Patent Grant
9809863
This disclosure relates to Theiler's disease-associated virus (“TDAV”), reagents relating thereto, and methods for detecting, using, and/or treating diseases associated with TDAV.
Theiler's disease is a fulminant hepatic disease affecting horses. The cause of Theiler's disease has not yet been elucidated and represents a significant problem related to the diagnosis and treatment of the disease. The disease has been associated with the antecedent administration of biologics of equine origin (e.g., botulinal antitoxin, tetanus antitoxin). A significant delay between exposure to biologics and the onset of acute hepatitis has been observed and the associated histopathologic lesions in the liver determined to be remarkably similar to those associated with acute human hepatitis A virus or hepatitis B virus infection.
This disclosure describes a new virus that has now been linked to Theiler's disease (Theiler's disease-associated Virus (“TDAV”)). TDAV was determined to be a member of the Flaviviridae family that includes hepatitis C virus (HCV), GB virus B, canine hepacvirus (CHV), and equine Non-Primate Hepacivirus (NPHV). This new virus, the genomic nucleotide sequence, amino acid sequence, as well as compositions and methods for preparing, using, and/or detecting the same are described herein. Also provided are reagents and methods for detecting TDAV within biological samples. Thus, this disclosure provides a solution to the problems relating to the detection, diagnosis, treatment and prevention of Theiler's disease.
TDAV is disclosed herein to comprise the nucleic acid and amino acid sequences of SEQ ID NOS.: 1, 2 and/or 3. Nucleic acid molecules comprising such nucleic acid sequences and/or encoding such amino acid sequences are described. Methods and reagents for detecting TDAV (which may also include TDAV-like viruses), in a sample (e.g., a biological sample such as whole blood (e.g., undiluted or processed), cord blood, plasma, serum, cord serum, saliva, lymphatic fluid, cerebrospinal fluid, urine, semen, pleural fluid, breast milk, sweat, ascites, a tissue sample e.g. liver, a food (e.g., meat) or beverage (e.g., milk) product, etc.) are also provided herein. Compositions comprising TDAV, nucleic acids, peptides, and/or polypeptides corresponding to TDAV are also disclosed. Other embodiments are also provided, as described herein.
This disclosure relates to solutions to the current and unmet need for the identification and detection of the causitive agent(s) of diseases such as Theiler's Disease. As described herein, a possible causitive agent has been identified as Theiler's disease-associated virus (TDAV, which may include, for instance, “TDAV-like” viruses) as well as isolates and compositions thereof. Further provided are nucleic acid sequences and amino acid sequences representing the same (e.g., SEQ ID NOS.: 1-3). Nucleic acid molecules comprising such nucleic acid sequences and/or encoding such amino acid sequences are also provided. Methods and reagents for detecting TDAV (which may also include TDAV-like viruses), in a sample (e.g., a biological sample such as whole blood (e.g., undiluted or processed), cord blood, plasma, serum, cord serum, saliva, lymphatic fluid, cerebrospinal fluid, urine, semen, pleural fluid, breast milk, sweat, ascites, a tissue sample, a food (e.g., meat), beverage (e.g., milk) product, etc.), and/or organism (e.g., insect) are also provided herein. For instance, TDAV virus may be present in a biological sample of an animal (e.g., mammal) such as a horse. Such a horse (e.g., one having Theiler's disease) may have TDAV circulating in a bodily fluid such as, for instance, blood. In some embodiments, TDAV (e.g., a virus sharing at least some identity with that described herein) may be identified and/or detected by detecting and/or isolating the virus or a portion thereof from a biological sample. In some embodiments, TDAV may be detected by detecting a nucleic acid sequence and/or amino acid sequence of the virus, and/or the virus per se (e.g., as an intact virus or viral particle) in the biological sample. Other embodiments are also contemplated as will be clear to one of ordinary skill in the art from this disclosure.
TDAV typically comprises any one or more nucleic acid and/or amino acid sequences that correspond to, may be used to identify, and/or distinguish TDAV from another virus, and/or may be used to detect TDAV in a sample (e.g., a biological sample), and/or used to generate an antibody reactive with TDAV, such as, for example: SEQ ID NO.: 1 or 2 or a portion thereof; a nucleic acid sequence having at least about 50-99%, identity to SEQ ID NO.: 1 or 2 or a portion thereof; a nucleic acid sequence comprising at least any of five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive nucleotides of SEQ ID NO.: 1 or 2 or a portion thereof; a nucleic acid sequence encoding SEQ ID NO.: 3 or a portion thereof; a nucleic acid sequence encoding a polypeptide or peptide having at least about 50-99% identity to SEQ ID NO.: 3 or a portion thereof; a nucleic acid sequence encoding at least three, four, five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive amino acid residues of SEQ ID NO.: 3 or a portion thereof; a polypeptide comprising SEQ ID NO.: 3 or a portion thereof; a polypeptide having at least about 50-99% identity or similarity to SEQ ID NO.: 3 or a portion thereof; a peptide or polypeptide comprising at least three contiguous amino acids of SEQ ID NO.: 3 or a portion thereof, and the like. A suitable “portion of” SEQ ID NO.: 1, 2 or 3 may be, for example, any nucleotide sequence (e.g., an oligonucleotide) and/or amino acid sequence (e.g., a peptide or any amino acid sequence to which a binding agent (e.g., antibody) binds) of any number of nucleotides and/or amino acid residues that is specific to TDAV, may be used to identify TDAV, and/or may be used to differentiate TDAV from, for example, another virus in, for example, a biological sample (e.g., using an assay). The sequence of these nucleic acid sequences may be determined by any method available to those of ordinary skill in the art. Any of such nucleotide and/or amino acid sequences may be “unique to Theiler's disease-associated virus (TDAV)”. “Used to identify” may include the use of a binding of a binding agent having specificity for a nucleotide and/or amino acid sequence of TDAV described herein. A virus comprising any such nucleotide (e.g., within the viral genome) and/or amino acid sequence (e.g., expressed by the virus) described herein and/or binding to a binding agent having specificity therefor may be referred to herein as a “TDAV-like” virus. In some instances herein, “TDAV” and “TDAV-like” may be used interchangeably. Assays for identifying TDAV (e.g., within a product) may be conducted in any manner set forth herein or otherwise available to one of ordinary skill in the art. For instance, the assay may include the use of one or more oligonucleotides, primer pair(s), method(s), kit(s), solid support(s), and/or antibodies described herein. Other embodiments of such products are also contemplated as will be clear to one of ordinary skill in the art from this disclosure.
As described herein, Theiler's disease has been associated with the antecedent administration of biologics of equine origin (e.g., botulinal antitoxin, tetanus antitoxin, snake antitoxins, anti-thymocyte preparations, general colostral products and the like). It is therefore important to produce products that are known not to contain an infectious agent that may cause Theiler's disease. The reagents and methods described herein provide one of ordinary skill in the art to make such determinations. Accordingly, using the reagents and methods described herein (e.g., assays for detecting TDAV), one may provide a product (e.g., a biologic of equine origin such as botulinal antitoxin or tetanus antitoxin) that has been screened and/or assayed for the presence of a Theiler's disease-associated virus therein. In certain embodiments, the product may be derived from serum or plasma (e.g., horse serum or plasma). The product, for example, may be one screened and/or assayed to detect the presence of TDAV. A preferred “assayed product”, for instance, may be one determined not to contain TDAV and/or to contain less TDAV than the original product.
TDAV may be detected as a viral particle per se or a portion thereof (e.g., nucleic acid sequence and/or antigen) may be detected using any of several well-known techniques. A viral particle may be detected by, for example, observing the virus directly (e.g., by electron microscopy), detecting cells expressing an antigen of the virus (e.g., by staining and/or flow cytometry), and/or detecting a nucleic acid molecule (e.g., a target nucleic acid sequence) corresponding to the virus. Other techniques for detecting TDAV in a sample are also available to those of ordinary skill in the art and are contemplated herein.
TDAV nucleic acid sequences (and/or oligonucleotides used to identify and/or detect such nucleic acid sequences) may include those that hybridize (e.g., under highly stringent and/or moderately stringent conditions) to all or any portion of a hybridization probe having a nucleotide sequence encoding a polypeptide of SEQ ID NO.: 3 or a portion thereof, such as SEQ ID NOS.: 1 or 2 (or a complement thereof). The hybridizing portion of the hybridizing nucleic acid is typically at least about five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 nucleotides in length. The hybridizing portion is typically at least about 50%, 55%, 60%, 50-60%, 65%, 70%, 60-70%, 75% 80%, 70-80%, 85%, 90%, 80-90%, 95%, 95-99%, 97.5%, 99% or 100% identical to the nucleotide sequence to which it hybridizes. Hybridizing nucleic acids are useful, for example, as cloning probes, primers (e.g., PCR primer), and/or diagnostic probes. Nucleic acid duplex or hybrid stability is expressed as the melting temperature or Tm, which is the temperature at which a probe dissociates from a target DNA. This melting temperature is typically used to define the required stringency conditions. If sequences are identified that are related and substantially identical to the probe, rather than identical, then it is useful to first establish the lowest temperature at which only homologous hybridization occurs with a particular concentration of salt (e.g., SSC or SSPE). Assuming that a 1% mismatching results in a 1° C. decrease in Tm, the temperature of the final wash in the hybridization reaction is reduced accordingly (for example, if sequences having more than 95% identity are sought, the final wash temperature is decreased by 5° C.). In practice, the change in Tm can be between 0.5 and 1.5° C. per 1% mismatch. Highly stringent conditions may involve hybridizing at 68° C. in 5×SSC/5×Denhardt's solution/1.0% SDS, and washing in 0.2×SSC/0.1% SDS at room temperature. Moderately stringent conditions may include washing in 3×SSC at 42° C. Salt concentrations and temperatures can be varied to achieve the optimal level of identity between the probe and the target nucleic acid. Additional guidance regarding such conditions is readily available in the art, for example, in Molecular Cloning: A Laboratory Manual, Third Edition by Sambrook et al., Cold Spring Harbor Press, 2001.
A nucleic acid sequence corresponding to (e.g., sharing at least some identity with) TDAV may also be a “target nucleic acid” and/or “target nucleic acid sequence” (which terms may be used interchangeably). A target nucleic acid sequence may be detected and/or identified and/or quantified by any of several techniques widely available in the art. The target nucleic acid sequence may, for example, correspond to SEQ ID NO.: 1 and/or encode any number of contiguous amino acid residues (e.g., at least any of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive amino acid residues) encoded thereby (e.g., the amino acid sequence encoded by nucleotides 618-10,479 of SEQ ID NO.: 1 (including stop codon GTG) and/or as in SEQ ID NO.: 2)) and/or a derivative thereof. In some embodiments, the target nucleic acid sequence may be at least about 50%, 55%, 60%, 50-60%, 65%, 70%, 60-70%, 75% 80%, 70-80%, 85%, 90%, 80-90%, 95%, 95-99%, 97.5%, 99% or 100% complementary (e.g., identical to or capable of binding to under, for instance, stringent nucleic acid hybridization conditions) to a portion of or over the entirely of nucleic acid sequence of TDAV (e.g., SEQ ID NO.: 1). The target nucleic acid sequence may comprise a region (e.g., a “target-specific region”) that is, for instance, about 4-30, about 5-25, about 6-20, about 7-15, about 8-10, about 10-15, about 15-20, about 20-25, about 25-30, about 30-35, about 35-40, about 40-45, about 45-50 or more nucleotides in length.
