Nucleic acid primers and probes for detecting oncogenic human papillomaviruses

Abstract

Probe sequences that are useful for detecting oncogenic HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 are herein provided. These sequences can be used in hybridization assays or amplification based assays designed to detect the presence of these oncogenic HPV types in a test sample. Additionally, the sequences can be provided as part of a kit.

What is claimed is:  
     
         1 . A oligonucleotide cocktail for detecting the presence of at least one oncogenic HPV type 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 in a test sample, said cocktail comprising at least two probes selected from the group consisting of: SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 29, SEQ ID NO. 31, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 38, SEQ ID NO. 40 and SEQ ID NO. 41.  
     
     
         2 . The cocktail of  claim 1  wherein one of said at least two probes is selected from the group consisting of: SEQ ID NO. 37, SEQ ID NO. 38, SEQ ID NO. 40 and SEQ ID NO. 41.  
     
     
         3 . A probe selected from the group consisting of: SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 29, SEQ ID NO. 31, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 38, SEQ ID NO. 40 and SEQ ID NO. 41.  
     
     
         4 . A method of detecting the presence of an oncogenic HPV type in a test sample comprising the steps of: 
 a) contacting said test sample with at least one probe of claim  3 ; and    b) detecting hybridization between said probe and an oncogenic HPV type target sequence as an indication of the presence of an oncogenic HPV type in said test sample.    
     
     
         5 . The method of  claim 4  wherein said oligonucleotide is labeled.  
     
     
         6 . The method of  claim 4  wherein said test sample is contacted with a cocktail of probes comprising at least two probes.  
     
     
         7 . The method of  claim 6  wherein said at least two probes include SEQ ID NO. 37 and SEQ ID NO. 40  
     
     
         8 . A method for detecting the presence of at least one oncogenic HPV type in a test sample comprising the steps of: 
 a) forming a reaction mixture comprising nucleic acid amplification reagents, at least one amplification primer for amplifying an oncogenic HPV target sequence, a test sample containing an oncogenic HPV type target sequence, and at least one probe according to claim  3 ; and    b) subjecting said mixture to hybridization conditions to generate at least one nucleic acid sequence complementary to said target sequence;    c) hybridizing said probe to said nucleic acid complementary to said target sequence so as to form a hybrid comprising said probe and said nucleic acid; and    d) detecting said hybrid as an indication of the presence of at least one oncogenic HPV type in said sample.    
     
     
         9 . The method of  claim 8  wherein said probe is labeled with a capture label and said primer is labeled with a detection label.  
     
     
         10 . The method of  claim 8  wherein said probe is labeled with a detection label and said primer is labeled with a capture label.  
     
     
         11 . A kit comprising: 
 a) at least one probe according to  claim 3 , and    b) amplification reagents.