Specific TT virus sequences and chimeric TT virus host cell DNA molecules for use in diagnosis, prevention and treatment of cancer and autoimmunity

Abstract

Described are single-stranded new sequences of TT viruses, rearranged TTV sequences and hybrid molecules of a specific TT virus sequence and host cell DNA that are capable of replicating autonomously for use in diagnosis, prevention and treatment of diseases like cancer and autoimmunity. In addition, it relates to the use of such molecules as gene vectors and artificial chromosomes.

Description

FIELD OF THE INVENTION

[0001] The present invention relates to single-stranded new sequences of TT viruses and hybrid molecules of a specific TT virus sequence and host cell DNA that are capable of replicating autonomously for use in diagnosis, prevention and treatment of diseases like cancer and autoimmunity. In addition, it relates to the use of such molecules as gene vectors and artificial chromosomes.

BACKGROUND OF THE TECHNOLOGY

[0002] Since their discovery in 1997 by Okamoto and colleagues TT viruses (TTV) have been found to be widely spread in all human populations, in domestic animals, and in old world primates (1,2). A large number of types and pseudotypes have been identified in humans, pointing to a remarkable heterogeneity of this virus family now being assigned as a new virus family, Anelloviridae (3). Viral DNA can be demonstrated in sera of almost every human being and some reports even document such DNA in newborn children and cord blood, suggesting prenatal transmission of these agents (4,5). In spite of the widespread occurrence of these viruses, intensive research performed during more than 10 years failed to demonstrate a pathogenic role of such infections in human disease. TT viruses have not been successfully replicated in human tissue culture cells, although indications exist that replication can be achieved in human cells of epithelial or hematopoietic origin. In the latter, replicative cycles of herpes group viruses (Epstein-Barr virus) seem to exert an enhancing effect for the amplification of latent or transfected TTV genomes (6). In addition, TT viruses frequently reveal intramolecular rearrangements which lead to subviral DNA genomes in part defective and with novel open reading frames. They replicate autonomously over prolonged periods of time in infected tissues (7). These subviral DNAs are found in normal and malignant human biopsy materials.

[0003] During the past years, some data have been compiled indicative of an association of TT virus infection with human malignant tumors. A high rate of TT virus load has been noted in a spleen biopsy of a patient with Hodgkin's lymphoma (24 individual TTV genotypes) (8). Similarly, other reports describe a higher rate of TTV prevalence in colorectal and esophageal cancer and in hematopoietic malignancies in comparison to non-tumorous tissue from the same or other patients (9,10). Yet, the ubiquity of these infections rendered an interpretation of these results rather difficult and did not permit a linkage of these observations with tumor development.

SUMMARY OF THE INVENTION

[0004] The technical problem underlying the present invention is to identify specific TTV sequences that might be clearly associated with diseases like cancer or autoimmune diseases and, thus, to provide means for diagnosis and therapy.

[0005] The solution to said technical problem is achieved by providing the embodiments characterized in the claims. Recent observations of the persistence of a 71 base highly conserved region (HCR), present with only minor variation in all TTV isolates characterized thus far, in a larger number of human cancer and immortalized cell lines were somewhat surprising in view of the regular long-time non-permissibility of the same cells for transfected TTV DNA. Even more surprising has been the linkage of host cell DNA sequences in an apparently single-stranded form to the TTV-HCR. The frequency and regularity of persistence of this obviously extrachromosomal genetic material in a large number of cancer cell lines as well as in biopsies of affected brain tissue from patients with multiple sclerosis prompted the following hypothesis: Host cell genes either modified in the recombinatory process or dysregulated by novel TTV regulatory sequences play a significant role in human carcinogenesis and also in some autoimmune reactions. They may even replace or, in a certain sense, functionally correspond to retrovirus infections in rodent and chicken cells.

A Novel Role for TT Viruses in Human Cancer and Autoimmunity

[0006] The surprising observation of host cell DNA linked to an apparently single-stranded form to TT virus HCR is the basis for the following conclusion: TT viral sequences have not yet been demonstrated as integrated into double-stranded cellular DNA, persisting within host cell chromosomes. Thus, the opposite finding of host cell DNA, linked in a single-stranded state to the TTV HCR should have biological significance. The present data indicate their long-time persistence as episomes in human cancer cell lines, pointing to a role of this persistence in cell proliferation. Two aspects seem to require specific consideration: a possible role of those recombinants in cancer and in autoimmunity.

[0007] One possibility is the random integration of host cell sequences into TTV episomes. This may happen after strand displacement in the course of aberrant DNA replication or after reverse transcription of cellular RNA. In case of random integration a larger number of recombinants should be innocuous and harmless for cells carrying these recombinants. A growth-promoting property of transcripts of the TTV HCR, as well as integration and transcription of growth-stimulating host cell genes, their modification in the process of integration or their dysregulation by the TTV HCR however, will result in proliferative consequences. These episomes should acquire immortalizing and under certain conditions transforming properties. In combination with additional modifications of the host cell genome they may direct malignant growth. This mode of action reveals a distant resemblance to the insertion of cellular oncogenes into retroviral genomes.

The TTV-Oncogene Concept

[0008] The previous considerations are summarized in FIG. 4. Obviously, the recombination between the TTV regulatory region and cellular nucleic acids must be a relatively frequent process, since such recombinants are found in the majority of cell lines thus far analyzed. It also should contribute to cell proliferation, otherwise the regular persistence of such molecules, in part over decades of continuous proliferation, would be difficult to explain. It is assumed that this type of recombination is a random process, involving different types of cellular genes. The coding function of the TTV HCR and/or the uptake of genes steering cell proliferation, or blocking the function of proliferation antagonists, or inhibiting cell differentiation should lead to an accumulation of cells containing these types of recombinants. It is envisaged that this, in combination with additional mutational or recombinational events of the cells harbouring such TTV-host cell nucleic acid recombinants, provides a selective advantage for cells carrying such episomes. The presence of the latter would represent a prime risk factor for malignant conversion. In this sense those recombinations should be of general importance for different types of human cancers, although a certain degree of specificity for a limited set of genes would be expected for individual cancer types.

[0009] The implications of this model are profound. They reach from cancer prevention, early detection into cancer therapy. The important role of TTV infections and of the persistence of TTV HCR is stressed by the available information. Prevention of these infections should reduce the risk for the development of the described recombinants. The diagnosis of specific recombinants would probably contribute to cancer risk assessment. Profound implications would be expected for cancer therapy: the TTV HCR emerges as the prime determinant for the persistence and maintenance of the single-stranded episomes. Since this region appears to be part of an open reading frame, it should be vulnerable to small interfering RNAs or DNAs. Thus, it offers a suitable target for future therapeutic deliberations.

[0010] Two other aspects deserve discussion: certain parallels which seem to exist to retroviral carcinogenesis in rodents and chicken and the use of autonomously replicating TTV-based vector systems for gene therapy. Insertional mutagenesis, the uptake and modification of cellular growth-stimulating genes, rendering them into oncogenes has frequently been analyzed in animal systems. This has thus far not been reported for human cancers. Do TT viruses replace this niche in human and other primate cells? Do TTV compete successfully with retrovirus infections in taking over their role in specific species? The episomal persistence of single-stranded DNA, however, emerges as a remarkable difference to retrovirus-induced carcinogenesis.

[0011] Autonomously replicating subviral DNA molecules of approximately 400 bases of TTV origin have been described before (11). It is tempting to speculate that they or specific TTV-host cell recombinants may represent optimal vector systems for future approaches in gene therapy and for the construction of artificial chromosomes.

The Recombinant TTV-host Cell DNA Autoimmunity Concept

[0012] The existence of TTV host cell nucleic acid recombinants also permits a novel view on aspects of autoimmune diseases and other chronic diseases (potentially even conditions like arteriosclerosis and Alzheimer's disease). Modification or dys-regulation of cellular proteins may originate from insertional events of cellular genes into single-stranded DNA or to the different HCRs exerted by TTV elements (FIG. 5). They could provide a convenient explanation for autoimmune reactions, even for local ones, like in multiple sclerosis (MS) or Crohn's disease. In the latter two cases in particular, the reactivation of other local infections (potentially herpes-type viruses) would provide a stimulus for the local amplification and gene activity of the respective TTV-host cell nucleic acid recombinants. In MS, this could explain recurrent episodes of disease progression. A model of the autoimmunity concept is depicted in FIG. 5.

[0013] Similarly, rearranged TT virus molecules of 719, 642, and 621 bases have been identified which replicate autonomously upon transfection of specific cell lines. Their DNA composition and derivation from specific complete TTV genotypes is shown in FIG. 6. Here the rearrangement results in novel open reading frames in part with epitopes related to those of juvenile diabetes and rheumatoid arthritis.

Conclusion

[0014] The models of the present invention for a role of TTV-host cell nucleic acid recombinants is based on the demonstration of the single-stranded chimeric molecules between the TTV HCR and host cell DNA and rearranged autonomously replicating TTV molecules of substantially reduced molecular weights. Both, the TTV oncogene concept and the TTV autoimmunity concept will clearly provide novel approaches to prevention, diagnosis, and in particular to therapy of these conditions and will improve the prognosis of the respective patients.

[0015] Thus, in a first aspect, the present invention relates to a TT virus polynucleic acid comprising

[0016] (a) a 71 base nucleotide sequence (HCR) shown in FIG. 6;

[0017] (b) a nucleotide sequence which shows 70% identity with an HCR of (a) and is capable of replicating autonomously;

[0018] (c) a fragment of a nucleotide sequence of (a) or (b) which is capable of replicating autonomously;

[0019] (d) a nucleotide sequence which is the complement of the nucleotide sequence of (a), (b) or (c); or

[0020] (e) a nucleotide sequence which is redundant as a result of the degeneracy of the genetic code compared to any of the above-given nucleotide sequences.

[0021] In a second aspect, the present invention provides oligonucleotide primers and probes comprising part of a polynucleic acid of a TTV polynucleic acid of the invention, with (a) said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid, and (b) said probe being capable of specifically hybridizing to said polynucleic acid.

[0022] The present invention also provides an expression vector comprising a TT virus polynucleic acid (HCR) of the invention operatively linked to prokaryotic, eukaryotic or viral transcription and translation control elements as well as a host cell transformed with an expression vector according to claim 11.

[0023] Moreover, the present invention provides a polypeptide being encoded by a TT virus polynucleic acid (HCR) of the invention and an antibody specifically binding to such polypeptide.

[0024] A diagnostic kit is also provided. Such kit is for use in determining the presence of a TT virus polynucleic acid of the invention and comprises a primer, a probe, a polypeptide or an antibody of the invention. Said primer, probe, polypeptide or antibody are useful for the diagnosis of a predisposition or an early stage of cancer or an autoimmune disease.

[0025] The present invention also provides an antisense oligonucleotide abolishing the persistence of this DNA or reducing or inhibiting the expression of the TTV polynucleic acid of the invention, preferably an iRNA comprising a sense sequence and an antisense sequence, wherein the sense and antisense sequences form an RNA duplex and wherein the antisense sequence comprises a nucleotide sequence sufficiently complementary to the nucleotide sequence of the TT virus polynucleic acid of the invention.

[0026] The present invention also relates to the construction of transgenic mice, carrying the TTV sequences of the invention, for diagnostic and experimental therapeutic purposes.

[0027] In a further aspect, the present invention relates to a pharmaceutical composition comprising the antibody, antisense oligonucleotide or oligopeptide (aptamer) of the invention and a suitable pharmaceutical carrier.

[0028] Said antibody, antisense oligonucleotide or oligopeptide are useful for the prevention or treatment of cancer (preferably breast cancer, ovarian cancer, lung cancer, liver cancer, colon or rectal cancer, pancreatic cancer, prostate cancer, skin cancer, stomach cancer, a cancer of the urinary system (e.g., kidney cancer), Hodgkin's lymphoma, B-lymphoma, acute lymphocytic leukemia, Burkitt's lymphoma or brain tumors) or an autoimmune disease (preferably multiple sclerosis (MS), asthma, Crohn's disease, polyarthritis, juvenile diabetes) or early stages thereof. Said compounds are also useful in the treatment/prevention of arteriosclerosis and Alzheimer's disease (AD).

[0029] Finally, the present invention provides a vaccine comprising a polypeptide of the invention for use in a method of immunizing a mammal against a TT virus infection.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

[0030] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art to which the invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, preferred methods and materials are described. For the purposes of the present invention, the following terms are defined below.

[0031] By "antibody" is meant a protein of the immunoglobulin family that is capable of combining, interacting or otherwise associating with an antigen. The term "antigen" is used herein in its broadest sense to refer to a substance that is capable of reacting in and/or inducing an immune response. Typically, but not necessarily, antigens are foreign to the host animal in which they produce immune reactions.

[0032] By "epitope" is meant that part of an antigenic molecule against which a particular immune response is directed. Typically, in an animal, antigens present several or even many antigenic determinants simultaneously. Thus, the terms "epitope" and "antigenic determinant" mean an amino acid sequence that is immunoreactive. Generally an epitope consists of 4, and more usually 5, 6, 7, 8 or 9 contiguous amino acids. However, it should also be clear that an epitope need not be composed of a contiguous amino acid sequence. The immunoreactive sequence may be separated by a linker, which is not a functional part of the epitope. The linker does not need to be an amino acid sequence, but can be any molecule that allows the formation of the desired epitope.

[0033] The term "biological sample" as used herein refers to a sample that may be extracted, untreated, treated, diluted or concentrated from an animal. Biological sample refers to any biological sample (tissue or fluid) containing a TTV polynucleic acid of the invention and refers more particularly to blood serum samples, plasma samples, biopsy samples, cerebrospinal fluid samples etc.

[0034] By "carrier" is meant any substance of typically high molecular weight to which a non- or poorly immunogenic substance (e.g., a hapten) is naturally or artificially linked to enhance its immunogenicity.

[0035] The term "diagnosis" is used herein in its broadest sense to include detection of an antigen reactive to a sub-immunoglobulin antigen-binding molecule. Also included within its scope, is the analysis of disorder mechanisms. Accordingly, the term "diagnosis" includes the use of monoclonal antibodies for research purposes as tools to detect and understand mechanisms associated with a disease or condition of interest. It also includes the diagnostic use of TTV polynucleic acid of the invention for the detection of homologous or complementary RNA transcribed from such molecules.

[0036] The term "immunogenicity" is used herein in its broadest sense to include the property of evoking an immune response within an organism. Inmunogenicity typically depends partly upon the size of the substance in question, and partly upon how unlike host molecules it is. It is generally considered that highly conserved proteins tend to have rather low immunogenicity.

[0037] The term "patient" refers to patients of human or other mammal origin and includes any individual it is desired to examine or treat using the methods of the invention. However, it will be understood that `patient" does not imply that symptoms are present. Suitable mammals that fall within the scope of the invention include, but are not restricted to, primates, livestock animals (e.g., sheep, cows, horses, donkeys, pigs), laboratory test animals (e.g., rabbits, mice, rats, guinea pigs, hamsters), companion animals (e.g., cats, dogs) and captive wild animals (e.g., foxes, deer, dingoes).

[0038] By `pharmaceutically acceptable carrier" is meant a solid or liquid filler, diluent or encapsulating substance that may be safely used in any kind of administration.

[0039] The term "related disease or condition" is used herein to refer to a disease or condition that is related anatomically, physiologically, pathologically and/or symptomatically to a reference disease or condition. For example, diseases or conditions may be related to one another by affecting similar anatomical locations (e.g., affecting the same organ or body part), affecting different organs or body parts with similar physiological function (e.g., the oesophagus, duodenum and colon which rely an peristalsis to move food from one end of the alimentary canal to the other), by having similar or overlapping pathologies (e.g., tissue damage or rupture, apoptosis, necrosis) or by having similar or overlapping symptoms (i.e., allergic response, inflammation, lymphocytosis). Thus, for example, an antigen associated with ulcerated colitis may also be associated with perforation of the colon because these disease affects the same organ (i.e., colon).

[0040] The term "treating" is used herein in its broadest sense to include both therapeutic and prophylactic (i.e., preventative) treatment designed to ameliorate the disease or condition.

