HCV core protein sequences

Abstract

The present invention describes peptides and recombinant proteins containing Hepatitis C virus core protein sequence in which one or more of the amino acids have been modified or deleted to remove the ability of these proteins to bind to specific anti-HCV murine monoclonal antibodies. The deletions and modifications are designed as to maintain the ability of this protein to be used in immunoassays used for the detection of anti-HCV antibodies in individuals infected with HCV.

Description

BACKGROUND OF THE INVENTION

[0001] An estimated 170 million people worldwide have been infected by hepatitis C virus (HCV). In the next few years, the number of U.S. deaths for HCV-caused liver disease and cancer may overtake deaths caused by Acquired Immune Deficiency Syndrome (AIDS).

[0002] The transmission of HCV seems to require blood-to-blood contact. Carrying a single strand of ribonucleic acid (RNA), HCV contains just one gene, coding for a polyprotein that is subsequently cleaved into at least 10 functional proteins. Clearly, the ability to test the blood supply for HCV is of great importance. A sensitive assay that can detect infection at an early stage would be helpful.

[0003] HCV detection assays typically detect antibodies against HCV virus. These antibodies are detected in immunoassays using recombinant proteins and peptides containing HCV protein sequences. Most commercial anti-HCV assays use proteins from the following regions, core protein, NS3, NS4, and NS5 protein sequences.

[0004] Anti-HCV core antibodies are one of the most prevalent anti-HCV antibodies detected in chronic HCV infected individuals. HCV core protein contains multiple epitopes. Using synthetic peptides in the HCV core region, it has been shown that most of these epitopes are in the amino terminal end of this protein. For example, using overlapping peptides, each approximately 15 amino acids in length, an ELISA was developed to screen for anti-HCV antibodies in chronic HCV infected individuals. Table 1 below shows the peptide sequences. As shown in Table 2 below, HCV infected individuals have antibodies to two or more of these core peptides. Thus, it has been shown that the complete core peptide is not required to detect anti-core antibodies.

TABLE 1
		HCV
Peptide	Amino Acid	Polyprotein
ID #	Sequence	AA Location
0	MSTNPKPQKKNKRNT	1-15	SEQ ID NO.:1
1	KNKRNTNRRPQDVKF	10-24	SEQ ID NO.:2
2	QDVKFPGGGQIVGGV	20-34	SEQ ID NO.:3
3	QIVGGVYLLPRRGPR	29-43	SEQ ID NO.:4
4	RRGPRLGVPATRKTS	39-53	SEQ ID NO.:5
5	ATRKTSERSQPRGRR	48-62	SEQ ID NO.:6
6	PRGRRQPIPKARRPE	58-72	SEQ ID NO.:7
7	KARRPEGRTWAQPGY	67-81	SEQ ID NO.:8
8	AQPGYPWPLYGNEGC	77-91	SEQ ID NO.:9
9	YGNEGCGWAGWLLSP	86-100	SEQ ID NO.:10
10	WLLSPRGSRPSWGPT	96-110	SEQ ID NO.:11
11	SWGPTDPRRRSRLNG	106-120	SEQ ID NO.:12
12	SRLNGKVIDTLTCGF	116-130	SEQ ID NO.:13
13	LTCGFADLMGYIPLV	126-140	SEQ ID NO.:14
14	YIPLVGAPLGGAARA	136-150	SEQ ID NO.:15
15	GAARALAHGVRVLED	146-160	SEQ ID NO.:16
16	RVLEDGVNYATGNLP	156-170	SEQ ID NO.:17
17	TGNLPGCSFSIFLLA	166-180	SEQ ID NO.:18

[0005]

