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US6416944: Methods of typing hepatitis C virus and reagents for use therein

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Filing Information

Inventor(s) David Y. Chien · George Kuo ·
Assignee(s) Chiron Corporation ·
Attorney/Agent(s) Roberta L. Robins · Alisa A. Harbin · Robert P. Blackburn ·
Primary Examiner Donna C. Wortman ·
Application Number US8439157
Filing date 05/11/1995
Issue date 07/09/2002
Predicted expiration date 05/10/2013
U.S. Classifications 435/5  · 436/820  · 435/6  ·
International Classifications --
Kind CodeB1
International Classifications 536 2372 · 435 5 · 435 6 · 436820 ·
Related U.S. Application DataThis application is a divisional, of application Ser. No. 08/336,553, filed Nov. 9, 1994 U.S. Pat. No. 6,054,264, which is a continution of application Ser. No. 08/060,400, filed May 10, 1993, now abandoned.
26 Claims, 4 Drawings


Abstract

The claimed invention provides methods of detecting and typing HCV using nucleic acid molecules encoding type specific and type-cluster specific epitopes. The nucleic acid molecules flanking regions encoding type specific or type cluster specific epitopes are useful in priming the polymerase chain reaction to determine the genotype an HCV isolate.

Independent Claims | See all claims (26)

  1. 1. A method for detecting one or more types of hepatitis C virus (HCV) in a sample, said method comprising the steps of: (a) providing a biological sample from an individual suspected of being infected by a hepatitis C virus; (b) contacting the sample with a first nucleic acid molecule wherein said first nucleic acid molecule encodes at least one first HCV epitope selected from the group consisting of an epitope within amino acid residues 67 to 84 of the core domain, relative to the HCV-1 viral polyprotein sequence; an epitope within amino acid residues 1689 to 1718 of the NS4 domain, relative to the HCV-1 viral polyprotein sequence; and an epitope within amino acid residues 2281 to 2313 the NS5 domain, relative to the HCV-1 viral polyprotein sequence; wherein said at least one first epitope is from 5 to 15 amino acids in length and wherein said first epitope is further selected from the group consisting of a first type-specific epitope specific for a first type of hepatitis C virus and a first type-cluster specific epitope specific for a first type-cluster of hepatitis C virus, under conditions that allow the selective hybridization of said nucleic acid molecule to a HCV polynucleotide or the complement thereof in said sample; and (c) determining whether polynucleotide duplexes comprising said first nucleic acid molecule are formed, where formation of such duplexes indicates detection of a first type or type-cluster of HCV in the sample; (d) contacting the samples containing said polynucleotide duplexes with a second nucleic acid molecule wherein said second nucleic acid molecule encodes at least one second HCV epitope different from said first HCV epitope, said at least one second epitope selected from the group consisting of an epitope within amino acids 67 to 84 of the core domain, relative to the HCV-1 viral polyprotein sequence; an epitope within amino acids 1689 to 1718 of the NS4 domain, relative to the HCV-1 viral polyprotein sequence; and an epitope within amino acids 2281 to 2313 of the NS5 domain, relative to the HCV-1 viral polyprotein sequence; wherein said at least one second epitope is from 5 to 15 amino acids in length and wherein said second epitope is further selected from the group consisting of a second type-specific epitope specific for a second type of hepatitis C virus and a second type-cluster specific epitope specific for a second type-cluster of hepatitis C virus, under conditions that allow the selective hybridization of said second nucleic acid molecule to a HCV polynucleotide or the complement thereof in said sample; and (e) determining whether polynucleotide duplexes comprising said second nucleic acid molecule are formed, where formation of such duplexes indicates detection of a second type or type-cluster of HCV in the sample.
  2. 7. A method for typing one or more types or type-clusters of a hepatitis C virus (HCV) in a sample, said method comprising the steps of: (a) providing a biological sample from an individual suspected of being infected by a hepatitis C virus; (b) contacting the sample with a first nucleic acid molecule wherein said first nucleic acid molecule encodes at least one first HCV epitope selected from the group consisting of an epitope within amino acids 67 to 84 of the core domain, relative to the HCV-1 viral polyprotein sequence; an epitope within amino acids 1689 to 1718 of the NS4 domain, relative to the HCV-1 viral polyprotein sequence; and an epitope within amino acids 2281 to 2313 of the NS5 domain, relative to the HCV-1 viral polyprotein sequence; wherein said at least one first epitope is from 5 to 15 amino acids in length and wherein said first epitope is further selected from the group consisting of a first type-specific epitope specific for a first type of hepatitis C virus and a first type-cluster specific epitope specific for a first type-cluster of hepatitis C virus, under conditions that allow the selective hybridization of said nucleic acid molecule to a HCV polynucleotide or the complement thereof in said sample; and (c) determining whether polynucleotide duplexes comprising said first nucleic acid molecule are formed, wherein the presence of said duplexes is indicative of a type or typecluster of HCV being present in the sample.
  3. 17. A method for typing one or more types or type-clusters of a hepatitis C virus comprising the steps of: (a) providing a nucleic acid molecule capable of selectively hybridizing to a target region within a genome of a hepatitis C virus (HCV), or its complement, wherein the nucleic acid molecule encodes at least one first HCV epitope selected from the group consisting of an epitope within amino acids 67 to 84 of the core domain, relative to the HCV-1 viral polyprotein sequence; an epitope within amino acids 1689 to 1718 of the NS4 domain, relative to the HCV-1 viral polyprotein sequence; and an epitope within amino acids 2281 to 2313 of the NS5 domain, relative to the HCV-1 viral polyprotein sequence; wherein said at least one first epitope is from 5 to 15 amino acids in length and wherein said first epitope is further selected from the group consisting of a first type-specific epitope specific for a first type of hepatitis C virus and a first type-cluster specific epitope specific for a first type-cluster of hepatitis C virus, or its complement; (b) providing a set of primer nucleic acid molecules which are primers for the polymerase chain reaction method and which flank the target region; (c) amplifying the target region via a polymerase chain reaction method to obtain an amplified test sample; (d) incubating the amplified test sample with the nucleic acid molecule of step (a) under conditions which allow hybrid duplexes to form between the nucleic acid molecule and the target region; and (e) detecting any hybrids formed between the target region and the nucleic acid molecule, wherein the presence of said hybrid duplex is indicative of a type or type-cluster of HCV being present in the test sample.