[0041] The term "episome" is used herein to refer to a portion of genetic material that can exist independent of the main body of genetic material (chromosome) at some times or continuously and replicate autonomously, while at other times is able to integrate into the chromosome. Examples of episomes include insertion sequences, transposons and the TTV of the invention.

FIGURE LEGENDS

[0042] FIG. 1: PCR amplification of a 71 base fragment containing the highly conserved TTV region (HCR) in 4 different cell lines, L1236 (EBV-negative Hodgkin's lymphoma line), HSB-2 (acute lymphoblastic leukemia line), KR and IGL (melanoma cell lines) and placenta DNA

[0043] FIG. 2: Spooled DNA remaining in the supernatant of L1236 cells after precipitation and removal of high molecular weight DNA and RNase digestion

[0044] Two bands are visible in the region between 4.3 and 6.6 base bands.

[0045] FIG. 3: Outwards-directed long-PCR, using primers of the 71 base TTV HCR region in HSB-2 DNA

[0046] Two bands are visible in regions corresponding to 4.5 to 7 kb. In addition, bands emerge in the region corresponding to 0.4 to 0.7 kb.

[0047] FIG. 4: Schematic outline of the TTV oncogene concept

[0048] The left part represents the genomic organization of wild-type TTV genomes. The right part envisages the integration of host cell DNA into the single-stranded plasmids.

[0049] FIG. 5: Schematic outline of the TTV host cell DNA autoimmunity concept

[0050] The modified host cell genes should code for immuno-reactive antigenic epitopes.

[0051] FIG. 6: PCR amplification of the 71 base HCR from the DNA of 4 different cell lines

[0052] The arrows point to the two sites with variations in the nucleotide sequences.

[0053] FIG. 7:

[0054] (A) The autonomously replicating 719 base TTV DNA (right) and the complete TTV sequence from which it is derived. The nucleotide composition of both molecules is found in FIG. 11A+B.

[0055] (B) The autonomously replicating 621 base TTV DNA (right) and the complete DNA sequence from which it is derived. The nucleotide composition of both molecules is found in FIG. 12A+B.

[0056] (C) The autonomously replicating 642 base TTV DNA (right) and the complete DNA sequence from which it is derived. The nucleotide composition of both molecules is found in FIG. 13A+B.

[0057] FIG. 8: Three exemplary chimeric TTV/truncated host cell DNA sequences from brain biopsies of patients with multiple sclerosis

[0058] (A) Chimeric cellular sequences derived from chromosome 1 with some homologies to prion and Wilms tumor sequences and the 3' end of myeloid lymphoid leukemia 3 (MLL3) pseudogene. Human DNA sequence from clone RP11-14N7 on chromosome 1. Contains 3'end of a myeloid/lymphoid or mixed lineage leukemia 3 (MLL3) pseudogene, a seven transmembrane helix receptor pseudogene, the 5'-end of a novel gene.

[0059] (B) Chimeric cellular sequences derived from chromosome 16. Homologies to transcription factor 3 (TF 3C), protein signatures for chemokine receptors and leukotriene B4 receptor.

[0060] (C) Chimeric cellular sequences derived from chromosome 10, truncated sequence of myosin, reactivity reported for multiple sclerosis patients and those with rheumatoid arthritis (sequence contains both full primers front and back).

[0061] FIG. 9: Three exemplary chimeric TTV/truncated host cell DNA sequences from cell lines derived from patients with Hodgkin's disease or leukemia

[0062] (A) Chromosome 1 sequences with part of transgelin 2, the IGSF9 gene for immunoglobulin superfamily member 9, the SLAM9 gene.

[0063] (B) Translated protein sequences with substantial homology to the oncogenes v-myb (avian myeloblastosis viral oncogene), but also to c-myb. This sequence was amplified with the forward primer at both ends.

[0064] (C) Derived from chromosome 10. High homology with "Deleted in malignant 1 Protein" (DMBT), an identified tumor suppressor gene. This sequence was amplified with the forward primer at both ends.

[0065] FIG. 10: Primer sequences used in the reactions described in the Examples, derived from the 71 base HCR.

[0066] FIG. 11:

[0067] (A) Complete TTV sequence from which autonomously replicating 719 base DNA has been obtained.

[0068] (B) Complete sequence of the autonomously replicating 719 base TTV DNA.

[0069] FIG. 12:

[0070] (A) Complete TTV sequence (tth25) from which autonomously replicating 621 base DNA has been obtained.

[0071] (B) Complete sequence of the autonomously replicating 621 base TTV DNA.

[0072] FIG. 13:

[0073] (A) Complete TTV sequence (ttrh215) from which autonomously replicating 642 base DNA has been obtained.

[0074] (B) Complete sequence of the autonomously replicating 642 base TTV DNA.

[0075] FIG. 14: Open reading frames (ORFs) found within the nucleotide sequence of 71 nt

[0076] zyb2.1.pep, zyb9.1.pep, and zkb69.1.pep are starting at the first triplet, zyb2.3.pep, zyb9.3.pep, zkb5.3.pep, and zkb69.3.pep are starting from the third triplet. This region is actively transcribed.

[0077] FIG. 15: Digestion of single-stranded DNA by mung-bean nuclease (MBN)

[0078] Lanes 2 and 3 show that the amplified DNA can be digested by pre-treatment with MBN. Lanes 5 and 6 demonstrate that plasmid-DNA pretreated in the same way is not digested by MBN.

[0079] The present invention provides an isolated TT virus polynucleic acid comprising a nucleotide sequence shown in FIG. 6.

[0080] The present invention also provides an isolated nucleotide sequence which shows 70%, preferably 80%, more preferably 90% and most preferably 95% identity to the corresponding regions of a nucleotide sequence of FIGS. 6 to 13 and is capable of replicating autonomously.

[0081] The present invention also provides fragments of the nucleotide sequences of the present invention described above that are capable of replicating autonomously. The skilled person can derive at fragments still having the biological activity of the full length molecule without undue experimantation. The lengths of the fragments are not critical, however, fragments having a length of at least 45, at least 55, or at least 65 nt are preferred.

[0082] The person skilled in the art can easily determine which nucleic acid sequences are related to the nucleotide sequence of FIG. 6 or which fragments are still capable of replicating autonomously by using standard assays or the assays described in the examples, below.

[0083] The present invention more specifically relates to an isolated TT virus polynucleic acid having (a) a nucleotide sequence shown in FIG. 6, (b) a nucleotide sequence which shows 70% (80%, 90%, or 95%) identity to the nucleotide sequence of (a) and is capable of replicating autonomously, (c) a fragment of the nucleotide of (a) or (b) which is capable of replicating autonomously, or (d) the complement of (a), (b), or (c).

[0084] The present invention also provides polynucleic acid sequences which are redundant as a result of the degeneracy of the genetic code compared to any of the above-given nucleotide sequences. These variant polynucleic acid sequences will thus encode the same amino acid sequence as the polynucleic acids they are derived from.

[0085] The term "polynucleic acid" refers to a single-stranded or double-stranded nucleic acid sequence. A polynucleic acid may consist of deoxyribonucleotides or ribonucleotides, nucleotide analogues or modified nucleotides, or may have been adapted for therapeutic purposes. Preferably, the TT virus polynucleic acid is a single-stranded DNA.

[0086] The TT virus polynucleic acid of the invention might be present as an extrachromosomal episome, might be integrated into the host's genome and/or might be linked to a host cell DNA, e.g., a DNA comprising a growth-stimulating host cell gene, oncogene or containing truncated host cell genes with altered immunogenicity.

[0087] Preferably, the TT virus polynucleic acid of the invention comprises a nucleotide sequence being selected from the group of nucleotide sequences shown in FIGS. 8, 9 and 11 to 13.

[0088] The present invention also relates to an oligonucleotide primer comprising or consisting of part of a polynucleic acid as defined above, with said primer being able to act as primer for specifically sequencing or specifically amplifying TT virus HCR polynucleic acid of the invention and attached cellular DNA sequences.

[0089] The term "primer" refers to a single stranded DNA oligonucleotide sequence capable of acting as a point of initiation for synthesis of a primer extension product which is complementary to the nucleic acid strand to be copied. The length and the sequence of the primer must be such that they allow priming the synthesis of the extension products. Preferably the primer is about 5-50 nucleotides. Specific length and sequence will depend on the complexity of the required DNA or RNA targets, as well as on the conditions of primer use such as temperature and ionic strength.

[0090] The fact that amplification primers do not have to match exactly with corresponding template sequence to warrant proper amplification is amply documented in the literature (17). The amplification method used can be either polymerase chain reaction (PCR; (18)), ligase chain reaction (LCR; (19, 20)), nucleic acid sequence-based amplification (NASBA; (21, 22)), transcription-based amplification system (TAS; (23)), strand displacement amplification (SDA; (24)) or amplification by means of Qβ replicase (25, 26) or any other suitable method to amplify nucleic acid molecules using primer extension. During amplification, the amplified products can be conveniently labelled either using labelled primers or by incorporating labelled nucleotides.

[0091] Labels may be isotopic (32P, 35S, etc.) or non-isotopic (biotin, digoxigenin, etc.). The amplification reaction is repeated between 20 and 70 times, advantageously between 25 and 45 times.

[0092] Any of a variety of sequencing reactions known in the art can be used to directly sequence the viral genetic information and determine the orf by translating the sequence of the sample into the corresponding amino acid sequence. Exemplary sequencing reactions include those based on techniques developed by Sanger or Maxam and Gilbert. It is also contemplated that a variety of automated sequencing procedures may be utilized when performing the subject assays including sequencing by mass spectrometry (see, for example: PCT publication WO 94/16101). It will be evident to one skilled in the art that, for example the occurrence of only two or three nucleic bases needs to be determined in the sequencing reaction.

[0093] Preferably, these primers are about 5 to 50 nucleotides long, more preferably from about 10 to 25 nucleotides. Most preferred are primers having a length of at least 13 bases.

[0094] In a preferred embodiment, a primer of the present invention has a nucleotide sequence as indicated in FIG. 10.

[0095] The present invention also relates to an oligonucleotide probe comprising or consisting of part of a TT virus polynucleic acid as defined above, with said probe being able to act as a hybridization probe for specific detection of a TTV nucleic acid according to the invention.

[0096] The probe can be labelled or attached to a solid support.

[0097] The term "probe" refers to single stranded sequence-specific oligonucleotides which have a sequence which is complementary to the target sequence of the TTV polynucleic acid to be detected.

[0098] Preferably, these probes are about 5 to 50 nucleotides long, more preferably from about 10 to 25 nucleotides. Most preferred are probes having a length of at least 13 bases.

[0099] The term "solid support" can refer to any substrate to which an oligonucleotide probe can be coupled, provided that it retains its hybridization characteristics and provided that the background level of hybridization remains low. Usually the solid substrate will be a microtiter plate, a membrane (e.g. nylon or nitrocellulose) or a microsphere (bead). Prior to application to the membrane or fixation it may be convenient to modify the nucleic acid probe in order to facilitate fixation or improve the hybridization efficiency. Such modifications may encompass homopolymer tailing, coupling with different reactive groups such as aliphatic groups, NH₂ groups, SH groups, carboxylic groups, or coupling with biotin or haptens.

[0100] The oligonucleotides according to the present invention, used as primers or probes may also contain or consist of nucleotide analoges such as phosphorothioates (12), alkylphosphoriates (13) or peptide nucleic acids (14, 15) or may contain intercalating agents (16). These modifications will necessitate adaptions with respect to the conditions under which the oligonucleotide should be used to obtain the required specificity and sensitivity. However, the eventual results will be essentially the same as those obtained with the unmodified oligonucleotides.

[0101] The introduction of these modifications may be advantageous in order to positively influence characteristics such as hybridization kinetics, reversibility of the hybrid-formation, biological stability of the oligonucleotide molecules, etc.

[0102] The polynucleic acids of the invention may be comprised in a composition of any kind. Said composition may be for diagnostic, therapeutic or prophylactic use.

[0103] Also included within the present invention are sequence variants of the polynucleic acids as selected from any of the nucleotide sequences with said sequence variants containing either deletions and/or insertions of one or more nucleotides, especially insertions or deletions of 1 or more codons, mainly at the extremities of oligonucleotides (either 3' or 5'), or substitutions of some non-essential nucleotides by others (including modified nucleotides an/or inosine).

[0104] Particularly preferred variant TTV polynucleic acids of the present invention include also sequences which hybridise under stringent conditions with any of the polynucleic acid sequences of the present invention. Particularly, sequences which show a high degree of homology (similarity) to any of the polynucleic acids of the invention as described above. Particularly preferred sequences are at least 70%, 80%, 85%, 90%, 95% or more homologous to said polynucleic acid sequences of the invention. Preferably said sequences will have less than 20%, 15%, 10%, or 5% variation of the original nucleotides of said polynucleic acid sequence.

[0105] TTV polynucleic acid sequences according to the present invention which are similar to the sequences as shown in FIG. 6 can be characterized and isolated according to any of the techniques known in the art, such as amplification by means of sequence-specific primers, hybridization with sequence-specific probes under more or less stringent conditions, sequence determination of the genetic information of TTV, etc.

[0106] The present invention also relates to a recombinant expression vector comprising a TTV polynucleic acid of the invention as defined above operably linked to prokaryotic, eukaryotic or viral transcription and translation control elements.

[0107] The term "vector" may comprise a plasmid, a cosmid, an artificial chromosome, a phage, or a virus or a transgenic non-human animal. Particularly useful for vaccine development may be TT virus recombinant molecules, BCG or adenoviral vectors, as well as avipox recombinant viruses.

[0108] The term "recombinantly expressed" used within the context of the present invention refers to the fact that the polypeptides of the present invention are produced by recombinant expression methods be it in prokaryotes, or lower or higher eukaryotes as discussed in detail below.

[0109] The term "lower eukaryote" refers to host cells such as yeast, fungi and the like. Lower eukaryotes are generally (but not necessarily) unicellular. Preferred lower eukaryotes are yeasts, particularly species within Saccharomyces, Schizosaccharomyces, Kluiveromyces, Pichia (e. g. Pichia pastoris), Hansenula (e. g. Hansenula polymorph), Schwaniomyces, Schizosaccharomyces, Yarowia, Zygosaccharomyces and the like. Saccharomyces cerevisiae, S. carlsbergensis and K. lactis are the most commonly used yeast hosts, and are convenient fungal hosts.

[0110] The term "higher eukaryote" refers to host cells derived from higher animals, such as mammals, reptiles, insects, and the like. Presently preferred higher eukaryote host cells are derived from Chinese hamster (e. g. CHO), monkey (e. g. COS and Vero cells), baby hamster kidney (BHK), pig kidney (PK15), rabbit kidney 13 cells (RK13), the human osteosarcoma cell line 143 B, the human cell line HeLa and human hepatoma cell lines like Hep G2, and insect cell lines (e.g. Spodoptera frugiperda). The host cells may be provided in suspension or flask cultures, tissue cultures, organ cultures and the like. Alternatively the host cells may also be transgenic non-human animals.

[0111] The term "prokaryotes" refers to hosts such as E. coli, Lactobacillus, Lactococcus, Salmonella, Streptococcus, Bacillus subtilis or Streptomyces. Also these hosts are contemplated within the present invention.

[0112] The term "host cell" refers to cells which can be or have been, used as recipients for a recombinant vector or other transfer polynucleotide, and include the progeny of the original cell which has been transfected.

[0113] It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation or recombination.

[0114] The term "replicon" is any genetic element, e. g., a plasmid, a chromosome, a virus, a cosmid, etc., that behaves as an autonomous unit of polynucleotide replication within a cell, i. e., capable of replication under its own control.

[0115] The term "vector" is a replicon further comprising sequences providing replication and/or expression of a desired open reading frame.

[0116] The term "control element" refers to polynucleotide sequences which are necessary to effect the expression of coding sequences to which they are ligated. The nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include promoter, ribosomal binding site, splicing sites and terminators; in eukaryotes, generally, such control sequences include promoters, splicing sites, terminators and, in some instances, enhancers. The term "control elements" is intended to include, at a minimum, all components whose presence is necessary for expression, and may also include additional components whose presence is advantageous, for example, leader sequences which govern secretion.

