Compositions and methods for detecting certain flaviviruses including members of the japanese encephalitis virus serogroup

Abstract

The present invention provides rapid and accurate methods, primers, probes and kits for identifying the presence of a certain flaviviruses in a sample. Flaviviruses that can be detected include members of the Japanese encephalitis virus serogroup, Dengue virus, St. Louis encephalitis virus, Montana myotis leukoencephalitis virus, Modoc virus, and Yellow Fever virus. The primers and probes of the invention can hybridize to regions in the 3′ untranslated region of the viral genomes to be detected.

What is claimed is: 
     
         1 . A method for detecting the presence or absence of a St. Louis encephalitis virus (SLEV) nucleic acid in a sample, the method comprising:
 contacting the sample with a nucleic acid polymerase and a plurality of primers and a probe;   amplifying at least a portion of an SLEV 3′ untranslated region (UTR), the SLEV 3′ UR region selected from SEQ ID NO: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, and 40, thereby generating an amplicon if the SLEV 3′ UTR is present in the sample; and   detecting the presence or absence of specific binding of the probe to the portion, thereby detecting the presence or absence of a St. Louis encephalitis virus (SLEV) nucleic acid in the sample.   
     
     
         2 . The method of  claim 1 , wherein the plurality of primers comprises one or more primer comprising a sequence selected from SEQ ID NO: 64, 66, 68, or 69. 
     
     
         3 . The method of  claim 1 , wherein the plurality of primers comprises a primer comprising SEQ ID NO:4. 
     
     
         4 . The method of  claim 1 , wherein the probe is detectably-labeled. 
     
     
         5 . The method of  claim 1 , wherein at least one of the plurality of primers is at least 30 nucleotides long.