Process for typing of HCV isolates

• US 6,891,026 B2
• Filed: 07/06/2001
• Issued: 05/10/2005
• 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:
  US09/899,082
• Publication Number:
  US 20020106638A1
• Time in Patent Office: 1,404 Days
• Field of Search: 536/23.1, 536/24.3, 435/6
• US Class Current: 536/23.1
• 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 polynucleic acid selected from the group consisting of

CCC TGT GAG GAA CTW CTG TCT TCA CGC,(SEQ ID NO 1)GGT GCA CGG TCT ACG AGA CCT,(SEQ ID NO 2)TCT AGC CAT GGC GTT AGT RYG AGT GT,(SEQ ID NO 3)TTG GGC GYG CCC CCG C,(SEQ ID NO 20)andTCT GCG GAA CCG GTG A,(SEQ ID NO 27)

or the complement thereof, wherein W represents A or T, R represents G or A, and Y represents T or C,

or a corresponding sequence wherein T has been replaced by U.

27. A method for detecting the presence of an infection with an HCV virus in a biological sample by means of a hybridization reaction with a polynucleic acid of any of claims 1, 3, 4, 10, 12-15.

28. A method according to claim 27 wherein said polynucleic acids are coupled to a solid support.

29. A diagnostic kit for the detection of HCV in a biological sample comprising at least one of the polynucleic acids of any of claim 1, 3, 4, 10 or 12-15.

30. A method for the identification of a previously amplified HCV 5′

untranslated region fragment comprising hybridizing a polynucleic acid according to any of claims 1, 3, 4, 10 and 12-15 to said 5′

region.

31. A method according to claim 27 wherein said polynucleic acids are capture probes.

2. A set of oligonucleotides comprising at least one oligonucleotide of 15 to 50 nucleotides, said at least one oligonucleotide comprising at least 15 contiguous nucleotides chosen from any of SEQ ID NOs:

1, 2 or 3, or the complement thereof wherein W represents A or T, R represents G or A, and Y represents T or C, or a corresponding sequence wherein T has been replaced by U.

3. A polynucleic acid consisting of 10 to 50 nucleotides which specifically hybridizes with the sequence of SEQ ID NO:

20 wherein Y represents T or C, or a corresponding sequence wherein T has been replaced by U.

4. A polynucleic acid consisting of 27 to 50 nucleotides which specifically hybridizes with the sequence of SEQ ID NO 27, or the complement thereof, or a corresponding sequence wherein T has been replaced by U.

5. A method for detecting the presence of an infection with an HCV virus in a biological sample by means of a hybridization reaction with a polynucleic acid of SEQ ID NO 20 or 27 or the complement thereof wherein Y represents T or C, or with a corresponding polynucleic acid wherein T has been replaced by U.

6. A method according to claim 5 wherein said polynucleic acids are coupled to a solid support.

18. A method according to claim 5 wherein said polynucleic acids are capture probes.

7. A method for detecting the presence of an infection with an HCV virus in a biological sample by means of an amplification reaction using (a set of) primers that specifically hybridize to SEQ ID NO:

1 or SEQ ID NO;

3, or the complement thereof wherein W represents A or T, R represents G or A and Y represents T or C; and

with SEQ ID NO;

2 or SEQ ID NO;

4, or the complement thereof.

8. The method according to claim 7 wherein said amplification method is PCR, LCR, NASBA, TAS or amplification by means of Qb replicase.

9. Process for general amplification of the 5′

UR region of HCV isolates involving at least one of the following primers

a primer of 15 to 50 nucleotides specifically hybridizing with SEQ ID NO;

1 or the complement thereof, wherein W represents A or T, and

a primer of 15 to 50 nucleotides specifically hybridizing with SEQ ID NO;

3 or the complement thereof, wherein R represents A or G and Y represents T or C.

24. The process of claim 9 wherein said primer of 15 to 50 nucleotides specifically hybridizing with SEQ ID NO:

1 is combined with a primer hybridizing to the region extending from nucleotide −

68 to nucleotide −

1 or the complement of said region.

25. The process of claim 9 wherein said primer of 15 to 50 nucleotides specifically hybridizing with SEQ ID NO:

3 is combined with a primer hybridizing to the region extending from nucleotide −

68 to nucleotide −

1 or the complement of said region.

26. The process according to claim 24 or 25 wherein said primer hybridizing to the region extending from nucleotide −

68 to nucleotide −

1 or the complement of said region is defined by SEQ ID NO;

2 or SEQ ID NO;

4.

10. A polynucleic acid consisting of 15 to 50 nucleotides which specifically hybridizes with at least one of SEQ ID NO:

1, SEQ ID NO;

2 or SEQ ID NO;

3.

11. A set of oligonucleotides comprising at least a first oligonucleotide of 15 to 50 nucleotides and a second oligonucleotide of 15 to 50 nucleotides, said first and second oligonucleotides each independently comprising at least 15 contiguous nucleotides chosen from any of SEQ ID NOs:

1, 2, 3, 4, 20 and 27, or the complement thereof wherein W represents A or T, R represents G or A and Y represents T or C, or a corresponding sequence wherein T has been replaced by U.

16. A method for detecting the presence of an infection with an HCV virus in a biological sample by means of a hybridization reaction with a set of oligonucleotides of claim 2 or 11.

17. A method according to claim 16 wherein said oligonucleotides are coupled to a solid support.

19. A method according to claim 16 wherein said oligonucleotides are capture probes.

22. A diagnostic kit for the detection of HCV in a biological sample comprising a set of oligonucleotides of claim 2 or 11.

23. A method for the identification of a previously amplified HCV 5′

untranslated region fragment comprising hybridizing a set of oligonucleotides of claim 2 or 11 to said 5′

region.

12. A polynucleic acid consisting of 10 to 50 nucleotides which specifically hybridizes under conditions allowing discrimination of up to 1 nucleotide mismatch with the sequence of SEQ ID NO:

20 wherein Y represents T or C, or with a corresponding sequence wherein T has been replaced by U.

13. A polynucleic acid consisting of 21 to 50 nucleotides which specifically hybridizes with the sequence of SEQ ID NO:

20 or the complement thereof wherein Y represents T or C, or with a corresponding sequence wherein T has been replaced by U.

14. A polynucleic acid consisting of 21 to 50 nucleotides which specifically hybridizes under conditions allowing discrimination of up to 1 nucleotide mismatch with the sequence of SEQ ID NO:

20 or the complement thereof wherein Y represents T or C, or with a corresponding sequence wherein T has been replaced by U.

15. A polynucleic acid consisting of 27 to 50 nucleotides which specifically hybridizes under conditions allowing discrimination of up to 1 nucleotide mismatch with the sequence of SEQ ID NO:

27 or the complement thereof, or with a corresponding sequence wherein T has been replaced by U.

20. A method for detecting the presence of an infection with an HCV virus in a biological sample by means of an amplification reaction using (a set of) primers that specifically hybridize with SEQ ID NO:

1 or SEQ ID NO;

3, or the complement thereof wherein W represents A or T, R represents G or A and Y represents T or C; and

with SEQ ID NO;

20 or SEQ ID NO;

27, or the complement thereof wherein Y represents T or C.

21. A method for detecting the presence of an infection with an HCV virus in a biological sample by means of an amplification reaction using (a set of) primers that specifically hybridize with SEQ ID NO:

20 or SEQ ID NO;

27, or the complement thereof wherein Y represents T or C; and

with SEQ ID NO;

2 or SEQ ID NO;

4, or the complement thereof.