[0117] The term "promoter" is a nucleotide sequence which is comprised of consensus sequences which allow the binding of RNA polymerase to the DNA template in a manner such that mRNA production initiates at the normal transcription initiation site for the adjacent structural gene.

[0118] The expression "operably linked" refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. A control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences.

[0119] The segment of the TTV DNA encoding the desired sequence inserted into the vector sequence may be attached to a signal sequence. Said signal sequence may be that from a non-TTV source, but particularly preferred constructs according to the present invention contain signal sequences appearing in the TTV genome before the respective start points of the proteins.

[0120] Higher eukaryotes may be transformed with vectors, or may be infected with a recombinant virus, for example a recombinant vaccinia virus. Techniques and vectors for the insertion of foreign DNA into vaccinia virus are well known in the art, and utilize, for example homologous recombination. A wide variety of viral promoter sequences, possibly terminator sequences and poly(A)-addition sequences, possibly enhancer sequences and possibly amplification sequences, all required for the mammalian expression, are available in the art. Vaccinia is particularly preferred since vaccinia halts the expression of host cell proteins. For vaccination of humans the avipox and Ankara Modified Virus (AMV) are particularly useful vectors.

[0121] Also known are insect expression transfer vectors derived from baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV), which is a helper-independent viral expression vector. Expression vectors derived from this system usually use the strong viral polyhedrin gene promoter to drive the expression of heterologous genes. Different vectors as well as methods for the introduction of heterologous DNA into the desired site of baculovirus are available to the man skilled in the art for baculovirus expression. Also different signals for posttranslational modification recognized by insect cells are known in the art.

[0122] The present invention also relates to a host cell as defined above transformed with a recombinant vector as defined above.

[0123] The present invention also relates to a polypeptide having an amino acid sequence encoded by a TTV polynucleic acid as defined above, or a part or an analogue thereof being substantially similar and biologically equivalent.

[0124] The term "polypeptide" refers to a polymer of amino acids and does not refer to a specific length of the product. Thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide. This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. Included within the definition are, for example, polypeptides containing one or more analogues of an amino acid (including, for example, unnatural amino acids, peptide nucleic acid (PNA), etc.), polypeptides with substituted linkages, as well as other modifications known in the art, both naturally occurring and non-naturally occurring.

[0125] By "biologically equivalent" as used throughout the specification and claims, it is meant that the compositions are immunogenically equivalent to the polypeptides of the invention as defined above and below.

[0126] By "substantially homologous" as used throughout the specification and claims to describe polypeptides, it is meant a degree of homology in the amino acid sequence to the polypeptides of the invention. Preferably the degree of homology is in excess of 70%, preferably in excess of 80%, with a particularly preferred group of proteins being in excess of 90% or even 95% homologous with the polypeptides of the invention.

[0127] The term "analogue" as used throughout the specification to describe the polypeptides of the present invention, includes any polypeptide having an amino acid residue sequence substantially identical to a sequence specifically shown herein in which one or more residues have been conservatively substituted with a biologically equivalent residue. Examples of conservative substitutions include the substitution of one nonpolar (hydrophobic) residue such as isoleucine, valine, leucine or methionine for another, the substitution of one polar (hydrophillic) residue for another such as between arginine and lysine, between glutamine and asparagine, between glycine and serine, the substitution of one basic residue such as lysine, arginine or histidine for another, or the substitution of one acidic residue, such as aspartic acid or glutamic acid for another.

[0128] The phrase "conservative substitution" also includes the use of a chemically derivatized residue in place of a non-derivatized residue provided that the resulting protein or peptide is biologically equivalent to the protein or peptide of the invention.

[0129] "Chemical derivative" refers to a protein or peptide having one or more residues chemically derivatized by reaction of a functional side group. Examples of such derivatized molecules, include but are not limited to, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, tbutyloxycarbonyl groups, chloracetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or O-alkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-imbenzylhistidine. Those proteins or peptides are also included as chemical derivatives which contain one or more naturally-occurring amino acid derivatives of the twenty standard amino acids. For examples: 4-hydroxyproline may be substituted for proline; 5-hydroxylysine may be substituted for lysine; 3-methylhistidine may be substituted for histidine; homoserine may be substituted for serine; and ornithine may be substituted for lysine. The polypeptides of the present invention also include any polypeptide having one or more additions and/or deletions or residues relative to the sequence of a polypeptide whose sequence is shown herein, so long as the polypeptide is biologically equivalent to the polypeptides of the invention.

[0130] The polypeptides according to the present invention contain preferably at least 3, preferably 4 or 5 contiguous TTV amino acids, 6 or 7 preferably however at least 8 contiguous TTV amino acids, at least 10 or at least 15.

[0131] The polypeptides of the invention, and particularly the fragments, can be prepared by classical chemical synthesis. The synthesis can be carried out in homogeneous solution or in solid phase. For instance, the synthesis technique in homogeneous solution which can be used is the one described by Houbenweyl in the book entitled "Methode der organischen Chemie" (Method of organic chemistry) edited by E. Wunsh, vol. 15-I et II. THIEME. Stuttgart 1974.

[0132] The polypeptides of the invention can also be prepared in solid phase according to for example the methods described by Atherton and Shepard in their book entitled "Solid phase peptide synthesis" (IRL Press, Oxford, 1989).

[0133] The polypeptides according to this invention can also be prepared by means of recombinant DNA techniques as for example described by Maniatis et al., Molecular Cloning: A Laboratory Manual, New York, Cold Spring Harbor Laboratory, 1982.

[0134] The present invention also relates to a method for production of a recombinant polypeptide as defined above, comprising: (a) transformation of an appropriate cellular host with a recombinant vector, in which a polynucleic acid or a part thereof as defined above has been inserted under the control of the appropriate regulatory elements, (b) culturing said transformed cellular host under conditions enabling the expression of said insert, and (c) harvesting said polypeptide.

[0135] The present invention also relates to an antibody raised upon immunization with at least one polypeptide as defined above, with said antibody being specifically reactive with any of said polypeptides, and with said antibody being preferably a monoclonal antibody. The term "antibody", preferably, relates to antibodies which consist essentially of pooled monoclonal antibodies with different epitopic specifities, as well as distinct monoclonal antibody preparations. Monoclonal antibodies are made from an antigen containing, e.g., a polypeptide encoded by the TTV polynucleic acid of the invention or a fragment thereof by methods well known to those skilled in the art (see, e.g. (27)). As used herein, the term "antibody"(Ab) or "monoclonal antibody" (Mab) is meant to include intact molecules as well as antibody fragments (such as, for example, Fab and F(ab')2 fragments) which are capable of specifically binding to protein. Fab and F(ab')2 fragments lack the Fc fragment of intact antibody, clear more rapidly from the circulation, and may have less non-specific tissue binding than an intact antibody (28). Thus, these fragments are preferred, as well as the products of a FAB or other immunoglobulin expression library. Moreover, antibodies useful for the purposes of the present invention include chimerical, single chain, and humanized antibodies.

[0136] Preferably, the antibody or antigen binding fragment thereof carries a detectable label. The antibody/fragment can be directly or indirectly detectably labeled, for example, with a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator or an enzyme. Those of ordinary skill in the art will know of other suitable labels for binding to the antibody, or will be able to ascertain such, using routine experimentation.

[0137] The present invention also relates to a diagnostic kit for use in determining the presence of a TT virus polynucleic acid or polypeptide of the invention, said kit comprising a primer, a probe, and/or an antibody of the invention.

[0138] The present invention also relates to a method for the detection of a TTV polynucleic acid according to the invention present in a biological sample, comprising: (a) optionally extracting sample polynucleic acid, (b) amplifying the polynucleic acid as described above with at least one primer as defined above, optionally a labelled primer, and (c) detecting the amplified polynucleic acids.

[0139] The term "polynucleic acid" can also be referred to as analyte strand and corresponds to a single- or double-stranded polynucleic acid molecule.

[0140] The term "labelled" refers to the use of labelled nucleic acids. This may include the use of labelled nucleotides incorporated during the polymerase step of the amplification such as illustrated by Saiki et al. (1989) or Bej et al. (1990) or labelled primers, or by any other method known to the person skilled in the art.

[0141] The present invention also relates to a method for the detection of a TTV polynucleic acid according to the invention present in a biological sample, comprising: (a) optionally extracting sample polynucleic acid, (b) hybridizing the polynucleic acid as described above with at least one probe as defined above, and (c) detecting the hybridized polynucleic acids.

[0142] The hybridization and washing conditions are to be understood as stringent and are generally known in the art (e. g. Maniatis et al., Molecular Cloning: A Laboratory Manual, New York, Cold Spring Harbor Laboratory, 1982). However, according to the hybridization solution (SSC, SSPE, etc.), these probes should be hybridized at their appropriate temperature in order to attain sufficient specificity.

[0143] According to the hybridization solution (SSC, SSPE, etc.), these probes should be stringently hybridized at their appropriate temperature in order to attain sufficient specificity. However, by slightly modifying the DNA probes, either by adding or deleting one or a few nucleotides at their extremities (either 3' or 5'), or substituting some non-essential nucleotides (i. e. nucleotides not essential to discriminate between types) by others (including modified nucleotides or inosine) these probes or variants thereof can be caused to hybridize specifically at the same hybridization conditions (i. e. the same temperature and the same hybridization solution). Also changing the amount (concentration) of probe used may be beneficial to obtain more specific hybridization results. It should be noted in this context, that probes of the same length, regardless of their GC content, will hybridize specifically at approximately the same temperature in TMACI solutions (29).

[0144] Suitable assay methods for purposes of the present invention to detect hybrids formed between the oligonucleotide probes and the polynucleic acid sequences in a sample may comprise any of the assay formats known in the art, such as the conventional dot-blot format, sandwich hybridization or reverse hybridization. For example, the detection can be accomplished using a dot blot format, the unlabelled amplified sample being bound to a membrane, the membrane being incorporated with at least one labelled probe under suitable hybridization and wash conditions, and the presence of bound probe being monitored.

[0145] An alternative and preferred method is a "reverse" dot-blot format, in which the amplified sequence contains a label. In this format, the unlabelled oligonucleotide probes are bound to a solid support and exposed to the labelled sample under appropriate stringent hybridization and subsequent washing conditions. It is to be understood that also any other assay method which relies on the formation of a hybrid between the polynucleic acids of the sample and the oligonucleotide probes according to the present invention may be used.

[0146] The present invention also relates to a method for detecting a polypeptide encoded by a TTV polynucleic acid of the present invention or an antibody against said polypeptide present in a biological sample, comprising: (a) contacting the biological sample for the presence of such polypeptide or antibody as defined above, and (b) detecting the immunological complex formed between said antibody and said polypeptide.

[0147] The immunoassay methods according to the present invention may utilize antigens from different domains of the new and unique polypeptide sequences of the present invention. It is within the scope of the invention to use for instance single or specific oligomeric antigens, dimeric antigens, as well as combinations of single or specific oligomeric antigens. The TTV antigens of the present invention may be employed in virtually any assay format that employs a known antigen to detect antibodies. Of course, a format that denatures the TTV conformational epitope should be avoided or adapted. A common feature of all of these assays is that the antigen is contacted with the body component suspected of containing TTV antibodies under conditions that permit the antigen to bind to any such antibody present in the component. Such conditions will typically be physiologic temperature, pH and ionic strength using an excess of antigen. The incubation of the antigen with the specimen is followed by detection of immune complexes comprised of the antigen.

[0148] Design of the immunoassays is subject to a great deal of variation, and many formats are known in the art. Protocols may, for example, use solid supports, or immunoprecipitation. Most assays involve the use of labeled antibody or polypeptide; the labels may be, for example, enzymatic, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays which amplify the signals from the immune complex are also known; examples of which are assays which utilize biotin and avidin or streptavidin, and enzyme-labeled and mediated immunoassays, such as ELISA assays.

[0149] The immunoassay may be in a heterogeneous or in a homogeneous format, and of a standard or competitive type. In a heterogeneous format, the polypeptide is typically bound to a solid matrix or support to facilitate separation of the sample from the polypeptide after incubation. Examples of solid supports that can be used are nitrocellulose (e. g., in membrane or microtiter well form), polyvinyl chloride (e. g., in sheets or microtiter wells), polystyrene latex (e. g., in beads or microtiter plates, polyvinylidine fluoride (known as Immunolon), diazotized paper, nylon membranes, activated beads, and Protein A beads. The solid support containing the antigenic polypeptides is typically washed after separating it from the test sample, and prior to detection of bound antibodies. Both standard and competitive formats are known in the art.

[0150] In a homogeneous format, the test sample is incubated with the combination of antigens in solution. For example, it may be under conditions that will precipitate any antigen-antibody complexes which are formed. Both standard and competitive formats for these assays are known in the art.

[0151] In a standard format, the amount of TTV antibodies in the antibody-antigen complexes is directly monitored. This may be accomplished by determining whether (labelled) anti-xenogeneic (e.g. anti-human) antibodies which recognize an epitope on anti-TTV antibodies will bind due to complex formation. In a competitive format, the amount of TTV antibodies in the sample is deduced by monitoring the competitive effect on the binding of a known amount of labeled antibody (or other competing ligand) in the complex.

[0152] Complexes formed comprising anti-TTV antibody (or in the case of competitive assays, the amount of competing antibody) are detected by any of a number of known techniques, depending on the format. For example, unlabeled TTV antibodies in the complex may be detected using a conjugate of anti-xenogeneic Ig complexed with a label (e. g. an enzyme label).

[0153] In an immunoprecipitation or agglutination assay format the reaction between the TTV antigens and the antibody forms a network that precipitates from the solution or suspension and forms a visible layer or film of precipitate. If no anti-TTV antibody is present in the test specimen, no visible precipitate is formed.

[0154] There currently exist three specific types of particle agglutination (PA) assays. These assays are used for the detection of antibodies to various antigens when coated to a support. One type of this assay is the hemagglutination assay using red blood cells (RBCs) that are sensitized by passively adsorbing antigen (or antibody) to the RBC. The addition of specific antigen/antibodies present in the body component, if any, causes the RBCs coated with the purified antigen to agglutinate.

[0155] To eliminate potential non-specific reactions in the hemagglutination assay, two artificial carriers may be used instead of RBC in the PA. The most common of these are latex particles.

[0156] The solid phase selected can include polymeric or glass beads, nitrocellulose, microparticles, microwells of a reaction tray, test tubes and magnetic beads. The signal generating compound can include an enzyme, a luminescent compound, a chromogen, a radioactive element and a chemiluminescent compound. Examples of enzymes include alkaline phosphatase, horseradish peroxidase and beta-galactosidase. Examples of enhancer compounds include biotin, anti-biotin and avidin. Examples of enhancer compounds binding members include biotin, anti-biotin and avidin.

[0157] The above methods are useful for evaluating the risk of developing diseases like cancer or an autoimmune disease due to the deleterious effects of the presence of a subgenomic TTV polynucleotide sequence by itself or linked to a particular host gene or gene fragment within the patient's cells and allow taking appropriate counter measures.

[0158] The present invention also relates to an antisense oligonucleotide or iRNA specific for the TT virus polynucleic acid of the invention.

[0159] The generation of suitable antisense oligonucleotides or iRNAs includes determination of a site or sites within the TT virus polynucleic acid for the antisense interaction to occur such that the desired effect, e.g., inhibition of expression of the polypeptide, will result. A preferred intragenic site is (a) the region encompassing the translation initiation or termination codon of the open reading frame (ORF) of the gene or (b) a region of the mRNA which is a "loop" or "bulge", i.e., not part of a secondary structure. Once one or more target sites have been identified, oligonucleotides are chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect. In the context of this invention, "hybridization" means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases. "Complementary" as used herein, refers to the capacity for precise pairing between two nucleotides. For example, if a nucleotide at a certain position of an oligonucleotide is capable of hydrogen bonding with a nucleotide at the same position of a DNA or RNA molecule, then the oligonucleotide and the DNA or RNA are considered to be complementary to each other at that position. The oligonucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides which can hydrogen bond with each other. Thus, "specifically hybridizable" and "complementary" are terms which are used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the oligonucleotide and the DNA or RNA target. It is understood in the art that the sequence of an antisense compound does not need to be 100% complementary to that of its target nucleic acid to be specifically hybridizable. An antisense compound is specifically hybridizable when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., in the case of therapeutic treatment.

