COMPOSITIONS FOR DETECTING BORDETELLA PERTUSSIS NUCLEIC ACID

1 . A composition for determining the presence or absence of Bordetella pertussis (Bp) in a sample, said composition comprising:

an amplification oligomer combination comprising first and second Bp-specific amplification oligomers capable of amplifying a target region of a Bp target nucleic acid, wherein the first and second Bp-specific amplification oligomers comprise, respectively, a first Bp-specific target-hybridizing sequence and a second Bp-specific target-hybridizing sequence, wherein

(a) the first Bp-specific target-hybridizing sequence is SEQ ID NO:9, SEQ ID NO: 12, SEQ ID NO:45, a sequence having at least 85% identity with SEQ ID NO: 4, a sequence having at least 85% identity with SEQ ID NO:6, or an RNA equivalent or DNA/RNA chimeric thereof, and

the second Bp-specific target-hybridizing sequence is SEQ ID NO:5, SEQ ID NO: 8, SEQ ID NO:11, SEQ ID NO:14, or SEQ ID NO:46, or an RNA equivalent or DNA/RNA chimeric thereof; or

(b) the first Bp-specific target-hybridizing sequence is SEQ ID NO:18, SEQ ID NO: 21, or SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimeric thereof, and

the second Bp-specific target-hybridizing sequence is SEQ ID NO:20, SEQ ID NO:23, or SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric thereof; and

a Bp-specific detection probe oligomer comprising a Bp-specific detection probe target-hybridizing sequence that is from about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a Bp amplicon amplifiable by the first and second Bp-specific amplification oligomers, wherein the Bp-specific detection probe oligomer comprises a fluorescent or chemiluminescent label.

2 . The composition of claim 1 , wherein the first and second Bp specific target-hybridizing sequences are, respectively, selected from the group consisting of

(i) SEQ ID NO:3, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:5, or an RNA equivalent or DNA/RNA chimeric thereof;

(ii) SEQ ID NO:6, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:8, or an RNA equivalent or DNA/RNA chimeric thereof;

(iii) SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimeric thereof;

(iv) SEQ ID NO:12, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:14, or an RNA equivalent or DNA/RNA chimeric thereof;

(v) SEQ ID NO:18, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:20, or an RNA equivalent or DNA/RNA chimeric thereof;

(vi) SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimeric thereof; and

(vii) SEQ ID NO:27, or an RNA equivalent or DNA/RNA chimeric thereof, and SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric thereof.

3 . The composition of claim 1 , wherein

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (i) and the Bp-specific detection probe target-hybridizing sequence is a sequence having at least 85% identity with SEQ ID NO:4, or an RNA equivalent or DNA/RNA chimeric thereof;

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (ii) and the Bp-specific detection probe target-hybridizing sequence is a sequence having at least 85% identity with SEQ ID NO:7, or an RNA equivalent or DNA/RNA chimeric thereof;

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (iii) and the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO: 10, or an RNA equivalent or DNA/RNA chimeric thereof;

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (iv) and the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO: 13, or an RNA equivalent or DNA/RNA chimeric thereof;

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (v) and the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO: 16, or an RNA equivalent or DNA/RNA chimeric thereof;

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (vi) and the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO: 19, or an RNA equivalent or DNA/RNA chimeric thereof;

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (vii) and the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO: 22, or an RNA equivalent or DNA/RNA chimeric thereof; or

the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (viii) and the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO: 28, or an RNA equivalent or DNA/RNA chimeric thereof.

4 . The composition of claim 1 , wherein the Bp-specific detection probe oligomer comprises the fluorescent label.

5 . The composition of claim 4 , wherein the Bp-specific detection probe oligomer further comprises a non-fluorescent quencher.

6 . The composition of claim 3 , wherein the Bp-specific detection probe oligomer comprises the fluorescent label.

7 . The composition of claim 6 , wherein the Bp-specific detection probe oligomer further comprises a non-fluorescent quencher.

8 . The composition of claim 1 , further comprising a second amplification oligomer combination capable of amplifying a target region of a Bordetella parapertussis (Bpp) target nucleic acid.

9 . The composition of claim 1 , wherein the first Bp-specific target-hybridizing sequence having at least 85% identity with SEQ ID NO:3 is SEQ ID NO:3 or SEQ ID NO:6, or an RNA equivalent or DNA/RNA chimeric thereof.

10 . The composition of claim 3 , wherein the first and second Bp-specific target-hybridizing sequences are target-hybridizing sequences of (i) and the Bp-specific detection probe target-hybridizing sequence is the sequence having at least 85% identity with SEQ ID NO: 4, or an RNA equivalent or DNA/RNA chimeric thereof.

11 . The composition of claim 10 , wherein the Bp-specific detection probe target-hybridizing sequence is SEQ ID NO:4 or SEQ ID NO:7, or an RNA equivalent or DNA/RNA chimeric thereof.

12 . The composition of claim 1 , wherein the first and second Bp-specific amplification oligomers comprise the first and second Bp-specific target-hybridizing sequences of (a).

13 . The composition of claim 12 , wherein the first Bp-specific target-hybridizing sequence is the sequence having at least 85% identity with SEQ ID NO:3, a sequence having at least 85% identity with SEQ ID NO:6, or an RNA equivalent or DNA/RNA chimeric thereof.

14 . The composition of claim 13 , wherein the second Bp-specific target-hybridizing sequence is SEQ ID NO:5 or SEQ ID NO:8, or an RNA equivalent or DNA/RNA chimeric thereof.

15 . The composition of claim 12 , wherein the Bp-specific detection probe target-hybridizing sequence is a sequence having at least 85% identity with SEQ ID NO:4, a sequence having at least 85% identity with SEQ ID NO:7, or an RNA equivalent or DNA/RNA chimeric thereof.

16 . A kit for determining the presence or absence of Bordetella pertussis (Bp) in a sample, said kit comprising the composition of claim 1 .

17 . A reaction mixture for determining the presence or absence of Bordetella pertussis (Bp) in a sample, said reaction mixture comprising the composition of claim 1 .

18 . The reaction mixture of claim 17 , further comprising at least one enzyme selected from the group consisting of a thermostable DNA polymerase, a reverse transcriptase, and an RNA polymerase.

19 . An aqueous formulation for determining the presence or absence of Bordetella pertussis (Bp) in a sample, said aqueous formulation comprising:

the composition of claim 1 , and

an organic buffer.

20 . A dried formulation for determining the presence or absence of Bordetella pertussis (Bp) in a sample, said dried formulation comprising:

the composition of claim 1 , and

a bulking agent.