The target nucleic acid sequence may be of any kind such as, for example, single- or double-stranded RNA, DNA, or a RNA/DNA hybrid, for example. In some embodiments, the target nucleic acid may be contained on a RNA (e.g., as in the case of simultaneous analysis of gene expression by RT-PCR) or DNA molecule (e.g., cDNA). Target nucleic acid preparation may be carried out in a manner appropriate for the particular detection process to be implemented, as would be known by those of ordinary skill in the art. For example, DNA or RNA nucleic acid molecules may be extracted from any type of sample (e.g., blood) and processed according to standard procedures. Typically, detection involves the use of a nucleic acid (e.g., an oligonucleotide (e.g., probe)) that hybridizes to and/or may be used to amplify (e.g., is specific for) a target nucleic acid sequence. In some embodiments, 1-1000 different oligonucleotides (e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11-50, 51-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, or 951-1000 oligonucleotides) may be used separately or together in a single or multiple reactions to detect and/or identify and/or detect one or more target nucleic acid sequences in a sample. Suitable, exemplary detection techniques may include northern blot and/or polymerase chain reaction and/or variations thereof. Other techniques may also be utilized as may be described herein or elsewhere.
A commonly used technique for detecting nucleic acids involves amplification of one or more target nucleic acids (which may or may not also include one or more non-target nucleic acids) prior to detection and/or identification. Any amplification and/or detection method may be used. The method used to amplify the target nucleic acid(s) may be chosen from any one or more methods available to one of skill in the art including but not limited to linear, logarithmic, and/or any other amplification methods. While the term “amplifying” typically refers to an “exponential” increase in target nucleic acid (e.g., as in a polymerase chain reaction (“PCR”)), the term may be used herein to describe both linear and exponential increases in the numbers of the target nucleic acid sequence(s). The term “amplification reaction mixture” typically refers to an aqueous solution comprising the various reagents used to amplify the target nucleic acid sequence(s) such as, for example, enzyme(s), aqueous buffer(s), salt(s), oligonucleotide(s) (e.g., amplification primer(s)), target nucleic acid, and nucleoside triphosphates. Depending upon the context, the mixture can be either a complete or incomplete amplification reaction mixture. Exemplary methods include polymerase chain reaction (PCR; see, e.g., U.S. Pat. Nos. 4,683,202; 4,683,195; 4,965,188; and/or 5,035,996), isothermal procedures (using one or more RNA polymerases (see, e.g., WO 2006/081222)), strand displacement (see, e.g., U.S. Pat. No. RE39007E), partial destruction of primer molecules (see, e.g., WO2006087574)), ligase chain reaction (LCR) (see, e.g., Wu, et al., Genomics 4: 560-569 (1990) and/or Barany, et al. PNAS USA 88:189-193 (1991)), Qβ RNA replicase systems (see, e.g., WO/1994/016108), RNA transcription-based systems (e.g., TAS, 3SR), rolling circle amplification (RCA) (see, e.g., U.S. Pat. No. 5,854,033; U.S. Pub. No. 2004/265897; Lizardi et al. Nat. Genet. 19: 225-232 (1998); and/or Barrer et al. Nucleic Acid Res., 26: 5073-5078 (1998)), and/or strand displacement amplification (SDA) (Little, et al. Clin Chem 45:777-784 (1999)), among others. In some embodiments, such as while carrying out PCR, the melting temperature (e.g., Tm) of the target nucleic acid sequence (or region thereof, e.g., a “target specific region”) may be about 5° C. below the anneal/extend temperature used for PCR cycling. In some embodiments, the Tm of the target specific region may range from about 51° C. to 60° C., about 52° C. to 59° C., about 53° C. to 58° C., about 54° C. to 57° C., about 55° C. to 56° C., or about 50° C. to about 60° C. Many systems are suitable for use in amplifying target nucleic acid sequences and are contemplated herein as would be understood by one of skill in the art.
In some embodiments, amplification may be accomplished by forming a reaction mixture containing the biological sample comprising nucleic acid of TDAV (or, e.g., a target nucleic acid thereof), a nucleic acid molecule such as a plasmid and/or oligonucleotide (optionally comprising a detectable label) corresponding to TDAV, and other reagents that may be required (e.g., buffers, enzymes (e.g., polymerase)) to amplify and/or detect and/or identify and/or quantify the target nucleic acid. In some embodiments, these methods may involve isolating and/or amplifying the target nucleic acid, and detecting the same using an oligonucleotide probe (e.g., an oligonucleotide corresponding to the nucleotide sequence of the TDAV-like virus described herein). For instance, for a PCR reaction, a pair of primers (a “forward” and a “reverse” primer) such as:
Variants of such target nucleic acids may also be suitable, as would other target nucleic acids that correspond to TDAV.
In some embodiments, the methods may involve preparing a sample of RNA and processing the same using a northern blot technique in which target nucleic acid is detected using an oligonucleotide probe that may include a detectable label. A suitable probe in a northern blot reaction may include any corresponding to TDAV such as, for instance, SEQ ID NO.: 3, which may include a detectable label. The types and/or amount of sample nucleic acid and/or primer and/or probe used in such reactions may vary as would be understood by one of ordinary skill in the art. For example, an amplification reaction may be performed using a nucleic acid polymerase (e.g., Taq polymerase), at least one oligonucleotide primer capable of specifically hybridizing to a target polynucleotide (typically two oligonucleotides as would be used in a polymerase chain reaction (PCR)) and, optionally, at least one (directly or indirectly) detectable oligonucleotide probe that hybridizes to the amplified target nucleic acid. A detectable label and/or probe may, for instance, be incorporated into the at least one oligonucleotide primer and/or probe. In some embodiments, at least one detectable nucleic acid binding agent (e.g., an intercalating or non-intercalating dye) may also be introduced before, during or after amplification. Any of these or other methods may be used to detect a TDAV in a sample as would be understood by one of ordinary skill in the art.
The oligonucleotide probe(s) described above may contain a detectable label that provides a signal that may be monitored to ascertain whether the target nucleic acid sequence has been amplified. Many different reagents, systems, and/or detectable labels may be used in the methods described herein. These include, for example, TaqMan® systems, detectable label-quencher systems (e.g., FRET, salicylate/DTPA ligand systems (see, e.g., Oser et al. Angew. Chem. Int. Engl. 29(10):1167 (1990), displacement hybridization, homologous probes, assays described in EP 070685), molecular beacons (e.g., NASBA), Scorpion, locked nucleic acid (LNA) bases (Singh, et al. Chem Commum 4:455-456 (1998)), peptide nucleic acid (PNA) probes (Pellestor, et al. European J. Human Gen. 12:694-700 (2004)), Eclipse probes (Afonina, et al. Biotechniques 32:940-949 (2002)), light-up probes (Svanvik, et al. Anal Biochem 281:26-35 (2001)), molecular beacons (Tyagi, et al. Nat. Biotechnol. 14:303-308 (1996)), tripartite molecular beacons (Nutiu, et al. Nucleic Acids Res. 30:e94 (2002)), QuantiProbes (www.qiagen.com), HyBeacons (French, et al. Mol. Cell. Probes 15:363-374 (2001)), displacement probes (Li, et al. Nucliec Acids Res. 30:e5 (2002)), HybProbes (Cardullo, et al. PNAS 85:8790-8794 (1988)), MGB Alert (www.nanogen.com), Q-PNA (Fiandaca, et al. Genome Res. 11:609-611 (2001)), Plexor (www.Promega.com), LUX primers (Nazarenko, et al. Nucleic Acids Res. 30:e37 (2002)), Scorpion primers (Whitcombe, et al. Nat Biotechnol 17:804-807 (1999)), AmpliFluor (Sunrise) primers (Nazarenko, et al. Nucleic Acids Res. 25:2516-2521 (1997)), DzyNA primers (Todd, et al. Clin. Chem. 46:625-630 (2000)), and the like. In each of these assays, the generation of amplification products may be monitored while the reaction is in progress. An apparatus for detecting the signal generated by the detectable label may be used to detect, measure, and quantify the signal before, during, and/or after amplification. The particular type of signal may dictate the choice of detection method. For example, in some embodiments, fluorescent dyes are used to label probes and/or amplified products. The probes may bind to single-stranded and/or double-stranded amplified products, and/or the dyes intercalate into the double-stranded amplified products, and consequently, the resulting fluorescence increases as the amount of amplified product increases. In some embodiments, the Tm may be ascertained by observing a fluorescence decrease as the double-stranded amplified product dissociates and the intercalating dye is released therefrom. The amount of fluorescence may be quantitated using standard equipment such as a spectra-fluorometer, for example. One or more detectable labels and/or quenching agents may also be attached to a primer or probe. The detectable label may emit a signal when free or when bound to one the target nucleic acid. The detectable label may also emit a signal when in proximity to another detectable label. Detectable labels may also be used with quencher molecules such that the signal is only detectable when not in sufficiently close proximity to the quencher molecule. For instance, in some embodiments, the assay system may cause the detectable label to be liberated from the quenching molecule. Any one or more of such detectable labels may be used to label and/or detect the primers and/or probes used in the methods described herein. As mentioned above, in some embodiments the detectable label may be attached to a probe, which may be incorporated into a primer, or may otherwise bind to amplified target nucleic acid (e.g., a detectable nucleic acid binding agent such as an intercalating or non-intercalating dye). In some embodiments, the probe is an oligonucleotide that hybridizes to a target nucleic acid 3′ relative to the at least one primer. In some embodiments, the polymerase has nuclease activity (e.g., 5′-3′) for releasing the probe from the amplified nucleic acid. In some embodiments, release from the amplified nucleic acid renders the probe detectable. In some embodiments, the probe may have a detectable label and a quencher molecule that quenches the detectable label when free but does not quench when the probe is hybridized to the amplified nucleic acid. In some embodiments, two or more probes may be used where at least one probe has a detectable label and at least one other probe has a quencher molecule. When in sufficiently close proximity of one another, the quencher molecule typically suppresses the signal of the detectable label on the other probe. In some embodiments, two or more probes, each having a different detectable label, may be used without quencher molecules. In such embodiments, the probes may be rendered detectable (e.g., de novo or by exhibiting a different signal than either probe alone) when in sufficiently close proximity to one another. Such reactions may also be combined with other detection steps, such as melting temperature analysis and the like. When using more than one detectable label, each should differ in their spectral properties such that the labels may be distinguished from each other, or such that together the detectable labels emit a signal that is not emitted by either detectable label alone.