[0160] "Oligonucleotide" (in particular in the context of antisense compounds) refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases. While antisense oligonucleotides are a preferred form of the antisense compound, the present invention comprehends other oligomeric antisense compounds, including but not limited to oligonucleotide mimetics such as are described below. The antisense compounds in accordance with this invention comprise from about 8 to about 50 nucleobases (i.e. from about 8 to about 50 linked nucleosides). Particularly preferred antisense compounds are antisense oligonucleotides, even more preferably those comprising from about 15 to about 25 nucleobases. Antisense compounds include ribozymes, external guide sequences (EGS), oligonucleotides (oligozymes), and other short catalytic RNAs or catalytic oligonucleotides which hybridize to the target nucleic acid and inhibit its expression. The antisense compounds also include an iRNA comprising a sense sequence and an antisense sequence, wherein the sense and antisense sequences form an RNA duplex and wherein the antisense sequence comprises a nucleotide sequence sufficiently complementary to the nucleotide sequence of the TT virus polynucleic acid of the present invention.

[0161] Alternatively, the invention provides a vector allowing to transcribe an antisense oligonucleotide of the invention, e.g., in a mammalian host. Preferably, such a vector is a vector useful for gene therapy. Preferred vectors useful for gene therapy are viral vectors, e.g. adenovirus, herpes virus, vaccinia, or, more preferably, an RNA virus such as a retrovirus. Even more preferably, the retroviral vector is a derivative of a murine or avian retrovirus. Examples of such retroviral vectors which can be used in the present invention are: Moloney murine leukemia virus (MoMuLV), Harvey murine sarcoma virus (HaMuSV), murine mammary tumor virus (MuMTV) and Rous sarcoma virus (RSV). Most preferably, a non-human primate retroviral vector is employed, such as the gibbon ape leukemia virus (GaLV), providing a broader host range compared to murine vectors. Since recombinant retroviruses are defective, assistance is required in order to produce infectious particles. Such assistance can be provided, e.g., by using helper cell lines that contain plasmids encoding all of the structural genes of the retrovirus under the control of regulatory sequences within the LTR. Suitable helper cell lines are well known to those skilled in the art. Said vectors can additionally contain a gene encoding a selectable marker so that the transduced cells can be identified. Moreover, the retroviral vectors can be modified in such a way that they become target specific. This can be achieved, e.g., by inserting a polynucleotide encoding a sugar, a glycolipid, or a protein, preferably an antibody. Those skilled in the art know additional methods for generating target specific vectors. Further suitable vectors and methods for in vitro- or in vivo-gene therapy are described in the literature and are known to the persons skilled in the art; see, e.g., WO 94/29469 or WO 97/00957. The TTV polynucleotide sequences of the invention may also serve as a suitable vector itself, either composed solely of rearranged TT viral sequences or of chimeric TTV host cell DNA sequences. In addition, the nucleotide sequences of the invention may be used for the construction of artificial chromosomes.

[0162] In order to achieve expression only in the target organ, the DNA sequences for transcription of the antisense oligonucleotides can be linked to a tissue specific promoter and used for gene therapy. Such promoters are well known to those skilled in the art (30-33).

[0163] Within an oligonucleotide structure, the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide. The normal linkage or backbone of RNA and DNA is a 3' to 5' phosphodiester linkage. Specific examples of preferred antisense compounds useful in the present invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. Oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. Modified oligonucleotide backbones which can result in increased stability are known to the person skilled in the art, preferably such modification is a phosphorothioate linkage.

[0164] A preferred oligonucleotide mimetic is an oligonucleotide mimetic that has been shown to have excellent hybridization properties, and is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone (34).

[0165] Modified oligonucleotides may also contain one or more substituted or modified sugar moieties. Preferred oligonucleotides comprise one of the following at the 2' position: OH; F; O--, S--, or N-alkyl; O--, S--, or N-alkenyl; O--, S-- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C₁ to C₁0 alkyl or C₂ to C₁0 alkenyl and alkynyl. A particularly preferred modified sugar moiety is a 2'-O-methoxyethyl sugar moiety.

[0166] Antisense-oligonucleotides of the invention may also include nucleobase modifications or substitutions. Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine etc., with 5-methylcytosine substitutions being preferred since these modifications have been shown to increase nucleic acid duplex stability.

[0167] Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include lipid moieties such as a cholesterol moiety, cholic acid, a thioether, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.

[0168] The present invention also includes antisense compounds which are chimeric compounds. "Chimeric" antisense compounds or "chimeras," in the context of this invention, are antisense compounds, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound. These oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the oligonucleotide increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. An additional region of the oligonucleotide may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of oligonucleotide inhibition of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligonucleotides hybridizing to the same target region. Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above. Such compounds have also been referred to in the art as hybrids or gapmers.

[0169] The present invention also relates to a pharmaceutical composition comprising an antibody or antisense oligonucleotide of the invention and a suitable excipient, diluent or carrier. Preferably, in a pharmaceutical composition, such compound as described above is combined with a pharmaceutically acceptable carrier. "Pharmaceutically acceptable" is meant to encompass any carrier, which does not interfere with the effectiveness of the biological activity of the active ingredient and that is not toxic to the host to which it is administered. Examples of suitable pharmaceutical carriers are well known in the art and include phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions etc. Such carriers can be formulated by conventional methods and the active compound can be administered to the subject at an effective dose.

[0170] An "effective dose" refers to an amount of the active ingredient that is sufficient to prevent the disease or to affect the course and the severity of the disease, leading to the reduction or remission of such pathology. An "effective dose" useful for treating and/or preventing these diseases or disorders may be determined using methods known to one skilled in the art (35).

[0171] Administration of the suitable compositions may be effected by different ways, e.g. by intravenous, intraperitoneal, subcutaneous, intramuscular, topical or intradermal administration. The route of administration, of course, depends on the kind of therapy and the kind of compound contained in the pharmaceutical composition. The dosage regimen will be determined by the attending physician and other clinical factors. As is well known in the medical arts, dosages for any one patient depends on many factors, including the patient's size, body surface area, age, sex, the particular compound to be administered, time and route of administration, the kind of therapy, general health and other drugs being administered concurrently.

[0172] In a preferred embodiment of the present invention, the disease that can be prevented/treated is cancer, preferably breast cancer, colorectal cancer, pancreatic cancer, Hodgkin's lymphoma, B-lymphoma, acute lymphocytic leukaemia, and Burkitt's lymphoma, or an autoimmune disease such as multiple sclerosis (MS), asthma, lupus erythematosus or Crohn's disease. The terms "cancer" and "autoimmune disease" also comprise early stages of said diseases.

[0173] The present invention also relates to a vaccine for immunizing a mammal against TTV infection, comprising at least one polypeptide or TT virus polynucleic acid as defined above, in a pharmaceutically acceptable carrier.

[0174] A "vaccine" is an immunogenic composition capable of eliciting protection against TTV, whether partial or complete. A vaccine may also be useful for treatment of an individual, in which case it is called a therapeutic vaccine.

[0175] The term "therapeutic" refers to a composition capable of treating TTV infection. The term "effective amount" refers to an amount of epitope-bearing polypeptide sufficient to induce an immunogenic response in the individual to which it is administered, or to otherwise detectably immunoreact in its intended system (e. g., immunoassay). Preferably, the effective amount is sufficient to effect treatment, as defined above. The exact amount necessary will vary according to the application. For vaccine applications or for the generation of polyclonal antiserum/antibodies, for example, the effective amount may vary depending on the species, age, and general condition of the individual, the severity of the condition being treated, the particular polypeptide selected and its mode of administration, etc. Effective amounts will be found within a relatively large, non-critical range. An appropriate effective amount can be readily determined using only routine experimentation. Preferred ranges of proteins for prophylaxis of TTV caused diseases are 0.01 to 100 μg/dose, preferably 0.1 to 50 μg/dose. Several doses may be needed per individual in order to achieve a sufficient immune response and subsequent protection against a TTV infection and a TTV caused disease, respectively.

[0176] Pharmaceutically acceptable carriers include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the vaccine. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, and amino acid copolymers. Such carriers are well known to those of ordinary skill in the art.

[0177] Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: aluminim hydroxide (alum), N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP) as found in U.S. Pat. No. 4,606,918, N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1'-2'-dipalmitoyl sn-glycero-3-hydroxy-phosphoryloxy)-ethylamine (MTP-PE) and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate, and cell wall Skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion. Any of the 3 components MPL, TDM or CWS may also be used alone or combined 2 by 2. Additionally, adjuvants such as Stimulon (Cambridge Bioscience, Worcester, Mass.) or SAF-1 (Syntex) may be used. Further, Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA) may be used for non-human applications and research purposes.

[0178] The immunogenic compositions typically will contain pharmaceutically acceptable vehicles, such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, preservatives, and the like, may be included in such vehicles.

[0179] Typically, the immunogenic compositions are prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. The preparation also may be emulsified or encapsulated in liposomes for enhanced adjuvant effect. The proteins may also be incorporated into Immune Stimulating Complexes together with saponins, for example Quil A (ISCOMS).

[0180] Immunogenic compositions used as vaccines comprise a "sufficient amount" or "an immunologically effective amount" of the proteins of the present invention, as well as any other of the above mentioned components, as needed. "Immunologically effective amount" means that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment, as defined above. This amount varies depending upon the health and physical condition of the individual to be treated, the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials. Usually, the amount will vary from 0.01 to 1000 μg/dose, more particularly from 0.1-100 μg/dose.

[0181] Finally, the present invention also provides [0182] (a) a method for the generation of a database for determining the risk to develop cancer or an autoimmune disease, comprising the following steps [0183] (i) determining the nucleotide sequence of a host cell DNA linked to TT virus polynucleic acids according to the invention and being present in episomal form, if present, in a sample from a patient suffering from at least one of said diseases; and [0184] (ii) compiling sequences determined in step (a) associated with said diseases in a database; as well as [0185] (b) a method for evaluating the risk to develop cancer or an autoimmune disease of a patient suspected of being at risk of developing such disease, comprising the following steps [0186] (i) determining the nucleotide sequence of a host cell DNA linked to TT virus polynucleic acids according to the invention and being present in episomal form, if present, in a sample from said patient; and [0187] (ii) comparing sequences determined in step (a) with the sequences compiled in the database generated to the method described above, wherein the absence of a host cell DNA linked to a TT virus polynucleic acid or the presence only of host cell DNA linked to a TT virus polynucleic acid not represented in said database indicates that the risk of developing such disease is decreased or absent.

[0188] The following examples are intended to illustrate, but not to limit the invention. While such examples are typical of those that might be used, other methods known to those skilled in the art may alternatively be utilized.

EXAMPLE 1

Demonstration of the Persistence of TTV DNA in Cells from Tissue Culture Lines Derived from Malignant Tumors

[0189] Cell lines derived from malignant tumors possess one advantage over primary tumor biopsy material. They commonly represent pure preparations of cancer cells, whereas primary materials are commonly contaminated by normal mesenchymal cells, by cells of the hematopoietic system and normal epithelial cells. On the other hand, one disadvantage of tissue culture lines may arise from the selection of specific clones growing under tissue culture conditions and the acquisition of secondary genetic modifications in the course of long-term cultivation. In addition, fetal calf sera may pose a risk due to the introduction of cattle viruses which survive serum inactivation procedures (e.g. bovine polyomavirus); see Table 1 summarizing these advantages/disadvantages.

TABLE-US-00001 TABLE 1 Analysis of primary tumor biopsies vs established cell lines for TTV-related sequences Biopsies Cell lines Advantage Disadvantage Advantage Disadvantage Authentic Contaminated by Pure Selection of specific materials admixture of preparations Clones adapted to normal cells of cancer cells tissue culture Search for TTV Available in conditions sequences clouded unlimited Secondary genetic by the uniform amounts changes during presence of TTV in long-term cultivation the peripheral blood Use of fetal calf serum Availability limited poses the risk of contaminations with cattle viruses

[0190] Attempts to find TTV DNA in human primary tumor materials suffers from one disadvantage: the plurality of TTV genotypes in human material (8). This renders it virtually impossible to identify a specific genotype as an etiologic agent for a human cancer type. For these reasons studies on the persistence of TTV DNA sequences in cells derived from cancer tissue culture lines were initiated. Thus far the results have been extremely surprising: PCR primers used to discover regions of the TTV large open reading frame have been entirely unsuccessful. However, other primer combinations, discovering exclusively a short GC-rich regulatory region of the TTV genome of about 71 bases, detected this sequence in a larger number of cell lines (FIG. 1). This regulatory region is highly conserved among different TTV genotypes and is not present in the human genome data bank.

[0191] In a first series of experiments the same sequence was discovered in a number of additional cell lines. These included the following lines: [0192] MCF7 (breast cancer line); [0193] HAK-1, KMH-2, L1236 (all Epstein-Barr virus negative Hodgkin's lymphoma lines); [0194] Y69 (Epstein-Barr virus negative B-lymphoma) [0195] HSB-2 (acute lymphocytic leukemia); [0196] P3HR-1 (Epstein-Barr virus-positive Burkitt's lymphoma); [0197] BJAB (Epstein-Barr virus negative Burkitt's lymphoma); [0198] Ng (EBV-immortalized B lymphoblasts from a patient with multiple sclerosis)-

[0199] Besides these 9 positive lines, two melanoma cell lines (IGL and KR, FIG. 1) and human placenta DNA were negative in initial experiments. Interestingly, after removal of spooled DNA from L1236 cells and RNase treatment of the remaining solution, besides mitochondrial DNA two faint bands of similar size became visible banding between positions 4.3-6.6 kb (double-stranded DNA size marker) in the agarose gels (FIG. 2). Analysis of these sequences revealed again the presence of the TTV regulatory region. Mung-bean nuclease, digesting selectively single-stranded DNA, completely abolished the cellular DNA-containing bands from four multiple sclerosis biopsies in contrast to double-stranded control DNA, underlining the single-stranded nature of the former. Similar studies are presently conducted for isolates from tumor DNA.

EXAMPLE 2

Analyses of Chimeric TTV/Truncated Host Cell DNA Sequences

[0200] Initially, all attempts failed to use primers in outwards orientation starting within the regulatory region in order to find flanking TT viral DNA, surrounding this region. Invariably, however, human cellular DNA was demonstrated in the respective clones (FIG. 3).

[0201] The human genes in these clones and their arrangements within the single-stranded episomal DNA, obviously controlled by the TTV 71 base region, are presently being analyzed. The available data indicate a substantial variation in the uptake of commonly truncated host cell genes. Their possible conversion into growth-stimulating oncogenes or into functions interfering with tumorsuppressor genes requires functional tests which are presently under investigation. The same accounts for rearranged TTV virus sequences. Some of the available data are presented in FIGS. 7, 8, 9, and 11 to 13.

