Hepatitic C virus (HCV) core gene nucleotide sequences and related methods of detecting major and minor genotypes of HCV isolates

• US 5,882,852 A
• Filed: 08/15/1994
• Issued: 03/16/1999
• Est. Priority Date: 06/29/1993
• Status: Expired due to Term

• Current Assignee: Secretary, Department of Health And Human Services Office of Technology Transfer, National Institutes of Health
• Original Assignee: United States Department Of Health And Human Services (Government of the United States of America)
• Inventors: Bukh, Jens, Miller, Roger H., Purcell, Robert H.
• Primary Examiner(s): Sisson, Bradley L.
• Application Number:
  US08/290,665
• Time in Patent Office: 1,674 Days
• Field of Search: 435/5, 435/6, 435/91.1, 435/91.2, 435/91.31, 435/91.32, 435/91.33, 435/810, 435/183, 536/23.1, 536/23.72, 536/24.33, 536/25.3, 935/5, 935/8, 935/16, 935/18, 935/77, 935/78
• US Class Current: 435/5
• CPC Class Codes: A61K 39/00 Medicinal preparations containing antigens or antibodies materials for immunoassay G01N33/53
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 2770/24222 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12Q 1/707 non-A, non-B Hepatitis, excluding hepatitis D
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

The nucleotide and deduced amino acid sequences of cDNAs encoding the envelope 1 genes and core genes of isolates of hepatitis C virus (HCV) are disclosed. The invention relates to the oligonucleotides, peptides and recombinant envelope 1 and core proteins derived from these sequences and their use in diagnostic methods and vaccines.

Claims

1. A method for detecting the presence of a hepatitis C virus in a biological sample comprising:

(a) amplifying reverse transcription products of RNA via polymerase chain reaction using universal primers consisting of at least 15 contiguous nucleotides selected from the following regions of SEQ ID NOs;

103-154;

(i) sense nucleotide regions 1-33, 50-89, 51-90, 52-91, 53-92, 61-100, 62-101, 77-116, 78-117, 79-118, 80-119, 81-120, 82-121, 83-122, 84-123, 85-124, 86-125, 329-368, 330-369, 331-370, 332-371, 354-393, 355-394, 356-395, 442-481, 443-482, 457-496, 458-497, 475-514, 476-515, 477-516 and,

(ii) antisense nucleotide regions 40-1, 41-2, 42-3, 43-4, 51-12, 52-13, 55-16, 56-17, 57-18, 58-19, 61-22, 62-23, 63-24, 64-25, 70-31, 124-85, 125-86, 126-87, 127-88, 128-89, 129-90, 517-478, 518-479, 519-480, 532-493, 533-494, 550-511, 551-512; and

(b) detecting said amplification products, wherein detection of said product indicates the presence of hepatitis C virus in the biological sample.

2. A method for determining the major genotype of a hepatitis C virus isolate comprising:

(a) amplifying reverse transcription products of RNA via polymerase chain reaction using amplification primers consisting of at least 15 contiguous nucleotides selected from the following major genotype-specific nucleotide domains;

(i) major genotype 1-specific nucleotide domains located in sense nucleotide regions 427-466, 444-483, 447-486 and antisense nucleotide regions 505-466, 522-483 and 525-486 of SEQ ID NOs;

103-124;

(ii) major genotype 2-specific nucleotide domains located in sense nucleotide regions 153-192, 162-201, 164-203, 168-207, 171-210, 182-221, 192-231, 197-242 and antisense nucleotide regions 231-192, 240-201, 242-203, 246-207, 249-210 and 380-341 of SEQ ID NOs;

125-134;

(iii) major genotype 3-specific nucleotide domains located in SEQ ID NOs;

135-138;

(iv) major genotype 4-specific nucleotide domains located in SEQ ID NOs;

139-145;

(v) major genotype 5-specific nucleotide domains located in SEQ ID NOs;

146-153; and

(vi) major genotype 6-specific nucleotide domains located in SEQ ID NO;

154; and

(b) detecting said amplification products, where the detection of said products indicates that the hepatitis C virus belongs to a single major genotype selected from major genotypes 1-6.

