Rapid genotyping analysis for human papillomavirus and the device thereof

Abstract

The present invention discloses methods and devices for rapid genotyping. In one embodiment, the present invention is applied to human papillomavirus (HPV) genotyping, comprising the use of viral genotype-specific-oligonucleotide probes, reversed-dot-blotting genotype array format and flow through hybridization process, thereby providing a more efficient, faster and less expensive method for HPV genotyping. The genotyping method further comprises the use of generic probes to expand the detection of HPV genotypes.

1 . A method for rapid detection of human papillomavirus (HPV), comprising the steps of:
 (a) obtaining a sample comprising a template nucleic acid;   (b) amplifying the template nucleic acid with primers having the sequences of SEQ ID NOs:116-118, thereby generating HPV L1 amplicons; and   (c) hybridizing the HPV L1 amplicons with immobilized oligonucleotide probes selected from the group consisting of SEQ ID NOs:121-173, wherein the resulting hybridization profile would indicate the presence of HPV.   
     
     
         2 . The method of  claim 1 , wherein the primers further comprise primers complimentary to an internal control. 
     
     
         3 . The method of  claim 2 , wherein the primers complimentary to the internal control have the sequences of SEQ ID NOs:119-120. 
     
     
         4 . The method of  claim 1 , wherein the primers comprise a signal generating label. 
     
     
         5 . The method of  claim 1 , wherein the oligonucleotide probes further comprise probes capable of capturing generic HPV viral DNA. 
     
     
         6 . The method of  claim 5 , wherein the probes capable of capturing generic HPV viral DNA are selected from the group consisting of SEQ ID NOs:170-173. 
     
     
         7 . The method of  claim 1 , wherein hybridization of the HPV L1 amplicons with the plurality of immobilized oligonucleotide probes is carried out in a flow-through process or a lateral flow-through process. 
     
     
         8 . The method of  claim 1 , wherein hybridization of the HPV L1 amplicons with the plurality of immobilized oligonucleotide probes is carried out in a flow-through process with recirculation of target analyte solution, thereby resulting in increased sensitivity. 
     
     
         9 . The method of  claim 1 , wherein the method can detect the presence of HPV with a HPV genotype selected from the group consisting of HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 66, 68, 70, 71, 72, 73, 81, 82, and 84. 
     
     
         10 . The method of  claim 9 , wherein the HPV genotypes are separately detected, or the genotypes are detected collectively in one or more groups. 
     
     
         11 . The method of  claim 9 , wherein HPV genotypes 16 and 18 are separately detected, and HPV genotypes 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 73 and 82 are detected collectively in one or more groups. 
     
     
         12 . The method of  claim 11 , wherein the method further detects HPV genotypes 6, 11, 26, 40, 42, 43, 44, 53, 54, 55, 57, 61, 66, 70, 71, 72, 73, 81 and 84 collectively in one or more groups. 
     
     
         13 . A kit for human papillomavirus (HPV) genotyping, comprising primers having the sequences of SEQ ID NOs:116-118 and oligonucleotide probes selected from the group consisting of SEQ ID NOs:121-173. 
     
     
         14 . The kit of  claim 13 , wherein the primers further comprise primers complimentary to an internal control. 
     
     
         15 . The kit of  claim 14 , wherein the primers complimentary to the internal control have the sequences of SEQ ID NOs:119-120. 
     
     
         16 . The kit of  claim 13 , wherein the primers comprise a signal generating label. 
     
     
         17 . The kit of  claim 13 , wherein the oligonucleotide probes further comprise probes capable of capturing generic HPV viral DNA. 
     
     
         18 . The kit of  claim 17 , wherein the probes capable of capturing generic HPV viral DNA are selected from the group consisting of SEQ ID NOs:170-173. 
     
     
         19 . The kit of  claim 13 , wherein the kit can detect a HPV genotype selected from the group consisting of HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 66, 68, 70, 71, 72, 73, 81, 82, and 84. 
     
     
         20 . The kit of  claim 19 , wherein the HPV genotypes are separately detected, or the genotypes are detected collectively in one or more groups.