LIST OF REFERENCES

[0202] 1. Nishizawa, T., Okamoto, H., Kato, N. et al. A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology. Biochem. Biophys. Fes. Commun. 241: 92-97, 1997. [0203] 2. Okamoto, H. TT viruses in animals. Review. In: TT Viruses, the still Elusive Pathogens (de Villiers, E. -M., zur Hausen, H. eds.), Curr. Topics Microbiol. Immunol. E. -M. de Villiers, H. zur Hausen (Eds), Vol. 331: 35-52, 2009. [0204] 3. Biagini, P., Todd, D., Bendinelli, M. et al., Anellovirus. In: Virus Taxonomy, VIIIth Report of the International Committee for the Taxonomy of Viruses. London: Elsevier/Academic Press pp. 335-341, 2005. [0205] 4. Gerner, P., Oettinger, R., Gerner, W., et al. Mother-to-infant transmission of TT virus: prevalence, extent and mechanism of vertical transmission. Pediatr. Infect. Dis. J. 19: 1074-1077, 2000. [0206] 5. Goto, K., Sugiyama, K., Ando, T., e al., Detection rates of TT virus DNA in serum of umbilical cord blood, breast milk and saliva. Tohoku J., Exp. Med. 191: 203-207, 2000. [0207] 6. Borkosky, S., Whitley, C., and de Villiers, E. -M., unpublished results. [0208] 7. Leppik, L., Gunst, K., Lehtinen, M., et al., In vivo and in vitro intragenomic rearrangement of TT viruses. J. Virol. 81: 9346-9356, 2007. [0209] 8. Jelcic, I., Hotz-Wagenblatt, A., Hunzicker, A., et al. Isolation of multiple TT virus genotypes from spleen biopsy tissue from a Hodgkin's disease patient: genome reorganization and diversity of the hypervariable region. J. Virol. 78: 7498-7507, 2004. [0210] 9. de Villiers, E. -M., Schmidt, R., Delius, H., et al. Heterogenetity of TT virus related sequences isolated from human tumour biopsy specimens. J. Mol. Med. 80: 44-50, 2002. [0211] 10. de Villiers, E. -M., Bulajic, M., Nitsch, C., et al. TTV infection in colorectal cancer tissues and normal mucosa. Int. J. Cancer 121: 2109-2112, 2007. [0212] 11. de Villiers, E. M., Kimmel, R., Leppik, L., and Gunst, K. Intragenomic rearrangements in TT viruses; a possible role in the pathogenesis of disease. In: TT Viruses, the still Elusive Pathogens (de Villiers, E. -M., zur Hausen, H. eds.), Curr. Topics Microbiol. Immunol. 331: 91-107, 2009. [0213] 12. Matsukara, M., Shinozuka, K., Zon, G., Mitsuya, H., Reitz, M., Cohen, J., Broder, S. Proc. Natl. Acad. Sci. USA 84 (21): 7706-10 (1987). [0214] 13. Miller, P., Yano, J., Yano, E., Carroll, C., Jayaram, K., Ts'o, P. (1979) Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry 18 (23): 5134-43. [0215] 14. Nielsen, P., Egholm, M., Berg, R., Buchardt, O. (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254(5037): 1497-500. [0216] 15. Nielsen, P., Egholm, M., Berg, R., Buchardt, O. (1993) Sequence specific inhibition of DNA restriction enzyme cleavage by PNA. Nucleic-Acids-Res. 21(2): 197-200. [0217] 16. Asseline, U., Delarue, M., Lancelot, G., Toulme, F., Thuong, N. (1984) Nucleic acid-binding molecules with high affinity and base sequence specificity: intercalating agents covalently linked to oligodeoxynucleotides. Proc. Natl. Acad. Sci. USA 81(11): 3297-301. [0218] 17. Kwok, S., Kellogg, D E., McKinney, N., Spasic, D., Goda, L., Levenson, C., Sninsky, J J. (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res 18: 999-1005. [0219] 18. Landgren, U., Kaiser, R., Sanders, J., Hood, L. (1988) A ligase-mediated gene detection technique. Science 241:1077-1080. [0220] 19. Wu, D., Wallace, B. (1989) The ligation amplification reaction (LAR)-amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 4: 560-569. [0221] 20. Walker, G T., Fraiser, M S., Schram, J L., Little, M C., Nadeau, J G., Malinowski, D P. (1992) Strand displacement amplification--an isothermal, in vitro DNA amplification technique. Nucleic Acids Res 20: 1691-6. [0222] 21. Guatelli, J., Whitfield, K., Kwoh, D., Barringer, K., Richman, D., Gengeras, T. (1990) Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci USA 87: 1874-1878. [0223] 22. Compton, J. (1991) Nucleic acid sequence-based amplification. Nature 350: 91-92. [0224] 23. Kwoh, D Y., Davis, G R., Whitfield, K M., Chappelle, H L., DiMichele, L J., Gingeras, T R. (1986) Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc Natl Acad Sci USA, 86: 1173-7. [0225] 24. Duck, P. (1990) Probe amplifier system based on chimeric cycling oligonucleotides. Biotechniques 9: 142-147. [0226] 25. Lizardi, P M., Kramer, F R. (1991) Exponential amplification of nucleic acids: new diagnostics using DNA polymerases and RNA replicases. Trends Biotechnol 19: 53-8. [0227] 26. Lomeli, H., Tyagi, S., Pritchard, C G., Lizardi, P M., Kramer, F R. (1989) Quantitative assays based on the use of replicatable hybridization probes. Clin Chem 35: 1826-31. [0228] 27. Kohler et al., Nature 256 (1975), 495. [0229] 28. Wahl et al., J. Nucl. Med. 24: 316-325 (1983). [0230] 29. Jacobs, K A. et al. (1988) The thermal stability of oligonucleotide duplexes is sequence independent in tetraalkylammonium salt solutions: application to indeifying recobinant DNA clones. Nucleic Acids Res 16:4637-50. [0231] 30. Zimmermann et al., (1994) Neuron 12, 11-24. [0232] 31. Vidal et al.; (1990) EMBO J. 9, 833-840. [0233] 32. Mayford et al., (1995), Cell 81, 891-904. [0234] 33. Pinkert et al., (1987) Genes & Dev. 1, 268-76). [0235] 34. Nielsen et al., Science 254 (1991), 1497-1500. [0236] 35. Fingl et al., The Pharmocological Basis of Therapeutics, Goodman and Gilman, eds. Macmillan Publishing Co., New York, pp. 1-46 (1975).

