Detection of human immunodeficiency virus type 1
AssigneeGen-Probe Incorporated
InventorsSherrol H. McDonough, Thomas B. Ryder, Yeasing Yang
Life of this patent
Estimating the term…
Abstract
Amplification oligonucleotides and hybridization assay probes which distinguish Human Immunodeficiency Virus type 1 from other viruses.
Claims152
An oligonucleotide for use in determining the presence of HIV Type 1 nucleic acid in a sample, said oligonucleotide being up to 100 nucleotide bases in length and comprising an at least 10 contiguous nucleoride base sequence consisting of or contained within a sequence selected from the group consisting of SEQ ID NO:
- 3, SEQ ID NO:
- 5, SEQ ID NO:
- 6, SEQ ID NO:
- 7, SEQ ID NO:
- 8, SEQ ID NO:
- 13, SEQ ID NO:
- 15, SEQ ID NO:
- 16, SEQ ID NO:
- 17, SEQ ID NO:
- 18, SEQ ID NO:
- 55, SEQ ID NO:
- 57, SEQ ID NO:
- 58, SEQ ID NO:
- 59, SEQ ID NO:
- 60, SEQ ID NO:
- 65, SEQ ID NO:
- 69, SEQ ID NO:
- 71, SEQ ID NO:
- 72, SEQ ID NO:
- 73, SEQ ID NO:
- 74, SEQ ID NO:
- 79, SEQ ID NO:
- 83, SEQ ID NO:
- 85, SEQ ID NO:
- 86, SEQ ID NO:
- 87, SEQ ID NO:
- 88, SEQ ID NO:
- 93, SEQ ID NO:
- 95, SEQ ID NO:
- 96, SEQ ID NO:
- 97, SEQ ID NO:
- 98, SEQ ID NO:
- 132, SEQ ID NO:
- 133, SEQ ID NO:
- 134, SEQ ID NO:
- 135, SEQ ID NO:
- 136, SEQ ID NO:
- 137, SEQ ID NO:
- 138 and SEQ ID NO:
- 139, provided that if said oligonucleotide comprises an at least 10 contiguous nucleotide base sequence consisting of or contained within the sequence of SEQ ID NO:
- 3, SEQ ID NO:
- 55, SEQ ID NO:
- 69 or SEQ ID NO:
- 83, then said oligonucleotide further comprises a detectable moiety, wherein said oligonucleotide hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions, and wherein said oligonucleotide does not hybridize to human nucleic acid in said sample to form an oligonucleotide:non-target duplex under said conditions.
An oligonucleotide for use in determining the presence of HIV Type 1 nucleic acid in a sample, said oligonucleotide being up to 100 nucleotide bases in length and comprising an at least 10 contiguous nucleotide base sequence consisting of or is contained within a sequence selected from the group consisting of SEQ ID NO:
- 14, SEQ ID NO:
- 66, SEQ ID NO:
- 80 and SEQ ID NO:
- 94,
- wherein said oligonucleotide hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions,
- wherein said oligonucleotide does not hybridize to human nucleic acid in said sample to form an oligonucleotide:non-target duplex under said conditions, and
- wherein said oligonucleotide includes a detectable moiety.
An oligonucleotide for use in determining the presence of HIV Type 1 nucleic acid in a sample, said oligonucleotide consisting essentially of a nucleotide base sequence selected from the group consisting of SEQ ID NO:
- 14, SEQ ID NO:
- 66, SEQ ID NO:
- 80 and SEQ ID NO:
- 94, wherein said oligonucleotide hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions, wherein said oligonucleotide does not hybridize to human nucleic acid in said sample to form an oligonucleotide:non-target duplex under said conditions.
