Detection of human papillomavirus by the polymerase chain reaction

• US 5,527,898 A
• Filed: 06/07/1995
• Issued: 06/18/1996
• Est. Priority Date: 09/09/1988
• Status: Expired due to Term

• Current Assignee: Roche Molecular Systems Inc (Roche Holding AG)
• Original Assignee: Hoffmann-La Roche Incorporated (Roche Holding AG)
• Inventors: Zhang, Tracy Y., Greer, Catherine E., Resnick, Robert M., Bauer, Heidi M., Manos, M. Michele, Gravitt, Patti E.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/474,542
• Time in Patent Office: 377 Days
• Field of Search: 435/5, 435/6, 435/91.1, 435/91.2, 436/501, 536/22.1, 536/23.1, 536/24.1, 536/24.3-.33, 935/7, 935/9, 935/77, 935/78
• US Class Current: 536/24.3
• 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 generic probes. The HPV is typed by the use of type-specific DNA probes specific for the amplified region of DNA.

Claims

1. A purified oligonucleotide probe, wherein said probe consists of a nucleotide sequence which hybridizes to a nucleic acid from a human papillomavirus (HPV) type under sequence-specific, stringent hybridization conditions and does not hybridize to a nucleic acid from HPV types 6, 11, 16, 18, and 33 under said conditions, and wherein said probe is chosen from the group consisting of

MYB186 (Seq ID No. 29), MYB187 (Seq ID No. 30), MYB188 (Seq ID No. 31), MYB189 (Seq ID No. 32), MYB202 (Seq ID No. 33), and sequences fully complementary thereto, which hybridize to HPV-26;

WD126 (Seq ID No.

     170), WD127 (Seq ID No.

     171), WD128 (Seq ID No.

     172), MY109 (Seq ID No.

     173), MY110 (Seq ID No.

     174)), WD165 (Seq ID No.

     79), WD166 (Seq ID No.

     80) and sequences fully complementary thereto, which hybridize to HPV-31;

MY92 (Seq ID No.

     175), MY127 (Seq ID No.

     176), MY128 (Seq ID No.

     177), and sequences fully complementary thereto, which hybridize to HPV-31 and HPV-31 B;

MY115 (Seq ID No.

     181), MY116 (Seq ID No.

     182), MY117 (Seq ID No.

     183), MYB168 (Seq ID No.

     34), MYB169 (Seq ID No.

     35), and sequences fully complementary thereto, which hybridize to HPV-35;

MY89 (Seq ID No.

     184), MY90 (Seq ID No.

     185), MY91 (Seq ID No.

     186), WD167 (Seq ID No.

     81), WD168 (Seq ID No.

     82), and sequences fully complementary thereto, which hybridize to HPV-39;

MY118 (Seq ID No.

     187), MY119 (Seq ID No.

     188), MY120 (Seq ID No.

     189), MYB174 (Seq ID No.

     36), MYB175 (Seq ID No.

     37), MYB176 (Seq ID No.

     52), and sequences fully complementary thereto, which hybridize to HPV-40;

MY33 (Seq ID No.

     192), MY34 (Seq ID No.

     193), MY121 (Seq ID No.

     190), MY122 (Seq ID No.

     122), WD169 (Seq ID No.

     83), and sequences fully, complementary thereto, which hybridize to HPV-42;

MY68 (Seq ID No.

     194), MY69 (Seq ID No.

     195), MY70 (Seq ID No.

     196), MY98 (Seq ID No.

     197), MY99 (Seq ID No.

     198), MY100 (Seq ID No.

     199), MY108 (Seq ID No.

     200), MY129 (Seq ID No.

     201), WD171 (Seq ID No.

     91), and sequences fully complementary hereto, which hybridize to HPV-45;

MY87 (Seq ID No.

     202), MY88 (Seq ID No.

     203), and sequences fully complementary thereto, which hybridize HPV-51;

MY80 (Seq ID No.

     204), MY81 (Seq ID No.

     205), MY82 (Seq ID No.

     206), and sequences fully complementary thereto, which hybridize to HPV-52;

MY101 (Seq ID No.

     207), MY102 (Seq ID No.

     208), MY103 (Seq ID No.

     209), MYB182 (Seq ID No.

     38), MYB159 (Seq ID No.

     39), and sequences fully complementary thereto, which hybridize to HPV-53;

MY111 (Seq ID No.

     210), MY112 (Seq ID No.

     211), MY113 (Seq ID No.

     212), MY114 (Seq ID No.

     213), MYB160 (Seq ID No.

     40), MYB161 (Seq ID No.

     41), and sequences fully complementary thereto, which hybridize to HPV-54;

MYB170 (Seq ID No.

