the polyprotein ORF1. Finally, this selection process resulted in a list of 100 peptides for the ten most common HLA allotypes covering all different proteins of the virus (Table 1).









TABLE 1







SARS-CoV-2-derived HLA class I-binding peptides






















ORF1




dupli-


SEQ




polyprotein
HLA
Syfpeithi
NetMHC
further
cate


ID
Immuno ID
Sequence
Protein
Protein name
region
restriction
Score
Score
allotypes
ID




















1
SARS_A01_P01
TTDPSFLGRY
ORF1
polyprotein
Papain-like
A01
89.7
0.00









proteinase







2
SARS_A01_P02
LTDEMIAQY
ORF2
spike protein

A01
80.0
0.00




3
SARS_A01_P03
ISEHDYQIGGY
ORF3
ORF3

A01
69.2
0.13




4
SARS_A01_P04
AGDSGFAAY
ORF5
membrane

A01
72.5
0.16








protein








5
SARS_A01_P05
RTFKVSIWNLDY
ORF6
ORF6

A01
65.9
1.57




6
SARS_A01_P06
RQEEVQELY
ORF7
ORF7

A01
60.0
0.33
B15
77


7
SARS_A01_P07
VDEAGSKSPIQY
ORF8
ORF8

A01
73.2
1.23




8
SARS_A01_P08
SPDDQIGYY
ORF9
nucleocapsid

A01
67.5
0.23








protein








9
SARS_A01_P09
GTGPEAGLPY
ORF9
nucleocapsid

A01
64.1
0.27








protein








10
SARS_A01_P10
LIDLQELGKY
ORF2
spike protein

A01
74.4
0.09




11
SARS_A02_P01
FLLPSLATV
ORF1
polyprotein
Non-structural
A02
91.7
0.01









protein 6







12
SARS_A02_P02
FIAGLIAIV
ORF2
spike protein

A02
83.3
0.13




13
SARS_A02_P03
ALSKGVHFV
ORF3
ORF3

A02
80.6
0.04




14
SARS_A02_P04
FLAFVVFLL
ORF4
envelope protein

A02
72.2
0.30




15
SARS_A02_P05
KLLEQWNLV
ORF5
membrane protein

A02
72.2
0.06




16
SARS_A02_P06
SIWNLDYIINL
ORF6
ORF6

A02
73.5
1.10




17
SARS_A02_P07
FLIVAAIVFI
ORF7
ORF7

A02
79.4
1.33




18
SARS_A02_P08
YIDIGNYTV
ORF8
ORF8

A02
69.4
0.03




19
SARS_A02_P09
LLLLDRLNQL
ORF9
nucleocapsid

A02
85.3
0.93








protein








20
SARS_A02_P10
VLQLPQGTTL
ORF9
nucleocapsid

A02
67.7
1.07








protein








21
SARS_A03_P01
KLFAAETLK
ORF1
polyprotein
Helicase
A03
83.9
0.01




22
SARS_A03_P02
RLFRKSNLK
ORF2
spike protein

A03
87.1
0.01




23
SARS_A03_P03
RIFTIGTVTLK
ORF3
ORF3

A03
81.3
0.14
A11



24
SARS_A03_P04
NIVNVSLVK
ORF4
envelope protein

A03
71.0
0.44
A11



25
SARS_A03_P05
RIAGHHLGR
ORF5
membrane protein

A03
74.2
0.08




26
SARS_A03_P06
NLIIKNLSK
ORF6
ORF6

A03
77.4
0.28
A11
36


27
SARS_A03_P07
QLRARSVSPK
ORF7
ORF7

A03
67.7
0.78




28
SARS_A03_P08
KTFPPTEPKK
ORF9
nucleocapsid

A03
90.3
0.01
A11







protein








29
SARS_A03_P09
KLDDKDPNFK
ORF9
nucleocapsid

A03
80.7
0.32








protein








30
SARS_A03_P10
VTYVPAQEK
ORF2
spike protein

A03
71.0
0.02
A11



31
SARS_A11_P01
ASMPTTIAK
ORF1
polyprotein
Papain-like
A11
82.4
0.00









proteinase







32
SARS_A11_P02
SVLNDILSR
ORF2
spike protein

A11
79.4
0.06
A03



33
SARS_A11_P03
ASKIITLKK
ORF3
ORF3

A11
79.4
0.11




34
SARS_A11_P04
VTLAILTALR
ORF4
envelope protein

A11
66.7
1.12




35
SARS_A11_P05
GTITVEELKK
ORF5
membrane protein

A11
87.9
0.18
A03



36
SARS_A11_P06
NLIIKNLSK
ORF6
ORF6

A11
61.8
0.65
A03
26


37
SARS_A11_P07
GVKHVYQLR
ORF7
ORF7

A11
67.7
1.80




38
SARS_A11_P08
ATEGALNTPK
ORF9
nucleocapsid

A11
72.7
0.23








protein








39
SARS_A11_P09
ASAFFGMSR
ORF9
nucleocapsid

A11
67.7
0.06








protein








40
SARS_A11_P10