3. A method for detecting the presence of hepatitis C virus in a biological sample comprising:

(a) amplifying reverse transcription products of RNA via polymerase chain reaction to produce amplification products;

(b) contacting said products with a probe having at least one nucleic acid sequence shown in SEQ ID NO;

103 through SEQ ID NO;

154 under conditions which permit the formation of complexes between said products and said nucleic acid sequence; and

(c) detecting sail complexes, where the detection of said complexes indicates the presence of hepatitis C virus in the biological sample.

4. The method of claim 3, wherein said amplification of step (a) uses universal primers consisting of at least 15 contiguous nucleotides selected from the following regions of SEQ ID Nos:

103-154;

(i) sense nucleotide regions 1-33, 50-89, 51-90, 52-91, 53-92, 61-100, 62-101, 77-116, 78-117, 79-118, 80-119, 81-120, 82-121, 83-122, 84-123, 85-124, 86-125, 329-368, 330-369, 331-370, 332-371, 354-393, 355-394, 356-395, 442-481, 443-482, 457-496, 458-497, 475-514, 476-515, 477-516 and

(ii) antisense nucleotide regions 40-1, 41-2, 42-3, 43-4, 51-12, 52-13, 55-16, 56-17, 57-18, 58-19, 61-22, 62-23, 63-24, 64-25, 70-31, 124-85, 125-86, 126-87, 127-88, 128-89, 129-90, 517-478, 518-479, 519-480, 532-493, 533-494, 550-511, 551-512.

5. A method for determining the major genotype of a hepatitis C virus isolate comprising:

(a) amplifying reverse transcription products of RNA via polymerase chain reaction to produce amplification products;

(b) contacting said products with at least one oligonucleotide consisting of at least 15 contiguous nucleotides selected from the following major genotype specific nucleotide domains;

(i) major genotype 1-specific nucleotide domains located in sense nucleotide regions 427-466, 444-483, 447-486 and antisense nucleotide regions 505-466, 522-483 and 525-486 of SEQ ID NOs;

103-124;

(ii) major genotype 2-specific nucleotide domains located in sense nucleotide regions 153-192, 162-201, 164-203, 168-207, 171-210, 182-221, 192-231, 197-242 and antisense nucleotide regions 231-192, 240-201, 242-203, 246-207, 249-210 and 380-341 of SEQ ID NOs;

125-134;

(iii) major genotype 3-specific nucleotide domains located in SEQ ID NOs;

135-138;

(iv) major genotype 4-specific nucleotide domain located in SEQ ID NOs;

139-145;

(v) major genotype 5-specific nucleotide domain located in SEQ ID NOs;

146-153; and

(vi) major genotype 6-specific nucleotide domains located in SEQ ID NO;

154; and

(c) detecting complexes of said products and said oligonucleotide(s), the detection of said complexes indicating that the hepatitis C virus belongs to a single major genotype selected from major genotypes 1-6.

6. A method for determining the minor genotype of a hepatitis C virus isolate comprising:

(a) amplifying reverse transcription products of RNA via polymerase chain reaction using amplification primers consisting of at least 15 contiguous nucleotides selected from the following minor genotype-specific domains;

(i) minor genotype I/1a-specific nucleotide domains located in sense nucleotide regions 141-180, 279-318 and antisense nucleotide regions 246-207 of SEQ ID NOs;

103-108;

(ii) minor genotype II/1b-specific nucleotide domains located in sense nucleotide regions 67-106, 127-186, 234-273 and antisense nucleotide regions 144-106 and 225-186 of SEQ ID NOs;

109-124;

(iii) minor genotype III/2a-specific nucleotide domains located in antisense nucleotide regions 354-315, 394-355 and 571-532 of SEQ ID NOs;

125-128;

(iv) minor genotype IV/2b-specific nucleotide domains located in sense nucleotide regions 6-45, 135-174, 177-216, 309-348, 337-376, 375-414, 501-540 and antisense nucleotide regions 84-45, 213-174, 255-216, 387-348, 415-376, 453-414, 571-532 and 573-540 of SEQ ID NOs;

129-133;

(v) minor genotype 2c-specific nucleotide domains located in SEQ ID NO;

134;

(vi) minor genotype V/3a-specific nucleotide domains located in SEQ ID NOs;