Exemplary detectable labels include, for instance, a fluorescent dye or fluorphore (e.g., a chemical group that can be excited by light to emit fluorescence or phosphorescence), “acceptor dyes” capable of quenching a fluorescent signal from a fluorescent donor dye, and the like. Suitable detectable labels may include, for example, fluorosceins (e.g., 5-carboxy-2,7-dichlorofluorescein; 5-Carboxyfluorescein (5-FAM); 5-HAT (Hydroxy Tryptamine); 5-Hydroxy Tryptamine (HAT); 6-JOE; 6-carboxyfluorescein (6-FAM); FITC); Alexa fluors (e.g., 350, 405, 430, 488, 500, 514, 532, 546, 555, 568, 594, 610, 633, 635, 647, 660, 680, 700, 750); BODIPY fluorophores (e.g., 4921515, 493/503, 500/510, 505/515, 530/550, 542/563, 558/568, 564/570, 576/589, 581/591, 630/650-X, 650/665-X, 665/676, FL, FL ATP, FI-Ceramide, R6G SE, TMR, TMR-X conjugate, TMR-X, SE, TR, TR ATP, TR-X SE), coumarins (e.g., 7-amino-4-methylcoumarin, AMC, AMCA, AMCA-S, AMCA-X, ABQ, CPM methylcoumarin, coumarin phalloidin, hydroxycoumarin, CMFDA, methoxycoumarin), calcein, calcein AM, calcein blue, calcium dyes (e.g., calcium crimson, calcium green, calcium orange, calcofluor white), Cascade Blue, Cascade Yellow; Cy™ dyes (e.g., 3, 3.18, 3.5, 5, 5.18, 5.5, 7), cyan GFP, cyclic AMP Fluorosensor (FiCRhR), fluorescent proteins (e.g., green fluorescent protein (e.g., GFP. EGFP), blue fluorescent protein (e.g., BFP, EBFP, EBFP2, Azurite, mKalamal), cyan fluorescent protein (e.g., ECFP, Cerulean, CyPet), yellow fluorescent protein (e.g., YFP, Citrine, Venus, YPet), FRET donor/acceptor pairs (e.g., fluorescein/tetramethylrhodamine, IAEDANS/fluorescein, EDANS/dabcyl, fluorescein/fluorescein, BODIPY FL/BODIPY FL, Fluorescein/QSY7 and QSY9), LysoTracker and LysoSensor (e.g., LysoTracker Blue DND-22, LysoTracker Blue-White DPX, LysoTracker Yellow HCK-123, LysoTracker Green DND-26, LysoTracker Red DND-99, LysoSensor Blue DND-167, LysoSensor Green DND-189, LysoSensor Green DND-153, LysoSensor Yellow/Blue DND-160, LysoSensor Yellow/Blue 10,000 MW dextran), Oregon Green (e.g., 488, 488-X, 500, 514); rhodamines (e.g., 110, 123, B, B 200, BB, BG, B extra, 5-carboxytetramethylrhodamine (5-TAMRA), 5 GLD, 6-Carboxyrhodamine 6G, Lissamine, Lissamine Rhodamine B, Phallicidine, Phalloidine, Red, Rhod-2, 5-ROX (carboxy-X-rhodamine), Sulphorhodamine B can C, Sulphorhodamine G Extra, Tetramethylrhodamine (TRITC), WT), Texas Red, Texas Red-X, VIC and other labels described in, e.g., US Pub. No. 2009/0197254), among others as would be known to those of skill in the art. Other detectable labels may also be used (see, e.g., US Pub. No. 2009/0197254), as would be known to those of skill in the art. The use of other methods and/or reagents is also contemplated herein as would be understood by one of skill in the art.
Polymerase enzymes suitable for the practicing the methods described herein are well known in the art and can be derived from a number of sources. For instance, thermostable polymerases may be obtained from a variety of thermophilic bacteria that are commercially available (for example, from American Type Culture Collection, Rockville, Md.) using methods that are well-known to one of ordinary skill in the art (see, e.g., U.S. Pat. No. 6,245,533). Bacterial cells may be grown according to standard microbiological techniques, using culture media and incubation conditions suitable for growing active cultures of the particular species that are well-known to one of ordinary skill in the art (See, e.g., Brock, T. D., and Freeze, H., J. Bacteriol. 98(1):289-297 (1969); Oshima, T., and Imahori, K, Int. J. Syst. Bacteriol. 24(1):102-112 (1974)). Suitable sources of thermostable polymerases may include the thermophilic bacteria Thermus aquaticus, Thermus thermophilus, Thermococcus litoralis, Pyrococcus furiosus, Pyrococcus woosii and other species of the Pyrococcus genus, Bacillus stearothermophilus, Sulfolobus acidocaldarius, Thermoplasma acidophilum, Thermus flavus, Thermus ruber, Thermus brockianus, Thermotoga neapolitana, Thermotoga maritima and other species of the Thermotoga genus, and Methanobacterium thermoautotrophicum, and mutants of each of these species. Preferable thermostable polymerases can include, but are not limited to, Taq DNA polymerase, Tne DNA polymerase, Tma DNA polymerase, or mutants, derivatives or fragments thereof.
Sources of nucleic acids (e.g., target nucleic acids) in the compositions, methods and/or kits include, but are not limited to, biological samples (e.g., mammalian, non-mammalian) described herein. For instance, mammalian tissue, blood, cultured cells, and/or other culture samples (e.g., containing virus) may also be suitable sources of template nucleic acids. In addition, viruses, bacteriophage, bacteria, fungi and other micro-organisms may be the source of nucleic acid for analysis. The DNA may be genomic or it may be cloned in plasmids, bacteriophage, bacterial artificial chromosomes (BACs), yeast artificial chromosomes (YACs) or other vectors. RNA may be isolated directly from the relevant cells or it may be produced by in vitro priming from a suitable RNA promoter or by in vitro transcription. Other sources may also be suitable as would be understood by one of ordinary skill in the art.
Nucleic acid molecules corresponding to and/or derived from and/or encoding TDAV and/or an antigen (or immunogen) thereof may also be contained within a vector (e.g., a recombinant vector) such as one or more non-viral and/or viral vectors. In one embodiment, such a vector may be utilized to deliver such nucleic acid molecules (e.g., to a cell in vitro or in vivo). Where such vectors are used to induce and/or enhance an immune response, the vector may also encode other proteins (e.g., co-stimulatory molecules, cytokines or chemokines) and/or be combined with other factors (e.g., exogenous cytokines) (Xiang et al., Immunity, 2:129-135, 1995; Kim et al., Eur. J. Immunol., 28:1089-1103, 1998; Iwasaki et al., J. Immunol. 158:4591-3601, 1997; Sheerlinck et al., Vaccine, 19:2647-2656, 2001). Other strategies may also be utilized to improve the efficiency of such delivery systems including, for example, the use of self-replicating viral replicons (Caley et al., Vaccine, 17:3124-2135, 1999; Dubensky et al., Mol. Med. 6:723-732, 2000; Leitner et al., Cancer Res. 60: 51-55, 2000), codon optimization (Liu et al., Mol. Ther., 1:497-500, 2000; Dubensky, supra; Huang, et al., J. Virol. 75:4947-4951, 2001), in vivo electroporation (Widera et al., J. Immunol. 164:4635-3640, 2000), incorporation of stimulatory motifs such as CpG (Gurunathan, supra; Leitner, supra), sequences for targeting of the endocytic or ubiquitin-processing pathways (Thomson et al., J. Virol. 72:2246-2252, 1998; Velders et al., J. Immunol. 166:5366-5373, 2001), prime-boost regimens (Gurunathan supra; Sullivan et al., Nature 408:605-609, 2000; Hanke et al., Vaccine, 16:439-445, 1998; Amara et al., Science 292:69-74, 2001), proteasome-sensitive cleavage sites, and the use of mucosal delivery. “Non-viral” vectors may include, for instance, plasmid vectors (e.g., compatible with bacterial, insect, and/or mammalian host cells). Exemplary vectors may include, for example, PCR-ii, PCR3, and pcDNA3.1 (Invitrogen, San Diego, Calif.), pBSii (Stratagene, La Jolla, Calif.), pet15 (Novagen, Madison, Wis.), pGEX (Pharmacia Biotech, Piscataway, N.J.), pEGFp-n2 (Clontech, Palo Alto, Calif.), pETI (Bluebacii, Invitrogen), pDSR-alpha (PCT pub. No. WO 90/14363) and pFASTBACdual (Gibco-BRL, Grand island, NY) as well as Bluescript® plasmid derivatives (a high copy number COLe1-based phagemid, Stratagene Cloning Systems, La Jolla, Calif.), PCR cloning plasmids designed for cloning TAQ-amplified PCR products (e.g., TOPO™ TA Cloning® kit, PCR2.1® plasmid derivatives, Invitrogen, Carlsbad, Calif.). Bacterial vectors may also be used including, for instance, Shigella, Salmonella (e.g., for mucosal delivery), Vibrio cholerae, Lactobacillus, Bacille Calmette Guérin (BCG), and Streptococcus (see for example, WO 88/6626; WO 90/0594; WO 91/13157; WO 92/1796; and WO 92/21376). The vectors may be constructed using standard recombinant techniques widely available to one skilled in the art. Many other non-viral plasmid expression vectors and systems are known in the art and may be used. Various viral vectors that have been successfully utilized for introducing a nucleic acid to a host include retrovirus, adenovirus, adeno-associated virus (AAV), herpes virus, and poxvirus, among others. Viral vectors may be constructed using standard recombinant techniques widely available to one skilled in the art.
Other delivery techniques may also suffice including, for example, DNA-ligand complexes, adenovirus-ligand-DNA complexes, direct injection of DNA, CaPO4 precipitation, gene gun techniques, electroporation, and colloidal dispersion systems. Colloidal dispersion systems include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. The preferred colloidal system is a liposome, which are artificial membrane vesicles useful as delivery vehicles in vitro and in vivo. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley, R. et al. Trends Biochem. Sci., 6:77, 1981). The composition of the liposome is usually a combination of phospholipids, particularly high-phase-transition-temperature phospholipids, usually in combination with steroids, especially cholesterol. Other phospholipids or other lipids may also be used. The physical characteristics of liposomes depend on pH, ionic strength, and the presence of divalent cations. Examples of lipids useful in liposomes include, for instance, phosphatidyl compounds, such as phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides. Particularly useful are diacylphosphatidylglycerols, where the lipid moiety contains from 14-18 carbon atoms, particularly from 16-18 carbon atoms, and is saturated. Illustrative phospholipids include egg phosphatidylcholine, dipalmitoylphosphatidylcholine and distearoylphosphatidylcholine.
As would be understood by those of ordinary skill in the art, methods for preparing and using such non-viral vectors, viral vectors, and variations thereof are available in the art. For instance, useful techniques may be found in common molecular biology references such as Molecular Cloning: A Laboratory Manual (Sambrook et al., Cold Spring Harbor Laboratory Press, 1989), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), and PCR Protocols: A Guide to Methods and Applications (Innis et al., 1990. Academic Press, San Diego, Calif.), for instance.
TDAV polypeptides described herein may be the same as or similar to those specific to TDAV (e.g., SEQ ID NO.: 3 or a portion thereof), and may contain and/or be modified to contain substitutions that may be considered, for instance, conservative or non-conservative. A conservative substitution may be, for example, the substitution of one type of amino acid residue with a similar type of amino acid residue. A non-conservative substitution may be, for example, the substitution of one type of amino acid residue with a different type of amino acid residue. Amino acids may be similar to one another if, for example, based on size, hydrophobicity, polarity, aliphaticity (or not), aromaticity (or lack thereof), charge (positive or negative), or other attributes. Non-limiting, exemplary and preferred substitutions are shown in Table 1:
A cultured cell comprising nucleic acid molecules corresponding to and/or derived from and/or encoding TDAV and/or an antigen (or immunogen) thereof may also be provided. The cultured cell may be transfected and/or infected by a vector or progeny thereof such that the may express a polypeptide (e.g., an antigen). Suitable cell lines are known to those of skill in the art and are commercially available, for example, through established cell culture collections. Such cells may then be used to produce viral particles, polypeptides, reagents for detecting and/or isolating TDAV, or for other uses. An exemplary method may comprise culturing a cell comprising the nucleic acid molecule (e.g., optionally under the control of an expression sequence) under conditions that allow for the production of viral particles or expression a polypeptide. The viral particle, polypeptide and/or other reagent may then be isolated from the cell or the cell culture medium using standard techniques.