TABLE 2
Peptide	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17
Neg	0.044	0.004	0.021	0.075	0.059	0.069	0.076	0.103	0.020	0.034	0.002	0.088	0.051	0.028	0.023	0.034	0.041	0.042
Neg	0.045	0.065	0.017	0.081	0.051	0.081	0.103	0.111	0.033	0.035	0.002	0.085	0.038	0.030	0.023	0.030	0.038	0.052
Neg	0.050	0.003	0.014	0.075	0.087	0.079	0.094	0.102	0.025	0.034	0.002	0.071	0.038	0.033	0.021	0.031	0.039	0.047
Neg	0.014	0.043	0.134	0.023	0.034	0.039	0.034	0.039	0.012	0.018	−0.001	0.025	0.009	0.009	0.008	0.013	0.010	0.020
Neg	0.015	0.039	0.119	0.021	0.033	0.030	0.030	0.034	0.013	0.019	0.000	0.026	0.011	0.010	0.005	0.012	0.010	0.016
Neg	0.013	0.036	0.126	0.027	0.053	0.032	0.037	0.042	0.013	0.016	0.001	0.037	0.013	0.009	0.009	0.012	0.009	0.017
Neg	0.016	0.004	0.104	0.020	0.039	0.034	0.003	0.041	0.019	0.019	0.000	0.041	0.011	0.017	0.006	0.010	0.008	0.021
9	0.256	2.500	2.500	0.425	1.443	0.016	0.218	0.248	0.062	0.015	0.025	0.049	0.030	0.013	0.012	0.021	0.012	0.028
11	0.413	2.500	2.500	0.917	0.229	0.647	0.114	0.262	0.166	0.159	0.002	0.055	0.022	0.027	0.021	0.042	0.247	0.088
15	0.044	0.661	2.500	0.067	0.577	0.057	0.110	0.072	0.061	0.032	−0.003	0.045	0.018	0.031	0.020	0.039	0.035	0.080
18	1.643	0.887	2.500	0.641	0.100	0.052	0.032	0.576	0.037	0.022	−0.001	0.040	0.006	0.010	0.009	0.025	0.036	0.039
20	0.021	0.111	2.500	2.500	0.482	0.032	0.029	0.045	0.028	0.015	0.011	0.035	0.009	0.014	0.009	0.017	0.019	0.059
21	2.500	2.500	2.500	2.262	2.500	0.516	2.259	0.080	0.378	0.018	0.022	0.064	0.013	0.024	0.017	0.024	0.135	0.035
27	0.032	2.500	2.500	0.089	2.500	1.652	1.349	0.043	0.039	0.034	0.033	0.026	0.012	0.018	0.013	0.028	0.287	0.008
30	2.500	2.500	2.500	2.500	0.183	0.044	0.075	0.993	0.078	0.035	0.028	0.190	0.023	0.025	0.022	0.028	0.042	0.043
35	0.022	0.278	0.912	0.031	0.036	0.116	0.079	0.049	0.062	0.010	0.005	0.026	0.005	0.006	0.009	0.020	0.007	0.020
36	0.059	0.129	2.500	0.090	0.131	0.060	0.093	0.148	0.090	0.037	0.003	0.050	0.018	0.060	0.077	0.062	0.129	0.079
37	2.500	2.500	2.500	0.219	0.130	0.090	0.169	0.223	0.147	0.040	0.018	0.065	0.016	0.051	0.051	0.025	0.080	0.110
39	0.165	2.500	2.500	2.500	0.124	1.217	2.351	2.500	0.397	0.056	0.015	1.319	0.017	0.050	0.056	0.041	0.200	0.190
40	0.058	2.500	2.500	2.500	0.098	0.066	0.060	0.755	0.093	0.024	0.000	0.059	0.013	0.028	0.017	0.032	0.068	0.101
42	0.022	0.043	2.500	0.031	0.023	0.150	0.018	0.036	0.023	0.011	−0.001	0.032	0.005	0.014	0.006	0.010	0.012	0.031
43	0.158	0.612	0.368	0.033	0.065	0.103	0.069	0.075	0.053	0.051	0.001	0.055	0.025	0.022	0.015	0.023	0.029	0.035
44	0.042	2.240	2.500	0.511	0.070	0.060	0.086	0.301	0.108	0.066	−0.002	0.143	0.028	0.041	0.028	0.047	0.061	0.076
45	1.002	2.500	2.500	0.174	0.713	0.055	0.129	1.722	1.896	0.029	−0.003	0.069	0.038	0.038	0.055	0.022	0.136	0.039