An oligonucleotide for use in determining the presence of HIV Type 1 nucleic acid in a sample, said oligonucleotide having a target binding region of from 18 to 38 nucleotide bases in length, wherein the nucleotide base sequence of said target binding region consists of or is contained within a sequence selected from the group consisting of SEQ ID NO:
- 25, SEQ ID NO:
- 26, SEQ ID NO:
- 28, SEQ ID NO:
- 29, SEQ ID NO:
- 30, SEQ ID NO:
- 31, SEQ ID NO:
- 32, SEQ ID NO:
- 33, SEQ ID NO:
- 34, SEQ ID NO:
- 35, SEQ ID NO:
- 36, SEQ ID NO:
- 37, SEQ ID NO:
- 38, SEQ ID NO:
- 40, SEQ ID NO:
- 42, SEQ ID NO:
- 43, SEQ ID NO:
- 46, SEQ ID NO:
- 47, SEQ ID NO:
- 48, SEQ ID NO:
- 49, SEQ ID NO:
- 51, SEQ ID NO:
- 105, SEQ ID NO:
- 106, SEQ ID NO:
- 108, SEQ ID NO:
- 109, SEQ ID NO:
- 110, SEQ ID NO:
- 111, SEQ ID NO:
- 112, SEQ ID NO:
- 113, SEQ ID NO:
- 114, SEQ ID NO:
- 115, SEQ ID NO:
- 116, SEQ ID NO:
- 117, SEQ ID NO:
- 118, SEQ ID NO:
- 120, SEQ ID NO:
- 122, SEQ ID NO:
- 123, SEQ ID NO:
- 126, SEQ ID NO:
- 127, SEQ ID NO:
- 128, SEQ ID NO:
- 129 and SEQ ID NO:
- 131, wherein said oligonucleotide hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions, and wherein said oligonucleotide does not hybridize to human nucleic acid in said sample to form an oligonucleotide:non-target duplex under said conditions.
A probe mix for use in determining the presence of HIV Type 1 nucleic acid in a sample, said probe mix comprising:
- a first oligonucleotide up to 100 nucleotide bases in length and comprising an at least 10 contiguous nucleotide base sequence consisting of or contained within a sequence selected from the group consisting of SEQ ID NO:
- 3, SEQ ID NO:
- 5, SEQ ID NO:
- 6, SEQ ID NO:
- 7, SEQ ID NO:
- 8, SEQ ID NO:
- 9, SEQ ID NO:
- 10, SEQ ID NO:
- 11, SEQ ID NO:
- 55, SEQ ID NO:
- 57, SEQ ID NO:
- 58, SEQ ID NO:
- 59, SEQ ID NO:
- 60, SEQ ID NO:
- 61, SEQ ID NO:
- 63, SEQ ID NO:
- 69, SEQ ID NO:
- 71, SEQ ID NO:
- 72, SEQ ID NO:
- 73, SEQ ID NO:
- 74, SEQ ID NO:
- 75, SEQ ID NO:
- 77, SEQ ID NO:
- 83, SEQ ID NO:
- 85, SEQ ID NO:
- 86, SEQ ID NO:
- 87, SEQ ID NO:
- 88, SEQ ID NO:
- 89 and SEQ ID NO:
- 91;
- and
- a second oligonucleotide having a first target binding region of from 18 to 38 nucleotide bases in length, wherein the nucleotide base sequence of said first target binding region consists of or is contained within a sequence selected from the group consisting of SEQ ID NO:
- 23, SEQ ID NO:
- 25, SEQ ID NO:
- 26, SEQ ID NO:
- 28, SEQ ID NO:
- 29, SEQ ID NO:
- 30, SEQ ID NO:
- 31, SEQ ID NO:
- 32, SEQ ID NO:
- 33, SEQ ID NO:
- 34, SEQ ID NO:
- 35, SEQ ID NO:
- 36, SEQ ID NO:
- 39, SEQ ID NO:
- 40, SEQ ID NO:
- 42, SEQ ID NO:
- 43, SEQ ID NO:
- 103, SEQ ID NO:
- 105, SEQ ID NO:
- 106, SEQ ID NO:
- 108, SEQ ID NO:
- 109, SEQ ID NO:
- 110, SEQ ID NO:
- 111, SEQ ID NO:
- 112, SEQ ID NO:
- 113, SEQ ID NO:
- 114, SEQ ID NO:
- 115, SEQ ID NO:
- 116, SEQ ID NO:
- 119, SEQ ID NO:
- 120, SEQ ID NO:
- 121, SEQ ID NO:
- 122 and SEQ ID NO:
- 123,
- wherein said second oligonucleotide optionally includes a 5′ sequence which is recognized by an RNA polymerase, and
- wherein each of said first and second oligonucleotides hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions, and wherein said first and second oligonucleotides do not hybridize to human nucleic acid in said sample to form oligonucleotide:non-target duplexes under said conditions.