Binding agents reactive with antigens of TDAV are also provided. For example, an antigen of TDAV may include any minimum number of contiguous amino acid residues (e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) of SEQ ID NO.: 3 (and/or encoded by SEQ ID NO.: 1 and/or SEQ ID NO.: 2) unique to TDAV. The binding agent may therefore be utilized to identify, isolate and/or remove TDAV from a sample (e.g., a biological sample). As described above, in some embodiments, binding agents may be antibodies. The term “antibody” or “antibodies” may refer to whole or fragmented antibodies in unpurified or partially purified form (e.g., hybridoma supernatant, ascites, polyclonal antisera) or in purified form, or to derivatives of antibodies. A purified antibody may be one that is separated from at least about 50%, 60%, 75%, 90%, or 95% of the proteins with which it is initially found (e.g., as part of a hybridoma supernatant or ascites preparation). The antibodies may be of any suitable origin or form including, for example, murine (e.g., produced by murine hybridoma cells), or expressed as humanized antibodies, chimeric antibodies, human antibodies, and the like. For instance, antibodies may be of any suitable type including, for example, human (e.g., IgG (IgG1, IgG2, IgG3, IgG4), IgM, IgA (IgA1 and IgA2), IgD, and IgE), canine (e.g., IgGA, IgGB, IgGC, IgGD), chicken (e.g., IgA, IgD, IgE, IgG, IgM, IgY), goat (e.g., IgG), mouse (e.g., IgG, IgD, IgE, IgG, IgM), pig (e.g., IgG, IgD, IgE, IgG, IgM), rat (e.g., IgG, IgD, IgE, IgG, IgM) and/or a fragment and/or derivative thereof (e.g., as chimeric antibodies). Suitable derivatives may include, for example, an Fab, F(ab′)2, Fab′ single chain antibody, Fv, single domain antibody, mono-specific antibody, bi-specific antibody, tri-specific antibody, multi-valent antibody, chimeric antibody, canine-human chimeric antibody, canine-mouse chimeric antibody, antibody comprising a canine Fc, humanized antibody, human antibody, caninized, CDR-grafted antibody, shark antibody, nanobody (e.g., antibody consisting of a single monomeric variable domain), camelid antibody (e.g., antibodies of members of the Camelidae family), microbody, intrabody (e.g., intracellular antibody), or mimetic. Mimetics may also include, for example, organic compounds that specifically bind TDAV virus or an antigen thereof such as, for example, an affibody (Nygren, et al., FEBS J. 275(11):2668-76, 2008), affilin (Ebersbach, et al., J. Mol. Biol. 372 (1):172-85, 2007), affitin (Krehenbrink et al., J. Mol. Biol. 383(5):1058-68, 2008), anticalin (Skerra, A., FEBS J. 275(11):2677-83, 2008), avimer (Silverman et al., Nat. Biotechnol. 23(12): 1556-61, 2005), DARPin (Stumpp et al., Drug Discov. Today 13(15-16):695-701, 2008), Fynomer (Grabulovski et al., J. Biol. Chem. 282(5):3196-3204, 2007), Kunitz domain peptide (Nixon et al., Curr. Opin. Drug Discov. Devel. 9(2):261-8, 2006), and/or a monobody (Koide et al., Methods Mol. Biol. 352:95-109, 2007). Other binding agents are also provided herein as would be understood by one of ordinary skill in the art.
Methods of preparing and utilizing various types of antibodies are well-known to those of skill in the art and would be suitable in practicing the present invention (see, for example, Harlow, et al. Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; Harlow, et al., Using Antibodies: A Laboratory Manual, Portable Protocol No. 1, 1998; Kohler and Milstein, Nature, 256:495, 1975; Jones et al., Nature, 321:522-525, 1986; Riechmann et al., Nature, 332:323-329, 1988; Presta, Curr. Op. Struct. Biol. 2:593-596, 1992; Verhoeyen et al., Science, 239:1534-1536, 1988; Hoogenboom et al., J. Mol. Biol., 227:381, 1991; Marks et al., J. Mol. Biol., 222:581, 1991; Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77, 1985; Boerner et al., J. Immunol., 147(1):86-95, 1991; Marks et al., Bio/Technology 10, 779-783, 1992; Lonberg et al., Nature 368:856-859, 1994; Morrison, Nature 368:812-13, 1994; Fishwild et al., Nature Biotechnology 14, 845-51, 1996; Neuberger, Nature Biotechnology 14, 826, 1996; Lonberg and Huszar, Intern. Rev. Immunol. 13:65-93, 1995; as well as U.S. Pat. Nos. 4,816,567, 5,545,807, 5,545,806, 5,569,825, 5,625,126, 5,633,425, and 5,661,016). In certain applications, the antibodies may be contained within hybridoma supernatant or ascites and utilized either directly as such or following concentration using standard techniques. In other applications, the antibodies may be further purified using, for example, salt fractionation and ion exchange chromatography, or affinity chromatography using Protein A, Protein G, Protein A/G, and/or Protein L ligands covalently coupled to a solid support such as agarose beads, or combinations of these techniques. The antibodies may be stored in any suitable format, including as a frozen preparation (e.g., −20° C. or −70° C.), in lyophilized form, or under normal refrigeration conditions (e.g., 4° C.). When stored in liquid form, a suitable buffer such as Tris-buffered saline (TBS) or phosphate buffered saline (PBS) may be utilized.
Where the binding agent is an antibody, it may be identified with reference to the nucleotide and/or amino acid sequence corresponding to the variable and/or complementarity determining regions (“CDRs”) thereof. For instance, an exemplary binding agent that is, is derived from, or is related to the monoclonal antibody that binds TDAV or antigen thereof may comprise a heavy and/or a light chain that each comprise one or more constant and/or variable regions. The variable regions typically comprise one or more CDRs that in large part determine the binding specificity of the antibody. These monoclonal antibodies may be identified by analysis of the nucleotide sequences encoding the variable regions. The monoclonal antibodies may also be identified by analysis of the amino acid sequences of (e.g., which may be encoded by the nucleotide sequences) the variable regions. The binding agent may also be a derivative of an antibody (of, for example, the monoclonal antibody 1E4, 1G10, and/or 1G1) such as, for example, an Fab, F(ab′)2, Fab′ single chain antibody, Fv, single chain, mono-specific antibody, bi-specific antibody, tri-specific antibody, multi-valent antibody, chimeric antibody, canine-human chimeric antibody, canine-mouse chimeric antibody, antibody comprising a canine Fc, humanized antibody, human antibody, caninized, CDR-grafted antibody, shark antibody, nanobody (e.g., antibody consisting of a single monomeric variable domain), camelid antibody (e.g., antibodies members of the Camelidae family) microbody, intrabody (e.g., intracellular antibody), and/or de-fucosylated antibody and/or derivative thereof. Mimetics of binding agents and/or antibodies are also provided. The binding agent may also comprise a detectable label and/or function/effector moiety fixably attached thereto. Functional/effector moieties may include, for example, cytotoxic drugs or toxins, or active fragments thereof such as diphtheria A chain, exotoxin A chain, ricin A chain, abrin A chain, curcin, crotin, phenomycin, enomycin, among others. Functional moieties may also include radiochemicals. In one embodiment, the effector moieties may be fixably attached to the binding agents. In one example, the detectable labels are fixably attached to the binding agents by chemical bonds. In one example, the chemical bonds are covalent chemical bonds. In one example, the effector moieties are conjugated to the binding agents.
The skilled artisan has many suitable techniques available for using the binding agents (e.g., antibodies) described herein to identify biological samples containing proteins that bind thereto. For instance, antibodies may be utilized to isolate TDAV and/or an antigen thereof using, for example, immunoprecipitation or other capture-type assay. This well-known technique may be performed by attaching the antibody to a solid support or chromatographic material (e.g., a bead coated with Protein A, Protein G and/or Protein L), contacting a sample (e.g., a solution) either containing or believed to contain the TDAV and/or an antigen thereof (e.g., a biological sample such as blood) with the material such that the TDAV and/or an antigen thereof binds to the antibody, thereby separating it from other components in the sample. The bound TDAV and/or an antigen thereof may then be separated from the antibody and analyzed as desired. Similar methods for isolating TDAV and/or an antigen thereof using a binding agent are well-known in the art. The binding agents (e.g., antibodies) may also be utilized to detect, isolate, and/or remove TDAV and/or an antigen thereof within or from a biological sample. Assays such as, for example, flow cytometric analysis, ELISA, immunoblotting (e.g., western blot), in situ detection, immunocytochemistry, and/or immunohistochemistry may be utilized in such methods. Other uses for the binding agents described herein may also be suitable, as would many other methods and/or assay systems.
In certain embodiments, preparations and/or compositions comprising the TDAV viral particles, nucleic acids corresponding thereto (e.g., contained within a vector), polypeptides and/or peptides corresponding thereto, and/or binding agents thereof are also provided. For example, a preparation or composition may comprise, for example, a TDAV viral particle, nucleic acid, polypeptide, peptide, and/or binding agent as a partially purified (e.g., about any of 50%, 60%, 75%, 90%, 95% purity (e.g., w/w)) or purified (e.g., about 98-100% (w/w)) preparation or composition. Typically, such preparations include a buffer such as phosphate- or tris-buffered saline (PBS or TBS, respectively). The preparations may also be formulated to contain excipients, like stabilizers, for example. The TDAV viral particles, nucleic acids corresponding thereto (e.g., contained within a vector), polypeptides and/or peptides corresponding thereto, and/or binding agents thereof may also be combined with one or more pharmaceutically acceptable carriers prior to use (e.g., administration to a host). A pharmaceutically acceptable carrier may be a material that is not biologically or otherwise undesirable, e.g., the material may be administered to a cell and/or subject, without causing significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
Suitable pharmaceutical carriers and their formulations that may be suitable are available to those of ordinary skill in the art as described in, for example, Remington's: The Science and Practice of Pharmacy, 21st Edition, David B. Troy, ed., Lippicott Williams & Wilkins (2005). Typically, an appropriate amount of a pharmaceutically-acceptable salt is used in the formulation to render the formulation isotonic. Examples of the pharmaceutically-acceptable carriers include, but are not limited to, sterile water, saline, buffered solutions like Ringer's solution, and dextrose solution. The pH of the solution is generally from about 5 to about 8 or from about 7 to about 7.5. Other carriers include sustained-release preparations such as semipermeable matrices of solid hydrophobic polymers containing polypeptides or fragments thereof. Matrices may be in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered. Pharmaceutical compositions may also include carriers, thickeners, diluents, buffers, preservatives, surface active agents, adjuvants, immunostimulants, in addition to the binding agent and/or nucleic acid. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, antiinflammatory agents and anesthetics. Adjuvants may also be included in the immunuostimulatory compositions to stimulate or enhance the immune response. Non-limiting examples of suitable classes of adjuvants include those of the gel-type (e.g., aluminum hydroxide/phosphate (“alum adjuvants”), calcium phosphate, microbial origin (muramyl dipeptide (MDP)), bacterial exotoxins (cholera toxin (CT), native cholera toxin subunit B (CTB), E. coli labile toxin (LT), pertussis toxin (PT), CpG oligonucleotides, BCG sequences, tetanus toxoid, monophosphoryl lipid A (MPL) of, for example, E. coli, Salmonella minnesota, Salmonella typhimurium, or Shigella exseri), particulate adjuvants (biodegradable, polymer microspheres), immunostimulatory complexes (ISCOMs)), oil-emulsion and surfactant-based adjuvants (Freund's incomplete adjuvant (FIA), microfluidized emulsions (MF59, SAF), saponins (QS-21)), synthetic (muramyl peptide derivatives (murabutide, threony-MDP), nonionic block copolymers (L121), polyphosphazene (PCCP), synthetic polynucleotides (poly A:U, poly I:C), thalidomide derivatives (CC-4407/ACTIMID), RH3-ligand, or polylactide glycolide (PLGA) microspheres, among others. Metallic salt adjuvants such as alum adjuvants are well-known in the art as providing a safe excipient with adjuvant activity. The mechanism of action of these adjuvants are thought to include the formation of an antigen depot such that antigen may stay at the site of injection for up to 3 weeks after administration, and also the formation of antigen/metallic salt complexes which are more easily taken up by antigen presenting cells. In addition to aluminium, other metallic salts have been used to adsorb antigens, including salts of zinc, calcium, cerium, chromium, iron, and berilium. The hydroxide and phosphate salts of aluminium are the most common. Formulations or compositions containing aluminium salts, antigen, and an additional immunostimulant are known in the art. An example of an immunostimulant is 3-de-O-acylated monophosphoryl lipid A (3D-MPL). Other homologs and/or derivatives of any of these toxins may also suitable, provided that they retain adjuvant activity.