SSTASALGK
ORF2
spike protein

A11
85.3
0.10




41
SARS_A24_P01
VYIGDPAQL
ORF1
polyprotein
Helicase
A24
80.7
0.03
C07



42
SARS_A24_P02
QYIKWPWYI
ORF2
spike protein

A24
77.4
0.03




43
SARS_A24_P03
VYFLQSINF
ORF3
ORF3

A24
71.0
0.01
C07



44
SARS_A24_P04
FYVYSRVKNL
ORF4
envelope protein

A24
70.0
1.56




45
SARS_A24_P05
SYFIASFRLF
ORF5
membrane protein

A24
76.7
0.07




46
SARS_A24_P06
PFHPLADNKF
ORF7
ORF7

A24
60.0
0.44




47
SARS_A24_P07
EYHDVRVVLDF
ORF8
ORF8

A24
70.0
0.63




48
SARS_A24_P08
DYKHWPQIAQF
ORF9
nucleocapsid

A24
66.7
0.32








protein








49
SARS_A24_P09
GYINVFAFPF
ORF10


A24
76.7
0.24




50
SARS_A24_P10
YYLGTGPEAGL
ORF9
nucleocapsid

A24
73.3
0.63








protein








51
SARS_B07_P01
APHGHVMVEL
ORF1
polyprotein
Host translation
B07
86.7
0.04









inhibitor nsp1







52
SARS_B07_P02
TPINLVRDL
ORF2
spike protein

B07
63.6
0.15




53
SARS_B07_P03
APFLYLYAL
ORF3
ORF3

B07
69.7
0.09




54
SARS_B07_P04
KPSFYVYSRV
ORF4
envelope protein

B07
63.3
1.87




55
SARS_B07_P05
RPLLESELVI
ORF5
membrane protein

B07
66.7
0.86




56
SARS_B07_P06
HPLADNKFAL
ORF7
ORF7

B07
73.3
0.11




57
SARS_B07_P07
EPKLGSLVV
ORF8
ORF8

B07
60.6
0.37




58
SARS_B07_P08
FPRGQGVPI
ORF9
nucleocapsid

B07
72.7
0.02








protein








59
SARS_B07_P09
FPFTIYSLLL
ORF10


B07
73.3
1.63




60
SARS_B07_P10
NPANNAAIVL
ORF9
nucleocapsid

B07
73.3
0.32








protein








61
SARS_B08_P01
YLKLRSDVL
ORF1
polyprotein
Non-structural
B08
81.4
0.01









protein 4







62
SARS_B08_P02
EPVLKGVKL
ORF2
spike protein

B08
69.8
0.17
B07



63
SARS_B08_P03
IIKNLSKSL
ORF6
ORF6

B08
60.5
0.17




64
SARS_B08_P04
TLDSKTQSL
ORF2
spike protein

B08
60.5
0.19
A02



65
SARS_B08_P05
TPKYKFVRI
ORF1
polyprotein
3C-like
B08
79.1
0.02









proteinase







66
SARS_B08_P06
VPMEKLKTL
ORF1
polyprotein
Papain-like
B08
69.8
0.01
B07








proteinase







67
SARS_B08_P07
FVKHKHAFL
ORF1
polyprotein
Non-structural
B08
72.1
0.02









protein 6







68
SARS_B08_P08
DLKGKYVQI
ORF1
polyprotein
Non-structural
B08
76.7
0.04









protein 10







69
SARS_B08_P09
GAKLKALNL
ORF1
polyprotein
Non-structural
B08
83.7
0.07









protein 2







70
SARS_B08_P10
EAFEKMVSL
ORF1
polyprotein
Non-structural
B08
67.4
0.03









protein 7







71
SARS_B15_P01
YQKVGMQKY
ORF1
polyprotein
Helicase
B15
85.2
0.01




72
SARS_B15_P02
VLKGVKLHY
ORF2
spike protein

B15
88.9
0.04




73
SARS_B15_P03
FLYLYALVY
ORF3
ORF3

B15
81.5
1.14
A03



74
SARS_B15_P04
LVKPSFYVY
ORF4
envelope protein

B15
77.8
0.09




75
SARS_B15_P05
WLSYFIASF
ORF5
membrane protein

B15
74.1
1.41




76
SARS_B15_P06
KVSIWNLDY
ORF6
ORF6

B15
74.1
1.19
A03



77
SARS_B15_P07
RQEEVQELY
ORF7
ORF7

B15
85.2
0.11
A01
 6


78
SARS_B15_P08
IQYIDIGNY
ORF8
ORF8

B15
77.8
0.02




79
SARS_B15_P09
LLNKHIDAY
ORF9
nucleocapsid

B15
81.5
0.06








protein








80
SARS_B15_P10
NVFAFPFTIY
ORF10


B15
60.6
1.37




81
SARS_B40_P01
AEIVDTVSAL
ORF1
polyprotein
Helicase
B40
71.9
0.02




82
SARS_B40_P02
SEPVLKGVKL
ORF2
spike protein

B40
90.6
0.29




83
SARS_B40_P03
SELVIGAVIL
ORF5
membrane protein

B40
87.5
0.12




84
SARS_B40_P04
YEGNSPFHPL
ORF7
ORF7

B40
62.5
0.27




