Patent ID: 8067208

Claim:
A closed-tube method for determining the type of a hepatitis C virus (HCV) in a sample, the method comprising: a) amplifying a portion of the HCV genome from the sample, thereby producing at least one amplicon; b) hybridizing the amplicon with at least a first probe and a second probe in a single hybridization reaction to form at least two target hybridization complexes, wherein: i) each probe has a nucleotide sequence that targets the probe to the same target region in the HCV genome and contains a minimum of six nucleotide overlap with the other probe, and is complementary or partially complementary to nucleotide sequences within the HCV genome; ii) the regions of hybridization complex complementarity or partial complementarity show sequence heterogeneity among at least two HCV types; iii) hybridization complexes comprising the first probe have a distinguishing range of melting temperature (T m ) that differentiates more than two HCV types but is indistinguishable for at least two other HCV types, wherein said range of melting temperature (T m ) is caused by sequence variations within a particular HCV type; iv) hybridization complexes comprising the second probe have a distinguishing range of melting temperature (T m ) that differentiates more than two HCV types but is indistinguishable for at least two other HCV types, wherein the more than two virus types differentiated by the first probe are different than the more than two HCV types differentiated by the second probe, wherein said range of melting temperature (T m ) is caused by sequence variations within a particular HCV type; and v) each probe comprises a different FRET donor moiety having a different excitation and emission spectra; c) simultaneously measuring the distinguishing range of melting temperature (T m ) of the target hybridization complexes; and, d) correlating the measured distinguishing range of melting temperature (T m ) of the target hybridization complexes with one of at least five HCV types, wherein an assignment of an HCV type is made based on the distinguishing range of melting temperature (T m ) of the hybridization complexes comprising the first probe and second probe in a multidimensional analysis.