COMPOSITIONS FOR USE IN IDENTIFICATION OF ADVENTITIOUS CONTAMINANT VIRUSES

• US 20110045456A1
• Filed: 06/12/2008
• Published: 02/24/2011
• Est. Priority Date: 06/14/2007
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Sampath, Rangarajan, Hall, Thomas A.
• Application Number:
  US12/664,619
• Publication Number:
  US 20110045456A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 1/702 for retroviruses
• CPC Class Codes: C12Q 1/706 for hepatitis

Abstract

The present invention provides oligonucleotide primers, compositions, and kits containing the same for rapid identification of viruses by amplification of a segment of viral nucleic acid followed by molecular mass analysis.

Claims

1. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 80% complementarity to a first portion of a region of Genbank Accession Number NC_—

002077.1, and said reverse primer configured to hybridize with at least 80% complementarity to a second portion of said region of Genbank Accession Number NC_—

002077.1, wherein said region of Genbank Accession Number NC_—

002077.1 begins at nucleotide position 1339 and continues to nucleotide position 1483 (SEQ ID NO;

     411).

19. The purified oligonucleotide primer pair of claim 1 wherein said forward member has at least 90% sequence identity to SEQ ID NO:

152.

20. The purified oligonucleotide primer pair of claim 1 wherein said forward member is SEQ ID NO:

152.

21. The purified oligonucleotide primer pair of claim 1 wherein said reverse member has at least 90% sequence identity to SEQ ID NO:

361.

22. The purified oligonucleotide primer pair of claim 1 wherein said reverse member is SEQ ID NO:

361.

2. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 80% complementarity to a first portion of a region of Genbank Accession Number NC_—

002077.1, and said reverse primer configured to hybridize with at least 80% complementarity to a second portion of said region of Genbank Accession Number NC_—

002077.1, wherein said region of Genbank Accession Number NC_—

002077.1 begins at nucleotide position 2870 and continues to nucleotide position 3132 (SEQ ID NO;

     412).

23. The purified oligonucleotide primer pair of claim 2 wherein said forward member has at least 90% sequence identity to SEQ ID NO:

154, SEQ ID NO;

155, SEQ ID NO;

156 or SEQ ID NO;

159.

24. The purified oligonucleotide primer pair of claim 2 wherein said forward member is SEQ ID NO:

154, SEQ ID NO;

155, SEQ ID NO;

156 or SEQ ID NO;

159.

25. The purified oligonucleotide primer pair of claim 2 wherein said reverse member has at least 90% sequence identity to SEQ ID NO:

364;

SEQ ID NO;

365;

SEQ ID NO;

366 or SEQ ID NO;

368.

26. The purified oligonucleotide primer pair of claim 2 wherein said reverse member is SEQ ID NO:

364;

SEQ ID NO;

365;

SEQ ID NO;

366 or SEQ ID NO;

368.

3. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 80% complementarity to a first portion of a region of Genbank Accession Number NC_—

000883.1, and said reverse primer configured to hybridize with at least 80% complementarity to a second portion of said region of Genbank Accession Number NC_—

000883.1, wherein said region of Genbank Accession Number NC_—

000883.1 begins at nucleotide position 2923 and continues to nucleotide position 3207 (SEQ ID NO;

     413)

27. The purified oligonucleotide primer pair of claim 3 wherein said forward member has at least 90% sequence identity to SEQ ID NO:

170.

28. The purified oligonucleotide primer pair of claim 3 wherein said forward member is SEQ ID NO:

170.

29. The purified oligonucleotide primer pair of claim 3 wherein said reverse member has at least 90% sequence identity to SEQ ID NO:

379.

30. The purified oligonucleotide primer pair of claim 3 wherein said reverse member is SEQ ID NO:

379.

4. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 80% complementarity to a first portion of a region of Genbank Accession Number NC_—

001510.1, and said reverse primer configured to hybridize with at least 80% complementarity to a second portion of said region of Genbank Accession Number NC_—

001510.1, wherein said region of Genbank Accession Number NC_—

001510.1 begins at nucleotide position 1670 and continues to nucleotide position 1877 (SEQ ID NO;

     414).