85
SARS_B40_P05
LEYHDVRVVL
ORF8
ORF8

B40
90.6
0.11




86
SARS_B40_P06
MEVTPSGTWL
ORF9
nucleocapsid

B40
68.8
0.21








protein








87
SARS_B40_P07
NESLIDLQEL
ORF2
spike protein

B40
71.9
0.50




88
SARS_B40_P08
TEAFEKMVSL
ORF1
polyprotein
Non-structural
B40
84.4
0.15









protein 7







89
SARS_B40_P09
IEYPIIGDEL
ORF1
polyprotein
Guanine-N7
B40
71.9
0.06









methyl-












transferase







90
SARS_B40_P10
TEVPANSTVL
ORF1
polyprotein
Non-structural
B40
75.0
0.10









protein 10







91
SARS_C07_P01
NYMPYFFTL
ORF1
polyprotein
Papain-like
C07
86.7
0.01
A24








proteinase







92
SARS_C07_P02
VRFPNITNL
ORF2
spike protein

C07
76.7
0.00




93
SARS_C07_P03
YYQLYSTQL
ORF3
ORF3

C07
73.3
0.05
A24



94
SARS_C07_P04
NRFLYIIKL
ORF5
membrane protein

C07
80.0
0.07




95
SARS_C07_P05
IRQEEVQEL
ORF7
ORF7

C07
80.0
0.10




96
SARS_C07_P06
EYHDVRVVL
ORF8
ORF8

C07
80.0
0.10
A24



97
SARS_C07_P07
QRNAPRITF
ORF9
nucleocapsid

C07
76.7
0.04








protein








98
SARS_C07_P08
KKADETQAL
ORF9
nucleocapsid

C07
60.0
1.62








protein








99
SARS_C07_P09
VYDPLQPEL
ORF2
spike protein

C07
76.7
0.08
A24



100
SARS_C07_P10
IYNDKVAGF
ORF1
polyprotein
RNA-directed
C07
80.0
0.02
A24








RNA












polymerase









4. Prediction of SARS-CoV-2-Derived HLA class II-Binding Peptides

For HLA class II predictions all ten ORFs were split into 15 amino acid long peptides. The prediction algorithm SYFPEITHI 1.0 was used to predict the binding to HLA DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*07:01, DRB1*11:01, and DRB1*15:01. The 5% top-scoring peptides of each ORF (related to the total length of each ORF, 2% for ORF1) were selected and sorted according to their position within the protein. Peptide clusters containing different length variants around a common 9 amino acid long core sequence were preselected for each protein, respectively. Thereby, the inventors selected one cluster for each protein as well as two and ten clusters for the spike protein and the nucleocapsid protein, respectively. From these clusters the inventors chose those clusters for further analyses, which cover most different HLA-DR allotypes. From each selected cluster one representative peptide was produced as synthetic peptide, thereby avoiding peptides containing cysteines. Finally, this selection process resulted in a list of 10 promiscuous HLA-DR peptides covering all different proteins of the virus (Table 2).









TABLE 2







SARS-CoV-2-derived HLA class II-binding peptides











SEQ
Immuno-

Start



ID
ID
Protein
Position
Sequence





101

ORF1
6751
LDDFVEIIKSQDLSV





102

ORF2
 235
ITRFQTLLALHRSYL





103

ORF2
 855
FNGLTVLPPLLTDEM





104

ORF3
   4
FMRIFTIGTVTLKQG





105

ORF4
  56
FYVYSRVKNLNSSRV





106

ORF5
 176
LSYYKLGASQRVAGD





107

ORF6
  26
IWNLDYIINLIIKNL





108

ORF7
  90
QEEVQELYSPIFLIV





109

ORF8
  43
SKWYIRVGARKSAPL





110

ORF10
   4
INVFAFPFTIYSLLL









In the event of discrepancies between the sequences specified in Tables 1 and 2 and those specified in the sequence listing, the information in the sequence listing takes precedence and applies.