(vii) minor genotype 4a-specific nucleotide domains located in SEQ ID NO;

139;

(viii) minor genotype 4b-specific nucleotide domains located in SEQ ID NO;

141;

(ix) minor genotype 4c-specific nucleotide domains located in SEQ ID NO;

143;

(x) minor genotype 4d-specific nucleotide domains located in SEQ ID NO;

145;

(xi) minor genotype 4e-specific nucleotide domains located in SEQ ID NO;

142;

(xii) minor genotype 4f-specific nucleotide domains located in SEQ ID NO;

140;

(xiii) minor genotype 5a-specific nucleotide domains located in SEQ ID NOs;

146-153; and

(xiv) minor genotype 6a-specific nucleotide domains located in SEQ ID NO;

154; and

(b) detecting complexes of said products and said oligonucleotides where the detection of said complexes indicates that the hepatitis C virus belongs to a single minor genotype selected from minor genotypes I/1a, II/1b, III/2a, IV/2b, 2c, V/3a, 4a, 4b, 4c, 4d, 4e, 4f, 5a and 6a.

7. A method for determining the minor genotype of a hepatitis C virus isolate comprising:

(a) amplifying reverse transcription products of RNA via -polymerase chain reaction to produce amplification products;

(b) contacting said products with at least one oligonucleotide consisting of at least 15 contiguous nucleotides selected from one of the following minor genotype-specific nucleotide domains;

(i) minor genotype I/1a-specific nucleotide domains located in sense nucleotide regions 141-180, 279-318 and antisense nucleotide regions 246-207 of SEQ ID NOs;

193-108;

(ii) minor genotype II/1b-specific nucleotide domains located in sense nucleotide region 67-106, 127-186, 234-273 and antisense nucleotide regions 144-106 and 225-186 of SEQ ID NOs;

109-124;

(iii) minor genotype III/2a-specific nucleotide domains located in antisense nucleotide regions 354-315, 394-355 and 571-532 of SEQ ID NOs;

125-128;

(iv) minor genotype IV/2b-specific nucleotide domains located in sense nucleotide regions 6-45, 135-174, 177-216, 309-348, 337-376, 375-414, 501-540 and antisense nucleotide regions 84-45, 213-174, 255-216, 387-348, 415-376, 453-414, 571-532 and 573-540 of SEQ ID NOs;

129-133;

(v) minor genotype 2c-specific nucleotide domains located in SEQ ID NO;

134;

(vi) minor genotype V/3a-specific nucleotide domains located in SEQ ID NOs;

;

(vii) minor genotype 4a-specific nucleotide domains located in SEQ ID NO;

139;

(viii) minor genotype 4b-specific nucleotide domains located in SEQ ID NO;

141;

(ix) minor genotype 4c-specific nucleotide domains located in SEQ ID NO;

143;

(x) minor genotype 4d-specific nucleotide domains located in SEQ ID NO;

145;

(xi) minor genotype 4e-specific nucleotide domains located in SEQ ID NO;

142;

(Xii) minor genotype 4f-specific nucleotide domains located in SEQ ID NO;

140;

(xiii) minor genotype 5a-specific nucleotide domains located in SEQ ID NOs;

146-153; and

(xiv) minor genotype 6a-specific nucleotide domains located in SEQ ID NO;

154; and

(c) detecting complexes of said products and said oligonucleotide(s), the detection of said complexes indicating that the hepatitis C virus belongs to a single major genotype selected from mayor genotypes 1-6.

8. An isolated oligonucleotide consisting of at least 15 contiguous nucleotides selected from the following regions of SEQ ID Nos:

103-154;

(i) sense nucleotide regions 1-20, 1-25, 1-26, 1-27, 1-33, 50-89, 51-90, 52-91, 53-92, 61-100, 62-101, 77-116, 78-117, 79-118, 80-119, 81-120, 82-121, 83-122, 84-123, 85-124, 86-125, 329-368, 330-369, 331-370, 332-371, 354-393, 355-394, 356-395, 442-481, 443-482, 457-496, 458-497, 475-514, 476-515, 477-516 and

(ii) antisense nucleotide regions 40-1, 41-2, 42-3, 43-4, 51-12, 52-13, 55-16, 56-17, 57-18, 58-19, 61-22, 62-23, 63-24, 64-25, 70-31, 124-85, 125-86, 126-87, 127-88, 128-89, 129-90, 517-478, 518-479, 519-480, 532-493, 533-494, 550-511, 551-512.