31. The purified oligonucleotide primer pair of claim 4 wherein said forward member has at least 90% sequence identity to SEQ ID NO:

177.

32. The purified oligonucleotide primer pair of claim 4 wherein said forward member is SEQ ID NO:

177.

33. The purified oligonucleotide primer pair of claim 4 wherein said reverse member has at least 90% sequence identity to SEQ ID NO:

386.

34. The purified oligonucleotide primer pair of claim 4 wherein said reverse member is SEQ ID NO:

386.

5. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer having at least 80% sequence identity with SEQ ID NO:

184, and said reverse primer having at least 80% sequence identity with SEQ ID NO;

393 (SEQ ID NO;

     415).

35. The purified oligonucleotide primer pair of claim 5 wherein said forward member is SEQ ID NO:

184.

36. The purified oligonucleotide primer pair of claim 5 wherein said reverse member is SEQ ID NO:

393.

6. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 80% complementarity to a first portion of a region of Genbank Accession Number NC_—

001662.1, and said reverse primer configured to hybridize with at least 80% complementarity to a second portion of said region of Genbank Accession Number NC_—

001662.1, wherein said region of Genbank Accession Number NC_—

001662.1 begins at nucleotide position 1446 and continues to nucleotide position 1704.

37. The purified oligonucleotide primer pair of claim 6 wherein said forward member has at least 90% sequence identity to SEQ ID NO:

190.

38. The purified oligonucleotide primer pair of claim 6 wherein said forward member is SEQ ID NO:

190.

39. The purified oligonucleotide primer pair of claim 6 wherein said reverse member has at least 90% sequence identity to SEQ ID NO:

399.

40. The purified oligonucleotide primer pair of claim 6 wherein said reverse member is SEQ ID NO:

399.

7. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer having at least 80% sequence identity with SEQ ID NO:

195, and said reverse primer having at least 80% sequence identity with SEQ ID NO;

404

41. The purified oligonucleotide primer pair of claim 7 wherein said forward member is SEQ ID NO:

195.

42. The purified oligonucleotide primer pair of claim 7 wherein said reverse member is SEQ ID NO:

404.

8. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer having at least 80% sequence identity with SEQ ID NO:

194, and said reverse primer having at least 80% sequence identity with SEQ ID NO;

403

43. The purified oligonucleotide primer pair of claim 8 wherein said forward member is SEQ ID NO:

194.

44. The purified oligonucleotide primer pair of claim 8 wherein said reverse member is SEQ ID NO:

403.

9. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer having at least 80% sequence identity with SEQ ID NO:

198, and said reverse primer having at least 80% sequence identity with SEQ ID NO;

407

45. The purified oligonucleotide primer pair of claim 9 wherein said forward member is SEQ ID NO:

198.

46. The purified oligonucleotide primer pair of claim 9 wherein said reverse member is SEQ ID NO:

407.

10. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer having at least 80% sequence identity with SEQ ID NO:

201, and said reverse primer having at least 80% sequence identity with SEQ ID NO;

410

47. The purified oligonucleotide primer pair of claim 10 wherein said forward member is SEQ ID NO:

201.

48. The purified oligonucleotide primer pair of claim 10 wherein said reverse member is SEQ ID NO:

410.

11. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, configured to generate an amplicon that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 80% complementarity to a first portion of a region of Genbank Accession Number U26342.1, and said reverse primer configured to hybridize with at least 80% complementarity to a second portion of said region of Genbank Accession Number U26342.1, wherein said region of Genbank Accession Number U26342.1 begins at nucleotide position 2723 and continues to nucleotide position 2937 (SEQ ID NO:

416).

49. The purified oligonucleotide primer pair of claim 11 wherein said forward member has at least 90% sequence identity to SEQ ID NO:

167 or SEQ ID NO;

199.

50. The purified oligonucleotide primer pair of claim 11 wherein said forward member is SEQ ID NO:

167 or SEQ ID NO;

199.

51. The purified oligonucleotide primer pair of claim 11 wherein said reverse member has at least 90% sequence identity to SEQ ID NO:

408.

52. The purified oligonucleotide primer pair of claim 11 wherein said reverse member is SEQ ID NO:

408.

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