Compositions for use in identification of adventitious viruses

• US 20060205040A1
• Filed: 03/03/2006
• Published: 09/14/2006
• Est. Priority Date: 03/03/2005
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Sampath, Rangarajan
• Application Number:
  US11/368,233
• Publication Number:
  US 20060205040A1
• Time in Patent Office: Days
• US Class Current: 435/91.100
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/701 Specific hybridization probes

Abstract

The present invention provides compositions, kits and methods for rapid identification and quantification of adventitious contaminant viruses by molecular mass and base composition analysis.

Claims

1. An oligonucleotide primer 14 to 35 nucleobases in length comprising at least 70% sequence identity with SEQ ID NO:

47.

3. A composition comprising the primer of claim 1.

4. The composition of claim 3 further comprising an oligonucleotide primer 14 to 35 nucleobases in length comprising at least 70% sequence identity with SEQ ID NO:

286.

5. The composition of claim 4 wherein either or both of said primers comprises at least one modified nucleobase.

6. The composition of claim 5 wherein said modified nucleobase is 5-propynyluracil or 5-propynylcytosine.

7. The composition of claim 4 wherein either or both of said primers comprises at least one universal nucleobase.

8. The composition of claim 7 wherein said universal nucleobase is inosine.

9. The composition of claim 4 wherein either or both of said primers further comprises a non-templated T residue on the 5′

-end.

10. The composition of claim 4 wherein either or both of said primers comprises at least one non-template tag.

11. The composition of claim 4 wherein either or both of said primers comprises at least one molecular mass modifying tag.

12. A kit comprising the composition of claim 4.

13. The kit of claim 12 further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs:

70;

286, 165;

286, 122;

275, 100;

336, and 61;

324.

14. The kit of claim 12 further comprising at least one calibration polynucleotide.

15. The kit of claim 12 further comprising at least one anion exchange functional group linked to a magnetic bead.

16. A method for identification of a polyomavirus in a sample comprising:

amplifying nucleic acid from said polyomavirus using the composition of claim 4 to obtain an amplification product;

determining the molecular mass of said amplification product;

optionally, determining the base composition of said amplification product from said molecular mass; and

comparing said molecular mass or base composition with a plurality of molecular masses or base compositions of known polyomavirus identifying amplicons, wherein a match between said molecular mass or base composition and a member of said plurality of molecular masses or base compositions identifies said polyomavirus.

17. The method of claim 16 wherein said sample is a biological product.

18. A method of determining the presence or absence of a polyomavirus in a sample comprising:

amplifying nucleic acid from said sample using the composition of claim 4 to obtain an amplification product;

determining the molecular mass of said amplification product;

optionally, determining the base composition of said amplification product from said molecular mass; and

comparing said molecular mass or base composition of said amplification product with the known molecular masses or base compositions of one or more known polyomavirus identifying amplicons, wherein a match between said molecular mass or base composition of said amplification product and the molecular mass or base composition of one or more known polyomavirus identifying amplicons indicates the presence of said polyomavirus in said sample.

19. The method of claim 18 wherein said sample comprises a biological product.

20. A method for determination of the quantity of an unknown polyomavirus in a sample comprising:

contacting said sample with the composition of claim 4 and a known quantity of a calibration polynucleotide comprising a calibration sequence;

concurrently amplifying nucleic acid from said unknown polyomavirus and nucleic acid from said calibration polynucleotide in said sample with the composition of claim 4 to obtain a first amplification product comprising a polyomavirus identifying amplicon and a second amplification product comprising a calibration amplicon;

determining the molecular mass and abundance for said polyomavirus identifying amplicon and said calibration amplicon; and

distinguishing said polyomavirus identifying amplicon from said calibration amplicon based on molecular mass, wherein comparison of polyomavirus identifying amplicon abundance and calibration amplicon abundance indicates the quantity of polyomavirus in said sample.

2. An oligonucleotide primer 14 to 35 nucleobases in length comprising at least 70% sequence identity with SEQ ID NO:

286.