Detection of human papillomavirus by the polymerase chain reaction

• US 5,447,839 A
• Filed: 04/20/1993
• Issued: 09/05/1995
• Est. Priority Date: 09/09/1988
• Status: Expired due to Term

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Hoffmann-La Roche Incorporated (Roche Holding AG)
• Inventors: Greer, Catherine E., Resnick, Robert M., Bauer, Heidi M., Ting, Yi, Manos, M. Michele
• Primary Examiner(s): Zitomer, Stephanie W.
• Assistant Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/050,743
• Time in Patent Office: 868 Days
• Field of Search: 435/5, 435/6, 435/91.2, 436/501, 536/23.1, 536/24.31, 536/24.32, 536/24.33, 536/24.3, 935/7, 935/78, 935/88
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/708 for papilloma

Abstract

The presence of human papillomavirus (HPV) in a sample can be detected and the HPV typed by a method that involves the amplification of HPV DNA sequences by the polymerase chain reaction (PCR). The primers used in the method are consensus primers that can be used to amplify a particular region of the genome of any HPV. The presence of HPV in a sample is indicated by the formation of amplified DNA. The HPV nucleic acid is detected by consensus probes that may be short oligonucleotide probes or long genetic probes. The HPV is typed by the use of type-specific DNA probes specific for the amplified region of DNA.

Claims

1. A method for detecting any one or more of human papillomavirus (HPV) type 5, 6, 8, 11, 16, 18, 26, 27, 30, 31, 33, 35, 39, 40, 41, 42, 43, 45, 47, 48, 51, 52, 53, 54, 55, 57, 58, or 59 nucleic acids in a sample that comprises the steps of:

(a) treating said sample under conditions for amplifying a nucleic acid sequence in an amplification reaction mixture that comprises a consensus HPV primer pair, wherein said consensus HPV primer pair consists of MY09 and MY11, to provide an amplified nucleic acid sequence if said HPV nucleic acid is present, and

(b) detecting said HPV nucleic acid by determining if amplification has occurred.

2. The method of claim 1, wherein at step (b) said amplified nucleic acid sequence is detected by hybridization to a consensus probe composition which composition comprises an equimolar mixture of oligonucleotides MY18, MY46, MY57 and WD147.

3. The method of claim 1, wherein at step (b) said amplified nucleic acid sequence is detected by hybridization to an oligonucleotide probe selected from the group consisting of:

MY12, MY62, MY63, MY125 (Seq ID No.

     10), MY126 (Seq ID No.

     11), MY13, MY61, MY65, WD150, WD151, MY14, MY58, MY71 (Seq ID No.

     12), MY72 (Seq ID No.

     13), MY95 (Seq ID No.

     14), MY96 (Seq ID No.

     15), MY97 (Seq ID No.

     16), MY133 (Seq ID No.

     17), WD152, WD153, MY60, MY73 (Seq ID No.

     18), MY107 (Seq ID No.

     19), MY130 (Seq ID No.

     20), MY131 (Seq ID No.

     21), MY132 (Seq ID No.

     22), WD74, WD75 (Seq ID No.

     23), WD126, WD127, WD128, MY109 (Seq ID No.

     24), MY110 (Seq ID No.

     25), MY92 (Seq ID No.

     26), MY127 (Seq ID No.

     27), MY128 (Seq ID No.

     28), MY16, MY59, MY64, MY115 (Seq ID No.

     29), MY116 (Seq ID No.

     30), MY117 (Seq ID No.

     31), MY89 (Seq ID No.

     32), MY90 (Seq ID No.

     33), MY91 (Seq ID No.

     34), MY118 (Seq ID No.

     35), MY119 (Seq ID No.

     36), MY120 (Seq ID No.

     37), MY121 (Seq ID No.

     38), MY122 (Seq ID No.

     39), MY33 (Seq ID No.

     40), MY34 (Seq ID No.

     41), MY68 (Seq ID No.

     42), MY69, MY70, MY98 (Seq ID No.

     43), MY99 (Seq ID No.

     44), MY100 (Seq ID No.

     45), MY108 (Seq ID No.

     46), MY129 (Seq ID No.

     47), MY87 (Seq ID No.

     48), MY88 (Seq ID No.

