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US 2012/0070820 A1Published application
Probes and Methods for Hepatitis C Virus Typing Using Multidimensional Probe Analysis
AssigneeRoche Molecular Systems, Inc.
InventorsAmar P. Gupta, Stephen Gordon Will
Life of this patent
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Abstract
This invention provides compositions and methods for HCV typing, e.g., genotyping and/or subtyping. The compositions and methods of the invention can be used to assign an HCV isolate to one of at least five HCV types (for example, selected from types 1, 2, 3, 4, 5 or 6), or to one of at least five subtypes (for example, subtypes 1a/b/c, 2a/c, 2b, 3a, 4a, 5a or 6a). These methods integrate the hybridization data from a plurality of HCV typing probes in a multidimensional analysis to make an HCV type assignment for an HCV in an experimental sample. The invention also provides related compositions, including, for example, the HCV typing probes and HCV typing diagnostic kits.
Claims18
1-34. (canceled)
A composition comprising a plurality of probes, wherein:
- a) each probe comprises a nucleotide sequence that targets the probe to a same target region within a hepatitis C virus (HCV) genome and is complementary or partially complementary to a nucleotide sequence within the HCV genome;
- b) the regions of complementarity or partial complementarity show sequence heterogeneity among at least two HCV types;
- c) hybridization complexes comprising (i) any one probe from the plurality of probes, and (ii) nucleotide sequences from at least two HCV types have a distinguishing range of melting temperature (Tm) that permits differentiation of more than two HCV types;
- d) the more than two HCV types differentiated by any one probe from the plurality of probes are different than the more than two HCV types differentiated by a second different probe from the plurality of probes;
- and,
- e) the distinguishing range of melting temperature (Tm) of each of the hybridization complexes comprising at least two probes from the plurality of probes correlates with one of at least five HCV types, wherein an assignment of an HCV type is made by considering the distinguishing range of melting temperature (Tm) of the hybridization complexes.
3 more elements
(canceled)
A diagnostic kit for determining the type of a hepatitis C virus (HCV) in a sample, the kit comprising:
- a) a plurality of HCV typing probes, wherein:
- i) each typing probe comprises a nucleotide sequence that targets the probe to a same target region within an HCV genome and is complementary or partially complementary to a nucleotide sequence within the HCV genome;
- ii) the regions of complementarity or partial complementarity show sequence heterogeneity among at least two HCV types;
- iii) hybridization complexes comprising (i) any one probe from the plurality of probes and (ii) nucleotide sequences from at least two HCV types have a distinguishing range of melting temperature (Tm) that permits differentiation of more than two virus types;
- iv) the more than two HCV types differentiated by one probe from the plurality of probes are different than the more than two HCV types differentiated by a second different probe from the plurality of probes;
- and,
- v) the distinguishing range of melting temperature (Tm) of each of the hybridization complexes comprising at least two probes from the plurality of probes correlates with one of at least five HCV types, wherein an assignment of an HCV type is made by considering the distinguishing range of melting temperature (Tm) of the hybridization complexes;
- and,
- b) instructions for measuring the distinguishing range of melting temperature (Tm) of hybridization complexes comprising a target probe from the plurality of target probes.
6 more elements
A system that correlates detection of a plurality of signals with a hepatitis C virus (HCV) type, the system comprising:
- a) a detector for detecting the signals, wherein the signals correlate with a distinguishing range of melting temperature (Tm) of a plurality of hybridization complexes;
- and,
- b) a correlation module operably coupled to the detector, wherein the correlation module receives the signals detected by the detector and correlates the signals with an HCV type by collating the detected signals with predicted or predetermined signals observed when detecting the distinguishing range of melting temperature (Tm) of hybridization complexes comprising a plurality of known HCV types, wherein during operation of the system:
- i) the signals are generated from a plurality of hybridization complexes comprising an amplicon comprising an HCV nucleotide sequence and at least a first and second probe;
- the first and second probe nucleotide sequences comprise a nucleotide sequence that targets the probe to a same target region within an HCV genome and are complementary or partially complementary to nucleotide sequences within the HCV genome;
- iii) the regions of hybridization complex complementarity or partial complementarity show sequence heterogeneity among at least two HCV types;
- iv) hybridization complexes comprising the first probe have a distinguishing range of melting temperature (Tm) that differentiates more than two HCV types;
- v) hybridization complexes comprising the second probe have a distinguishing range of melting temperature (Tm) that differentiates more than two HCV types, wherein the more than two virus types differentiated by the first probe are different than the more than two virus types differentiated by the second probe;
- and,
- vi) the distinguishing range of melting temperature (Tm) of each of the hybridization complexes comprising each of the at least two probes correlates with one of at least five HCV types.
7 more elements
Dependencies are inferred from the claim text.