Process for typing of HCV isolates

• US 6,495,670 B1
• Filed: 08/23/1999
• Issued: 12/17/2002
• 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:
  US09/378,900
• Time in Patent Office: 1,212 Days
• Field of Search: 536/23.1, 536/24.3, 435/6, 435/91.2, 935/76, 935/77, 935/78
• 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 consisting of 15 to 50 nucleotides which specifically hybridizes with at least one sequence selected from the group consisting of

TCT AGC CAT GGC GTT AGT RYG AGT GT (SEQ ID NO:

3),

CCG CGA GAC TGC TAG C (SEQ ID NO;

     7),

TTA CCG GGA AGA CTG G (SEQ ID NO;

     11),

TTT CTG GGT ATT GAG C (SEQ ID NO;

     14),

TCT TGG AGC AAC CCG C (SEQ ID NO;

     15),

AAT YGC CGG GAT GAC C (SEQ ID NO;

     17),

TTC TTG GAA CTA ACC C (SEQ ID NO;

     18),

TTT CCG GGC ATT GAG C (SEQ ID NO;

     19),

CCG CGA GAT CAC TAG C (SEQ ID NO;

     21),

CCG GGA AGA CTG GGT C (SEQ ID NO;

     22),

ATA GAG TGG GTT TAT C (SEQ ID NO;

     26),

wherein

Y is T or C,

K is G or T, and

R is G or A, or the complement thereof,

and the corresponding sequences wherein T had been replaced by U.

2. A polynucleic acid consisting of a polynucleic acid sequence selected from the group consisting of

TCT AGC CAT GGC GTT AGT RYG AGT GT (SEQ ID NO:

3),

AAT TGC CAG GAC GAC C (SEQ ID NO;

     5),

TCT CCA GGC ATT GAG C (SEQ ID NO;

     6),

CCG CGA GAC TGC TAG C (SEQ ID NO;

     7),

TAG CGT TGG GTT GCG A (SEQ ID NO;

     8),

TTR CCG GRA AGA CTG G (SEQ ID NO;

     9),

TGR CCG GGC ATA GAG T (SEQ ID NO;

     10),

TTA CCG GGA AGA CTG G (SEQ ID NO;

     11),

TGA CCG GAC ATA GAG T (SEQ ID NO;

     12),

AAT CGC TGG GGT GAC C (SEQ ID NO;

     13),

TTT CTG GGT ATT GAG C (SEQ ID NO;

     14),

TCT TGG AGC AAC CCG C (SEQ ID NO;

     15),

TCT TGG AAC AAC CCG C (SEQ ID NO;

     16),

AAT YGC CGG GAT GAC C (SEQ ID NO;

     17),

TTC TTG GAA CTA ACC C (SEQ ID NO;

     18),

TTT GGG CCC ATT GAG C (SEQ ID NO;

     19),

TTG GGC GYG CCC CCG C (SEQ ID NO;

     20),

CCG CGA GAT CAC TAG C (SEQ ID NO;

     21),

CCG GGA AGA CTG GGT C (SEQ ID NO;

     22),

CCG GAA AGA CTG GGT C (SEQ ID NO;

     23),

ACC CAC TCT ATG CCC G (SEQ ID NO;

     24),

ACC CAC TCT ATG TCC G (SEQ ID NO;

     25),

ATA GAG TGG GTT TAT C (SEQ ID NO;

     26), and

TCT GCG GAA CCG GTG A (SEQ ID NO;

     27),

wherein

Y is T or C,

K is G or T, and

R is G or A, or the complement of said polynucleic acid sequence.

3. A polynucleic acid consisting of 15 to 50 nucleotides which specifically hybridizes with at least one sequence selectcd from the group consisting of

CCC CGC AAG ACT GCT A (SEQ ID NO:

31),

CGT ACA GCC TCC AGG C (SEQ ID NO;

     32),

GGA CCC AGT CTT CCT G (SEQ ID NO;

     33),

TGC CTG GTC ATT TGG G (SEQ ID NO;

     34).

TKT CTG GGT ATT GAG C (SEQ ID NO;

     35),

CCG CAA GAT CAC TAG C (SEQ ID NO;

     36),

GAG TGT TGT ACA GCC T (SEQ ID NO;

     37),

AAT CGC CGG GAT GAC C (SEQ ID NO;

     38),

GAG TGT TGT GCA GCC T (SEQ ID NO;

     39),

AAT CGC CGG GAC GAC C (SEQ ID NO;

     40).