     49), MY80 (Seq ID No.

     50), MY81 (Seq ID No.

     51), MY82 (Seq ID No.

     52), MY101 (Seq ID No.

     53), MY102 (Seq ID No.

     54), MY103 (Seq ID No.

     55), MY111 (Seq ID No.

     56), MY112 (Seq ID No.

     57), MY113 (Seq ID No.

     58), MY114 (Seq ID No.

     59), MY151 (Seq ID No.

     60), MY152 (Seq ID No.

     61), MY153 (Seq ID No.

     62), MY154 (Seq ID No.

     63), MY155 (Seq ID No.

     64), MY156 (Seq ID No.

     65), MY123 (Seq ID No.

     66), MY124 (Seq ID No.

     67), MY83 (Seq ID No.

     68), MY84 (Seq ID No.

     69), MY86 (Seq ID No.

     70), MY85 (Seq ID No.

     71), MY93 (Seq ID No.

     72), MY94 (Seq ID No.

     73), MY104 (Seq ID No.

     74), MY105 (Seq ID No.

     75), MY106 (Seq ID No.

     76), MY66, MY55, MY39, MY56, MY57, MY46, and WD147.

4. A method for detecting any one or more of human papillomavirus (HPV) type 5, 6, 8, 11, 16, 18, 26, 27, 30, 31, 33, 35, 39, 40, 41, 42, 43, 45, 47, 48, 51, 52, 53, 54, 55, 57, 58, or 59 nucleic acids in a sample that comprises the steps of:

(a) treating said sample under conditions for amplifying a nucleic acid sequence in an amplification reaction mixture that comprises a pair of consensus HPV primers, wherein said consensus HPV primers consist of positive and negative strand primers and said positive primers are selected from the group consisting of;

WD72/WD73, WD72/WD76, WD72/WD77, WD65/WD64, WD83/WD64, and WD84/WD64; and

said negative strand primers are selected from the group consisting of WD70/ WD71;

WD86/WD69; and

WD66/WD67;

to provide an amplified nucleic acid sequence if said HPV nucleic acid is present, and

(b) detecting said HPV nucleic acid by determining if amplification has occurred.

5. The method of claim 4, wherein at step (b) said amplified nucleic acid sequence is detected by hybridization to a consensus probe selected from the group consisting of:

WD64, WD65, WD83, WD84, MY135 and MY136.

6. The method of claim 4, wherein at step (b) said amplified nucleic acid sequence is detected by hybridization to an oligonucleotide probe selected from the group consisting of:

WD78, WD79, WD80, WD81, WD82, WD165, WD166, WD167, WD168, WD169, WD104, WD102, WD103, WD132, WD133, WD134, RR₁ (Seq ID No.

     79), RR2 (Seq ID No.

     82) , WD170 (Seq ID No.

     81), WD171 (Seq ID No.

     80).

7. A method for detecting any one or more of human papillomavirus (HPV) type 5, 6, 8, 11, 16, 18, 26, 27, 30, 31, 33, 35, 39, 40, 41, 42, 43, 45, 47, 48, 51, 52, 53, 54, 55, 57, 58, or 59 nucleic acids in a sample that comprises the steps of:

(a) treating said sample under conditions for amplifying a nucleic acid sequence in an amplification reaction mixture that comprises a consensus HPV primer pair, wherein said consensus HPV primers consist of oligonucleotides selected from the group consisting of;

WD64/WD65 and TYN01/TYN02/TYN03;

WD64/WD65 and TYN04/TYN05/TYN06;

WD64/WD65 and TYN07/TYN08;

WD72/WD76 and TYN01/TYN02/TYN03;

WD72/WD76 and TYN04/TYN05/TYN06;

WD72/WD76 and TYN07/TYN08;

TYP01/TYP02 and TYN07/TYN08; and

TYP04/TYP05/TYP06 and TYN07/TYN08;

to provide an amplified sequence if said HPV nucleic acid is present, and

(b) detecting said HPV nucleic acid by determining if amplification has occurred.

8. The method of claim 7, wherein at step (b) said amplified nucleic acid sequence is detected by hybridization to an oligonucleotide probe selected from the group consisting of:

TYP09 and TYP12.