46	0.016	0.031	2.500	0.022	0.021	0.021	0.038	0.035	0.031	0.027	−0.002	0.027	0.016	0.015	0.013	0.026	0.019	0.037
47	2.484	2.500	2.500	0.449	0.750	0.593	0.102	2.006	0.331	0.017	−0.004	0.034	0.012	0.014	0.007	0.026	0.014	0.032
48	0.427	0.201	2.500	0.364	0.356	0.038	0.049	0.070	0.027	0.029	−0.001	0.040	0.018	0.011	0.013	0.025	0.014	0.095
49	0.019	0.483	2.500	0.044	0.045	0.047	0.050	0.246	0.039	0.025	−0.005	0.033	0.019	0.014	0.013	0.030	0.016	0.085
50	0.668	2.500	2.500	0.568	1.233	0.277	0.154	2.500	0.882	0.024	−0.001	0.035	0.014	0.012	0.007	0.017	0.044	0.055
52	2.500	2.500	2.500	0.948	1.116	1.619	0.026	0.267	0.112	0.019	0.026	0.042	0.012	0.007	0.009	0.019	0.008	0.044
53	0.823	2.500	2.500	0.428	2.500	0.780	0.086	2.500	1.566	0.025	0.001	0.050	0.014	0.020	0.011	0.022	0.019	0.028
54	1.577	2.500	2.500	2.500	2.500	2.500	2.500	2.500	2.500	0.020	0.032	0.053	0.021	0.012	0.012	0.020	0.017	0.038
55	0.017	0.083	2.500	0.047	0.018	0.023	0.071	0.042	0.019	0.017	−0.002	0.026	0.015	0.015	0.012	0.026	0.014	0.030
58	2.500	2.500	2.500	2.283	2.500	2.500	2.500	2.500	0.810	0.037	0.073	0.067	0.018	0.019	0.021	0.025	0.159	0.059
59	0.015	1.805	2.500	0.023	2.500	0.019	0.180	0.038	0.070	0.039	0.027	0.017	0.012	0.015	0.018	0.015	0.023	0.049
60	0.053	2.500	2.500	0.255	2.500	0.102	1.266	0.666	2.500	0.034	−0.003	0.153	0.026	0.019	0.022	0.039	0.097	0.063
62	0.018	0.053	2.500	1.178	0.025	0.031	0.041	0.060	0.028	0.017	−0.002	0.039	0.013	0.012	0.010	0.017	0.010	0.048
63	0.009	0.016	0.027	0.012	0.017	0.013	1.225	0.028	0.012	0.017	−0.004	0.026	0.007	0.007	0.006	0.010	0.057	0.020
65	1.440	0.041	0.026	0.040	0.032	0.056	0.052	0.062	0.020	0.040	0.023	0.051	0.018	0.023	0.023	0.019	0.020	0.035
66	2.060	2.500	2.500	1.030	2.500	0.508	0.144	2.500	2.500	0.013	0.009	0.060	0.007	0.009	0.009	0.014	0.025	0.018
67	2.500	2.500	2.500	2.500	2.500	1.338	0.406	2.500	0.135	0.031	0.003	0.091	0.021	0.027	0.028	0.032	0.042	0.077
68	2.500	2.500	2.500	1.105	0.415	0.358	1.025	2.500	0.263	0.028	0.006	0.039	0.023	0.025	0.022	0.024	0.034	0.037
70	0.745	2.500	2.500	0.342	2.500	0.200	0.049	0.075	1.730	0.030	0.009	0.119	0.015	0.025	0.022	0.027	0.056	0.050
73	0.031	2.392	2.500	0.049	0.629	0.935	0.596	1.119	0.081	0.040	0.009	0.052	0.028	0.036	0.031	0.038	0.043	0.059
75	0.037	2.500	2.500	1.435	1.342	0.107	0.287	0.094	0.080	0.049	0.012	0.031	0.013	0.030	0.017	0.021	0.058	0.050
78	2.500	2.500	2.500	0.269	2.500	0.298	0.051	2.500	0.040	0.057	0.006	0.084	0.013	0.022	0.014	0.021	0.022	0.030
80	0.280	2.500	2.500	0.674	0.318	0.972	0.048	2.118	0.040	0.021	0.022	0.024	0.015	0.010	0.008	0.014	0.066	0.031
84	0.012	0.075	2.500	0.025	0.190	0.145	0.106	0.099	0.019	0.028	0.050	0.018	0.009	0.010	0.009	0.013	0.009	0.026
90	0.019	0.306	2.500	0.039	2.500	0.689	0.033	0.301	0.195	0.021	0.005	0.033	0.011	0.017	0.010	0.013	0.014	0.018

