METHODS AND MICROARRAYS FOR DETECTING ENTERIC VIRUSES
First Claim
1. A method of detecting one or more human astrovirus serotypes in a group of astroviruses in a sample from an individual comprising:
- (a) amplifying nucleic acid molecules of the sample with one or more primers specific to a conserved region of the astrovirus serotypes being assessed to obtain an amplified nucleic acid product;
(b) contacting the amplified nucleic acid product with one or more serotype specific probes having a nucleic acid sequence specific for a single astrovirus serotype in the group of astroviruses being assessed, the nucleic acid sequence having from about 9 o about 25 nucleic acid bases; and
(c) detecting hybridization between the amplified nucleic acid product the serotype specific probe, the presence of absence of hybridization indicating the presence or absence of one or more specific astrovirus serotypes in the sample.
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Accused Products
Abstract
The present invention relates to methods, microarrays and kits for detecting one or more human astrovirus serotypes in a sample (e.g., a fecal sample) from an individual. The method includes amplifying nucleic acid molecules of the sample with one or more primers, to thereby obtain an amplified nucleic acid product; contacting the amplified nucleic acid product with one or more serotype specific probes having a nucleic acid sequence that is specific for only one astrovirus serotype in the group of astroviruses being assessed, wherein the nucleic acid sequence includes between about 9 and 25 nucleic acid bases (e.g., SEQ ID NO: 5-24); and detecting the hybridization complex. The presence of hybridization complexes with a serotype specific probe indicates the presence of one or more specific astrovirus serotypes, and the absence of hybridization complexes with a serotype specific probe indicates the absence of the specific astrovirus serotype. Identification of the astrovirus serotypes allows for one to diagnose an individual infected with the serotype. The present invention further includes microarrays having any one of the astrovirus specific probe, or kits having microarrays and reagents for carrying out the assay.
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Citations
31 Claims
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1. A method of detecting one or more human astrovirus serotypes in a group of astroviruses in a sample from an individual comprising:
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(a) amplifying nucleic acid molecules of the sample with one or more primers specific to a conserved region of the astrovirus serotypes being assessed to obtain an amplified nucleic acid product; (b) contacting the amplified nucleic acid product with one or more serotype specific probes having a nucleic acid sequence specific for a single astrovirus serotype in the group of astroviruses being assessed, the nucleic acid sequence having from about 9 o about 25 nucleic acid bases; and (c) detecting hybridization between the amplified nucleic acid product the serotype specific probe, the presence of absence of hybridization indicating the presence or absence of one or more specific astrovirus serotypes in the sample. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method of detecting one or more human astroviruses in a sample from an individual, the method comprising:
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(a) amplifying nucleic acid molecules of the sample with one or more primers specific to a conserved region of the astroviruses to produce an amplified nucleic acid product; (b) contacting the amplified nucleic acid product under suitable hybridization conditions with one or more nucleic acid probe having a nucleic acid sequence of any one of SEQ ID NO;
5-24 or a complement thereof, a nucleic acid sequence having from about 40% to about 100% of contiguous nucleotides of any one of SEQ ID NO;
5-24 or a complement thereof, or a nucleic acid having from about 9 to about 25 contiguous nucleotides of SEQ ID NO;
5-24 or a complement thereof; and
.(c) detecting the presence or absence of hybridization of the amplified nucleic acid product to the probe, the presence or absence of hybridization being indicative of the presence or absence of one or more serotype specific astroviruses. - View Dependent Claims (8, 9, 10, 11)
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12. A method for identifying an astrovirus serotype in a sample from an individual, the method comprises:
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(a) reverse transcribing RNA from the sample to using one or more primers specific to a conserved region of the astrovirus serotypes to obtain DNA; (b) optionally amplifying the DNA by PCR; (c) labeling the DNA, prior to and/or during step (a) and/or step(b); (d) contacting DNA of step (c) under conditions suitable for hybridization with one or more nucleic acid molecules having a nucleic acid sequence of any one of SEQ ID NO;
5-24 or complements thereof, or a nucleic acid sequence having between about 40% and about 100% of any contiguous nucleotides of SEQ ID NO;
5-24 or complements thereof, or a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides of SEQ ID NO;
5-24 or complements thereof; and(e) detecting the presence or absence of the hybridization, the presence of a complex indicates the presence of the serotype and the absence a complex indicates the absence of the serotype, wherein the serotype is astrovirus 1, astrovirus 2, astrovirus 3, astrovirus 4, astrovirus 5, astrovirus 6, astrovirus 7, or astrovirus 8.
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13. A method of detecting one or more human astroviruses in a sample from an individual, the method comprises:
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(a) isolating viral nucleic acid molecules from the sample; (b) contacting one or more primers with the sample, the primers comprising nucleic acid sequence of SEQ ID NO;
1 or 2 and at least one primer comprising a tag, under conditions suitable for amplifying nucleic acid molecules of the sample, to obtain an amplified nucleic acid product having a labeled nucleic acid strand and an unlabeled nucleic acid strand;(c) digesting the unlabeled nucleic acid strand to thereby obtained an amplified labeled single stranded nucleic acid product; (d) contacting the amplified nucleic acid product under stringency conditions suitable for hybridization with one or more nucleic acid molecules having a nucleic acid sequence of any one of SEQ ID NO;
5-24 or a complement thereof, or a nucleic acid sequence having between about 40% and about 100% contiguous nucleotides of any one of SEQ ID NO;
5-24, or a complement thereof, or a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides of SEQ ID NO;
5-24 or a complement thereof; and(e) detecting hybridization of the amplified nucleic acid product to one or more nucleic acid molecules, the presence or absence of hybridization being indicative of the presence or absence of one or more specific astroviruses.
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14. A method for diagnosing an individual having a disease or condition associated with an astrovirus, the method comprising:
determining the presence or absence of one or more nucleic acid molecules from a sample from the individual that hybridize to one or more nucleic acid molecules having a nucleic acid sequence of any one of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides or complements thereof, the presence or absence of one or more complexes indicates the presence or absence of the disease or condition.
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15. A method for monitoring treatment or efficacy of therapy for an individual having a disease or condition associated with an astrovirus, the method comprising:
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(a) determining the presence or absence of one or more nucleic acid molecules from at least two samples taken from the individual at different time points that hybridize to one or more nucleic acid molecules having a nucleic acid sequence one or more nucleic acid molecules having a nucleic acid sequence of any one of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides or complements thereof,(b) comparing the hybridization of the nucleic acid molecules in the samples, wherein said comparison indicates the efficacy of therapy.
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16. A device for the identification of one or more astrovirus serotypes, the device comprising a support having at least one array comprising a plurality of nucleic acid molecules deposited on the support in spatially distinct domains, the nucleic acid molecules having a nucleic acid sequence of any one of SEQ ID NO:
- 5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides or complements thereof. - View Dependent Claims (17, 18, 19, 20, 21, 22)
- 5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
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23. An isolated nucleic acid molecule from one or more astrovirus serotypes having a nucleic acid sequence of any one of SEQ ID NO:
- 5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides or complements thereof. - View Dependent Claims (24, 25)
- 5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
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26. A method of making a device for the identification of an astrovirus serotype comprising:
depositing on a support an array of spatially arranged domains one or more nucleic acid molecules having a nucleic acid sequence of any one of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 40% and about 100% of contiguous nucleotides of any of SEQ ID NO;
5-24 or complements thereof, a nucleic acid sequence having between about 9 and about 25 contiguous nucleotides or complements thereof.- View Dependent Claims (27, 28, 29, 30, 31)
Specification