Process for typing of HCV isolates
First Claim
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1. A method of genotyping HCV nucleic acids present in a biological sample comprising the steps ofcontacting nucleic acids of the 5′
- UTR of HCV in a biological sample with multiple oligonucleotide probes under reaction conditions in which said probes specifically hybridize to target sequences in said HCV 5′
UTR nucleic acids within the region extending from the nucleotides at positions −
291 to −
66, if present in the biological sample, anddetermining whether one or more of said probes have hybridized to said nucleic acids of HCV,wherein, under said reaction conditions, said probes can distinguish among at least three genotypes of HCV selected from the group consisting of HCV type 1, HCV type 2, HCV type 3, and HCV type 4, and classify the HCV nucleic acids into any of said at least three genotypes, if any of said at least three genotypes is present in said sample.
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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.
22 Citations
27 Claims
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1. A method of genotyping HCV nucleic acids present in a biological sample comprising the steps of
contacting nucleic acids of the 5′ - UTR of HCV in a biological sample with multiple oligonucleotide probes under reaction conditions in which said probes specifically hybridize to target sequences in said HCV 5′
UTR nucleic acids within the region extending from the nucleotides at positions −
291 to −
66, if present in the biological sample, anddetermining whether one or more of said probes have hybridized to said nucleic acids of HCV, wherein, under said reaction conditions, said probes can distinguish among at least three genotypes of HCV selected from the group consisting of HCV type 1, HCV type 2, HCV type 3, and HCV type 4, and classify the HCV nucleic acids into any of said at least three genotypes, if any of said at least three genotypes is present in said sample. - View Dependent Claims (2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
- UTR of HCV in a biological sample with multiple oligonucleotide probes under reaction conditions in which said probes specifically hybridize to target sequences in said HCV 5′
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3. A method of genotyping HCV nucleic acids present in a biological sample comprising the steps of
contacting nucleic acids of the 5′ - UTR of HCV in a biological sample with multiple oligonucleotide probes under reaction conditions in which said probes specifically hybridize to target sequences in said HCV 5′
UTR nucleic acids within the region extending from the nucleotides at positions −
291 to −
66, if present in the biological sample, anddetermining whether one or more of said probes have hybridized to said nucleic acids of HCV, wherein, under said reaction conditions, said probes can distinguish among at least three genotypes of HCV selected from the group consisting of HCV type 1, HCV type 2, HCV type 3, HCV type 4, HCV type 5 and HCV type 6, and classify the HCV nucleic acids into any of said at least three genotypes, if any of said at least three genotypes is present in said sample. - View Dependent Claims (4, 5, 6)
- UTR of HCV in a biological sample with multiple oligonucleotide probes under reaction conditions in which said probes specifically hybridize to target sequences in said HCV 5′
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26. A method of genotyping HCV Type 6 nucleic acids present in a biological sample comprising the steps of:
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contacting a biological sample comprising nucleic acids of the 5′
UTR of HCV Type 6 with at least one probe, anddetermining whether said at least one probe has hybridized to said nucleic acids of HCV, wherein said step of contacting is carried out under reaction conditions in which said at least one probe specifically hybridizes to a HCV type 6 specific sequence in the 5′
UTR, if said HCV type 6 specific sequence in the 5′
UTR is present in the biological sample. - View Dependent Claims (27)
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Specification
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Current AssigneeInnogenetics NV (H.U. Group Holdings, Inc.)
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Original AssigneeInnogenetics NV (H.U. Group Holdings, Inc.)
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InventorsMaertens, Geert, Van Heuverswyn, Hugo, Rossau, Rudi, Stuyver, Lieven
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Primary Examiner(s)WHISENANT, ETHAN C
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Application NumberUS10/822,711Publication NumberTime in Patent Office1,225 DaysField of Search435/6, 536/23.1, 536/24.3US Class Current435/5CPC Class CodesC12Q 1/6834 Enzymatic or biochemical co...C12Q 1/707 non-A, non-B Hepatitis, exc...C12Q 2525/101 incorporating non-naturally...C12Q 2531/113 PCRC12Q 2545/101 with an internal standard/c...C12Q 2563/131 the label being a member of...
