Detection of variola virus
First Claim
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1. A method for detecting the presence or absence of variola virus in a biological sample from an individual, said method comprising:
- performing at least one cycling step, wherein a cycling step comprises an amplifying step and a hybridizing step, wherein said amplifying step comprises contacting said sample with a pair of hemagglutinin (HA) primers to produce an HA amplification product if a variola virus HA nucleic acid molecule is present in said sample, wherein said hybridizing step comprises contacting said sample with a pair of HA probes, wherein the members of said pair of HA probes hybridize within no more than five nucleotides of each other, wherein a first HA probe of said pair of HA probes is labeled with a donor fluorescent moiety and said second HA probe of said pair of HA probes is labeled with a corresponding acceptor fluorescent moiety; and
detecting the presence or absence of fluorescence resonance energy transfer (FRET) between said donor fluorescent moiety of said first HA probe and said acceptor fluorescent moiety of said second HA probe, wherein the presence of FRET is indicative of the presence of variola virus in said biological sample, and wherein the absence of FRET is indicative of the absence of variola virus in said biological sample.
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Abstract
The invention provides methods to detect variola virus in biological samples using real-time PCR. Primers and probes for the detection of variola virus are provided by the invention. Articles of manufacture containing such primers and probes for detecting variola virus are further provided by the invention.
20 Citations
52 Claims
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1. A method for detecting the presence or absence of variola virus in a biological sample from an individual, said method comprising:
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performing at least one cycling step, wherein a cycling step comprises an amplifying step and a hybridizing step, wherein said amplifying step comprises contacting said sample with a pair of hemagglutinin (HA) primers to produce an HA amplification product if a variola virus HA nucleic acid molecule is present in said sample, wherein said hybridizing step comprises contacting said sample with a pair of HA probes, wherein the members of said pair of HA probes hybridize within no more than five nucleotides of each other, wherein a first HA probe of said pair of HA probes is labeled with a donor fluorescent moiety and said second HA probe of said pair of HA probes is labeled with a corresponding acceptor fluorescent moiety; and
detecting the presence or absence of fluorescence resonance energy transfer (FRET) between said donor fluorescent moiety of said first HA probe and said acceptor fluorescent moiety of said second HA probe, wherein the presence of FRET is indicative of the presence of variola virus in said biological sample, and wherein the absence of FRET is indicative of the absence of variola virus in said biological sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29)
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30. A method for detecting the presence or absence of variola virus in a biological sample from an individual, said method comprising:
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performing at least one cycling step, wherein a cycling step comprises an amplifying step and a hybridizing step, wherein said amplifying step comprises contacting said sample with a pair of thymidine kinase (TK) primers to produce a TK amplification product if a variola virus TK nucleic acid molecule is present in said sample, wherein said hybridizing step comprises contacting said sample with a pair of TK probes, wherein the members of said pair of TK probes hybridize within no more than five nucleotides of each other, wherein a first TK probe of said pair of TK probes is labeled with a donor fluorescent moiety and said second TK probe of said pair of TK probes is labeled with a corresponding acceptor fluorescent moiety; and
detecting the presence or absence of fluorescence resonance energy transfer (FRET) between said donor fluorescent moiety of said first TK probe and said acceptor fluorescent moiety of said second TK probe, wherein the presence of FRET is indicative of the presence of variola virus in said biological sample, and wherein the absence of FRET is indicative of the absence of variola virus in said biological sample.
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31. An article of manufacture, comprising:
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a pair of hemagglutinin (HA) primers;
a pair of HA probes; and
a donor fluorescent moiety and a corresponding acceptor fluorescent moiety. - View Dependent Claims (32, 33, 34, 35, 36, 37)
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38. An article of manufacture, comprising:
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a pair of thymidine kinase (TK) primers;
a pair of TK probes; and
a donor fluorescent moiety and a corresponding acceptor fluorescent moiety. - View Dependent Claims (39, 40, 41, 42, 43)
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44. A method for detecting the presence or absence of variola virus in a biological sample from an individual, said method comprising:
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performing at least one cycling step, wherein a cycling step comprises an amplifying step and a hybridizing step, wherein said amplifying step comprises contacting said sample with a pair of hemagglutinin (HA) primers to produce an HA amplification product if a variola virus HA nucleic acid molecule is present in said sample, wherein said hybridizing step comprises contacting said sample with an HA probe, wherein the HA probe is labeled with a donor fluorescent moiety and a corresponding acceptor fluorescent moiety; and
detecting the presence or absence of fluorescence resonance energy transfer (FRET) between said donor fluorescent moiety and said acceptor fluorescent moiety of said HA probe, wherein the presence or absence of fluorescence is indicative of the presence or absence of variola virus in said sample. - View Dependent Claims (45, 46, 47, 48, 49)
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50. A method for detecting the presence or absence of variola virus in a biological sample from an individual, said method comprising:
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performing at least one cycling step, wherein a cycling step comprises an amplifying step and a dye-binding step, wherein said amplifying step comprises contacting said sample with a pair of hemagglutinin (HA) primers to produce an HA amplification product if a variola virus HA nucleic acid molecule is present in said sample, wherein said dye-binding step comprises contacting said HA amplification product with a double-stranded DNA binding dye; and
detecting the presence or absence of binding of said double-stranded DNA binding dye, wherein the presence of binding is indicative of the presence of variola virus in said sample, and wherein the absence of binding is indicative of the absence of variola virus in said sample. - View Dependent Claims (51, 52)
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Specification