The TDAV viral particles, nucleic acids corresponding thereto (e.g., contained within a vector), polypeptides and/or peptides corresponding thereto, and/or binding agents may be used, for example, to stimulate an immune response against TDAV described herein in a host. In some embodiments, immunogenic compositions and vaccines comprising TDAV, antigen thereof (e.g., SEQ ID NO.: 2 or a fragment thereof), and/or nucleic acid corresponding thereto (e.g., SEQ ID NO.: 1 or a fragment thereof) may be used to treat diseases caused by or associated with the presence of TDAV in a host (e.g., an animal such as a horse). An immunological composition is one that, upon administration to a host (e.g., an animal such as a horse) induces or enhances an immune response directed against the antigen or immunogen (e.g., TDAV) contained within the composition. This response may include the generation of antibodies (e.g., through the stimulation of B cells) or a T cell-based response (e.g., a cytolytic response). These responses may or may not be protective or neutralizing. A protective or neutralizing immune response is one that may be detrimental to the cell containing or expressing the antigen (e.g., from which the antigen was derived) and beneficial to the host (e.g., by reducing or preventing tumor growth). As used herein, protective or neutralizing antibodies and/or cellular responses may be reactive to TDAV and/or an antigen thereof. An immunological composition that, upon administration to a host, results in a protective or neutralizing immune response may be considered a vaccine. Immunological compositions comprising at least one TDAV and/or antigen may also include one or more additional antigens.
Methods for treating disease caused by or associated with TDAV in a mammalian host by administering to the mammal at least one or more effective doses of one or more TDAV viral particles (e.g., inactivated), nucleic acids, polypeptides, peptides, and/or binding agents described herein are also provided. For instance, a TDAV viral particle (e.g., inactivated) or vector corresponding thereto, may be administered to a host in a suitable dose (e.g., about 104, 105, 106, 107 or 108 viral particles) and dosing schedule (e.g., once, twice, or three times a day/week/month), as may be determined by one of ordinary skill in the art. A polypeptide and/or peptide may be administered to a host in a suitable dose (e.g., about 1-100 mg/kg body weight) and dosing schedule (e.g., once, twice, or three times a day/week/month), as may be determined by one of ordinary skill in the art. A binding agent may be administered in a suitable dosage (e.g., about 1-50 mg/kg of body weight), about 1 to about 30 mg/kg, or about 1 to about 15 mg/kg (e.g., about any of 1, 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, 30, 35, or 40 mg/kg). In certain embodiments, these reagents may be administered via any route (e.g., intradermally, intravenously, orally, rectally) at one or more times. When multiple doses are administered, the doses may comprise about the same or different types and or amounts of reagent (e.g., in a prime-boost format). The doses may also be separated in time from one another by the same or different intervals. For instance, the doses may be separated by about any of 6, 12, 24, 36, 48, 60, 72, 84, or 96 hours, one week, two weeks, three weeks, one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, 10 months, 11 months, 12 months, 1.5 years, 2 years, 3 years, 4 years, 5 years, or any time period before, after, and/or between any of these time periods. In some embodiments, the binding agents may be administered in conjunction with other agents (e.g., chemotherapeutic agents), as described above. Such other agents may be administered about simultaneously with the binding agents, or at a different time and/or frequency. Other embodiments of such methods may also be appropriate as could be readily determined by one of ordinary skill in the art. Generally, a dose has the effect of decreasing the number of TDAV viral particles in a mammal is called an effective dose. Methods for preparing and/or using such preparations are well-known in the art.
In some embodiments, methods for detecting cells comprising TDAV viral particles and/or antigens thereof using binding agents are provided. In certain embodiments, cells expressing TDAV antigen(s) on the cell surface in an animal (e.g., a horse), may be detected by contacting a test biological sample with a binding agent and detecting the same bound to the cells (e.g., using flow cytometry). In certain embodiments, the method may comprise comparing the amount of binding to the test biological sample or components thereof to the amount of binding to a control biological sample or components thereof, wherein increased binding to the test biological sample or components thereof relative to the control biological sample or components thereof indicates the presence of a lymphoma cell in the test biological sample. In some embodiments, the biological sample is equine blood. Such methods are also provided in an in vivo and/or in vitro format. In some embodiments, methods for decreasing the viability and/or number of TDAV viral particles in a host using such the nucleic acids and/or binding agents described herein are also provided.
To assist the skilled artisan in using the nucleic acids and/or binding agents described herein, the same may be provided in kit format. A kit including such nucleic acids and/or binding agents (e.g., antibodies) and optionally other components necessary for using the same to detect, isolate and/or remove TDAV and/or antigen in and/or from a biological sample (e.g., cell or fluid) thereof is also provided herein. The nucleic acids and/or binding agents of the kit may be provided in any suitable form, including frozen, lyophilized, or in a pharmaceutically acceptable buffer such as TBS or PBS. The kit may also include other reagents required for utilization of the antibodies in vitro or in vivo such as buffers (e.g., TBS, PBS), blocking agents (solutions including nonfat dry milk, normal sera, Tween-20 Detergent, BSA, or casein), and/or detection reagents (e.g., goat anti-mouse IgG biotin, streptavidin-HRP conjugates, allophycocyanin, B-phycoerythrin, R-phycoerythrin, peroxidase, and/or detectable label) and other labels and/or staining kits (e.g., ABC Staining Kit, Pierce). The kits may also include other reagents and/or instructions for using the antibodies in commonly utilized assays described above such as, for example, flow cytometric analysis, ELISA, immunoblotting (e.g., western blot), in situ detection, immunocytochemistry, immunohistochemistry. In one embodiment, the detectable labels may be fixably attached to the binding agents. In one example, the detectable labels are fixably attached to the binding agents by chemical bonds. In one example, the chemical bonds are covalent chemical bonds. In one example, the detectable labels are conjugated to the binding agents.
In one embodiment, the kit provides a monoclonal antibody against TDAV and/or an antigen thereof in purified form. The monoclonal antibody may be provided in biotinylated form either alone or along with an avidin-conjugated detection reagent (e.g., antibody). The kit may include fluorescently-labelled antibodies that may be used to directly detect TDAV and/or an antigen thereof. Buffers and the like required for using any of these systems are well-known in the art and may be prepared by the end-user or provided as a component of the kit. The kit may also include a solid support containing positive- and negative-control protein and/or tissue samples. For example, kits for performing spotting or western blot-type assays may include control cell or tissue lysates for use in SDS-PAGE or nylon or other membranes containing pre-fixed control samples with additional space for experimental samples. Kits for visualization of TDAV and/or an antigen thereof on slides may include pre-formatted slides containing control cell or tissue samples with additional space for experimental samples. As mentioned above, the binding agents described herein and/or derivatives thereof may also be incorporated into compositions for use in vitro or in vivo. Other embodiments are also provided as would be understood by one of ordinary skill in the art.
As described above, this disclosure relates to SEQ ID NO.: 1, 2 or 3, any portion thereof, any derivative thereof, and/or any virus or viral particle comprising any of SEQ ID NOS.: 1, 2 or 3, any portion thereof, and/or any derivative thereof. This disclosure relates to, for example, an isolated nucleic acid sequence comprising SEQ ID NO.: 1 or 2 or a portion thereof; an isolated nucleic acid sequence having at least 50-99% identity to SEQ ID NO.: 1 or 2 or a portion thereof; an isolated nucleic acid sequence comprising at least five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive nucleotides of SEQ ID NO.: 1 or 2 or a portion thereof; an isolated nucleic acid sequence encoding SEQ ID NO.: 3 or a portion thereof; an isolated nucleic acid sequence encoding a polypeptide having at least 50-99% identity to SEQ ID NO.: 3 or a portion thereof; an isolated nucleic acid sequence encoding at least at least three, four, five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive amino acids of SEQ ID NO.: 3 or a portion thereof; a polypeptide comprising SEQ ID NO.: 3 or a portion thereof; a polypeptide having at least 50-99% identity or similarity to SEQ ID NO.: 3 or a portion thereof; a peptide or polypeptide comprising at least at least three, four, five, six, seven, eight, nine, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more consecutive contiguous amino acids of SEQ ID NO.: 3, optionally comprising a conservative and/or non-conservative substitution therein; an expression vector comprising or encoding SEQ ID NO.: 1, 2 and/or 3, and/or a complementary or similar (e.g., 50-99% identical) nucleic acid sequence, and/or a similar (e.g., 50-99% identical) amino acid sequence; a host cell comprising or encoding SEQ ID NO.: 1, 2 and/or 3, and/or a complementary or similar nucleic acid sequence, and/or a similar amino acid sequence; an oligonucleotide having a nucleic acid sequence hybridizable under highly or moderately stringent conditions to SEQ ID NO.: 1 or 2 or a portion thereof, complementary to a fragment of SEQ ID NO.: 1 or 2 or a portion thereof, corresponding to a nucleic acid sequence encoding at least a portion of SEQ ID NO.: 3, or complementary to a nucleic acid sequence encoding at least a portion of SEQ ID NO.: 3; an oligonucleotide corresponding to or complementary to at least portion of SEQ ID NO.: 1 or 2; an oligonucleotide selected from the group consisting of SEQ ID NO.: 1, SEQ ID NO.: 2, SEQ ID NO.: 3, SEQ ID NO.: 4, 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.: 12, SEQ ID NO.: 13, SEQ ID NO.: 14, SEQ ID NO.: 15, SEQ ID NO.: 16, SEQ ID NO.: 17, SEQ ID NO.: 18, and SEQ ID NO.: 19; an oligonucleotide comprising nucleotides encoding at least a portion of SEQ ID NO.: 3, optionally comprising one or more detectable labels; two or more oligonucleotides for amplifying a nucleic acid sequence of a virus (e.g., TDAV), each oligonucleotide comprising a nucleic acid sequence corresponding to at least a portion of SEQ ID NO.: 1 or 2, complementary to at least a portion of SEQ ID NO.: 1 or 2, corresponding to a nucleic acid sequence encoding at least a portion of amino acids of SEQ ID NO.: 3, or complementary to a nucleic acid sequence encoding a portion of SEQ ID NO.: 3, optionally comprising one or more detectable labels; a primer pair selected from the group consisting of SEQ ID NOS.: 4 and 5; SEQ ID NOS.: 6 and 7; SEQ ID NOS.: 8 and 9; SEQ ID NOS.: 10 and 11; SEQ ID NOS.: 12 and 13; SEQ ID NOS.: 14 and 15; SEQ ID NOS.: 16 and 17; and SEQ ID NOS.: 18 and 19, optionally comprising one or more detectable labels; methods for detecting and/or identifying and/or quantifying a virus (e.g., TDAV) in a sample (e.g., a biological sample such as serum), comprising amplifying from the sample a nucleic acid corresponding to TDAV; a kit for the detection of nucleic acid of a virus in a sample, the kit comprising an oligonucleotide, oligonucleotides, and/or primer pair for detecting and/or identifying and/or quantifying TDAV, the kit further optionally comprising a solid support, and/or one or more amplification reagents; a composition comprising a pharmaceutically acceptable carrier and a nucleic acid or complement thereof and/or a peptide and/or polypeptide corresponding to TDAV (which may be an immunogenic composition and/or a vaccine); a method of producing a nucleic acid molecule, peptide and/or polypeptide corresponding to TDAV, the method comprising transfecting a host cell with an expression vector encoding the peptide or polypeptide, culturing the host cell such that nucleic acid molecule, peptide and/or polypeptide is expressed, and isolating the peptide or polypeptide; a method of eliciting an immune response in a mammal by administering to the mammal a pharmaceutical composition comprising a nucleic acid molecule, peptide, and/or polypeptide corresponding to TDAV, and/or host cell comprising or expressing the same; a method of generating a binding agent (e.g., antibody) against a nucleic acid, peptide and/or polypeptide corresponding to TDAV and the binding agent(s) produced thereby (e.g., reactive with a polypeptide encoded by SEQ ID NO.: 1 or 2, a fragment of at least 9 nucleotides thereof). Other embodiments are also provided by this disclosure as would be recognized by one of ordinary skill in the art.