[0006] A recent report indicates that the HCV core protein can be detected in HCV infected individuals before the appearance of anti-HCV antibodies. (S. Lee et al., Vox Sanguinis, 2001; 80: 19-23). Therefore, we suggest that a more efficient way of early detection of HCV infection would be a combination assay able to detect HCV core protein and anti-HCV antibodies including anti-core antibodies.

SUMMARY OF THE INVENTION

[0007] The present invention describes peptides and recombinant proteins containing Hepatitis C virus core protein sequence in which one or more of the amino acids have been modified or deleted to remove the ability of these proteins to bind to specific anti-HCV murine monoclonal antibodies. These modifications were made in the in the underlined regions shown in Table 3 below. The deletions and modifications are designed as to maintain the ability of this protein to be used in immunoassays used for the detection of anti-HCV antibodies in individuals infected with HCV. These modified core proteins can be used in a combination assay for the simultaneous detection of HCV core protein and anti-HCV antibodies. The combination assay will be able to detect HCV assay earlier than the currently used antibody assays.

DETAILED DESCRIPTION OF THE INVENTION

[0008] One object of the invention is to develop peptide sequences that can detect anti-HCV antibodies in the presence of anti-core monoclonal antibodies to detect HCV core antigen. One use therefore of these modified core antigens will be to use them in an anti-HCV/HCV core assay, or “combination assay”.

[0009] For this purpose, two or more monoclonal antibodies from Table 4 can be co-coated with one or more modified HCV core proteins on a solid phase thereby enabling the solid phase to capture anti-HCV core antibodies and core antigen. The modification is accomplished by removing the epitope for the antibody being used for detection or capture of HCV core. The removal of epitopes can be achieved by means known in the art such as deleting parts of the core sequence or altering amino acids in the epitope sequence. This can be achieved, for example, by synthesizing these peptides by chemical synthesis using commercially available peptide synthesizers or by modifying recombinant clones expressing HCV core protein. The recombinant sequences can be modified by primer dependent single or multiple site mutagenesis or primer dependent deletions. (B. Tao and K. C. Lee, PCR Technology Current Innovations,1994 by CRC Press, Inc., Chapter 10, Mutagenesis by PCR).

[0010] Another object of the invention is to identify immunodominant regions of HCV core protein.

[0011] Another object of the present invention is to determine the pattern of reactivity to core peptides among HCV infected individuals presenting anti-core antibodies.

[0012] The peptides of the invention were generated by maintaining the highly reactive portions of the core protein and making modifications to the remaining parts of the sequence such that the peptide would not be detected by an antibody used to detect core protein in an assay.

[0013] In a preferred embodiment, the peptide would be modified by either substitution of amino acids or deletion of amino acids in the regions underlined in Table 1. The remainder of the sequence shown in Table 1 should not be altered.

[0014] In another preferred embodiment the peptides would be used in a combination assay. That is one that is capable of detecting both HCV antigens and antibodies simultaneously.

TABLE 3
HCV core protein sequence:
SEQ ID NO.:19
MSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVPATR
KTSERSQPRGRRQPIPKARRPEGRSWAQPGYPWPLYGNEGCGWAGWLLSP
RGSRPSWGPTDPRRRSRNLGKVIDTLTCGF

[0015] The effectiveness and advantages of the invention are further illustrated by the following examples.

EXAMPLE 1

[0016] Synthetic Peptides

[0017] Synthetic peptides covering the entire sequence of HCV core protein sequence were used. Eighteen overlapping peptides shown in Table 1 were chemically synthesized by solid phase peptide synthesis using a peptide synthesizer. All of the peptides were synthesized with a C-terminal cysteine amide residue. Peptides were cleaved form the resin and purified by reverse phase liquid chromatography. Purity of each of these peptides, based on reverse phase HPLC analysis was greater that ninety-five (95%). The sequence of each peptide was confirmed by amino acid analysis of the acid hydrolysate of the peptide. The structural identities of the peptides were confirmed mass spectrometry. All of the peptides had the molecular weight expected.