AAT GCC CGG CAA TTT G (SEQ ID NO;

     41),

AAT CGC CGA GAT GAC C (SEQ ID NO;

     42),

AAT GCT CGG AAA TTT G (SEQ ID NO;

     43).

GAG TGT CGA ACA GCC T (SEQ ID NO;

     44),

AAT TGC CGG GAT GAC C (SEQ ID NO;

     45),

GGG TCC TTT CCA TTG G (SEQ ID NO;

     48),

AAT CGC CAG GAT GAC C (SEQ ID NO;

     49),

TGC CTG GAA ATT TGG G (SEQ ID NO;

     50).

GAG TGT CGT ACA GCC T (SEQ ID NO;

     51),

AGT YCA CCG GAA TCG C (SEQ ID NO;

     52),

GGA ATC GCC AGG ACG A (SEQ ID NO;

     53),

GAA TCG CCG GGT TGA C (SEQ ID NO;

     54),

wherein

Y is T or C,

K is G or T, and

R is G or A, or the complement thereof,

and the corresponding sequence wherein T had been replaced by U.

4. A polynucleic acid consisting of a polynucleic acid sequence selected from the group consisting of

AAT TGC CAG GAY GAC C (SEQ ID NO:

28),

GCT CAG TGC CTG GAG A (SEQ ID NO;

     29),

CCG CGA GAC YGC TAG C (SEQ ID NO;

     30),

CCC CGC AAG ACT GCT A (SEQ ID NO;

     31),

CGT ACA GCC TCC AGG C (SEQ ID NO;

     32),

GGA CCC AGT CTT CCT G (SEQ ID NO;

     33),

TGC CTG GTC ATT TGG G (SEQ ID NO;

     34),

TKT CTG GGT ATT GAG C (SEQ ID NO;

     35),

CCG CAA GAT CAC TAG C (SEQ ID NO;

     36),

GAG TGT TGT ACA GCC T (SEQ ID NO;

     37),

AAT CGC CGG GAT GAC C (SEQ ID NO;

     38),

GAG TGT TGT GCA GCC T (SEQ ID NO;

     39),

AAT CGC CGG GAC GAC C (SEQ ID NO;

     40),

AAT GCC CGG CAA TTT G (SEQ ID NO;

     41),

AAT CGC CGA GAT GAC C (SEQ ID NO;

     42),

AAT GCT CGG AAA TTT G (SEQ ID NO;

     43),

GAG TGT CGA ACA GCC T (SEQ ID NO;

     44),

AAT TGC CGG GAT GAG C (SEO ID NO;

     45),

TCT CCG GGC ATT GAG C (SEO ID NO;

     46),

AAT TGC CGG GAC GAC C (SEQ ID NO;

     47),

GGG TCC TTT CCA TTG G (SEO ID NO;

     48),

AAT CGC CAG GAT GAC C (SEQ ID NO;

     49),

TGC CTG GAA ATT TGG G (SEQ ID NO;

     50),

GAG TGT CGT ACA GCC T (SEQ ID NO;

     51),

AGT YCA CCG GAA TCG C (SEQ ID NO;

     52),

GGA ATC GCC AGG ACG A (SEQ ID NO;

     53), and

GAA TCG CCG GGT TGA C (SEQ ID NO;

     54),

wherein

Y is T or C,

K is G or T, and

R is G or A, or the complement of said polynucleic acid sequence.

5. A polynucleic acid consisting of 15 to 50 nucleotides which specifically hybridizes with at least one sequence selected from the group consisting of

GAG TGT TGT ACA GCC TCC (SEQ ID NO:

93),

TGC CCG GAA ATT TGG GC (SEQ ID NO;

     94),

TGC CCG GAG ATT TGG G (SEQ ID NO;

     95),

GAG TGT CGA ACA GCC TC (SEQ ID NO;

     96), and

the corresponding sequence wherein T had been replaced by U.

6. A polynucleic acid consisting of the polynucleic acid sequence selected from the group consisting of

GAG TGT TGT ACA GCC TCC (SEQ ID NO:

93),

TGC CCG GAA ATT TGG GC (SEQ ID NO;

     94),

TGC CCG GAG ATT TGG G (SEQ ID NO;

     95), and

GAG TGT CGA ACA GCC TC (SEO ID NO;

     96),

or the complement of said polynucleic acid sequence.

7. A polynucleic acid consisting of the polynucleic acid sequence selected from the group consisting of SEQ ID NO:

55 to SEQ ID NO;

81 or the complement of said polynucleic acid sequence.