Detection of west nile virus nucleic acids in the viral 3' non-coding region

Abstract

Compositions for detecting flavivirus nucleic acids are for detecting West Nile virus nucleic acids in the 3′ non-coding region. The compositions can include oligonucleotides including nucleotide sequences that are substantially complementary to a West Nile virus target nucleic acid. The compositions can also include a detectable moiety.

What is claimed is: 
     
         1 . A hybridization assay probe for detecting a WNV nucleic acid, comprising:
 (a) a probe sequence that comprises a target-complementary sequence of bases and optionally one or more base sequences that are not complementary to said nucleic acid that is to be detected, and   (b) a detectable label,   wherein said target-complementary sequence of bases consists of 12-87 contiguous bases contained within the sequence of SEQ ID NO:101 or the complement thereof, allowing for the presence of RNA and DNA equivalents, nucleotide analogs and up to 10% base differences, and   wherein said hybridization assay probe has a length of up to 100 bases.   
     
     
         2 . The hybridization assay probe of  claim 1 , wherein the target-complementary sequence of bases consists of 12-69 contiguous bases contained within the sequence of SEQ ID NO:102 or the complement thereof, allowing for the presence of RNA and DNA equivalents, nucleotide analogs and up to 10% base differences. 
     
     
         3 . The hybridization assay probe of  claim 2 , wherein the hybridization assay probe comprises the optional one or more base sequences that are not complementary to the nucleic acid that is to be detected. 
     
     
         4 . The hybridization assay probe of  claim 3 , wherein the detectable label is a fluorophore moiety and the hybridization assay probe further comprises a quencher moiety. 
     
     
         5 . The hybridization assay probe of  claim 4 , wherein the hybridization assay probe is a molecular beacon. 
     
     
         6 . The hybridization assay probe of  claim 4 , wherein the target-complementary sequence of bases consists of a sequence selected from the group consisting of SEQ ID NO:179, SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, and SEQ ID NO:183, including complements and DNA equivalents thereof. 
     
     
         8 . The hybridization assay probe of  claim 4 , wherein the target-complementary sequence of bases consists of a sequence selected from the group consisting of SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:114, and SEQ ID NO:116, including complements and RNA equivalents thereof. 
     
     
         9 . The hybridization assay probe of  claim 2 , wherein the probe sequence does not comprise the optional one or more base sequences that are not complementary to the nucleic acid that is to be detected. 
     
     
         10 . The hybridization assay probe of  claim 9 , wherein the hybridization assay probe has a length of up to 69 bases. 
     
     
         11 . The hybridization assay probe of  claim 2 , wherein the target-complementary sequence of bases consists of 18-52 contiguous bases contained within the sequence of SEQ ID NO:103 or the complement thereof, allowing for the presence of RNA and DNA equivalents, nucleotide analogs and up to 10% base differences. 
     
     
         12 . The hybridization assay probe of  claim 11 , wherein the probe sequence does not comprise the optional one or more base sequences that are not complementary to the nucleic acid that is to be detected. 
     
     
         13 . The hybridization assay probe of  claim 12 , wherein the detectable label is selected from the group consisting of a chemiluminescent label and a fluorescent label. 
     
     
         14 . The hybridization assay probe of  claim 11 , wherein said hybridization assay probe has a length of up to 52 bases. 
     
     
         15 . The hybridization assay probe of  claim 14 , wherein the target-complementary sequence of bases consists of 18-22 contiguous bases contained within the sequence of SEQ ID NO:103 or the complement thereof, allowing for the presence of RNA and DNA equivalents, nucleotide analogs and up to 10% base differences, and wherein the hybridization assay probe has a length of up to 22 bases. 
     
     
         16 . The hybridization assay probe of  claim 15 , wherein the probe sequence is selected from the group consisting of SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:114, and SEQ ID NO:116, including complements and RNA equivalents thereof. 
     
     
         17 . The hybridization assay probe of  claim 1 , wherein the detectable label is a chemiluminescent label. 
     
     
         18 . The hybridization assay probe of  claim 17 , wherein the chemiluminescent label is an acridinium ester label. 
     
     
         19 . A hybridization assay probe for detecting a WNV nucleic acid, comprising:
 (a) a probe sequence that comprises a target-complementary sequence of bases and optionally one or more base sequences that are not complementary to the nucleic acid that is to be detected, and   (b) a detectable label,   wherein the target-complementary sequence of bases consists essentially of a sequence selected from the group consisting of SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108, SEQ ID NO:109, SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:114, and SEQ ID NO:116, including complements and RNA equivalents thereof.   
     
     
         20 . The hybridization assay probe of  claim 19 , wherein the detectable label is selected from the group consisting of a chemiluminescent label and a fluorescent label.