     42), MYB151 (Seq ID No.

     43), MYB171 (Seq ID No.

     44), MY151 (Seq ID No.

     43), MY152 (Seq ID No.

     215), MY153 (Seq ID No.

     216), and sequences fully complementary thereto, which hybridize to HPV-55;

MYB196 (Seq ID No.

     45), MYB197 (Seq ID No.

     46), MYB198 (Seq ID No.

     47), MYB199 (Seq ID No.

     48), and sequences fully complementary thereto, which hybridize to HPV-56;

MY154 (Seq ID No.

     217), MY155 (Seq ID No.

     218), MY156 (Seq ID No.

     219), and sequences fully complementary thereto, which hybridize to HPV-57;

MY93 (Seq ID No.

     220), MY94 (Seq ID No.

     221), MY179 (Seq ID No.

     59), and sequences fully complementary thereto, which hybridize HPV-58;

MY123 (Seq ID No.

     222), MY124 (Seq ID No.

     223), MYB172 (Seq ID No.

     49), MYB173 (Seq ID No.

     50), MYB162 (Seq ID No.

     51), and sequences fully complementary thereto, which hybridize to HPV-59; and

MYB191 (Seq ID No.

     66), MYB192 (Seq ID No.

     53), MYB193 (Seq ID No.

     54), MYB194 (Seq ID No.

     67), MYB195 (Seq ID No.

     55), and sequences fully complementary thereto, which hybridize to HPV-68.

2. A probe of claim 1, wherein said HPV type is HPV-26, and wherein said probe is selected from the group of probes consisting of MYB186 (Seq ID No. 29), MYB187 (Seq ID No. 30), MYB188 (Seq ID No. 31), MYB189 (Seq ID No. 32), MYB202 (Seq ID No. 33), and sequences fully complementary thereto.

3. A probe of claim 1, wherein said HPV type is HPV-31 or HPV-31 B, and wherein said probe is selected from the group of probes consisting of WD126 (Seq ID No. 170), WD127 (Seq ID No. 171), WD128 (Seq ID No. 172), MY109 (Seq ID No. 173), MY110 (Seq ID No. 174), MY92 (Seq ID No. 175), MY127 (Seq ID No. 176), MY128 (Seq ID No. 177), WD165 (Seq ID No. 79), WD166 (Seq ID No. 80), and sequences fully complementary thereto.

4. A probe of claim 1, wherein said HPV type is HPV-35, and wherein said probe is selected from the group of probes consisting of MY 115 (Seq ID No. 181), MY116 (Seq ID No. 182), MY 117 (Seq ID No. 183), MYB168 (Seq ID No. 34), MYB169 (Seq ID No. 35), and sequences fully complementary thereto.

5. A probe of claim 1, wherein said HPV type is HPV-39, and wherein said probe is selected from the group of probes consisting of MY89 (Seq ID No. 184), MY90 (Seq ID No. 185), MY91 (Seq ID No. 186), WD167 (Seq ID No. 81), WD168 (Seq ID No. 82), and sequences fully complementary thereto.

6. A probe of claim 1, wherein said HPV type is HPV-40, and wherein said probe is selected from the group of probes consisting of MY 118 (Seq ID No. 187), MY 119 (Seq ID No. 188), MY120 (Seq ID No. 189), MYB174 (Seq ID No. 36), MYB175 (Seq ID No. 37), MYB176 (Seq ID No. 52), and sequences fully complementary thereto.

7. A probe of claim 1, wherein said HPV type is HPV-42, and wherein said probe is selected from the group of probes consisting of MY33 (Seq ID No. 192), MY34 (Seq ID No. 193), MY121 (Seq ID No. 190), MY122 (Seq ID No. 191), WD169 (Seq ID No. 83), and sequences fully complementary thereto.

8. A probe of claim 1, wherein said HPV type is HPV-45, and wherein said probe is selected from the group of probes consisting of MY68 (Seq ID No. 194), MY69 (Seq ID No. 195), MY70 (Seq ID No. 196), MY98 (Seq ID No. 197), MY99 (Seq ID No. 198), MY100 (Seq ID No. 199), MY108 (Seq ID No. 200), MY129 (Seq ID No. 201), WD171 (Seq ID No. 91 ), and sequences fully complementary thereto.

9. A probe of claim 1, wherein said HPV type is HPV-51, and wherein said probe is selected from the group of probes consisting of MY87 (Seq ID No. 202), MY88 (Seq ID No. 203), and sequences fully complementary thereto.

10. A probe of claim 1, wherein said HPV type is HPV-52, and wherein said probe is selected from the group of probes consisting of MY80 (Seq ID No. 204), MY81 (Seq ID No. 205), MY82 (Seq ID No. 206), and sequences fully complementary thereto.

