Process for typing HCV isolates

• US 6,548,244 B2
• Filed: 07/06/2001
• Issued: 04/15/2003
• Est. Priority Date: 11/27/1992
• Status: Expired due to Fees

• Current Assignee: Innogenetics NV (H.U. Group Holdings, Inc.)
• Original Assignee: Innogenetics NV (H.U. Group Holdings, Inc.)
• Inventors: Maertens, Geert, Stuyver, Lieven, Van Heuverswyn, Hugo, Rossau, Rudi
• Primary Examiner(s): Whisenant, Ethan C.
• Application Number:
  US09/899,044
• Publication Number:
  US 20030036053A1
• Time in Patent Office: 648 Days
• Field of Search: 435/6, 536/23.1, 536/24.3
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/707 non-A, non-B Hepatitis, excluding hepatitis D
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin

Abstract

The invention relates to a process for genotyping any HCV isolate present in a biological sample, previously identified as being HCV positive, and for classifying said isolate according to the percentage of homology with other HCV isolates, comprising the steps of:

contacting said sample in which the ribonucleotides or deoxyribonucleotides have been made accessible, if need be, under suitable denaturation, with at least one probe from about 10 to about 40 nucleotides, with said probe being liable to hybridize to a region being in the domain extending from nucleotide at position −291 to nucleotide at position −66 of the 5′ untranslated region of one of the HCV isolates represented by their cDNA sequences, with said numbering of position beginning with the first ATG codon of the open reading frame encoding the HCV polyprotein, or with said probe being complementary to the above-defined probes,

detecting the complexes possibly formed between said probe and the nucleotide sequence of the HCV isolate to be identified.

Claims

1. A method for detecting the presence of an infection with an HCV virus in a biological sample on the basis of the presence of a genotype-specific sequence or an isolate-specific mutation present in any of SEQ ID NO 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81.

3. The method according to claim 1 or 2, wherein said method comprises the determination of the presence of said genotype-specific sequence or isolate-specific mutation of any of SEQ ID NO 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81 by means of a sequencing reaction.

6. An HCV genotyping method comprising the steps of a method according to claim 1.

8. An HCV genotyping method comprising the steps of a method according to claim 3.

19. A method according to any of claims 1, 2, 4-7, 9-13 or 15-17 wherein at least one primer is used.

20. A method according to claim 3 wherein at least one primer is used.

21. A method according to claim 8 wherein at least one primer is used.

2. A method for detecting the presence of an infection with an HCV virus in a biological sample on the basis of the presence of any of SEQ ID NO 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81.

7. An HCV genotyping method comprising the steps of a method according to claim 2.

4. A method comprising the determination of the presence in a biological sample of at least one of the following variable nucleotide regions or positions of any HCV 5′

UTR sequence by means of a sequencing reaction, wherein said method detects the nucleotide variation present between HCV strains in at least one of the following regions of HCV;

(a) the type-specific variable region between positions −

170 and −

155,

(b) the type-specific variable region between positions −

132 and −

117, and/or,

(c) the type-specific variable region between positions −

291 and −

55.

5. The method according to claim 4 wherein said method comprises the determination of said nucleotide variations present in said regions of any of SEQ ID NO 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81.

9. An HCV genotyping method comprising the steps of a method according to claim 4.

10. An HCV genotyping method comprising the steps of a method according to claim 5.

14. A method according to claim 10 or 11 wherein said method comprises the determination of the presence of said genotype-specific sequence or isolate-specific mutation by means of a sequencing reaction.

15. An HCV genotyping method comprising the steps of the method according to claim 10.

22. A method according to claim 14 wherein at least one primer is used.

11. A method for detecting the presence of an infection with an HCV virus in a biological sample on the basis of the presence of a genotype-specific sequence or an isolate-specific mutation present in a nucleic acid encoding any of SEQ ID NOs 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 or 92.

16. An HCV genotyping method comprising the steps of the method according to claim 11.

12. A method for detecting the presence of an infection with an HCV virus in a biological sample on the basis of the presence of a nucleotide sequence encoding any of SEQ ID NOs 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 or 92.

17. An HCV genotyping method comprising the steps of the method according to claim 12.

13. A method for detecting the presence of an infection with an HCV virus in a biological sample on the basis of the presence of at least part of an amino acid sequence of any of SEQ ID NOs 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 or 92.

18. An HCV genotyping method comprising the steps of the method according to claim 13.