Astrovirus species
AssigneeBlood Systems, Inc.
InventorsERIC DELWART, AMIT KAPOOR
Life of this patent
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Abstract
Provided herein are sequences of the genomes and encoded proteins of new astrovirus species, and variants thereof. Also provided are methods of detecting the new astrovirus species and diagnosing astrovirus infection, methods of treating or preventing astrovirus infection, and methods for identifying anti-astrovirus compounds. Provided are two new astrovirus species named HMOAstV-A and HMOAstV-B, and both are distantly related to known astroviruses. Also provided is a new method of classifying astroviruses, where there are three groups of human astroviruses, including HAstV, AstV-MLB, and HMOAstV.
Claims29
An isolated nucleic acid molecule comprising a nucleotide sequence having at least 75% identity to SEQ ID NO:1, SEQ ID NO:5, or a complement thereof, wherein the nucleotide sequence is at least 12, 20, 25, 30, 40, 50, 75, 100, or 200 nucleotides in length.
An isolated nucleic acid molecule comprising a nucleotide sequence that hybridizes under highly stringent conditions to at least 12, 25, 50, 100, or 150 contiguous nucleotides of a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:5, or a complement thereof, wherein the hybridization reaction is incubated at 42° C. in a solution comprising 50% formamide, 5×SSC, and 1% SDS and washed at 65° C. in a solution comprising 0.2×SSC and 0.1% SDS.
A substantially purified protein comprising an amino acid sequence at least 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7, and SEQ ID NO:8.
A method of detecting an astrovirus nucleic acid comprising:
- (a) contacting a sample suspected of containing an astrovirus nucleic acid with a nucleotide sequence that hybridizes under highly stringent conditions to a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:5, or a complement thereof;
- and
- (b) detecting the presence or absence of hybridization.
A method of detecting an astrovirus nucleic acid comprising:
- (a) amplifying the nucleic acid of a sample suspected of containing astrovirus nucleic acid with at least one primer that hybridizes to a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:5, or a complement thereof, to produce an amplification product;
- and
- (b) detecting the presence of an amplification product, thereby detecting the presence of the astrovirus nucleic acid.
A method of detecting an astrovirus infection in a sample comprising:
- (a) contacting a sample suspected of containing an astrovirus protein with an antibody that specifically binds to a polypeptide encoded by SEQ ID NO:1 or SEQ ID NO:5 to form a protein/antibody complex;
- and
- (b) detecting the presence of the protein/antibody complex, thereby detecting the presence of the astrovirus protein.
A kit for detecting an anstrovirus nucleic acid comprising at least one oligonucleotide primer that hybridizes to a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:5, or a complement thereof, under highly stringent PCR conditions.
A method of assaying for an anti-astrovirus compound comprising:
- (a) contacting a sample containing an astrovirus with a test compound, the astrovirus comprising a genome that hybridizes under highly stringent conditions to a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:5, or a complement thereof;
- and
- (b) determining whether the test compound inhibits astrovirus replication, wherein inhibition of astrovirus replication indicates that the test compound is an anti-astrovirus compound.
A method of treating or preventing an astrovirus infection in a subject comprising:
- administering to the subject an antigen encoded by an astrovirus, the astrovirus comprising a genome that hybridizes under highly stringent conditions to a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:5, or a complement thereof;
- thereby treating or preventing infection in the subject.
A method for detecting and serotyping astrovirus in a sample comprising:
- (a) contacting a first portion of the sample with a first pair of primers in a first amplification protocol, wherein the first pair of primers have an associated first characteristic amplification product if an astrovirus is present in the sample;
- (b) determining whether or not the first characteristic amplification product is present;
- (c) contacting a second portion of the sample with a second pair of primers in a second amplification protocol, wherein the second pair of primers have an associated second characteristic amplification product if an astrovirus is present in the sample and wherein the second pair of primers are different from the first pair of primers;
- (d) determining whether or not the second characteristic amplification product is present;
- (e) based on whether or not the first and second characteristic amplification product are present, selecting one or more subsequent pair of primers and contacting the one or more subsequent pair of primers with additional portions of the sample in subsequent amplification protocols, wherein each subsequent pair of primers is different from each pair of primers already used and wherein each subsequent pair of primers has an associated subsequent characteristic amplification product if an astrovirus is present in the sample;
- (f) determining whether or not the associated characteristic amplification product for each subsequent pair of primers used is present;
- (g) repeating steps (e) and (f) for one or more subsequent pairs of primers if the astrovirus cannot be serotyped based on the determinations of steps (b), (d), and (f) until the astrovirus can be serotyped, wherein the one or more subsequent pairs of primers are different from all pairs of primers used in earlier amplification protocols;
- and
- (h) determining the serotype or groups of serotypes of the astrovirus that may be present in the sample.
A method for detecting the presence of an astrovirus in a sample comprising:
- (a) purifying RNA contained in the sample;
- (b) reverse transcribing the RNA with primers effective to reverse transcribe astrovirus RNA to provide a cDNA;
- (c) contacting at least a portion of the cDNA with (i) a composition that promotes amplification of a nucleic acid and (ii) an oligonucleotide mixture wherein the mixture comprises at least one oligonucleotide that hybridizes to a highly conserved sequence of the sense strand of an astrovirus nucleic acid and at least one oligonucleotide that hybridizes to a highly conserved sequence of the antisense strand of an astrovirus nucleic acid;
- (d) carrying out an amplification procedure on the amplification mixture such that, if an astrovirus is present in the sample, an astrovirus amplicon is produced whose sequence comprises a nucleotide sequence of at least a portion of the astrovirus genome;
- and
- (e) detecting whether an amplicon is present;
- wherein the presence of the amplicon indicates that an astrovirus is present in the sample.
Dependencies are inferred from the claim text.