Any indication that a feature is optional is intended provide adequate support for claims that include closed or exclusive or negative language with reference to the optional feature. Exclusive language specifically excludes the particular recited feature from including any additional subject matter. For example, if it is indicated that A can be drug X, such language is intended to provide support for a claim that explicitly specifies that A consists of X alone, or that A does not include any other drugs besides X. “Negative” language explicitly excludes the optional feature itself from the scope of the claims. For example, if it is indicated that element A can include X, such language is intended to provide support for a claim that explicitly specifies that A does not include X. Non-limiting examples of exclusive or negative terms include “only,” “solely,” “consisting of,” “consisting essentially of,” “alone,” “without”, “in the absence of (e.g., other items of the same type, structure and/or function)” “excluding,” “not including”, “not”, “cannot,” or any combination and/or variation of such language.
All publications and patents cited in this specification are herein incorporated by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference. Genbank records referenced by GID or accession number, particularly any polypeptide sequence, polynucleotide sequences or annotation thereof, are incorporated by reference herein. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention.
Certain embodiments are further described in the following examples. These embodiments are provided as examples only and are not intended to limit the scope of the claims in any way.
Described below are the procedures utilized to isolate the genome of a novel virus termed “Theiler's disease-associated virus” (TDAV). The genome is presented as SEQ ID NO: 1; the amino acid coding sequence presented as SEQ ID NO.: 2; and the amino acid sequence is presented as SEQ ID NO.: 3.
A. Materials and Methods
1. RNA Extraction
Sera harvested from horses were stored at −80° C. RNA was extracted from 300 μl aliquots of stored sera using the TRIzol LS reagent (Life Technologies) as per the manufacturer's protocol. Briefly, 900 μl of TRIzol LS was added to 300 μl of sera; tube was shaken by hand; homogenized sample was incubated for 5 minutes (min) at room temperature; 0.24 ml of chloroform was added and shaken vigorously; sample was centrifuged at 12000×g for 15 min at 4° C.; the aqueous top phase was saved; 15 μg of GlycoBlue (Life Technologies) was added; 600 μl of 2-propanol was added; sample was incubated room temperature for 10 min; sample was centrifuged at 12000×g for 10 min at 4° C.; supernatant was discarded; RNA pellet was washed with 75% ethanol; pellet was dried and RNA was dissolved in 20 μl water. Extracted RNA samples were subjected to Turbo DNA-free (Life Technologies) treatment as per the manufacturer's protocol with one modification (include RNase inhibitor). Briefly, a mix of 2.9 μl Turbo DNase buffer, 5 μl H20, and 0.25 μl RNase Inhibitor (Life Technologies) was added to a 20 μl RNA sample; 1 μl Turbo DNase was added; sample was incubated at 37° C. for 20 min; 3 μl DNase inactivation reagent was added; sample was incubated at room temperature for 5 mM; sample was centrifuged at 10000×g for 1.5 min at room temperature; 21.5 μl of supernatant was saved for further analysis.
2. Library Preparation and Sequencing
Briefly, 4 μL of DNase-treated RNA was used as template for reverse transcription with the following conditions: 3Sol_N primer (final concentration, 8 uM) was mixed with RNA and denatured at 65° C. for 5 min before incubation on ice for 5 min. Superscript III reverse transcriptase (10 U/ul) reagents (Life Technologies) Superscript III buffer (1×), MgCl2 (5 mM), DTT (10 mM), dNTP (500 μM), and RNaseOUT (0.4 U/μL), were added and sample was incubated at 42° C. for 60 min followed by 94° C. for 4 mM. For second strand synthesis, a 5 μL mix of Sequenase buffer (0.33×) and Sequenase 2.0 (0.13 U/μL) was added. Reaction temperature was ramped from 4° C. to 37° C. over 8 mM, then held at 37° C. for 8 min. In an initial PCR step, 5 μL of this cDNA was amplified with Klentaq LA DNA polymerase (0.1 U/μL) (Sigma) in Klentaq buffer (1×), dNTP (200 μM), and 3_Sol primer (2 mM), and PCR was performed under the following cycling conditions: 94° C. for 3 mM, 25 cycles [94° C. for 30 seconds (s), 40° C. for 1 min, 68° C. for 1 min], 68° C. for 7 min. A final 4-primer PCR used 10 ng of the initial PCR reaction as a template with Klentaq buffer (1×), dNTP (200 μM), SolM1 primer (10 nM), SolM2_barcode (10 nM), two oligos manufactured with the CleanAmp Precision™ modification (TriLink BioTechnologies), 5SolM1_18** (200 nM), 5SolM2_19** (200 nM), and Klentaq LA DNA polymerase (0.1 U/μL). The following cycling conditions were used for this PCR step: 94° C. for 1 min, then two cycles [94° C. for 30 s, 40° C. for 30 s, 68° C. for 1 mM], 94° C. for 10 min, seven cycles [94° C. for 30 s, 58° C. for 30 s, 68° C. for 1 min], and 72° C. for 5 min. Resulting sequencing libraries were purified using DNA Clean & Concentrator-5 (Zymo Research) according to the manufacturer's protocol and eluted with 20 g, H2O. Ten microliters of purified libraries were size selected (423 bp+/−7%) using LabChip XT (DNA 750 assay kit, Caliper/Perkin Elmer) and further purified by Zymo column. Individual library concentration were determined by qPCR using a PhiX control library (Illumina) with primers 1.1 and 2.1 and Fast SYBR Green Master Mix (Life Technologies), as per manufacturer's protocol. Libraries were then pooled in equimolar concentrations and re-quantified prior to sequencing. Paired-end sequencing (100 cycles for each paired end) on the HiSeq2000 (Illumina) with v3 cluster generation reagents and SBS reagents was performed as per manufacturer's instructions.
3. Illumina Sequencing
Paired-end sequencing (100 cycles for each paired end) was performed by first generating clusters on flow cell (FC) on the cBot as described in the “cBot User Guide” (Part #: 15006165 Rev. G, Illumina); the clustered FC was subjected to paired-end sequencing on the HiSeq200 as described in the “HiSeq 2000 User Guide” (Part#: 15011190 Rev. K, Illumina).
4. Sequencing Analysis
The initial FASTQ sequence data were binned by sequencing index for each of the three samples. Sequence read pairs for which one of the reads had 10 or more uncalled bases (Ns) were removed. Low complexity reads were identified by analyzing the size of the compressed Lempel-Ziv-Welch sequence string after removing Ns from the string to avoid artificial increases in complexity. Sequence read pairs for which one of the reads had a compressed size below 37 were removed. The remaining sequencing reads were aligned to the horse genome (EquCab2.0, GCF_000002305.2) (33) by nucleotide BLAST (blastn) with default word size and E value (11 and 10, respectively). Sequence read pairs for which one of the reads had at least 80/100 nucleotides (80% total read identity) mapping identically to the horse genome were considered host-derived and removed from downstream analysis. The remaining sequencing reads were aligned by both blastn and translated BLAST (blastx) to all RefSeq (March 2012) viral genomes and protein sequences, respectively, with default word size (11 for blastn, 3 for blastx) and E value (10 for both blastn and blastx). Sequences matching the viral database were isolated and considered candidates. To confirm viral origin in an unbiased context, candidate viral sequences were aligned to the non-redundant nucleotide database (NT; April 2012) by blastn using the default parameters. Candidate viral reads that did not have an alignment to NT were aligned to the non-redundant protein database (NR; April 2012) by blastx using the default parameters. Candidate viral reads whose highest-scoring alignments mapped only to viral genomes were deemed viral in origin.
5. Genome Assembly
All reads mapping to the Flaviviridae family from each of the three samples were consolidated into FASTA files representing the starting point for genome assemblies. These reads were used as seeds for a targeted metatranscriptomic assembly using an alpha version (v0.16.2) of the Paired-Read Iterative Contig Extension (PRICE) assembler software (http://derisilab.ucsf.edu/software/price/index.html). PRICE uses paired-end information to generate local assemblies that extend existing contigs; in this case, the initial contigs were reads with blastx matches to the Flaviviridae family, and the contigs were repeatedly extended through as many cycles as possible. In some cases, if an assembly stalled, the unfiltered sequence data were mapped to the existing assembly, and reads with high percent identity were culled in an effort to gather more high-quality seeds for further assembly.
6. Phylogenetic Analysis
All RefSeq Flaviviridae polyprotein sequences, in addition to the polyprotein sequences from the recently-discovered non-primate hepaciviruses (NPHVs) (
7. Physical Recovery and Validation of TDAV Sequence
The TDAV genome assembly was validated by recovering and sequencing ten overlapping RT-PCR amplicons that span positions 57-10127 (see below). Successful recovery of each amplicon required optimization of the RT and PCR conditions. Two different reverse transcription (RT) approaches were used in combination with 4 different PCR conditions to recover the 10 overlapping TDAV clones shown in
†Source a = This study, Source b = Zhang YW, Davis EG and Bai J, 2009. Determination of internal control for gene expression studies in equine tissue and cell culture using quantitative RT-PCR. Veterinary Immunology and Immunopathology 130, 114-119; Source c = Runckel C, Flenniken, ML, Engel JC, Ruby JG, Ganem D, Andino R, and DeRisi JL, 2011. Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema and Crithidia. PLoS One. 6(6): e20656. Epub 2011 Jun 7.