EXAMPLE 2

[0018] Synthetic peptides were coated onto Immulon 2 microwells (made by Dyanatech) in 50 mM borate buffer at a concentration of 1 ug/ml. To each microwell, 200 ul of peptide solution was added and the microwells were incubated at 25 degrees Celsius for 16-20 hours. The microwells were aspirated and washed once with phosphate buffer saline (PBS) containing TWEEN 20 to remove any unbound peptide. The microwells were then post coated with 300 ul of PBS containing one percent (1%) bovine serum albumin (BSA) and three percent (3%) sucrose to block all of the available protein binding sites. After 2-4 hours, the plates were aspirated, turbo dried and stored in sealed pouches at 2-8 degrees Celsius.

EXAMPLE 3

[0019] Synthetic Peptide ELISA

[0020] The sample, 10 ul in 200 ul of diluent, suspected of being infected with HCV was added into the peptide coated microwell. After incubation for approximately one hour the microwells were washed. To the washed microwells anti-human IgG were labeled with horse radish peroxidase was added. After an incubation for thirty minutes the microwells were washed and a solution of ORTHO phenylenedaamine buffer and hydrogen peroxide added to each well. After approximately 30 minutes sulfuric acid were added to each well to stop the reaction. An orange or yellow color indicated the presence of anti-HCV antibodies in the sample.

[0021] Table 4

[0022] Monoclonal Antibodies

[0023] The table below identifies 15 antibodies. The antibodies were screened at every stage of antibody development with microtitrewell plates coated with immunogen. The immunogen used to immunize the mice that produced each strain of monoclonal antibody is identified as one of the following: peptide ODS 243, a large peptide further defined in Example 1; “FLC” means full length core antigen, defined in Example 1; or KLH conjugated core peptide #8, a short peptide, further defined herein. The specificity of each to a numbered peptide is shown and the amino acid sequences of each numbered peptide is identified herein. Furthermore, the epitope to which the antibody specifically binds is included in the last column, defined by the amino acids that encode for the epitope.

ATCC	AG-FUSION #,
#	clone	IMMUNOGEN	ISOTYPE	SPECIFICITY	AA
PTA-	ODS243, 7B4F11	Peptide	IgG 2b	HCV core	77-91
3811		ODS 243		peptide #8
PTA-	ODS243, 1E3D12	Peptide	IgG2a	HCV core	86-100
3803		ODS 243		peptide #9
PTA-	ODS243, 7C12C4	Peptide	IgG2b	HCV core	77-91
3802		ODS 243		peptide #8
PTA-	core#3,	FLC	IgG1	HCV core	106-120
3813	2A11C6			peptide# 11
PTA-	Core#12,	FLC	IgG1	HCV core	29-43
3809	1B7A1			peptide# 3
PTA-	CORE#13,	FLC	IgG1	HCV core	39-53
3805	5A12G12			peptide# 4
PTA-	Core#13,	FLC	IgG1	HCV core	48-62
3812	4H7E7			peptide# 5
PTA-	Core#13, 12F4A	FLC	IgG1	HCV core	58-72
3806	11			peptide# 6
PTA-	Core#13,	FLC	IgG1	HCV core	67-81
3804	14D12A12			peptide# 7
PTA-	c22-8#4,	KLH	IgG1	HCV core	77-91
3807	6D8E8	Conjugated		peptide# 8
		core
		peptide
		#8
PTA-	Core#12,	FLC	IgG2b	HCV core	96-110
3800	4G10G6			peptide# 10
PTA-	Core#13,	FLC	IgG2a	HCV core	106-120
3801	6E7E1			peptide# 11
PTA-	Core#13,	FLC	IgG2b	HCV core	106-120
3810	11D12A6			peptide# 11
PTA-	Core#13,	FLC	IgG3	HCV core	106-120
3808	14B7C3			peptide# 11
PTA-	Core#12,	FLC	IgG1	HCV core	156-170
3799	4A6H3			peptide# 16