9. A diagnostic kit for use in detecting the presence of hepatitis C virus in a biological sample, said kit comprising at least one oligonucleotide according to claim 8.

10. A diagnostic kit for use in detecting the presence of hepatitis C virus in a biological sample, said kit comprising at least one nucleic acid sequence selected from the group consisting of SEQ ID NO:

103-154.

11. An isolated oligonucleotide consisting of at least 15 contiguous nucleotides selected from the following major genotype-specific nucleotide domains:

(a) major genotype 1-specific nucleotide domains located in sense nucleotide regions 427-466, 435-495, 444-483, 447-486 and antisense nucleotide regions 505-466, 522-483 and 525-486 of SEQ ID NOs;

103-124;

(b) major genotype 2-specific nucleotide domains located in sense nucleotide regions 153-192, 162-201, 164-203, 168-207, 171-210, 182-221, 186-240, 192-231, 197-242, 320-360, 440-475 and antisense nucleotide regions 231-192, 240-201, 242-203, 246-207, 249-210 and 380-341 of SEQ ID NOs;

125-134;

(c) major genotype 3-specific nucleotide domains located in SEQ ID NOs;

135-138;

(d) major genotype 4-specific nucleotide domains located in SEQ ID NOs;

139-145;

(e) major genotype 5-specific nucleotide domains located in SEQ ID NOs;

146-153; and

(f) major genotype 6-specific nucleotide domains located in SEQ ID NO;

154.

12. A diagnostic kit for determining which major genotype a hepatitis C virus isolate belongs to, said kit comprising at least one oligonucleotide according to claim 11.

13. An isolated oligonucleotide consisting of at least 15 contiguous nucleotides selected from the following minor genotype-specific nucleotide regions:

(a) minor genotype I/1a-specific nucleotide domains located in sense nucleotide regions 141-180, 207-277, 279-318 and antisense nucleotide region 246-207 of SEQ ID NOS;

103-108;

(b) minor genotype II/1b-specific nucleotide domains located in sense nucleotide regions 67-106, 81-131, 127-186, 159-225, 411-472, 530-573 and antisense nucleotide regions 144-106 and 225-186 of SEQ ID NOS;

109-124;

(c) minor genotype III/2a-specific nucleotide domains located in sense nucleotide regions 35-75, 200-276, 330-380, 410-472, 530-573 and antisense nucleotide regions 354-315, 394-355 and 571-532 of SEQ ID NOs;

125-128;

(d) minor genotype IV/2b-specific nucleotide domains located in sense nucleotide regions 6-45, 20-70, 135-174, 149-199, 177-216, 191-241, 309-348, 323-373, 337-376, 351-401, 375-414, 389-439, 429-477, 530-573, 501-540 and antisense nucleotide regions 84-45, 213-174, 255-216, 387-348, 415-376, 453-414, 571-532 and 573-540 of SEQ ID NOs;

129-133;

(e) minor genotype 2c-specific nucleotide domains located in SEQ ID NO;

134;

(f) minor genotype V/3a-specific nucleotide domains located in SEQ ID NOs;

135-138;

(g) minor genotype 4a-specific nucleotide domains located in SEQ ID NO;

139;

(h) minor genotype 4b-specific nucleotide domains located in SEQ ID NO;

141;

(i) minor genotype 4c-specific nucleotide domains located in SEQ ID NO;

143;

(j) minor genotype 4d-specific nucleotide domains located in SEQ ID NO;

145;

(k) minor genotype 4e-specific nucleotide domains located in SEQ ID NO;

142;

(l) minor genotype 4f-specific nucleotide domains located in SEQ ID NO;

140;

(m) minor genotype 5a-specific nucleotide domains located in SEQ ID NOs;

146-153; and

(n) minor genotype 6a-specific nucleotide domains located in SEQ ID NO;

154.

14. A diagnostic kit for determining the minor genotype of a hepatitis C virus isolate, said kit comprising at least one oligonucleotide according to claim 13.