11. A probe of claim 1, wherein said HPV type is HPV-53, and wherein said probe is selected from the group of probes consisting of MY101 (Seq ID No. 207), MY102 (Seq ID No. 208), MY103 (Seq ID No. 209), MYB182 (Seq ID No. 38), MYB159 (Seq ID No. 39), and sequences fully complementary thereto.

12. A probe of claim 1, wherein said HPV type is HPV-54, and wherein said probe is selected from the group of probes consisting of MY111 (Seq ID No. 210), MY112 (Seq ID No. 211), MY113 (Seq ID No. 212), MY114 (Seq ID No. 213), MYB160 (Seq ID No. 40), MYB161 (Seq ID No. 41), and sequences fully complementary thereto.

13. A probe of claim 1, wherein said HPV type is HPV-55, and wherein said probe is selected from the group of probes consisting of MYB170 (Seq ID No. 42), MYB15 1 (Seq ID No. 43), MYB171 (Seq ID No. 44), MY151 (Seq ID No. 214), MY152 (Seq ID No. 215), MY153 (Seq ID No. 216), and sequences fully complementary thereto.

14. A probe of claim 1, wherein said HPV type is HPV-56, and wherein said probe is selected from the group of probes consisting of MYB196 (Seq ID No. 45), MYB197 (Seq ID No. 46), MYB198 (Seq ID No. 47), MYB199 (Seq ID No. 48), and sequences fully complementary thereto.

15. A probe of claim 1, wherein said HPV type is HPV-57, and wherein said probe is selected from the group of probes consisting of MY154 (Seq ID No. 217), MY155 (Seq ID No. 218), MY156 (Seq ID No. 219), and sequences fully complementary thereto.

16. A probe of claim 1, wherein said HPV type is HPV-58, and wherein said probe is selected from the group of probes consisting of MY93 (Seq ID No. 220), MY94 (Seq ID No. 221), MY179 (Seq ID No. 59), and sequences fully complementary thereto.

17. A probe of claim 1, wherein said HPV type is HPV-59, and wherein said probe is selected from the group of probes consisting of MY123 (Seq ID No. 222), MY124 (Seq ID No. 223), MYB172 (Seq ID No. 49), MYB173 (Seq ID No. 50), MYB162 (Seq ID No. 51), and sequences fully complementary thereto.

18. A probe of claim 1, wherein said HPV type is HPV-68, and wherein said probe is selected from the group of probes consisting of MYB191 (Seq ID No. 66), MYB192 (Seq ID No. 53), MYB193 (Seq ID No. 54), MYB194 (Seq ID No. 67), MYB195 (Seq ID No. 55), and sequences fully complementary thereto.

19. A purified sequence-specific oligonucleotide probe, wherein said probe consists of a nucleotide sequence which hybridizes under sequence-specific, stringent hybridization conditions to a nucleic acid sequence from a human papillomavirus (HPV), wherein said nucleic acid sequence is selected from the group consisting of

SEQ ID NO:

14 or the sequence fully complementary thereto, which is from HPV isolate 36A;

SEQ ID NO;

15 or the sequence fully complementary thereto, which is from HPV isolate 36B;

SEQ ID NO;

16 or the sequence fully complementary thereto, which is from HPV isolate 88;

SEQ ID NO;

17 or the sequence fully complementary thereto, which is from HPV isolate 238A;

SEQ ID NO;

18 or the sequence fully complementary thereto, which is from HPV isolate 238B;

SEQ ID NO;

19 or the sequence fully complementary thereto, which is from HPV isolate 155A or 155B;

SEQ ID NO;

20 or the sequence fully complementary thereto, which is from HPV isolate C14;

SEQ ID NO;

273 or the sequence fully complementary thereto, which is from HPV isolate B6062;

SEQ ID NO;

274 or the sequence fully complementary thereto, which is from HPV isolate D3173;

SEQ ID NO;

275 or the sequence fully complementary thereto, which is from HPV isolate 7552;

SEQ ID NO;

276 or the sequence fully complementary thereto, which is from HPV isolate JB10;

SEQ ID NO;

277 or the sequence fully complementary thereto, which is from HPV isolate Lavc5;

SEQ ID NO;

278 or the sequence fully complementary thereto, which is from HPV isolate D7515;

SEQ ID NO;

279 or the sequence fully complementary thereto, which is from HPV isolate Pap116;

SEQ ID NO;

280 or the sequence fully complementary thereto, which is from HPV isolate W13b;

SEQ ID NO;

281 or the sequence fully complementary thereto, which is from HPV isolate Lavb24a;

SEQ ID NO;