‡The X in the sequence indicates base positions of barcode sequences in Illumina library adapters used in this study.
†See Table 3 for PCR primer sequences.
The 5′-most sequence of TDAV was recovered by performing 5′ Rapid Amplification of cDNA Ends (5′-RACE) according to the manufacturer's protocol (Life Technologies. Briefly, 2 μl of RNA from two subjects (Horse A1 and Horse A2) and Antitoxin 2 were used as input to the initial RT step. Reverse transcription was primed by EVT-145 (Table 3). Purified cDNAs were subjected to a tailing reaction with dCTP. dCTP-tailed cDNA was used as a template for PCR with EVT-147 (Table 3) and the manufacturer-supplied Abridged Anchor Primer. PCR was performed according to the Taq polymerase manufacturer's protocol (New England BioLabs) with the following cycling conditions: 94° C. for 2 min, then 32 cycles of 94° C. for 30 s, 55° C. for 30 s, 72° C. for 1 min, followed by 72° C. for 7 min. PCR products were purified and concentrated by column purification (DNA Clean & Concentrator™-5, Zymo Research) according to the manufacturer's protocol. Purified 5′ RACE products were size selected (292-438 bp) using the LabChip XT (DNA 750 assay kit, Caliper/Perkin Elmer).
8. PCR-Based TDAV Diagnostic Assay
The TDAV qRT-PCR diagnostic assay used RNA isolated from 300 μL equine serum or plasma, as described above. Two microliters of RNA were used for random-primed reverse transcription performed according to the manufacturer's protocol (SuperScript III First-Strand Synthesis System, Life Technologies). Diluted cDNA (1:10) was added to qPCR reactions with Fast SYBR Green Master Mix (Life Technologies) and one of the following primer pairs: EVT-162/-163 (TDAV), EVT-146/147 (TDAV) and EVT-192/-193 (equine 18S rRNA). All samples were blinded and reactions were performed at least in triplicate. The qRT-PCR TDAV assay was designed to separate known positive and known negative samples by at least 9 Cts in initial pilot experiments. Pre-defined Ct threshold values for TDAV positivity could not be set because of small day-to-day variability in the assay; thus positivity was defined as i) detecting equine 18S rRNA with Cts substantially lower than in blinded samples predicted to be H2O and ii) detecting viral RNA with both TDAV primer sets with Cts substantially lower than in blinded samples predicted to be negative controls.
B. Results
1. Outbreak Summary
An outbreak of Theiler's disease that occurred on a horse farm in the western United States following prophylactic treatment of the animals for botulinum toxin poisoning was investigated. The farm (Farm A) housed a population of 75 horses, of which four were diagnosed with signs of botulism poisoning after consumption of contaminated feed. Two of the horses presented with a rapid onset of paralysis and were euthanized. The other two horses displayed milder symptoms, were treated with equine botulinum antitoxin plasma, and made a full recovery. As a prophylactic measure, botulinum antitoxin treatment was then administered to 21 other horses suspected of exposure to the contaminated feed. Because quantities of the initial antitoxin batch were limited, the first four horses were provided the same antitoxin used to treat the two symptomatic horses (‘Antitoxin 1’) and 17 horses were administered an independently sourced botulinum antitoxin (‘Antitoxin 2’). The remaining horses on the farm went untreated. One of the horses that was treated with Antitoxin 1 upon presentation with mild symptoms of botulism was removed from the farm and was unavailable for further monitoring, leaving a total of 22 horses that were treated with Antitoxin 1 (N=5) or Antitoxin 2 (N=17) for continued observation and testing. Within eight weeks, two of the horses treated with Antitoxin 2 (Horse A1 and Horse A2) displayed signs of Theiler's disease, including lethargy, poor appetite, photodermatitis, and jaundice. Serum levels of liver enzymes were also markedly elevated in both horses. All horses that received antitoxin treatment were subsequently monitored for overt symptoms of hepatitis and weekly serum samples were tested for signs of liver injury (elevated levels of aspartate amino transferase (AST), gamma glutamyl transferase (GGT), sorbitol dehydrogenase (SDH), glutamate dehydrogenase (GLDH or GD), and bilirubin). In total, eight of the 22 horses that received antitoxin treatment developed hepatitis over the following several weeks (
2. Viral Sequence Detection Leads to Assembly of a Novel Flaviviridae Genome
Massively parallel sequencing of libraries from Horse A1, Horse A2, and Antitoxin 2 resulted in an average of 22 million 100 nucleotide (nt) sequence reads for each sample. For the two serum specimens, complexity and host filtering of the raw sequence data removed approximately 95% of the reads from downstream analyses. For the Antitoxin 2 sample, complexity and host filtering removed approximately 50% of the reads. The remaining reads were mapped to all viral protein sequences in RefSeq. For Horses A1 and A2 approximately 0.01% of sequence reads (2954 and 3522 reads, respectively) mapped to members of the Flaviviridae; 0.06% (9116) of Antitoxin 2 reads mapped to the same virus family. In addition to the abundance of Flaviviridae reads in each sample, Horse A1 had a single read pair mapping to Baculoviridae, a family of insect viruses, and another read pair derived from Adenoviridae, mapping to the region found in laboratory recombination vectors; Horse A2 contained 80 read pairs deriving from a 298 nt contiguous region in Pepper Mild Mottle virus, a plant virus from the Virgaviridae family. These reads likely represent artifactual contamination introduced during sample collection and library preparation. Horse A2 additionally contained four read pairs derived from Equid herpesvirus 2, a common virus associated with mild respiratory disease in horses. No additional viral reads were detected in the Antitoxin 2 specimen. Sequence reads mapping to members of the Flaviviridae were used as the starting point for de novo genome assemblies using the assembly algorithm PRICE. A 10.5 kilobase (kb) contig corresponding to a previously unknown and divergent genome of the Flaviviridae family was assembled from the Horse A1 sequences, and long contigs from an essentially identical (>99% nucleotide sequence identity) genome were assembled from the Horse A2 and Antitoxin 2 samples (
3. Genome Features of Theiler's Disease-Associated Virus (TDAV)
In order to validate the computer-generated genome assembly, the presence of artificial structural rearrangements was first investigated. In an assembly free of artifacts, the computed amplicon sizes across the genome should match the amplicon size selected during library preparation. This was evaluated by calculating the distance between read pairs mapping back to the TDAV genome, and by plotting the median value of all calculated amplicon sizes at each position. The calculated amplicon sizes based on the Horse A1 data closely matched the experimentally-generated insert size of 300±30 nucleotides (nt) (
The TDAV genome assembly is approximately 10,479 nt in length, encompassing the 5′ untranslated region (UTR), a single open reading frame (ORF) initiating from an AUG at position 618 and encoding a putative polyprotein 3189 amino acid (aa) residues in length, and 292 nt of the 3′UTR. By comparison to related Flaviviridae, the TDAV genome encodes three putative structural (core, E1, E2) and seven non-structural (a gene product of variable length mapping between E2 and NS2, NS2, NS3, NS4A, NS4B, NS5A, and NS5B) proteins (
Although TDAV appears most closely related to the GB viruses and hepaciviruses in the Flaviviridae phylogeny (
4. PCR-Based Diagnostic Assay
Upon validation of TDAV genome sequence, a PCR-based diagnostic assay was developed to screen for the presence of TDAV in clinical specimens (e.g., serum). Eight candidate primer pairs targeting 130-200 nt products from across the TDAV genome were designed (Tables 3, 5). These and four previously described qRT-PCR primers for equine housekeeping genes were tested for performance in a SYBR green-based qPCR assay on samples collected from the outbreak. RNA prepared from the following sources were used to test these 1 primer pairs: three samples in which TDAV was identified by Illumina sequencing (the first samples collected from horses A1 and A2, and Antitoxin 2; these serve as confirmed positives for TDAV assays and suspected positives for equine housekeeping gene assays), three water samples (these serve as negative controls for both TDAV and equine housekeeping gene assays), eight specimens from horses treated with Antitoxin 1 (two available samples collected from horses A19, A20, A21 and A22; these serve as suspected negatives for TDAV assays, and expected positives for equine housekeeping gene assays), and two specimens from horses treated with Antitoxin 2 (two available samples collected from horse A18; these serve as suspected positives for TDAV assays and expected positive for equine housekeeping targets). Total RNA was extracted from 300 μl of serum specimen provided for the study as described in the Materials and Methods section of the manuscript. An aliquot of each sample was transferred to fresh tubes and provided to a second investigator to process in a blinded manner as follows: 2 μl of sample were used as template in random hexamer-primed 20 μl reaction with the Superscript III First Strand Synthesis System for RT-PCR kit (Life Technologies), according to the manufacturer's protocol. Resulting cDNAs were diluted 1:3 with nuclease-free H2O, and 2 μl were used as input template for SYBR green qPCR assays with each of the 12 primer pairs in a reaction mix containing 7.8 μl H2O, 0.2 μl 10 μM mix of qPCR primer pair, and 10 μl FAST SYBR Green Master mix (Life Technologies). The qPCR was performed on an ABI 7900HT Fast Real-Time PCR System Instrument as per manufacturer's recommended cycling parameters (95° C., 20 s denaturation step, 40 cycles of 95° C., 1 s, 60° C., 20 s), followed by dissociation analysis. The following criteria were used to identify primer pairs for calls on the presence or absence of viral RNA and equine host RNA prior to unmasking sample identifiers: a single peak in post-qPCR dissociation curve analysis and a single product of expected size in confirmatory agarose gel electrophoresis analyses; Ct values for suspected positive signals <30; Ct values for suspected negative signals >35; Ct values for suspected H2O samples >39; a minimum difference of 9 Cts between lowest Ct value for negative calls and highest Ct value for positive calls. A summary of results is provided in Table 6. TDAV primer pairs EVT146/147, EVT154/155, EVT162/163 and the equine housekeeping primers EVT192/193 met the above criteria. Using any one of these TDAV primers in combination with the EVT192/193 housekeeping primer pair yielded 100% accuracy in identification of the different sample types (TDAV+, TDAV−, or H2O) tested in this assay.
5. Epidemiological Survey for the Presence of TDAV
An epidemiological survey was conducted to understand the prevalence of TDAV in horses, to investigate the correlation between clinical symptoms and viremia, and to determine whether there is natural animal-to-animal transmission. A qRT-PCR-based TDAV assay was developed (see above) and employed to screen serum or plasma from 60 horses from three geographically distant facilities. Farm A, on which the Theiler's disease outbreak took place, provided samples from 37 horses. Some grazed common fields or were housed in common stables. Horses from Farm A stratified into three sub-groups: 15 horses had not been treated with botulinum antitoxin, 17 horses (including Horse A1 and Horse A2) had received the contaminated Antitoxin 2, and 5 horses had received the untainted Antitoxin 1. Farm B was located in a different state than Farm A and serum was analyzed from 20 Farm B horses with no history of exposure to antitoxin from either source. Farm D (donor) was the facility in which the botulinum Antitoxin 2 had been prepared by pooling plasma from three botulinal toxin-immunized horses; samples from the three donor horses were provided.