Sequence CWU 1

49171DNAartificial sequencezyb2 1cgggtgccga aggtgagttt acacaccgca gtcaaggggc aattcgggct cgggactggc 60cgggccatgg g 71271DNAartificial sequencezyb9 2cgggtgccga aggtgagttt acacaccgca gtcaaggggc aattcgggct cgggactggc 60cgggctatgg g 71371DNAartificial sequencezkb5 3cgggtgccgt aggtgagttt acacaccgca gtcaaggggc aattcgggct cgggactggc 60cgggctatgg g 71471DNAartificial sequencezkb69 4cgggtgccgg aggtgagttt acacaccgca gtcaaggggc aattcgggct cgggactggc 60cgggctatgg g 7152227DNAartificial sequencechimeric TTV, WV13038 clone 6 5caattcgtgc acgggactac aaggaaaggg gttgaccccc accctccccc gccatgccca 60ggagggtgca gacacaactg ggaaggtgct agagaccccg gggggaggct gggccagcac 120caggcattgg ggggcaggtt cccgtctcta caccccagcc ccaggcggac agcgcgtgcc 180cctcccgctg ccccacctgt cacccacctg ctggccccgg gctgtctctg ctcctggctc 240ccctcccagc tgcgtcccca gctgcctctc cagggaggag tgacagctgg cctgtgccac 300accctcgagc ccccccggac taccccctcc ctggggcagg acccctgcct gtggcacaac 360caaggggcct gctgatgggg gctcatgtga gcagtgcccc agctgtgggt gtgggtgctg 420ccagctgcca ccgcctttgc cctggtttcc cagatagacc ccgacccaca ctccgaagct 480gtatcatgaa cgctgtggtg ggcggctggt ggggagcggg gttgccgtcc cactaccctc 540tggaagcctc agccatgaag ggcccctgtg ggcacctttt cccggcacac ggtgctgtgt 600ttctccactc ttgggctctg cagtgacttg aggggtcaag tctatgatcc cacgggaggc 660tgggctaatg aggggaccag agacctcagt gctgtgcagg gagtcctgaa ccaccctggt 720ggaaggccca gcccaactcc ccagtcctcc cgccagctcc ctgtggtgtc caggagacct 780gtggtcaggc ctggaggaga agctcctcct cccctcgaca tcctccctgc agcccttgct 840cttcaccaga gcctcctgac tccccaggac cccagagagg actgaccctc tccagccgac 900ctctgggctc aggacagctg ggcggggcag ccacaggagc tgcctgtagg gagcagagtc 960aggacgggga ccgagccgga cacccattct ggaagtgtct gcacttccag gcaggggaag 1020gacggcagtg ggtagctggg agtgctgggc cgaagatggg cattgtcagg ccctcagtgg 1080ggactgggag gtagaggtgg ggaggtctgt ggaggaagga gaagaagggc cagtgtcccg 1140agttgggggt ggttggcagt ggacgaggcc gacaggaaca gacctgagct tggggagctc 1200cactcagaac gaggcatcct tcagggttct gtgcatactg gtgtccctgg ctgggggccg 1260ggccccgaag tggagcctgg gactgtgagg gtgggggggg tgtgctgggg tgggaggtgg 1320atggagcccc ccctccaccg cctggccgct tgggctgaac cttggacttc ggagccggaa 1380cagacatagg aaatggccta actgcatttg cgcaggaaca ccaaatccct cgcagctgca 1440cggggctgag ccagggccac gggcggggtc ggccatccca gagtcctgac agctccgtgg 1500tgtatgccaa ggggcctggg ccgctgaccg aggggcgcct ttcccaggcc agaggccccc 1560accccacccc aggagagctg cccccctttc agttcccaga acggagcccg gctgtggaat 1620agtgatgcgg tgaggtcatg gggagggggc ccgcatgact catatcctgg ggtaggggaa 1680agggaggaga cggagaaggg gcccagaggc ctccacgtcc tcagctctgc tgggtcagag 1740gccaggggct ggcggggctt ctccccagca ctgggtttta ggggagacac caggagatgc 1800ttactctgca tccccactct gtcccccagg cccctagcca gggagagctc agtcagagtg 1860atcctccagg ggcccagctc tgcatggatg atgttcccag agtacacacc tgggcctcgt 1920gccagggccg gcaccgccgt tgtcagggct atggcaaggc aaacagtcaa tgtttgcctc 1980actaaagtga ggctgcagca ccctgaaggg atccctggag ggggacgtgg tccccttgtt 2040cccaagcttg tctgcacatg cacgtggatg tcaagggttc ccgtgtgtga gcacatgcat 2100atttgtatgt gcatggggtg cgggcatgtg tgcctgtgtg gccggagcgt gggctcgtgg 2160agaatgtgtg tgagttgggt gtgcacctgc atgtgcccca ggcctaggga gtcccgtgcc 2220cgaattg 22276883DNAartificial sequencechimeric TTV, gb40.27 6cgggactggc cgggctatgc cccagacaca ctcacgtagg ggtgtccggc ctggcagccc 60aggaccatgg tctgcagggt ttcctctcgg ccattcagga caaccctagt ctccagggaa 120tagcgctggt gtcgcctatc agccgtgaag gtctcctgca ggaggaggct ctgcgggatg 180ggcaggtgca atgggtgcct ggtgtgcaga gggaaaaaca ggccaaagcc attaaagcag 240ctggcagtgc caggggacaa ttgtgcccca cggtctcagc ctgggcctgt cacgagcttg 300cagagttaag actctgccac agagaagaga acatcaggac acctggcagc cctatgcttt 360acaatgtggc atccagaacc cttcaccacc tcactgtgcc agagaagtgg gcatggctgg 420ggtccccgtc gccatttgac agcaaagacc caagaggata gatgacacac agcatctggt 480gtcacacaga ctgggattag aatccaggca cggtctttca ctagctgtgt gaccttggga 540aaaggacttg actgttctgt gcctcagttt ccccatctgt aaaacggagg ctaaaataat 600actgatcgga cacagtggtc agggttagag ataacataca tgaaacgacc acaagctccc 660caagggcaaa ggtttctgac attccggttc tctgccattt tccatgtgcc cagaagagca 720cttggtccat agtatgtgct caatgaatgt aaatgggata aaaacacgaa cgaacactct 780gccaacgatg ctgctgttcc tttgtcatca ctgcttctgt ttaggctgta gctgacttat 840ctaaggccat acagctgctc aatgcatagc ccggccagtc ccg 8837291DNAartificial sequencechimeric TTV, gb43.30 7ccccttgact tcggtgtgta aacttgtggt atagaacatg atgttttaag atacatgtac 60attgtggaat ggcttgatca tgctaattaa catatgaatt acctcactta gctatctttt 120ttatggtgaa agcacttaaa atctaccctc agcagttttc aagtacacaa tacatttcta 180ttaactatag tcaccatgtt gtacaataaa tctcttgaat ttattcctcc tgcctaactg 240acattttgta tcctttgact gatctctctc cccagtcccg tgcccgaatt g 2918293DNAHomo sapiens 8taattgacaa aacgtgtata aacttgtggt atagaacatg atgttttaag atacatgtac 60attgtggaat ggcttgatca tgctaattaa catatgaatt acctcactta gctatctttt 120ttatggtgaa agcacttaaa atctaccctc agcagttttc aagtacacaa tacatttcta 180ttaactatag tcaccatgtt gtacaataaa tctcttgaat ttattcctcc tgcctaactg 240acattttgta tcctttgact gatctctctc cccagtcccg tgaccagtgc cct 2939269DNAartificial sequencegbDhDi43.30.sequence 9gtgtgtaaac ttgtggtata gaacatgatg ttttaagata catgtacatt gtggaatggc 60ttgatcatgc taattaacat atgaattacc tcacttagct atctttttta tggtgaaagc 120acttaaaatc taccctcagc agttttcaag tacacaatac atttctatta actatagtca 180ccatgttgta caataaatct cttgaattta ttcctcctgc ctaactgaca ttttgtatcc 240tttgactgat ctctctcccc agtcccgtg 26910269DNAHomo sapiens 10tttaagtgta taaacttgtg gtatagaaca tgatgtgata catgtacatt gtggaatggc 60ttgatcatgc taattaacat atgaattacc tcacttagct atctttttta tggtgaaagc 120acttaaaatc taccctcagc agttttcaag tacacaatac atttctatta actatagtca 180ccatgttgta caataaatct cttgaattta ttcctcctgc ctaactgaca ttttgtatcc 240tttgactgat ctctctcccc agtcccgtg 2691149PRTartificial sequenceFASTA of gbDhDi43.30 11Met Phe Tyr Thr Thr Ser Leu His Thr Glu Val Lys Gly Gln Phe Gly1 5 10 15His Gly Thr Gly Glu Arg Asp Gln Ser Lys Asp Thr Lys Cys Gln Leu 20 25 30Gly Arg Arg Asn Lys Phe Lys Arg Phe Ile Val Gln His Gly Asp Tyr 35 40 45Ser12119PRTartificial sequenceTT virus variant 12Ala Gln Thr Gln Arg Arg Val Ile Pro Ala Ser Arg Gly Arg Val Pro1 5 10 15Glu Val Ser Leu His Thr Xaa Val Lys Gly Gln Phe Gly Leu Gly Thr 20 25 30Gly Arg Ala Met Gly Lys Ala Leu Lys Lys Asp Met Phe Leu Gly Lys 35 40 45Leu Tyr Lys Lys Lys Arg Ala Leu Ser Leu His Gly Leu Arg Thr Pro 50 55 60Glu Ala Lys Pro Pro Ala Met Ser Trp Arg Pro Pro Val His Asn Pro65 70 75 80Asn Arg Ile Glu Arg Asn Leu Trp Glu Ala Phe Phe Arg Ile His Ala 85 90 95Ser Ser Cys Gly Cys Gly His Leu Val Gly His Leu Thr Val Leu Ala 100 105 110Arg Arg Tyr Gly Ala Pro Pro 11513639DNAartificial sequencehod11 13ccccttgact gcggtgtgta aagcgcccca gcctgtgcct gcacagtgcc tgtgtggtgt 60gaacccatga ccaggcctct ggagggaagg aaggttaggc ttagtggaca ccagctttcc 120taaggtgggt cttagaccaa ctcattaaaa tggcaggatg ggcttttgtg ctgtatttct 180tgggattttc aagatgcccc acacagcaga agggatgtgc atttttttct ctgccctgag 240ttgtttgata aaaatcagtg acctcgttct ccacttagaa ctcccctgaa ctgcactcgg 300tgtctaggac tgttggggaa ggaagtgaag agccagcatg tagtctcctc tggactctta 360caggatctgt ccacctctgg gctctttatg taggggaagg tgtgagctcc tgggagtact 420cctgatagag gactgtttcc ctgaaaacct cagcagtgtt tgaggcccta gcagggggaa 480cccagacccc gcctgccaaa gcccctaatc cctcagggct attatcagca gcctaagcgc 540cttagggtgg ccagagtcca gcccagcaag cagcaaagtc agcagcctcc tcgccctatc 600ctctccatgc cccggggcac tccagtcccg accgaattg 63914358DNAartificial sequencehodL.VvWw.1.sequence 14tcccctgaac tgcactcggt gtctaggact gttggggaag gaagtgaaga gccagcatgt 60agtctcctct ggactcttac aggatctgtc cacctctggg ctctttatgt aggggaaggt 120gtgagctcct gggagtactc ctgatagagg actgtttccc tgaaaacctc agcagtgttt 180gaggccctag cagggggaac ccagaccccg cctgccaaag cccctaatcc ctcagggcta 240ttatcagcag cctaagcgcc ttagggtggc cagagtccag cccagcaagc agcaaagtca 300gcagcctcct cgccctatcc tctccatgcc ccggggcact ccagtcccga ccgaattg 35815360DNAHomo sapiens 15tcccctgaac tgcactcggt gtctaggact gttggggaag gaagtgaaga gccagcatgt 60agtctcctct ggactcttac aggatctgtc cacctctggg ctctttatgt aggggaaggt 120gtgagctcct gggagtactc ctgatagagg actgtttccc tgaaaacctc agcagtgttt 180gaggccctag cagggggaac ccagaccccg cctgccaaag cccctaatcc ctcagggcta 240ttatcagcag cctaagcgcc ttagggtggc cagagtccag cccagcaagc agcaaagtca 300gcagcctcct cgccctatcc tctccatgcc ccggggcact ccagtcccag ctggctgatc 36016288DNAartificial sequenceVvWw.1.sequence 16ccccttgact gcggtgtgta aagcgcccca gcctgtgcct gcacagtgcc tgtgtggtgt 60gaacccatga ccaggcctct ggagggaagg aaggttaggc ttagtggaca ccagctttcc 120taaggtgggt cttagaccaa ctcattaaaa tggcaggatg ggcttttgtg ctgtatttct 180tgggattttc aagatgcccc acacagcaga agggatgtgc annnnnnnct ctgccctgag 240ttgtttgata aaaatcagtg acctcgttct ccacttagaa ctcccctg 28817289DNAHomo sapiens 17ttcagttagc tgctgtgtgt aaagcgcccc agcctgtgcc tgcacagtgc ctgtgtggtg 60tgaacccatg accaggcctc tggagggaag gaaggttagg cttagtggac accagctttc 120ctaaggtggg tcttagacca actcattaaa atggcaggat gggcttttgt gctgtatttc 180ttgggatttt caagatgccc cacacagcag aagggatgtg catttttttc tctgccctga 240gttgtttgat aaaaatcagt gacctcgttc tccacttaga actcccctg 289183387DNAartificial sequencehoht33 18aattcggtcg ggactggcag agtgacgctc aggtcagcct gacagcaggg tgattgaagg 60ggccagatac cccagcaggg cctgaggcca gaacacagca taggctggct ctgatgggtg 120gaggaggtgg ccaggcatca tctggagctt ggagttgaga acatctgtga ctcctccttc 180aggagggtgc tctaggagtt gagagcatcc taggtaggac catacatcta cccccatcct 240agttccctcc agcctctctt ttcagctcca ggtctacctt aagggaccta ggacacctgg 300gctggggcat aacaggactt ggttttatgt aaaggagctg ggaagagact gagataacag 360agggctgcaa ggagagagac agagagagaa gaacctgcca gaagaagctc ctcagcaatc 420cactaagccc tgatctttgc ctcactgcct gtcccttccc atccgctctt ctgctctctc 480aatctctgcc ttcaagaaat ttggtgcata ttggaatagg gaggaataga agcaccctgg 540gtggagctct gggcttggct gtgcacgagc tttcagtggg tggtttgctg gtctccaaag 600atgaccctcc attagtcatg cttctcggtg tttgtcctca ggtagtctca tcccatcttg 660agtctgggct tgccctgtga ctcactttaa ccacaagaat gtggcagaaa ggatgttgtg 720ccagttctag aactaagcct tcagaaagcc tagcaccttc tgcttttagg agcactgagc 780ccccatgtta gaagtccact tttatactct gctctggaga ctagcagaat tagaaatgca 840ctgctgaatg ctgctcgaga gactaatgga gaggccatgt gaataaggag gcctgaaact 900acatggagat agagggccag ccaccccagc accacggctc agctgtgcct cccagccatc 960tctgccagtc ctccagggct atgagtgaac catcttggat gttctagctc ggtggagccc 1020ccaggtgatt gcagcctcag ccaccatctg actgtagctg catgagaggc ccccagtggg 1080accagcagga ctgccaagct gagccctgcc cacccacaga actgtgagaa ataaaaaaat 1140ggttgtttcc ttaagccatt aagttttgga atgatttgtt actcacaatt gataactgat 1200acagtctgtc tttagggaaa acaagggata actctgggct ccaggtgtct tctataggat 1260gaatgggact tggttgctga caagctgaca agtttgagca tgaaactctt tttttttttt 1320ggagaaggaa ttttgctctt gttatccagg ctggaataca gtggtgcgat ctcggcccaa 1380ggcaacctct gcctcctggg ttcaagcaat tctcctgcct cagcctcctg agtagctggg 1440attacaggca cccaccacta cacctggctc tttttttttt ttgtattttt agtagagaca 1500ggttttcatt atgttggcct ggtcaggttt tgaactcctg acctcaggtg atccacctgc 1560cttggcctcc taaaatgctg ggattacagg tgtgagccac cgtgcctggc ctgagcatga 1620aacttttatg ctcaaacatt aaagtgtaaa cactcaccag ctcagctgaa taagaacttc 1680tgggggcaag gcccaggaat ctacagttta gtaagtgccc ccaccactgg accctgggaa 1740agtggactgc attttgaaaa actctagatc agttgatacc caggagtcct cataacacta 1800agttgtaata cctcagtgtg aattagtctg atgcagctct tcttagaggt cattgacaga 1860gggcaagaca tttccaaaag gaaggaatag ccaatatgga atgacaggtg gattggatga 1920ccctctatta tttagtttca acctgccctt cctgccttcc ctcccacaaa ttccctttca 1980gatcctccgt cctaatcctc ttcgatagtt cattgttctt ctgcagacag agcagcgaag 2040tgttatctgt tgtacccact atgactagtt gatggtgcat ggcttccatg gagcagtgct 2100gtgatccatt agtcatggag cagtgctgtg atccattgtc atgtctgcca tgaacactgg 2160aaggggcagt ggtaatgaca gcctcttaca tttgccaact ctgcccaaca ttcttcccag 2220tgttgggaaa gcctttgctt attccattcc ttcttggaaa gctttgttcc tccatttcac 2280atttttaatt tttctcattt ttatggtgca ccatggatac cacctgtcca tatagctggc 2340ttctgatttt tccagatgaa agtaatcctt cctctcctaa cctcccatga cacctaacct 2400ggcactcatt tacggtgttc agctccttct cctgtacgtt ctcattgttc tcctctcatc 2460ttctccccag gaatggattc cccgccaagg gaggtaccag gtcagtttct tctttgtgca 2520acagggtgtc cctgatgagc acaaacctgg aacaagtgtt tgtagggctg gtgggcatct 2580ggttcctctg ggtgttgtgt agcctgagcc ggggggcaaa tgggtgtttg tttttctgaa 2640gaaggcaggc gttctgtggc agatgtgggt ggagggggtt ggggagtagt atcatggaga 2700ggctgggatc ctatctatct ccttcccctg cttgaagggc aacttgggag aagctcaaga 2760gggaggagtt gactgcagaa gctgggatac ctgcataact ctcaggttca agcatcactg 2820ctttagggcc ctgggggcct atgtgtgagt caagaaaggg agatagagag agaagagaga 2880gagaggagag agagagagag agagagaaga cagaggagag agagagagaa gaaagaggag 2940agagagagaa gagagagcag agagagagag catgctgtca gtgaggtggc cctaagccct 3000cttggaaata acttggaggc actgtggggt ggctctgagg tgctgaggta tacctgtagt 3060ggggctagga cctttccaac ctgggtctga aggttgaggc aaccttgggt gtacctgctg 3120gtgagctgag agccctgggg acctttggca gacattccca cccctgcagc ctggagggtt 3180tgcatgcagt gaggctgtcc tgctcatcac tacgtcctct gggacagcac attgcctgtg 3240ctgaacaggc attcagttgc gatttgtgga atcagtgttg gtgaggaggg caagtggcaa 3300cagaaatggg ggtgtgctcc ccccagttcc tcagctacaa tctccatgac cttctacact 3360gccctgggcc cagtcccgac cgaattg 3387191790DNAartificial sequencehoht22 19caattcggtc gggactgggg agctgtgaga aagagaagag aaggtcagat caggaacatt 60acacagaagt cggcaaaact ggaacgagga gggaaagaaa tgagcgagtc tgacactcag 120tccatcctag ttcctatcac acagggaggg acattgccat gcacatcccc acagagatgc 180accgtgtaag gggtcgaggc agatcctgtc cactattgcc agctctgagg tgatcaaatt 240gtgtctgccc agggtaaccc ggttgaccta aaccaaccca ctcccttgca catcttaggt 300gttcctgagt cagcaaggct gaggaagcca ctccagccaa aatcccttgt gcgatcttca 360agccccaatc acaggcaatg acaaggccat gtctggctgg cctcatgggg actgccctcc 420cctcaccaga cctagaacac aggcaatgct cagcagcgtt ctgagaagag ctgaggtcaa 480gaactccaac cccacgcaac ccagacctga tacaaacaga cacccatttg cactcctaac 540ccttgagcct ctatttccag acctcctcac tgggtctcag ctgagaaccc acttttagcc 600aagcatcttt agttcagagt tcctcgcagt gaggggatcc ctcccctgcc ttgctgtctg 660tgctgcatcc attataccct cacaccgtgc tactcagcag gggagaaatg gagccctggg 720gagccggcac ttttctcttc tgcctcttcc ttgccttgcc tcaggaaggg gaaaaactct 780gggttgtttt agtttgatcc cctgtcctaa gtgaccacag gaacactagg cagtgagtac 840atatggattc ttagcagaga gctgacaagt cttcagaaac atagaaaaca tagaagcttt 900gagtgaggag atcagaatgt aattaggagt ttcttttgga gcaaacccca ccccaagaga 960gtgagcccaa gttcttgaag gcccacctga gcagatgaca ccagcgtctt cactatggcc 1020acagttgtgg gtgagccagc cattgtgggg gcagctccac aggtaggact cgtgtcctga 1080gcagcgcaca tcatccagga caatgggtcc tgagccctgg ccaaactggg catttcctgg 1140ggctgacatg gcccagccac agcccggctg cctgcagacc acattggcat cattggtgtc 1200ccagtagtca tcacacacgg tgccccagga gcctcggtat aggacctcca ctcggcctcg 1260acacctgtcg cctccattca ccagcctcag ggccaaactg gattcagatc ctacagggga 1320acacaagaac ctttcatcca tccctatcat gaggtcaaga atctaaggta agttccacac 1380tcagggtact tcctaatgaa ctaagtcacc taggcaggca gtcacctttg catatgacta 1440cagactaggc ttcatcaccg tgaaagtagc actgataacc tactctgccc aggtctatgg 1500gtgctcaact tttggggaag cacctgtgac cccagtggat gtgatgggaa tggatgcccc 1560actccccagt tgggtacaca gaggatggag ctgctcagct ccagatggca ggcccagacc 1620cctcccttat tcaggagcat ggtcctatct gggatctgac tggcagagta ccagagatgg 1680cagggatgag gtccccatag gattagggag acccccaggg cttgttctga gcccatagat 1740aaggatcttt tctgaccact tggaacagga tcccagtccc gaccgaattg 17902018DNAartificial sequenceDhDi primer forward 20caattcgggc acgggact 182124DNAartificial sequenceDhDi primer reverse 21ccccttgact tcggtgtgta aact 242228DNAartificial sequencecd, primer forward 22cagcgagaac gccacggagg gagatcct 282328DNAartificial sequencecd; primer reverse 23cggacgggcg tggaaaactc agccattc 282418DNAartificial sequenceDfDg primer forward 24cgggactggc cgggctat 182519DNAartificial sequenceDfDg primer reverse 25agcccgaatt gccccttga 19263725DNAartificial sequencettgb33.35 26attttgtgca gcccgccaat ttctgttcaa acagaccaat caggaccttc tacgtgcact 60tcctggggcg tgtctacgag gtctatataa gcaacagcgg tgacgaatgg tagagttttt 120cttcgcccgt ccgcggcgag agcgcgagcg aagcgagcga tcgagcgtcc cgtgggcggg 180tgccgtaggt gagtttacac accgaagtca aggggcaatt cgggcacggg actggccggg 240ctatgggcaa ggctcttaaa aaattccccc gctctgctct ccggcaggac acaaagtcat 300gccgtggaga ccgccggtcc ataacgtgcc aggtagagag aatcaatggt ttgcagcgtt 360ctttcacggt catgctgctt tctgcgggtg tggtgaccct gttgggcatc ttaacggcat 420tgctcctcgc tttcctaacg ccggtccacc gagaccacct ccagggctag accagcttaa 480tcccgagggc ccggcaggtc ccggagggcc ccccgccatc ttgccagctc tgccggcccc 540ggcagaccct gaaccggcac cacggcgtgg tggtggggca gatggaggcg ccgccgctgg 600ggccgccgcc gacgcagacc ataccgggta cgaagaagga gacctagaag atcttttcgc 660cgccgcggcc gaggacgata