EXAMPLE 4

[0024] Use of Modified Core Peptides in an Anti-HCV ELISA

[0025] A peptide consisting of HCV core immunodominant region amino acids 1-43 was chemically synthesized. Another peptide with certain deletions in this region, namely, amino acids 1-8 and 31-33 were deleted, was also synthesized. These peptides were used to test 40 chronic HCV patients' serum samples for anti-HCV antibody status. The results indicated that 39 of the 40 patients were not affected by deletion of these sequences. The deletion peptides can be used in combination with anti-HCV monoclonal antibodies, such as the ones shown in Table 4, in a combination assay. Peptides with deletions of amino acids 31-33 can be used with any of the monoclonal antibodies shown in Table 4.

TABLE 5
Peptide/Specimen ID	265-2	266-2	271-2	272-2
11	2.500	2.500	2.500	2.500
15	2.500	2.500	2.500	2.500
18	2.500	2.500	2.500	2.500
20	2.500	2.500	2.500	2.500
21	2.500	2.500	2.500	2.500
27	2.500	2.500	2.500	2.500
30	2.500	2.500	2.500	2.500
35	0.762	0.911	0.507	0.611
36	2.500	2.500	2.500	2.500
37	2.500	2.500	2.500	2.500
39	2.500	2.500	2.500	2.500
40	2.500	2.500	2.500	2.500
42	2.500	2.500	2.500	2.500
43	1.621	1.255	1.382	1.443
44	2.500	2.500	2.500	2.500
45	2.500	2.500	2.500	2.500
46	2.003	1.863	1.058	1.829
47	2.500	2.500	2.500	2.500
48	2.500	2.500	2.500	2.500
49	2.500	2.500	2.500	2.500
50	2.500	2.500	2.500	2.500
52	2.500	2.500	2.500	2.500
53	2.500	2.500	2.500	2.500
54	2.500	2.500	2.500	2.500
55	2.500	2.500	2.500	2.500
58	2.500	2.500	2.500	2.500
59	2.500	2.500	2.500	2.500
60	2.500	2.500	2.500	2.500
62	2.500	2.500	2.500	2.500
65	0.056	0.045	2.237	1.704
66	2.500	2.500	2.500	2.500
67	2.500	2.500	2.500	2.500
68	2.500	2.500	2.500	2.500
70	2.500	2.500	2.500	2.500
73	2.500	2.500	2.500	2.500
75	2.500	2.500	2.500	2.500
78	2.500	2.500	2.500	2.500
80	2.500	2.500	2.500	2.500
84	2.500	2.500	2.170	2.500
90	2.500	2.500	2.500	2.500
Peptide 265 HCV Polyprotein Amino Acid Sequence 10-43
Peptide 266 HCV Polyprotein Amino Acid Sequence 8-43
Peptide 271 HCV polyprotein Amino Acid Sequence 1-43 with AA 31, 32 and 33 deleted
Peptide 272 HCV Polyprotein Amino Acid Sequence 1-43 Consensus sequence

[0026]

Claims

1. A kit for the detection of HCV comprising A) a solid phase coated with modified HCV core protein, HCV non-core protein, and at least one anti-HCV core monoclonal antibody, and B) a labeled anti-HCV core monoclonal antibody, wherein the modified core protein of part A) has been modified by removing the binding sites of the anti-core monoclonal antibodies of part A) and part B).

2. The kit according to claim 1 wherein the modified HCV core protein includes amino acids 10-43 of HCV core protein.

3. The kit according to claim 1 wherein the HCV non-core protein is selected from c200-3 and NS5.

4. The kit according to claim 1 wherein the labeled anti-HCV monoclonal antibody is labeled with an enzyme, a flourophore, or a radioactive label.

5. The kit according to claim 1 wherein the solid phase is a microtitre well, polystyrene bead, magnetic bead or membrane.

6. The kit according to claim 1 wherein the monoclonal antibody in part A) has at least one epitope in the region of amino acids 80-170 of HCV and the monoclonal antibody in part B) has at least one epitope in the region of amino acids 1-80 of HCV.