References Cited

U.S. Patent Documents

Document NumberAssigneesInventorsIssue/Pub Date
US4868105 Chiron Corporation Urdea et al. Sep 1989
US5106726 United Biomedical, Inc. Wang Apr 1992
US5124246 Chiron Corporation Urdea et al. Jun 1992
US5350671* Chiron Corporation Houghton et al. Sep 1994
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Foreign Patent Documents

Document NumberAssigneesInventorsIssue/Pub Date
EP318216May 1989
EP388232Sep 1990
EP0586065Advanced Life Science Institute, IncMar 1994
WO199115771Oct 1991
WO199300365Jan 1993
WO199306247Apr 1993
WO199310239May 1993
WO199411388May 1994
WO199425602Nov 1994
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Other Publications

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Okamoto et al., Full-length Sequence of a Hepatitis C Virus Genome Having Poor Homology to Reported Isolates: Comparative Study of Four Distinct Genotypes, Virology 188:331-341, 1992.*
Chan et al., Serological responses to infection with three different types of hepatitis C virus, Lancet 338:1391, 1991.*
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Referenced By

Patent Family

Document NumberAssigneeInventorsIssue/Pub Date
US6416944 Chiron Corporation David Y. Chien et al. Jul 2002
US6416946 Chiron Corporation David Y. Chien et al. Jul 2002