A probe mix for use in determining the presence of HIV Type 1 nucleic acid in a sample, said probe mix comprising:
- a first oligonucleotide up to 100 nucleotide bases in length and comprising an at least 10 contiguous nucleotide base sequence consisting of or contained within a sequence selected from the group consisting of SEQ ID NO:
- 1, SEQ ID NO:
- 12, SEQ ID NO:
- 53, SEQ ID NO:
- 64, SEQ ID NO:
- 67, SEQ ID NO:
- 78, SEQ ID NO:
- 81 and SEQ ID NO:
- 92;
- and
- a second oligonucleotide up to 100 nucleotide bases in length and comprising an at least 10 contiguous nucleotide base sequence consisting of or contained within a sequence selected from the group consisting of SEQ ID NO:
- 15, SEQ ID NO:
- 18, SEQ ID NO:
- 95, SEQ ID NO:
- 98, SEQ ID NO:
- 132, SEQ ID NO:
- 135, SEQ ID NO:
- 136 and SEQ ID NO:
- 139,
- wherein each of said first and second oligonucleotides hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions, and wherein said first and second oligonucleotides do not hybridize to human nucleic acid in said sample to form oligonucleotide:non-target duplexes under said conditions.
A kit for use in determining the presence of HIV Type 1 nucleic acid in a sample, said kit comprising first and second oligonucleotides, wherein each of said first and second oligonucleotides has a target binding region of from 18 to 38 nucleotide bases in length, wherein the nucleotide base sequence of each said target binding region consists of or is contained within a sequence selected from the group consisting of SEQ ID NO:
- 23, SEQ ID NO:
- 25, SEQ ID NO:
- 26, SEQ ID NO:
- 28, SEQ ID NO:
- 29, SEQ ID NO:
- 30, SEQ ID NO:
- 31, SEQ ID NO:
- 32, SEQ ID NO:
- 33, SEQ ID NO:
- 34, SEQ ID NO:
- 35, SEQ ID NO:
- 36, SEQ ID NO:
- 37, SEQ ID NO:
- 38, SEQ ID NO:
- 39, SEQ ID NO:
- 40, SEQ ID NO:
- 42, SEQ ID NO:
- 43, SEQ ID NO:
- 46, SEQ ID NO:
- 47, SEQ ID NO:
- 48, SEQ ID NO:
- 49, SEQ ID NO:
- 50, SEQ ID NO:
- 51, SEQ ID NO:
- 103, SEQ ID NO:
- 105, SEQ ID NO:
- 106, SEQ ID NO:
- 108, SEQ ID NO:
- 109, SEQ ID NO:
- 110, SEQ ID NO:
- 111, SEQ ID NO:112, SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:
- 117, SEQ ID NO:
- 118, SEQ ID NO:
- 119, SEQ ID NO:
- 120, SEQ ID NO:
- 122, SEQ ID NO:
- 123, SEQ ID NO:
- 126, SEQ ID NO:
- 127, SEQ ID NO:
- 128, SEQ ID NO:
- 129, SEQ ID NO:
- 130 and SEQ ID NO:
- 131,
- wherein said target binding regions of said first and second oligonucleotides are different from each other,
- wherein each of said first and second oligonucleotides optionally includes a 5′ sequence which is recognized by an RNA polymerase, and
- wherein each of said first and second oligonucleotides hybridizes to an HIV Type 1 target nucleic acid sequence in a sample to form an oligonucleotide:target duplex under hybridization conditions, and wherein said first and second oligonucleotides do not hybridize to human nucleic acid in said sample to form oligonucleotide:non-target duplexes under said conditions.
Dependencies are inferred from the claim text.