Compositions to detect adenovirus nucleic acids
The disclosure is related to compositions, for targeting Adenovirus nucleic acid. Compositions include amplification oligomers and/or detection probe oligomers.
1. A composition for determining the presence or absence of an Adenovirus target nucleic acid in a sample, the composition comprising:
a first amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74;
a second amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62; and
at least one additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61, 62, 71, 72, 73, and 74, wherein the at least one additional amplification oligomers is different from the first amplification oligomer and the second amplification oligomer.
2. The composition of claim 1 , wherein the at least one additional amplification oligomer comprises a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74.
3. The composition of claim 1 , wherein the at least one additional amplification oligomer comprises a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62.
4. The composition of claim 1 , wherein at least one of the first amplification oligomer, second amplification oligomer, and at least one additional amplification oligomer comprises a nucleic acid sequence that contains at least one 5-Me-C, at least one non-Watson Crick base, at least one degenerate base, or a combination thereof.
5. The composition of claim 1 , further comprising at least one detection probe oligomer configured to hybridize to a region of an Adenovirus amplicon amplifiable by the first, second, and at least one additional amplification oligomers, wherein the at least one detection probe oligomer comprises at least one of
(i) a detectable label,
(ii) a substitution at the 2′ position of at least one ribose moiety,
(iii) a blocking moiety at or near the 3′ end of the detection probe oligomer, wherein the blocking moiety is configured to prevent enzyme-mediated extension of the detection probe in an amplification reaction, and
(iv) a non-target-hybridizing sequence that contributes to the three-dimensional conformation of the detection probe oligomer.
6. The composition of claim 5 , wherein the at least one detection probe oligomer comprises a target hybridizing sequence selected from the group consisting of SEQ ID NOs:4, 10, 18, 20, 22, 24, 30, 36, 37, 39, 40, 63, 64, and 139.
7. The composition of claim 5 , wherein the at least one detection probe oligomer comprises a target hybridizing sequence that is from 18 to 36 nucleobases in length wherein the 18 to 36 nucleobases are all selected from contiguous nucleobases within SEQ ID NO:138.
8. The composition of claim 7 , wherein the at least one detection probe oligomer comprises
a detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:63,
a detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:64, or
a combination thereof.
9. The composition of claim 5 , wherein the at least one detection probe oligomer comprises the detectable label.
10. The composition of claim 9 , wherein the detectable label is a fluorophore.
11. The composition of claim 9 , wherein the at least one detection probe oligomer is a dual labeled detection probe oligomer comprising a fluorescent label and a quencher moiety that can quench a fluorescent emission from the fluorescent label.
12. The composition of claim 5 , wherein
(a) the at least one additional amplification oligomer comprises
a first additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74, and
a second additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62; and
(b) the at least one detection probe oligomer comprises
a first detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:63, and
a second detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:64.
13. The composition of claim 1 , further comprising
at least one additional first amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:1, 5, 11, 12, 25, 26, 31, 32, 33, 34, 35, and 38; and
at least one additional second amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:2, 3, 6, 7, 8, 9, 13, 14, 15, 16, 27, 28, 42, 43, 44, 45, 46, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and 149.
14. A dried composition comprising:
(A) an oligomer combination to amplify an Adenovirus amplicon, the oligomer combination comprising
(1) a first amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74;
(2) a second amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62; and
(3) at least one additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61, 62, 71, 72, 73, and 74, wherein the at least one additional amplification oligomers is different from the first amplification oligomer and the second amplification oligomer;
(B) an inorganic salt;
(C) a polymerase enzyme having 5′ to 3′ exonuclease activity;
(D) a reverse transcriptase; and
(E) dNTPs.
15. The dried composition of claim 14 , further comprising at least one detection probe oligomer that hybridizes to a region of the Adenovirus amplicon, wherein the at least one detection probe oligomer comprises at least one of
(i) a detectable label,
(ii) a substitution at the 2 ′ position of at least one ribose moiety,
(iii) a blocking moiety at or near within 5 residues of the 3 ′ end of the detection probe oligomer, wherein the blocking moiety prevents enzyme-mediated extension of the detection probe in an amplification reaction, and
(iv) a non-target-hybridizing sequence that contributes to the three-dimensional conformation of the detection probe oligomer.
16. The dried composition of claim 15 , wherein the at least one detection probe oligomer comprises
a detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:63,
a detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:64, or
a combination thereof.
17. The dried composition of claim 15 , wherein
(a) the at least one additional amplification oligomer comprises
a first additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74, and
a second additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62; and
(b) the at least one detection probe oligomer comprises
a first detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:63, and
a second detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:64.
18. A formulation for amplification and detection of an Adenovirus target nucleic acid, the formulation comprising:
(A) an oligomer combination to amplify an Adenovirus amplicon, the oligomer combination comprising
(1) a first amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74;
(2) a second amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62; and
(3) at least one additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61, 62, 71, 72, 73, and 74, wherein the at least one additional amplification oligomers is different from the first amplification oligomer and the second amplification oligomer;
(B) at least one detection probe oligomer that hybridizes to a region of the Adenovirus amplicon;
(C) a polymerase enzyme having 5′ to 3′ exonuclease activity;
(D) a reverse transcriptase;
(E) dNTPs;
(F) EDTA; and
(G) water.
19. The formulation of claim 18 , wherein the at least one detection probe oligomer comprises a detectable label.
20. The formulation of claim 18 , wherein the at least one detection probe oligomer comprises
a detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:63,
a detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:64, or
a combination thereof.
21. The formulation of claim 18 , wherein
(a) the at least one additional amplification oligomer comprises
a first additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:71, 72, 73, and 74, and
a second additional amplification oligomer comprising a target hybridizing sequence selected from the group consisting of SEQ ID NOs:61 and 62; and
(b) the at least one detection probe oligomer comprises
a first detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:63, and
a second detection probe oligomer comprising a target hybridizing sequence of SEQ ID NO:64.