The results of the TDAV qRT-PCR detection assay are displayed as Ct values plotted on an inverted y-axis (
During the Theiler's disease outbreak on Farm A, animals were broadly classified as either having hepatitis not having hepatitis. Horses with hepatitis were further stratified into horses that were “clinical” and “subclinical.” The clinical cases displayed significant elevation of liver enzymes in the serum along with common clinical signs of disease such as jaundice, lethargy, poor appetite and photodermatitis. The subclinical cases displayed varying degrees of elevation of liver enzymes in the serum, but with no overt clinical manifestations of liver disease. To investigate the correlation between viral load and clinical presentation, the qRT-PCR assay data from the Antitoxin 2 exposed animals were stratified by hepatitis status and symptom level (
6. Experimental Inoculation Study
To better understand the dynamics of TDAV infection and the role of the virus in disease progression, a small experimental inoculation study was performed. Four horses that were healthy and free of clinical or biochemical evidence of liver disease according to initial evaluations were administered standard doses of Antitoxin 2 (same lot as involved in Farm A outbreak). For the next 10-14 weeks, the animals were monitored daily for overt signs of illness. Serum specimens were collected on a weekly basis and tested for biochemical signs of liver injury and quantification of TDAV serum levels.
Over the course of the study, only 1 of the 4 animals (Horse C1) displayed clinical signs of illness. The symptoms, which arose approximately 7 to 9 weeks after inoculation, included a brief period of mild lethargy and diminished appetite, and appeared to resolve within <1 week. Consistent with the observation of clinical signs, Horse C1 had elevated liver enzyme levels in the serum that peaked within the week prior to the onset of illness (
The dynamics of TDAV infection were remarkably diverse among the four inoculated animals (
7. Acute TDAV Infection can Become Chronic
GB and hepaciviruses are known to cause chronic infection in some individuals. To examine the potential of TDAV to progress to chronicity, serum samples from thirty animals on Farm A were collected approximately one year after the initial Theiler's disease outbreak. In both index cases (Horses A1 and A2), which were TDAV positive and displayed clinical signs of illness during the outbreak, the virus was not detectable one year later (
The above-described TDAV diagnostic assay provides for the detection and/or identification and/or quantification of TDAV in a biological sample (e.g., serum). The TDAV qPCR-based diagnostic assay was employed to screen serum or plasma from an 60 horses from three geographically distant facilities (
As described herein, massively parallel sequencing and subsequent nucleic acid-based screening was utilized to identify a previously unknown, highly divergent member of the Flaviviridae and link it to an outbreak of Theiler's disease in horses. This virus, which we have termed Theiler's disease-associated virus (TDAV), is the first infectious agent to be unambiguously associated with equine acute serum hepatitis since the first description of the disease in 1918. Several lines of evidence implicate TDAV as the causative agent in this outbreak of Theiler's disease in horses. First, TDAV was the only virus common to all of the index cases, and there were few non-TDAV viral sequences detected in any of the samples. Second, although not all TDAV-positive horses had hepatitis, TDAV was detectable in every animal in the outbreak with clinical or biochemical evidence of hepatitis. Third, TDAV positivity was exclusively associated with antecedent exposure to Antitoxin 2, supporting the hypothesis that it was an infectious contaminant of the serum product and not a virus routinely found in farm horses. Fourth, the inoculation study indicated that TDAV infection precedes liver injury, excluding the possibility that the association of virus with hepatitis on Farm A reflects preferential infection of animals with antecedent liver injury. Finally, sequencing of the TDAV genome revealed a member of the Flaviviridae, which encompasses other blood-borne viruses linked to liver injury, including HCV. It is noted that this inoculation study does not formally fulfill Koch's postulates, as the TDAV in the inoculum was not first purified by cultivation in vitro (since we have yet to develop suitable culture systems). As such, the association of TDAV with Theiler's disease, while very strong, remains inferential. Similarly, it remains to be determined whether TDAV is the sole etiologic agent of Theiler's disease or one of several causative agents—as is the case in human hepatitis, which is linked to at least five unrelated viruses (hepatitis viruses A-E). In this regard, we note that we have been unable to link NPHV, the only known hepaci-like virus detected in horses, to hepatitis in this outbreak. Parallel qRT-PCR assays for NPHV RNA performed in this study identified the virus in only three horses: one TDAV-negative untreated, asymptomatic horse (Farm A), one asymptomatic TDAV-positive horse (Farm A), and one TDAV-negative horse with no history of antitoxin treatment (Farm B) (Table 7). Of course, this does not exclude a role for NPHV in hepatic (or extrahepatic) disease in other epidemiologic settings.
†Horse identifiers are coded according to farm location and a unique number assigned to each horse sampled for this study (A, Farm A where the outbreak occurred; B, non-outbreak Farm B located in a different state; D, donor horses whose serum was pooled to make the ETAV-contaminated Antitoxin 2 serum linked to the Theiler's disease outbreak on Farm A.
‡Ct = cycle threshold.
The closest relatives of TDAV appear to be the GB viruses. GB viruses are a group of highly prevalent Flaviviridae species that produce persistent but typically subclinical infections in their host species. GB viruses A, B, and C were first identified in studies of non-A non-B serum hepatitis in humans and non-human primates in the early 1990s, though none have been unequivocally linked to human liver injury in subsequent epidemiological investigations (Proc. Natl. Acad. Sci. USA, 19; 100(17):9962-7. Epub 2003 Aug. 7, Chronic hepatitis associated with GB virus B persistence in a tamarin after intrahepatic inoculation of synthetic viral RNA).
GBV-D, also thus far unlinked to disease, was recently identified in a serum survey of frugivorous bats native to south central Asia. Based on observed similarities in genome organization and sequence, tissue tropism, lack of detectable pathogenicity in humans, and the persistent nature of infection, it has been proposed to classify GBV-A, GBV-C, and GBV-D together in a new Flaviviridae genus termed pegivirus (persistent GB or G virus). At present, based on sequence features, TDAV would likely be considered a member of the proposed pegivirus genus, though it would be the first member for which a disease association has been identified. Membership of a virus in a given genus doesn't necessarily connote its natural host. While TDAV has been discovered in horses, the natural reservoirs and hosts of this virus are unknown; it could be an exclusively equine virus, or an agent introduced into the equine population from another source and amplified there by the practice of transfusion.
Divergence from Flaviviridae family members is evident in several interesting features of the TDAV genome. First, the virus harbors three amino acid insertions in the NS5A protein spanning approximately 160 amino acids not found in any of the related hepacivirus or GB virus species. HCV NS5A is a phosphoprotein with no known enzymatic activity but an essential, though poorly understood, role in the viral life cycle. NS5A is required for RNA replication, infectious HCV assembly, and interactions with a variety of cellular proteins; the protein is also the target of the most potent anti-HCV inhibitors discovered to date. The largest TDAV NS5A insertion resides in the equivalent of HCV NS5A domain I, a zinc-binding region with RNA-binding activity; the relevance of the insertions in the TDAV life cycle is not known. Second, TDAV lacks a microRNA (miR)-122 binding site in the 5′ UTR that has been detected in the hepaciviruses. In humans, miR-122 is an abundant liver-specific miRNA, which is essential for HCV replication. The role, if any, that miRNAs play in TDAV replication remains to be determined.
While genetically distinct from the hepaciviruses, TDAV resembles HCV in several elements of its biology, including the ability to engender both acute and chronic infections that can present with symptomatic or asymptomatic infection. TDAV is a blood-borne virus that showed no evidence of horizontal transmission via normal contact between uninfected and infected horses on Farm A over one year. This also resembles HCV, which is rarely transmitted by casual nonparenteral human contact and is inefficiently transmitted by sexual contact; indeed, for HCV as for TDAV, parenteral exposure appears to be the most efficient route of transmission. Of course, the absence of horizontal TDAV transmission observed in this study does not entirely preclude its occurrence, and vertical transmission also remains a possibility. As observed for HCV, TDAV-positive individuals may be asymptomatic for prolonged periods. Furthermore, as in HCV, TDAV serum RNA levels are not strongly correlated with the severity of clinical disease. This may indicate that viral replication itself is not cytocidal, and that damage to hepatocytes, where present, may result from secondary immune or inflammatory mechanisms. Finally, acute HCV infections can clear without any intervention in some individuals, although approximately 70% can progress to chronicity; in this study, we observed an TDAV chronicity rate of 4 of 17 (23.5%) animals after one year.
The availability of a qRT-PCR-based TDAV diagnostic assay and the future development of serology-based assays will permit screening of equine biologic products, as well as further investigations of TDAV prevalence and exposure. These studies provide insight into the expanding world of non-primate Flaviviridae, open opportunities to investigate an important pathogen of horses, and provide critical information for the control and potential eradication of equine serum hepatitis.
For the purposes of interpreting this specification, the following definitions apply and whenever appropriate, terms used in the singular will also include the plural and vice versa. In the event that any definition set forth below conflicts with the usage of that word in any other document, including any document incorporated herein by reference, the definition set forth below shall always control for purposes of interpreting this specification and its associated claims unless a contrary meaning is clearly intended. It is noted that, as used in this specification and the appended claims, the singular forms “a,” “an,” and “the,” include plural referents unless expressly and unequivocally limited to one referent. The use of “or” means “and/or” unless stated otherwise. The use of “comprise,” “comprises,” “comprising,” “include,” “includes,” and “including” are interchangeable and not intended to be limiting. Furthermore, where the description of one or more embodiments uses the term “comprising,” those skilled in the art would understand that, in some specific instances, the embodiment or embodiments can be alternatively described using the language “consisting essentially of” and/or “consisting of.” The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including but not limited to patents, patent applications, articles, books, and treatises are hereby expressly incorporated by reference in their entirety for any purpose. In the event that one or more of the incorporated documents defines a term that contradicts that term's definition in this application, this application controls. All references cited herein, including patents, patent applications, papers, text books, and the like, and the references cited therein, to the extent that they are not already, are hereby incorporated by reference in their entirety. In the event that one or more of the incorporated literature and similar materials differs.
TTCGGGTAAATCCCGGCGCGGTGTTTTGGGTTCAGGGCAGTAGGGGCAGACGGGCCAGC
AGTCGCTGGTTCCTGGTACCACCACCCTATCCGGACGACCTCCCTCACGAAAGGTCGCC
ACGGTCTGTGGCTCGACGACGCCTATAATTCAGTCCGAGGGGCGCAGCCCTCGTTAAAC
TTTGGCTACTAAAATGGTCTTGACTGCTAAATTACAACCCTTGTGGAGGAATCTTAACA
CTACCATTATGTGCTCAGTTATTCGGACTTCTGTCCATTGCTTTAGTTGCATCGGCTTG
CCATGGGTATGTTGACCGCGGTGTCGCATCGGGGGCCGGAAGTACACTCGGCCCTCTTT
GTCAAGCCGTGGGACAGCGTTCCCAGGGATGCCCAAACGGTTACGGACGTGGGTGCACC
TCCTGCGGTACCTGGCAAAGGCAACTACGAGGAGCGATCCTTGTTCTTGCCCACTGGCA
The present application is a national phase entry under 35 U.S.C. §371 of International Patent Application PCT/US2013/067669, filed on Oct. 31, 2013 and published in English as International Patent Publication WO 2014/070975A1 on May 8, 2014, which claims benefit of priority to U.S. Patent Application Ser. No. 61/721,858, filed Nov. 2, 2012; all of which are incorporated by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2013/067669 | 10/31/2013 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
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| WO2014/070975 | 5/8/2014 | WO | A |
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| Number | Date | Country | |
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| 20150292042 A1 | Oct 2015 | US |
| Number | Date | Country | |
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| 61721858 | Nov 2012 | US |
