Oligonucleotide probe for the detection of adenovirus

• US 9,487,838 B2
• Filed: 12/28/2010
• Issued: 11/08/2016
• Est. Priority Date: 12/28/2010
• Status: Expired due to Fees

• Current Assignee: Qiagen Hamburg GmbH (Qiagen NV)
• Original Assignee: Qiagen Hamburg GmbH (Qiagen NV)
• Inventors: Van De Sand, Claudia, Janssen-Weets, Melanie, Knigsfeld, Nele
• Primary Examiner(s): Wilder, Cynthia B
• Application Number:
  US13/977,411
• Publication Number:
  US 20140106335A1
• Time in Patent Office: 2,142 Days
• Field of Search: 435/91.2, 435/6.1
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/701 Specific hybridization probes
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The present invention relates to an oligonucleotide probe for the detection of adenoviral nucleic acid in a biological sample. In a further aspect, the invention relates to a method for the detection of an adenoviral nucleic acid in a biological sample. The invention also provides oligonucleotide primers for amplifying adenoviral nucleic acid. Kits comprising probes and/or primers of the invention are also provided. Finally, the invention also relates to the use of the oligonucleotide primers and/or probes for detecting adenoviral nucleic acid.

Claims

1. A method for detecting adenoviral nucleic acid from an adenovirus that causes respiratory infections in a biological sample, comprising:

a) obtaining viral nucleic acid from a biological sample that is suspected to include material from an adenovirus that causes respiratory infections;

b) amplifying the viral nucleic acid;

c) contacting an oligonucleotide probe with the amplified viral nucleic acid obtained in step b), said probe comprising;

i) the nucleotide sequence of SEQ ID NO;

1 or SEQ ID NO;

2;

or

ii) a sequence which is at least 85% identical to the nucleotide sequence of SEQ ID NO;

1 or SEQ ID NO;

2;

or

iii) the full complement of (i) or (ii), wherein said probe comprises a detectable moiety and wherein said probe is a universal probe that hybridizes specifically to adenovirus serotypes that causes respiratory infections in humans; and

d) detecting specific hybridization of the oligonucleotide probe to the amplified viral nucleic acid;

wherein the specific hybridization of said oligonucleotide probe in step c) i) indicates that the biological sample contains adenovirus nucleic acid from an adenovirus that causes respiratory infections, and wherein no hybridization of said oligonucleotide probe in step c) i) indicates that the biological sample does not contain nucleic acid from an adenovirus that causes respiratory infections.

2. The method according to claim 1, wherein said oligonucleotide probe comprises:

a) the nucleotide sequence of SEQ ID NO;

2;

or

b) a sequence which is at least 85% identical to the nucleotide sequence of SEQ ID NO;

2;

or

c) the full complement of (a) or (b).

3. The method according to claim 1, wherein said oligonucleotide probe consists of the sequence of SEQ ID NO:

1 or SEQ ID NO;

2.

4. The method according to claim 1, wherein the oligonucleotide probe is linked to a bead.

5. The method according to claim 4, wherein said bead is a colour-coded bead.

6. The method according to claim 1, wherein said biological sample is derived from a human.

7. The method according to claim 1, wherein the biological sample is a biopsy, blood, serum, plasma, urine, stool, sputum, bronchial lavage, or liquor sample or a nasal or throat swab.

8. The method according to any of claim 1, wherein the adenovirus nucleic acid to be detected is adenovirus DNA.

9. The method according to claim 8, wherein the adenovirus DNA is from the adenoviral hexon gene.

10. The method according to claim 1, wherein the amplification in step b) is effected using one or more oligonucleotide primers comprising:

a) the nucleotide sequence of any of SEQ ID NOS;

3-9;

or

b) a sequence which is at least 85% identical to a nucleotide sequence of any of SEQ ID NOS;

3-9;

or

c) the complement of (a) or (b).

11. The method according to claim 1, wherein the amplification in step b) is effected using one or more oligonucleotide primers comprising:

a) the nucleotide sequence of any of SEQ ID NOS;

10-13;

or

b) a sequence which is at least 85% identical to a nucleotide sequence of any of SEQ ID NOS;

3-5 and 10-13;

or

c) the complement of (a) or (b).

12. The method according to claim 1, wherein the amplification in step b) is effected using one or more oligonucleotide primers consisting of a nucleotide sequence of any of SEQ ID NOS:

3-13.

13. The method according to claim 1, wherein amplification in_step b) is effected using a multiplex PCR.

14. The method according to claim 13, wherein the multiplex PCR is effected using:

(i) as a first forward primer an oligonucleotide comprising;

a) the nucleotide sequence of SEQ ID NO;

6 or SEQ ID NO;

10;

or

b) a sequence which is at least 85% identical to the nucleotide sequence of SEQ ID NO;

6 or SEQ ID NO;

10;

or

c) the full complement of (a) or (b);

(ii) as a second forward primer an oligonucleotide comprising;

a) the nucleotide sequence of SEQ ID NO;

7 or SEQ ID NO;

11;

or

b) a sequence which is at least 85% identical to a nucleotide sequence of SEQ ID NO;

7 or SEQ ID NO;

11;

or

c) the full complement of (a) or (b);

(iii) as a first reverse primer an oligonucleotide comprising;

a) the nucleotide sequence of SEQ ID NO;

8 or SEQ ID NO;

12;

or

b) a sequence which is at least 85% identical to a nucleotide sequence of SEQ ID NO;

8 or SEQ ID NO;

12;

or

c) the full complement of (a) or (b); and

(iv) as a second reverse primer an oligonucleotide comprising;

a) the nucleotide sequence of SEQ ID NO;

9 or SEQ ID NO;

13;

or

b) a sequence which is at least 85% identical to a nucleotide sequence of SEQ ID NO;

9 or SEQ ID NO;

13;

or

c) the full complement of (a) or (b).

15. The method according to claim 14, wherein the multiplex PCR further uses

(i) as a third forward primer an oligonucleotide comprising:

a) the nucleotide sequence of SEQ ID NO;

3;

or

b) a sequence which is at least 85% identical to the nucleotide sequence of SEQ ID NO;

3;

or

c) the full complement of (a) or (b); and

(ii) as a third reverse primer an oligonucleotide comprising;

a) the nucleotide sequence of SEQ ID NO;

4 or SEQ ID NO;

5;

or

b) a sequence which is at least 85% identical to a nucleotide sequence of SEQ ID NO;

4 or SEQ ID NO;

5;

or

c) the full complement of (a) or (b).