tgtgagtagg cggaggcgcc gccgctacta caggcgcaga 720ctgagacggg gcagacgcag agggcgacga aagagacaca gacagactct agtagtgagg 780cagtggcaac ctgacgttgt taaaaagtgt aaaataacag gatggatgcc tcttataatc 840tgtggctctg gaagcacaca gatgaacttt ataactcaca tggacgatac tccccctatg 900ggatacacct acgggggcaa ctttgtaaat gtaactttca gtctagaggc catctatgaa 960caattcctgt accacagaaa caggtggtcc aggtctaacc atgacttaga cctggccaga 1020taccaaggaa ccactctaaa actttacaga caccaaaccg tggactatat agttagctac 1080aacagaacag gcccctttac tataagtgaa atgacttaca tgagcacaca cccggctctc 1140atgctactac aaaaacatag aatagttgta cccagcttca gaaccaagcc aaaaggcaaa 1200agagccataa aaattagaat aagggcccca aaactaatgc tcaccaagtg gtactttaca 1260aaagacattt gctccatggg cctctttcaa ctaatggcaa cagctgcaga acttacaaac 1320ccatggctca gagacaccac aaaaagccca gtaattggct tcagagtctt aaaaaacagc 1380ttatacacat gcctttccaa cttaaaagac caagcaatac aaggtgaaag aaagactgta 1440caaaatagat tacacccaga aaacctacat ggcacaggac ctaatgctaa aggctgggaa 1500tacacataca caaaactaat ggcatctaca tactactcag ccaacagaaa cagcacctac 1560aactggcaaa actatcaaac taactatgca aacacatata caaaatttaa agaaaaaaga 1620acagcaaact taaacttaat taaagcagaa tacctatatc attaccctaa caatgtcaca 1680caatctgact ttatattaga ctacacacta acacccgact ggggcatata cagcccctac 1740tacctaacac ccaccagaat tagcctagac tgggacacac catggacata tgtaagatac 1800aacccactat cagacaaagg cataggtaac agaatatatg cacagtggtg ctcagaaaaa 1860tctagtaaat tagacaccac aaagagcaag tgcatactaa gagacttccc actgtgggcc 1920atggcctatg gctactgtga ctgggtggtg aagtgcacag gagtgtccag tgcttggaca 1980gacatgagaa tagccattat atgtccctac acagaaccag cacttatagg gtcaacagaa 2040gacgtaggct tcattccagt aagtgacacc ttttgcaacg gagacatgcc gtttcttgca 2100ccatacatac ctattacatg gtggattaag tggtacccca tgattacaca ccaaaaggaa 2160gttcttgagg caatagttaa ctgtggaccg tttgtacccc gagaccaaac ttccccagct 2220tgggaataac catgggttac aaaatggatt ggaaatgggg cggctctccc ctgccttcac 2280aggcaatcga cgacccctgc cagaagtcca cccacgaact tcccgacccc gatagacacc 2340ctcgcatgtt acaagtctct gacccgacaa agctcggacc gaagacagtt tttcacaaat 2400gggactggag acgtgggatg cttagcaaaa gaagtattaa aagagtccaa gaagactcaa 2460cagacgatga atatgttgca ggacccttac caagaaaaag aaacaagttc gatactcgag 2520tccaaggccc tccaacccca gaaaaagaaa gttacacttt actccaagcc ctccaagagt 2580cggggcaaga gagcagctca gaggaccaag aacaagcacc ccaagaaaaa gaggaccaga 2640aggaagcgct catggagcag ctccagctcc agaaacacca ccagcgagtc ctcaagcgag 2700gcctcaaact cctcctcgga gacgtgctcc gactccggag aggagtccac tgggaccccc 2760tcctgtccta attcaaggtc ccagtatccc agacctgctt ttccctaaca cacaaaaaaa 2820aaaacgattt tccaactacg actgggtgtg cgagtacgag ctggccaaat ggatggatcg 2880gcccttgcgg cactacccat cagacccccc tcactacccc tggctaccaa aaaagcctcc 2940tacccctcct acatgtagag taagtttcaa attaaagctc aatgactaaa attcaaggcc 3000gtgggtgttt cacttcatcg gtgtctacct ctaaaagtca ctaagcactc cgagcgtaag 3060cgaggagtgc gacccccctg cccggtagca acttcctcgg ggtccggcgc tacgccttcg 3120gctgcgccgg gcgcctcgga ccccccctcg acccgaatcg ctcgcgcgat tcggacctgc 3180ggcctcgggg gggtcggggg ctttactaaa cagactctga ggtgccgttg gacactgagg 3240gggtgaacag caacgaaagt gagtggggcc aaacttcgcc ataaggcctt taactttggg 3300tcgcttgtca gcagcttccg ggtccgcctg gaggccgcca ttttacattc ggccgccatt 3360ttaggccctc gcgggcctcc atagtcgcac atcagtgacg tcacggcagc catcttggct 3420gtgacgtcaa cgtcacgtgg ggaggacggc gtgtaacccg gaagtcatcc tcatcacgcg 3480acctgacgtc acggccgcca ttttgtgctg tccgccatct tgtgacttcc ttccgctttt 3540tgtaaaaaaa agaggaagtg tgacgtagcg gcgggggggn nnnnnnnnnn nnnnnnncgc 3600caccaggggg cgctacgcgc ccccccccgc gcatgtgcgg gtcccccccc tcgggggggg 3660ctccgccccc ccggcccccc cccgggctaa atacaccgcg catgcgcggc cacgcccccg 3720ccgcc 372527719DNAartificial sequencezpr4.20 27caattcgggc acgggactgg ccgggctatg ggcaaggctc ttaaaaaatt cccccgctct 60gctctccggc aggacacaaa gtcatgccgt ggagaccgcc ggtccataac gtgccaggta 120gagagaatca atggtttgca gcgttctttc acggtcatgc tgctttctgc gggtgtggtg 180accctgttgg gcatcttaac ggcattgctc ctcgctttcc taacgccggt ccaccgagac 240cacctccagg gctagaccag cttaatcccg agggcccggc aggtcccgga gggccccccg 300ccatcttgcc agctctgccg gccccggcag accctgaacc ggcaccacgg cgtggtggtg 360gggcagatgg aggcgccgcc gctggggccg ccgccgacgc agaccatacc gggtacgaag 420aaggagacct cggggggggc tccgcccccc cggccccccc ccgggctaaa tacaccgcgc 480atgcgcggcc acgcccccgc cgccattttg tgcagcccgc caatttctgt tcaaacagac 540caatcaggac cttctacgtg cacttcctgg ggcgtgtcta cgaggtctat ataagcaaca 600gcggtgacga atggtagagt ttttcttcgc ccgtccgcgg cgagagcgcg agcgaagcga 660gcgatcgagc gtcccgtggg cgggtgccgt aggtgagttt acacaccgaa gtcaagggg 719283758DNAartificial sequencetth25 28aagtacgtca ctaaccacgt gactcccgca ggccaaccag agtctacgtc gtgcacttcc 60tgggcatggt ctacatcata atataagaac gtgcacttcc gaatggctga gttttccacg 120cccgtccgca gcgagaacgc cacggaggga gatcctcgcg tcccgagggc gggtgccgga 180ggtgagttta cacaccgcag tcaaggggca attcgggctc gggactggcc gggccccggg 240caaggctctt aaaaaatgcg ttttcgcagg gttgcccaga aaaggaaagt gcttttgcaa 300actgtgccag ctgcaaagaa ggctaggcgg cttctaggta tgtggcagcc ccccacgcac 360aatgtcccgg gcatcgagag aaactggtac gagagctgtt ttagatccca cgctgctgtt 420tgtggctgtg gcgattttgt tggccatctt aatcatctgg caactactct gggtcgtcct 480ccgcgtcctg ggcccccagg cggaccccgc acgccgcaaa taagaaacct gccagcgctc 540ccggcgcccc agggcgagcc cggtgacaga gcgccatggc atggggcttc tggggccgac 600gccgccggtg gagacgatgg agagcgcggc gcagacggtg gagaccccgc agacgtagga 660gacgacgccc tactcgccgc tttcgagctc gtcgaagagt aaggaggcgc ggggggaggt 720ggcgcagacg ctacagaaaa tggcgacggg gcagacgcag acggactcat agaaaaaaga 780tagtcataaa acagtggcaa ccaaacttta taagacgctg ctacgtcata gggtacttac 840cacttatatt ctgcggcgaa aatacaaccg cccagaactt tgccactcac tcggacgaca 900tgataagcaa aggaccgtac ggggggggca tgactaccac caaattcact ctgagaatac 960tgtacgacga gtttaccagg tttatgaact tttggactgt cagtaacgaa gacctagacc 1020tgtgtagata cgtgggctgc aaactaatat tttttaaaca ccccacggtg gactttatag 1080tacagataaa cactcagcct cctttcttag acacgcacct caccgcggcc agcatacacc 1140cgggcatcat gatgctcagc aagagacaca tactaatacc ctctctaaag acccggccca 1200gcagaaaaca cagggtggtc gtcagggtgg gcgccccaag actttttcag gacaagtggt 1260acccccagtc agacctgtgt gacacagttc tgctttccat atttgcaacc gcctgcgact 1320tgcaatatcc gttcggctca ccactaactg acaacccttg cgtcaacttc cagatcctgg 1380ggccccagta caaaaaacac cttagtatta gctccactat ggatcaaact aacgaaaacc 1440attataaaga aaacttattt aacaaaactg aactatacaa cacctttcaa accatagctc 1500agcttaaaga gacaggacac atttcaggca ttagtcctac ttggaatgaa gtccagaatt 1560caacaacact tactaaagga ggtgacaatg ccactcagag tagagacact tggtataaag 1620gaaatacata caacgagaag atatgcgagt tagcacaaat aaccagaaac agatttaaaa 1680atgcaaccaa aggagcacta ccaaactacc ccacaataat gtccacagac ctatatgaat 1740accactcagg catacactcc agcatatatc tatcagctgg caggagctac tttgaaacca 1800ccggggccta ctctgacatt atatacaacc ctttcacaga caaaggcaca ggcaacataa 1860tctggataga ctacctcaca aaagaagaca ccatttttgt gaaaaacaaa agcaaatgcg 1920agataatgga catgcccctg tgggcggcct gcacaggata cacagagttt tgtgcaaagt 1980atacaggcga ctctgccatt atctacaatg caagaatact cataagatgc ccatacactg 2040agcccatgtt aatagaccac tcagacccaa acaaaagctt cgttccctac tcatttaact 2100ttggcaacgg aaagatgccc ggaggcagct ccaacgtgcc cataagaatg agagccaagt 2160ggtacgtgaa catattccac caaaaagaag tattagagag catagtacag tccggaccgt 2220ttgggtacaa gggcgacata agatcagctg tactagccat gaaatacaga tttcactgga 2280agtggggcgg aaaccctata tccaaacagg tcgtcaggaa tccctgctcc aactccagct 2340cctccgcggc ccatagagga cctcgcagcg tacaagcggt tgacccgaaa tacaataccc 2400cagaggtcac gtggcactcg tgggacatta gacgaggact ctttggcaaa gcaggtatta 2460aaagaatgca acaggaatca gatgctcttt acattcctcc aggaccaatc aagagacctc 2520gcagggacac caacgcccaa gacccagaag agcaaaacga aagctcaggt ttcagagtcc 2580agcagcgact cccgtgggtc cactccagcc aagagacgca aagctcccaa gaagagacgg 2640aggcgcaggg gtcggtacaa gaccaactac tcctccagct ccgagagcag cgagttctcc 2700gactccagct ccagcaactc gcaacccaag tcctcaaagt ccaagcaggg cacagcctac 2760accccctatt atcttcccaa gcataaacaa agcctttatg tttgagcccc agggtcctaa 2820acccatacag gggtacaacg actggctaga agagtacact gcttgcaaat tctgggacag 2880accccccaga aagctacaca cagacatacc cttctacccc tgggcaccaa aaccccaaca 2940gcaagtcagg gtgtccttta aactcaactt tcaataaaaa ttctaggccg tgggagtttc 3000acttgtcggt gtctgcttct taaggtcgcc aagcactccg agcgccagcg aggagtgcga 3060ccccccctcc ggtagcaacg ccttcggagc cgcgcgctac gccttcggct gcgcgcggca 3120cctcagaccc cccctccacc cgaaacgctt gcgcgtttcg gaccttcggc gtcggggggg 3180tcgggagctt tattaaacag actccgagtt gccattggac actggagctg tgaatcagta 3240acgaaagtga gtggggccag acttcgccat agggccttta tcttctcgcc attggatagt 3300gtccggggtc gccgtaggct tcggcctcgt ttttaggcct tccggactac aaaaatggcg 3360gttttagtga cgtcacggcc gccattttaa gtaaggcgga agcagctcca ctttctcaca 3420aaatggcggc ggagcacttc cggcttgccc aaaatggcgg gcaagctctt ccgggtaaag 3480ggtcagcagc tacgtcacaa gtcacctgac tggggagggg tcacaacccg gaagccctcc 3540tcagtcacgt ggctgttcac gtggttgcta cgtcatcggc gccatcttgt gtcgcaaaat 3600ggcggacaac ttccgctttt ttaaaaaaag gcgcgaaaaa acggcggcgg cggcgcgcgc 3660gctgtgcgcg cgcgccgggg gggcgccagc gccccccccc ccgcgcatgc gcgggtcccc 3720ccccccgcgg ggggctccgc cccccggccc cccccccg 375829621DNAartificial sequencezpr9.6 29ccgcagcgag aacgccacgg agggagatcc tcgcgtcccg agggcgggtg ccggaggtga 60gtttacacac cgcagtcaag gggcaattcg ggctcgggac tggccgggcc ccgggcaagg 120ctcttaaaaa atgcgttttc gcagggttgc ccagaaaagg aaagtgcttt tgcaaactgt 180gccagctgca aagaaggcta ggcggcttct aggtatgtgg cagcccccca cgcacaatgt 240cccgggcatc gagagaaact ggtacgagag ctgttttaga tcccacgctg ctgtttgtgg 300ctgtggcgat tttgttggcc atcttaatca tctggcaact actctgggtc gtcctccgcg 360tcctgggccc ccaggcggac cccgcacgcc gcaaataaga aacctgccag cgctcccggc 420gccccagggc gagcccggtg acagagcgcc atggcatggg gcttctgggg ccgacgccgc 480cggtggagac gatggagagc gcggcgcaga cggtggagac cccgcaggcc aaccagagtc 540tacgtcgtgc acttcctggg catggtctac atcataatat aagaacgtgc acttccgaat 600ggctgagttt tccacgcccg t 621303758DNAartificial sequencettrh215 30aaagtacgtc actaaccacg tgactcccac aggccaacca cagtctacgt cgtgcatttc 60ctgggcatgg tctacatcat aatataagaa ggcgcacttc cgaatggctg agttttccac 120gcccgtccgc agcgagaacg ccacggaggg agatcctcgc gtcccgaggg cgggtgccgg 180aggtgagttt acacaccgca gtcaaggggc aattcgggct cgggactggc cgggccctgg 240gcaaggctct taaaaaatgc gctttcgcag ggttgcggag aaaaggaaag tgcttctgca 300aactctgcga gctgcaaagc aggctaggcg gcttctaggt atgtggcagc cccccgcgca 360caatgtcccc ggcatcgaga gaaactggta cgagagctgc ttcaggtctc acgctgctgt 420ttgtggctgt ggcgactttg ttggccatat taatcatttg gcaactactc tgggtcgtcc 480tccgcgtcct gggcccccag gcggaccccg cacgccgcaa ataagaaacc tgccagcgct 540cccggcgccc cagggcgagc ccggtgacag agcgccatgg cgtggggttt ctggggccga 600cgccgccggt ggagacggtg gagagcgcgg cgcagacggt ggagaccccg gagacgtagg 660agacgacgcc ctgctcgccg ctttcgagct cgtcgaagag taaggagacg cggggggagg 720tggcgcagac gctacagaaa atggcgacgg ggcagacgca gacggactca cagaaaaaag 780ataattataa aacagtggca accaaacttt attagacgct gctacataat aggatgccta 840cctctcgttt tctgtggcga aaatacaacc gcccagaact atgccactca ctcagacgat 900atgataagca aaggaccgta cggggggggc atgactacca cgaaattcac tctgagaata 960ctgtacgacg agtttaccag gtttatgaac ttttggactg tcagtaacga agacctagac 1020ctgtgtagat acgtgggctg caaactgata ttttttaaac accccacggt ggactttatg 1080gtacagataa acactcagcc tcctttctta gacacaagcc tcaccgcggc cagcatacac 1140ccgggcatca tgatgctcag caagagacgc atattaatac cctctctaaa gacccggccg 1200agcagaaaac acagggtggt cgtcagggtg ggcgccccaa gactttttca ggacaagtgg 1260tacccccagt cagacctatg tgacacagtt ctgctttcca tatttgcaac cgcccgcgac 1320ttgcaatatc cgttcggctc accactaact gacaaccctt gcgtcaactt ccagatcctg 1380gggccccagt acaaaaaaca ccttagtatt agctccacta tggatgatac taacaaacag 1440cactataaca gcaacttatt taataaaact gcactataca acacctttca aaccatagcc 1500cggcttaaag agacaggaca aactgcaaac attagtccaa gttggagtga agtacaaaac 1560acaaaactac tagatcacac aggtgctaat gcaactgcca gcagagacac ttggtacaag 1620ggaaacacat acaatgacta catacaacag ttagcagaga aaacaagaga aaggtttaaa 1680aaagcaacaa tgtcagcact accaaactac cccacaataa tgtccacaga cttatacgaa 1740taccactcag gcatatactc cagcatattt ctatcagctg gcaggagcta ctttgaaacc 1800actggggcct actctgacat tatatacaac cctttgacag acaaaggcac aggcaacata 1860atctggatag actaccttac aaaagacgac acaatctttg taaaaaacaa aagcaaatgt 1920gagataatgg acatgcccct gtgggcggcc ggcacaggat acacagagtt ttgtgcaaag 1980tacacaggag actctgccat tatttacaat gccagaatac tcataagatg cccatacact 2040gaacccatgc taatagacca ctcagaccca aacaaaggct ttgtaccgta ctcatttaac 2100tttggcaacg gaaagatgcc gggaggcagc tccaacgtgc ccataagaat gagagccaag 2160tggtacgtaa acatattcca ccaaaaagaa gtattggaga gcatagtaca gtccggaccg 2220ttcgggtaca ggggcgacat aaaatcagct gtactgtcca tgaaatacag atttcactgg 2280aaatggggcg gaaaccctat atccaaacag gtcgtcagga atccctgctc caactccagc 2340acctccgcgg cccatagagg acctcgcagc gtacaagcgg ttgacccgaa atacaatacc 2400ccagaagtca cttggcactc gtgggacatc agacgaggac tctttggcaa agcaggtatt 2460aaaagaatgc aacaagaatc agatgctctt tacgttcctg caggaccact caagaggcct 2520cgcagagaca ccaacgccca agacccggaa aagcaaaacg aaagctcacg tttcggagtc 2580cagcagcgac tcccgtgggt ccactccagc caagagacgc aaagctccga agaagagacg 2640caggcgcagg ggtcggtaca agaccaacta ctcctccagc tccgagagca gcgagtactc 2700cgactccagc tccaacaact cgcaccccaa gtcctcaaag ttcaagcagg acacagccta 2760caccccctat tatcctccca agcataaaca aagcctatat gtttgaaccc cagggtccta 2820aacccataca ggggtacaac gattggctag aggagtacac tagttgcaag ttccgggaca 2880gacccccgag aatgctacac acagacttac ccttttaccc ctgggcacca aaaccccaag 2940accaagtcag ggtaaccttt aaactcaact ttcaataaaa attctaggcc gtgggacttt 3000cacttgtcgg tgtctgcttc ttaaggtcgc caagcactcc gagcgtcagc gaggagtgcg 3060accccccccc tcggtagcaa cgccttcgga gccgcgcgct acgccttcgg ctgcgcgcgg 3120cacctcagac cccccctcca cccgaaacgc ttgcgcgttt cggaccttcg gcgtcggggg 3180ggtcgggagc tttattaaac agactccgag ttgccattgg acactggagc tgtgaatcag 3240taacgaaagt gagtggggcc agacttcgcc atagggcctt tatcttctcg ccattggata 3300gtgtccgggg ttgccgtagg cttcggcctc gtttttaggc cttccggact acaaaaatgg 3360cggattttgt gacgtcacgg ccgccatttt aagtaaggcg gaagcagctc caccctctca 3420cataatggcg gcggagcact cccggcttgc ccaaaatggc gggcaagctc ttccgggtca 3480aaggttggca gctacgtcac aagtcacctg actggggagg agttacatcc cggaagttct 3540cctcggtcac gtgactgtac acgtgactgc tacgtcattg acgccatctt gtgtcacaaa 3600atggcggtgc acttccgctt ttttgaaaaa aggcgcgaaa aaacggcggc ggcggcgcgc 3660gcgctgcgcg cgcgcgccgg gggggcgcca gcgccccccc ccccgcgcat gcacgggtcc 3720ccccccccac ggggggctcc gccccccggc cccccccc 375831642DNAartificial sequencezpr12.24 31cagcgagaac gccacggagg gagatcctcg cgtcccgagg gcgggtgccg gaggtgagtt 60tacacaccgc agtcaagggg caattcgggc tcgggactgg ccgggccccg ggcaaggctc 120ttaaaaaatg cgctttcgca gggttgctga gaaaaggaaa gtgcttctgc aaactgtgcg 180agctacacag aagactaggc ggcttctaag ccgcccacag gggcatgtct acatgcttcc 240gcagcgagaa cgccacggag ggagatcctc gcgtcccgag ggcgggtgcc ggaggtgagt 300ttacacaccg cagtcaaagg gcaattcggg ctcgggactg gccgggcccc gggcaaggct 360cttaaaaaat gcgctttcgc ggggttgctg agaaaaggaa agtgcttctg caaactgtgc 420gagctacaca gaagactagg cggcttctag gtatgtggca gccccccgtg cacaatgtcc 480ccggcatctt attagtactc tggcgttgta gataatggca gagtctccag tgtactttgc 540acagaactct gtgtatcctg tgcaggccgc ccacaggggc atgtctacat cataatataa 600taaggcgcac ttccgaatgg ctgagttttc cacgcccgtc cg 6423223PRTartificial sequencezyb2.1. peptide 32Arg Val Pro Lys Val Ser Leu His Thr Ala Val Lys Gly Gln Phe Gly1 5 10 15Leu Gly Thr Gly Arg Ala Met 203323PRTartificial sequencezyb9.1 peptide 33Arg Val Pro Lys Val Ser Leu His Thr Ala Val Lys Gly Gln Phe Gly1 5 10 15Leu Gly Thr Gly Arg Ala Met 203423PRTartificial sequencezyb69.1 peptide 34Arg Val Pro Glu Val Ser Leu His Thr Ala Val Lys Gly Gln Phe Gly1 5 10 15Leu Gly Thr Gly Arg Ala Met 203523PRTartificial sequencezyb2.3. peptide 35Gly Ala Glu Gly Glu Phe Thr His Arg Ser Gln Gly Ala Ile Arg Ala1 5 10 15Arg Asp Trp Pro Gly His Gly 203623PRTartificial sequencezyb9.3. peptide 36Gly Ala Glu Gly Glu Phe Thr His Arg Ser Gln Gly Ala Ile Arg Ala1 5 10 15Arg Asp Trp Pro Gly Tyr Gly 203723PRTartificial sequencezyb5.3. peptide 37Gly Ala Val Gly Glu Phe Thr His Arg Ser Gln Gly Ala Ile Arg Ala1 5 10 15Arg Asp Trp Pro Gly Tyr Gly 203823PRTartificial sequencezkb69.3 peptide 38Gly Ala Gly Gly Glu Phe Thr His Arg Ser Gln Gly Ala Ile Arg Ala1 5 10 15Arg Asp Trp Pro Gly Tyr Gly 203923PRTartificial sequenceQ9WB09_9Viru 39Arg Val Pro Lys Val Ser Leu His Thr Glu Val Lys Gly Gln Phe Gly1 5 10 15Leu Gly Thr Gly Arg Ala Met 2040204PRTartificial sequencetorque teno virus 40Cys Thr Ser Glu Trp Leu Ser Phe Pro Arg Pro Ser Ala Ala Ala Xaa1 5 10 15Pro Arg Arg Val Ile Pro Ala Ser Arg Trp Arg Val Pro Lys Val Ser 20 25 30Leu His Thr Ala Val Lys Gly Gln Phe Gly Leu Gly Thr Gly Arg Ala 35 40 45Met Gly Lys Ala Leu Lys Val Phe Ile Leu Lys Met His Phe Ser Arg 50 55 60Ile Ser Arg Ser Lys Arg Lys Val Leu Leu Pro Ala Leu Pro Ala Pro65 70 75 80Pro Pro Pro Arg Gln Leu Leu Met Trp Gln Pro Pro Ile Gln Asn Gly 85 90 95Thr Gln Leu Asp Arg His Trp Phe Glu Ser Val Trp Arg Ser His Ala 100 105 110Ala Tyr Cys Gly Cys Gly