282 or the sequence fully complementary thereto, which is from HPV isolate Lavb24b or PAP291;

SEQ ID NO;

283 or the sequence fully complementary thereto, which is from HPV isolate B8988;

SEQ ID NO;

284 or the sequence fully complementary thereto, which is from HPV type 35;

SEQ ID NO;

285 or the sequence fully complementary thereto, which is from HPV type 39;

SEQ ID NO;

286 or the sequence fully complementary thereto, which is from HPV type 40;

SEQ ID NO;

287 or the sequence fully complementary thereto, which is from HPV type 42;

SEQ ID NO;

288 or the sequence fully complementary thereto, which is from HPV type 45;

SEQ ID NO;

289 or the sequence fully complementary thereto, which is from HPV type 51;

SEQ ID NO;

290 or the sequence fully complementary thereto, which is from HPV type 52;

SEQ ID NO;

291 or the sequence fully complementary thereto, which is from HPV type 53;

SEQ ID NO;

292 or the sequence fully complementary thereto, which is from HPV type 54;

SEQ ID NO;

293 or the sequence fully complementary thereto, which is from HPV type 55;

SEQ ID NO;

294 or the sequence fully complementary thereto, which is from HPV type 56;

SEQ ID NO;

295 or the sequence fully complementary thereto, which is from HPV type 57; and

SEQ ID NO;

296 or the sequence fully complementary thereto, which is from HPV type 59; and

wherein said probe does not hybridize to a genomic sequence from HPV types 6, 11, 16, 18, and 33 under said conditions.

20. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

14 or the sequence fully complementary thereto, which is from HPV isolate 36A.

21. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

15 or the sequence fully complementary thereto, which is from HPV isolate 36B.

22. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO;

16 or the sequence fully complementary thereto, which is from HPV isolate 88.

23. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

17 or the sequence fully complementary thereto, which is from HPV isolate 238A.

24. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

18 or the sequence fully complementary thereto, which is from HPV isolate 238B.

25. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

19 or the sequence fully complementary thereto, which is from HPV isolate 155a or 155B.

26. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

20 or the sequence fully complementary thereto, which is from HPV isolate C14.

27. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

273 or the sequence fully complementary thereto, which is from HPV isolate B6062.

28. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

274 or the sequence fully complementary thereto, which is from HPV isolate D3173.

29. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

281 or the sequence fully complementary thereto, which is from HPV isolate Lavb24a.

30. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

283 or the sequence fully complementary thereto, which is from HPV isolate B8988.

31. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

279 or the sequence fully complementary thereto, which is from HPV isolate Pap116.

32. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

275 or the sequence fully complementary thereto, which is from HPV isolate 7552.

33. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

277 or the sequence fully complementary thereto, which is from HPV isolate Lavc5.

34. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

282 or the sequence fully complementary thereto, which is from HPV isolate Lavb24b or PAP291.

35. A probe of claim 19, wherein stud nucleic acid sequence is SEQ ID NO:

280 or the sequence fully complementary thereto, which is from HPV isolate W13b.

36. A probe of claim 19, wherein said nucleic acid sequence is SEQ. ID NO:

278 or the sequence fully complementary thereto, which is from HPV isolate D7515.

37. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

276 or the sequence fully complementary thereto, which is from HPV isolate JB10.

38. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

284 or the sequence fully complementary thereto, which is from HPV type 35.

39. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

285 or the sequence fully complementary thereto, which is from HPV type 39.

40. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

286 or the sequence fully complementary thereto, which is from HPV type 40.

41. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

287 or the sequence fully complementary thereto, which is from HPV type 42.

42. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

288 or the sequence fully complementary thereto, which is from HPV type 45.

43. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

289 or the sequence fully complementary thereto, which is from HPV type 51.

44. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

290 or the sequence fully complementary thereto, which is from HPV type 52.

45. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

291 or the sequence fully complementary thereto, which is from HPV type 53.

46. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

292 or the sequence fully complementary thereto, which is from HPV type 54.

47. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

293 or the sequence fully complementary thereto, which is from HPV type 55.

48. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

294 or the sequence fully complementary thereto, which is from HPV type 56.

49. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

295 or the sequence fully complementary thereto, which is from HPV type 57.

50. A probe of claim 19, wherein said nucleic acid sequence is SEQ ID NO:

296 or the sequence fully complementary thereto, which is from HPV type 59.

51. A primer for amplifying HPV-51 nucleic acid, wherein said primer is selected from the group of primers consisting of CEG05 (Seq ID No. 94), HMB01 (Seq ID No. 95), HMB02 (Seq ID No. 96), HMB03 (Seq ID No. 97), and HMB04 (Seq ID No. 98).