Method for detection of human papillomavirus

Abstract

The invention provides compositions and methods for the differential detection of high risk forms of HPV from a urine sample provided by a patient. Specifically, the invention provides primers and probes that specifically recognize and bind sequences within the E1 gene of HPV. Detection of high risk forms of HPV identifies individuals at risk of developing or in the early stages of cervical carcinoma.

What is claimed is: 
     
         1 - 20 . (canceled) 
     
     
         21 . A method of detecting a human papillomavirus (HPV) nucleic acid in a urine sample from a human subject, the method comprising:
 (a) isolating nucleic acids by combining the whole urine sample with an anion exchange resin;   (b) eluting nucleic acids from the anion exchange resin; and   (c) amplifying an HPV sequence from the eluted nucleic acids using PCR; and   (d) detecting the amplified HPV sequence.   
     
     
         22 . The method of  claim 21 , wherein the anion exchange resin is Q-Sepharose. 
     
     
         23 . The method of  claim 21 , wherein the amplifying produces an amplicon of less than 100 base pairs. 
     
     
         24 . The method of  claim 21 , wherein the amplifying produces an amplicon of 30-50 bp. 
     
     
         25 . The method of  claim 21 , wherein the amplifying amplifies a sequence in the HPV E1 gene. 
     
     
         26 . The method of  claim 21 , wherein the PCR uses a primer pair sufficiently complementary to hybridize with a sequence comprising SEQ ID NO: 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, or 96. 
     
     
         27 . The method of  claim 21 , wherein the PCR uses a primer pair comprising SEQ ID NOs: 43 and 55, 44 and 56, 45 and 30, 46 and 57, 47 and 58, 48 and 33, 49 and 34, 50 and 36, 51 and 59, 52 and 38, 53 and 39, or 54 and 40. 
     
     
         28 . The method of  claim 21 , wherein the PCR uses a forward primer comprising SEQ ID NO: 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, or 54. 
     
     
         29 . The method of  claim 21 , wherein the PCR uses a reverse primer comprising SEQ ID NO: 55, 56, 30, 57, 58, 33, 34, 35, 36, 59, 38, 39, or 40. 
     
     
         30 . The method of  claim 28 , wherein the PCR uses a reverse primer comprising SEQ ID NO: 55, 56, 30, 57, 58, 33, 34, 35, 36, 59, 38, 39, or 40. 
     
     
         31 . The method of  claim 21 , wherein the PCR uses a forward primer comprising the sequence CAGGCAGAATTAGAGRCAGC, wherein R is A or G (SEQ ID NO:41). 
     
     
         32 . The method of  claim 31 , wherein the forward primer is fluorescently labeled. 
     
     
         33 . The method of  claim 31 , wherein the PCR uses a reverse primer comprising the sequence 5′-TCCACCACAWACTTTCGTTTTA, wherein W is T or A (SEQ ID NO:42). 
     
     
         34 . The method of  claim 33 , wherein the forward primer is XEN-HPV-FAM-F (SEQ ID NO:98) and the reverse primer is XEN-HPV-R (SEQ ID NO:100).