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US 2023/0399708 A1Published application
Compositions and Methods for Detecting Influenza A, Influenza B, and SARS-CoV-2
OwnerCraig Brian CLARK, Jimmykim PHAM +2inventors
InventorsCraig Brian CLARK, Jimmykim PHAM, Paul M. DARBY, Yi-Hsuan Elisha HO
Life of this patent
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Abstract
Disclosed are nucleic acid oligonucleotides, including primers, probes, and target capture oligonucleotides, for detection of SARS-CoV-2, Influenza A, and Influenza B. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligonucleotides. Corresponding formulations, reaction mixtures, and kits and related methods for preparing aqueous reaction mixtures from dried formulations are described.
Claims38
A composition or kit for determining the presence or absence of SARS-CoV-2, influenza A, and/or influenza B in a sample, said composition or kit comprising one or more of the following primer sets:
- (a) a first primer set comprising first and second SARS-CoV-2 region 1 primers capable of amplifying a target region of a SARS-CoV-2 target nucleic acid wherein,
- (i) the SARS-CoV-2 region 1 first primer comprises a nucleotide sequence having no more than 0, 1, 2, 3, 4, or 5 mismatches from the nucleotide sequence of SEQ ID NO:
- 126 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the SARS-CoV-2 region 1 second primer comprises a target hybridizing region 18-35 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 140 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 141 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (b) a second primer set comprising first and second SARS-CoV-2 region 2 primers capable of amplifying a target region of a SARS-CoV-2 target nucleic acid wherein,
- (i) the SARS-CoV-2 region 2 first primer comprises a target hybridizing region 16-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 143 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 144 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the SARS-CoV-2 region 2 second primer comprises a target hybridizing region 11-35 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 147, 148, or 149 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 150, 151, or 152 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (c) a third primer set comprising first and second SARS-CoV-2 region 3 primers capable of amplifying a target region of a SARS-CoV-2 target nucleic acid wherein,
- (i) the SARS-CoV-2 region 3 first primer comprises target hybridizing region 18-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 155 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 156 or 157 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the SARS-CoV-2 region 3 second primer comprises a target hybridizing region 13-40 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 160, 161, or 162 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 163, 164, 165, or 166 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (d) a fourth primer set comprising first and second Influenza A region 1 primers capable of amplifying a target region of an Influenza A target nucleic acid,
- (i) the influenza A region 1 first primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:15 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:16 or SEQ ID NO:17 an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza A region 1 second primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:18 an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:19 or SEQ ID NO:20 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (e) a fifth primer set comprising first and second Influenza A region 2 primers capable of amplifying a target region of an Influenza A target nucleic acid,
- (i) the influenza A region 2 first primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 25 an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 26 or SEQ ID NO:
- 27 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza A region 2 second primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 21 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:22 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (f) a sixth primer set comprising first and second Influenza B region 1 primers capable of amplifying a target region of an Influenza B target nucleic acid,
- (i) the influenza B region 1 first primer comprises a target hybridizing region 20-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 90 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 91 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza B region 1 second primer comprises a target hybridizing region 17-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 85 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 86 or SEQ ID NO:
- 87 or an RNA equivalent or a DNA/RNA chimeric thereof;
- and
- (g) a seventh primer set comprising first and second Influenza B region 2 primers capable of amplifying a target region of an Influenza B target nucleic acid,
- (i) the influenza B region 2 first primer comprises a target hybridizing region 13-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 83 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 84 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza B region 2 second primer comprises a target hybridizing region 17-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 79 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 80 or an RNA equivalent or a DNA/RNA chimeric thereof.
43 more elements
3-11. (canceled)
18-24. (canceled)
(canceled)
29-39. (canceled)
(canceled)
(canceled)
48-57. (canceled)
60-62. (canceled)
64-66. (canceled)
(canceled)
A formulation for determining the presence or absence of SARS-CoV-2, influenza A, and/or influenza B in a sample, said formulation comprising one or more of the following primer sets:
- (a) a first primer set comprising first and second SARS-CoV-2 region 1 primers capable of amplifying a target region of a SARS-CoV-2 target nucleic acid wherein,
- (i) the SARS-CoV-2 region 1 first primer comprises a nucleotide sequence having no more than 0, 1, 2, 3, 4, or 5 mismatches from the nucleotide sequence of SEQ ID NO:
- 126 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the SARS-CoV-2 region 1 second primer comprises a target hybridizing region 18-35 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 140 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 141 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (b) a second primer set comprising first and second SARS-CoV-2 region 2 primers capable of amplifying a target region of a SARS-CoV-2 target nucleic acid wherein,
- (i) the SARS-CoV-2 region 2 first primer comprises a target hybridizing region 16-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 143 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 144 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the SARS-CoV-2 region 2 second primer comprises a target hybridizing region 11-35 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 147, 148, or 149 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 150, 151, or 152 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (c) a third primer set comprising first and second SARS-CoV-2 region 3 primers capable of amplifying a target region of a SARS-CoV-2 target nucleic acid wherein,
- (i) the SARS-CoV-2 region 3 first primer comprises target hybridizing region 18-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 155 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 156 or 157 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the SARS-CoV-2 region 3 second primer comprises a target hybridizing region 13-40 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 160, 161, or 162 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 163, 164, 165, or 166 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (d) a fourth primer set comprising first and second Influenza A region 1 primers capable of amplifying a target region of an Influenza A target nucleic acid,
- (i) the influenza A region 1 first primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:15 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:16 or SEQ ID NO:17 an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza A region 1 second primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:18 an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:19 or SEQ ID NO:20 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (e) a fifth primer set comprising first and second Influenza A region 2 primers capable of amplifying a target region of an Influenza A target nucleic acid,
- (i) the influenza A region 2 first primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 25 an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 26 or SEQ ID NO:
- 27 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza A region 2 second primer comprises a target hybridizing region 15-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 21 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:22 or an RNA equivalent or a DNA/RNA chimeric thereof;
- (f) a sixth primer set comprising first and second Influenza B region 1 primers capable of amplifying a target region of an Influenza B target nucleic acid,
- (i) the influenza B region 1 first primer comprises a target hybridizing region 20-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 90 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 91 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza B region 1 second primer comprises a target hybridizing region 17-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 85 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 86 or SEQ ID NO:
- 87 or an RNA equivalent or a DNA/RNA chimeric thereof;
- and
- (g) a seventh primer set comprising first and second Influenza B region 2 primers capable of amplifying a target region of an Influenza B target nucleic acid,
- (i) the influenza B region 2 first primer comprises a target hybridizing region 13-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 83 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 84 or an RNA equivalent or a DNA/RNA chimeric thereof, and
- (ii) the influenza B region 2 second primer comprises a target hybridizing region 17-30 nucleobases in length, wherein the target hybridizing region is contained within SEQ ID NO:
- 79 or an RNA equivalent or a DNA/RNA chimeric thereof and comprises a nucleotide sequence differing by no more than 0, 1, 2, 3, 4, or 5 nucleotides from the nucleotide sequence of SEQ ID NO:
- 80 or an RNA equivalent or a DNA/RNA chimeric thereof.
43 more elements
(canceled)
(canceled)
75-80. (canceled)
Dependencies are inferred from the claim text.