Claims
  • 1. A peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variants thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variants bind to molecule(s) of the major histocompatibility complex (MHC) or induces T cells cross-reacting with said variants; and a pharmaceutical acceptable salt thereof, wherein said peptide is not a full-length polypeptide.
  • 2. The peptide according to claim 1, wherein said peptide binds to an MHC class-1 or -II molecule, and wherein said peptide, when bound to said MHC, is recognized by CD4 and/or CD8 T cells.
  • 3. The peptide according to claim 1, wherein the amino acid sequence thereof comprises a continuous stretch of amino acids according to any one of SEQ ID NO: 1 to SEQ ID NO: 110.
  • 4. (canceled)
  • 5. A T-cell receptor or a fragment thereof, wherein the T-cell receptor or a fragment thereof is reactive with an HLA ligand when bound to an MHC molecule, wherein said HLA ligand is the peptide or variants thereof according to claim 1.
  • 6. A nucleic acid encoding the peptide or variant thereof according to claim 1.
  • 7. A recombinant host cell comprising the nucleic acid according to claim 6.
  • 8. An in vitro method for producing activated T lymphocytes, the method comprising contacting in vitro T cells with antigen loaded human class I or II MEW molecules expressed on the surface of a suitable antigen-presenting cell or an artificial construct mimicking an antigen-presenting cell for a period of time sufficient to activate said T cells in an antigen specific manner, wherein said antigen is a peptide according to claim 1.
  • 9. An activated T lymphocyte, produced by the method according to claim 8, wherein the activated T lymphocyte selectively recognizes a cell which presents a peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variants thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110.
  • 10. A pharmaceutical composition comprising at least one active ingredient, wherein the at least one active ingredient is the peptide according to claim 1, a pharmaceutically acceptable carrier, and pharmaceutically acceptable excipients or stabilizers.
  • 11. The pharmaceutical composition according to claim 10, wherein the pharmaceutical composition comprises at least five different peptides, each peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variants bind to molecule(s) of the major histocompatibility complex (MHC) or induce T cells cross-reacting with said variants.
  • 12. The pharmaceutical composition according to claim 11, wherein the pharmaceutical composition comprises at least six different peptides, each peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variants bind to molecule(s) of the major histocompatibility complex (MHC) or induce T cells cross-reacting with said variants.
  • 13. The pharmaceutical composition according to claim 11, wherein the pharmaceutical composition comprises at least seven different peptides, each peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variants bind to molecule(s) of the major histocompatibility complex (MHC) or induce T cells cross-reacting with said variants.
  • 14. The pharmaceutical composition according to claim 11, wherein the pharmaceutical composition comprises at least eight different peptides, each peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variant binds to molecule(s) of the major histocompatibility complex (WIC) or induces T cells cross-reacting with said variant peptide; and a pharmaceutical acceptable salt thereof, wherein said peptide is not a full-length polypeptide.
  • 15. The pharmaceutical composition according to claim 11, wherein the pharmaceutical composition comprises at least nine different peptides, each peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variant binds to molecule(s) of the major histocompatibility complex (WIC) or induces T cells cross-reacting with said variant peptide; and a pharmaceutical acceptable salt thereof, wherein said peptide is not a full-length polypeptide.
  • 16. The pharmaceutical composition according to claim 11, wherein the pharmaceutical composition comprises at least ten different peptides, each peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 1 to SEQ ID NO: 110, and variant sequences thereof which are at least 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 110, and wherein said variant binds to molecule(s) of the major histocompatibility complex (WIC) or induces T cells cross-reacting with said variant peptide; and a pharmaceutical acceptable salt thereof, wherein said peptide is not a full-length polypeptide.
  • 17. The pharmaceutical composition of claim 10, wherein the pharmaceutical composition is in the form of a vaccine.
  • 18. A method of preventing or treating an infection by SARS-CoV-2 (COVID-19) in a subject, the method comprising administering a pharmaceutically effective amount of the pharmaceutical composition of claim 10 to a subject in need thereof
  • 19. A kit comprising: (a) a container comprising a pharmaceutical composition comprising the peptide according to claim 1, wherein the peptide is in solution or in lyophilized form . and(b) a second container containing a diluent or reconstituting solution for the lyophilized form.
  • 20. (canceled)
  • 21. The kit of claim 19, further comprising: (c) at least one more peptide selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 110.
  • 22. (canceled)
  • 23. A nucleic acid molecule encoding the T cell receptor or fragment thereof according to claim 5.
Priority Claims (1)
Number Date Country Kind
20169047.6 Apr 2020 EP regional
CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of copending International Patent application PCT/EP2021/059232 filed on 8 Apr. 2021 and designating the United States of America, and claims priority of European Pat. application EP 20 169 047.6 filed on 9. Apr. 2020. The entire contents of these prior applications are incorporated herein by reference.

Continuations (1)
Number Date Country
Parent PCT/EP2021/059232 Apr 2021 US
Child 17962403 US