Asp Cys Val Gly His Leu Gln His Leu Ala 115 120 125Ala Asn Leu Gly Arg Pro Pro His Pro Gln Pro Pro Arg Glu Gln His 130 135 140Pro Pro Gln Ile Arg Gly Leu Pro Ala Leu Pro Ala Pro Pro Ser Asn145 150 155 160Arg Asn Ser Trp Pro Gly Thr Gly Gly Asp Ala Ala Gly Glu Gln Ala 165 170 175Gly Gly Ser Arg Gly Ala Gly Asp Gly Gly Asp Gly Glu Leu Ala Asp 180 185 190Asp Asp Leu Xaa Asp Ala Ala Ala Leu Val Glu Glu 195 20041138PRTartificial sequencetorque teno virus 41Ala Val Lys Pro Arg Arg Glu Ile Ser Ala Ser Arg Gly Arg Val Pro1 5 10 15Lys Val Ser Leu His Thr Glu Val Lys Gly Gln Phe Gly Leu Gly Thr 20 25 30Gly Arg Ala Met Gly Lys Ala Leu Lys Lys Ser Met Phe Ile Gly Arg 35 40 45His Tyr Arg Lys Lys Arg Ala Leu Ser Leu Cys Ala Val Arg Thr Thr 50 55 60Lys Lys Ala Cys Lys Leu Leu Ile Val Met Trp Thr Pro Pro Arg Asn65 70 75 80Asp Gln Gln Tyr Leu Asn Trp Gln Trp Tyr Ser Ser Val Leu Ser Ser 85 90 95His Ala Ala Met Cys Gly Cys Pro Asp Ala Ile Ala His Leu Ser His 100 105 110Leu Ala Phe Val Phe Arg Ala Pro Gln Asn Pro Pro Pro Pro Gly Pro 115 120 125Gln Arg Asn Leu Pro Leu Arg Arg Leu Pro 130 13542202PRTartificial sequencetorque teno virus 42Met Ala Glu Phe Ser Thr Pro Val Arg Ser Gly Glu Ala Thr Glu Gly1 5 10 15Asp His Arg Val Pro Arg Ala Gly Ala Glu Gly Glu Phe Thr His Arg 20 25 30Ser Gln Gly Ala Ile Arg Ala Arg Asp Trp Pro Gly Tyr Gly Gln Gly 35 40 45Ser Glu Lys Ser Met Phe Ile Gly Arg His Tyr Arg Lys Lys Arg Ala 50 55 60Leu Ser Leu Cys Ala Val Arg Thr Thr Lys Lys Ala Cys Lys Leu Leu65 70 75 80Ile Val Met Trp Thr Pro Pro Arg Asn Asp Gln Gln Tyr Leu Asn Trp 85 90 95Gln Trp Tyr Ser Ser Val Leu Ser Ser His Ala Ser Met Cys Gly Cys 100 105 110Pro Asp Ala Val Ala His Leu Ile Asn Leu Ala Ser Val Leu Arg Ala 115 120 125Pro Gln Asn Pro Pro Pro Pro Gly Pro Gln Arg Asn Leu Pro Leu Arg 130 135 140Arg Leu Pro Ala Leu Pro Ala Ala Pro Glu Ala Pro Gly Asp Arg Ala145 150 155 160Pro Trp Pro Met Ala Gly Gly Ala Glu Gly Glu Asn Gly Gly Ala Gly 165 170 175Gly Asp Ala Asp His Gly Gly Ala Ala Gly Gly Pro Glu Asp Ala Asn 180 185 190Leu Leu Asp Ala Val Ala Ala Ala Glu Thr 195 20043204PRTartificial sequencetorque teno virus 43Cys Thr Ser Glu Trp Leu Ser Phe Pro Arg Pro Ser Ala Ala Ala Xaa1 5 10 15Pro Arg Arg Val Ile Pro Ala Ser Arg Trp Arg Val Pro Lys Val Ser 20 25 30Leu His Thr Ala Val Lys Gly Gln Phe Gly Leu Gly Thr Gly Arg Ala 35 40 45Met Gly Lys Ala Leu Lys Val Phe Ile Leu Lys Met His Phe Ser Arg 50 55 60Ile Ser Arg Ser Lys Arg Lys Val Leu Leu Pro Ala Leu Pro Ala Pro65 70 75 80Pro Pro Pro Arg Gln Leu Leu Met Trp Gln Pro Pro Ile Gln Asn Gly 85 90 95Thr Gln Leu Asp Arg His Trp Phe Glu Ser Val Trp Arg Ser His Ala 100 105 110Ala Tyr Cys Gly Cys Gly Asp Cys Val Gly His Leu Gln His Leu Ala 115 120 125Ala Asn Leu Gly Arg Pro Pro His Pro Gln Pro Pro Arg Glu Gln His 130 135 140Pro Pro Gln Ile Arg Gly Leu Pro Ala Leu Pro Ala Pro Pro Ser Asn145 150 155 160Arg Asn Ser Trp Pro Gly Thr Gly Gly Asp Ala Ala Gly Glu Gln Ala 165 170 175Gly Gly Ser Arg Gly Ala Gly Asp Gly Gly Asp Gly Glu Leu Ala Asp 180 185 190Asp Asp Leu Xaa Asp Ala Ala Ala Leu Val Glu Glu 195 20044138PRTartificial sequencetorque teno virus 44Ala Val Lys Pro Arg Arg Glu Ile Ser Ala Ser Arg Gly Arg Val Pro1 5 10 15Lys Val Ser Leu His Thr Glu Val Lys Gly Gln Phe Gly Leu Gly Thr 20 25 30Gly Arg Ala Met Gly Lys Ala Leu Lys Lys Ser Met Phe Ile Gly Arg 35 40 45His Tyr Arg Lys Lys Arg Ala Leu Ser Leu Cys Ala Val Arg Thr Thr 50 55 60Lys Lys Ala Cys Lys Leu Leu Ile Val Met Trp Thr Pro Pro Arg Asn65 70 75 80Asp Gln Gln Tyr Leu Asn Trp Gln Trp Tyr Ser Ser Val Leu Ser Ser 85 90 95His Ala Ala Met Cys Gly Cys Pro Asp Ala Ile Ala His Leu Ser His 100 105 110Leu Ala Phe Val Phe Arg Ala Pro Gln Asn Pro Pro Pro Pro Gly Pro 115 120 125Gln Arg Asn Leu Pro Leu Arg Arg Leu Pro 130 13545138PRTartificial sequencetorque teno virus 45Ser Gly Glu Ala Thr Glu Gly Asp Leu Arg Val Pro Arg Ala Gly Ala1 5 10 15Glu Gly Glu Phe Thr His Arg Ser Gln Gly Ala Ile Arg Ala Arg Asp 20 25 30Trp Pro Gly Tyr Gly Gln Gly Ser Glu Lys Ser Met Phe Ile Gly Arg 35 40 45His Tyr Arg Lys Lys Arg Ala Leu Ser Leu Cys Ala Val Arg Thr Thr 50 55 60Lys Lys Ala Cys Lys Leu Leu Ile Val Met Trp Thr Pro Pro Arg Asn65 70 75 80Asp Gln Gln Tyr Leu Asn Trp Gln Trp Tyr Ser Ser Val Leu Ser Ser 85 90 95His Ala Ala Met Cys Gly Cys Pro Asp Ala Val Ala His Phe Asn His 100 105 110Leu Ala Ala Val Leu Arg Ala Pro Gln Asn Pro Pro Pro Pro Gly Pro 115 120 125Gln Arg Asn Leu Pro Leu Arg Arg Leu Pro 130 1354623PRTartificial sequencepeptide of subject 24 46Gly Ala Glu Gly Glu Phe Thr His Arg Ser Gln Gly Ala Ile Arg Ala1 5 10 15Arg Asp Trp Pro Gly Tyr Gly 2047202PRTartificial sequencetorque teno virus 47Met Ala Glu Phe Ser Thr Pro Val Arg Ser Gly Glu Ala Thr Glu Gly1 5 10 15Asp His Arg Val Pro Arg Ala Gly Ala Glu Gly Glu Phe Thr His Arg 20 25 30Ser Gln Gly Ala Ile Arg Ala Arg Asp Trp Pro Gly Tyr Gly Gln Gly 35 40 45Ser Glu Lys Ser Met Phe Ile Gly Arg His Tyr Arg Lys Lys Arg Ala 50 55 60Leu Ser Leu Cys Ala Val Arg Thr Thr Lys Lys Ala Cys Lys Leu Leu65 70 75 80Ile Val Met Trp Thr Pro Pro Arg Asn Asp Gln Gln Tyr Leu Asn Trp 85 90 95Gln Trp Tyr Ser Ser Val Leu Ser Ser His Ala Ser Met Cys Gly Cys 100 105 110Pro Asp Ala Val Ala His Leu Ile Asn Leu Ala Ser Val Leu Arg Ala 115 120 125Pro Gln Asn Pro Pro Pro Pro Gly Pro Gln Arg Asn Leu Pro Leu Arg 130 135 140Arg Leu Pro Ala Leu Pro Ala Ala Pro Glu Ala Pro Gly Asp Arg Ala145 150 155 160Pro Trp Pro Met Ala Gly Gly Ala Glu Gly Glu Asn Gly Gly Ala Gly 165 170 175Gly Asp Ala Asp His Gly Gly Ala Ala Gly Gly Pro Glu Asp Ala Asn 180 185 190Leu Leu Asp Ala Val Ala Ala Ala Glu Thr 195 20048152PRTartificial sequencetorque teno virus 48Ala Arg Thr Pro Arg Arg Gly Val Arg Ala Ser Arg Gly Arg Val Pro1 5 10 15Glu Val Ser Leu His Thr Ala Val Lys Gly Gln Phe Gly Leu Gly Thr 20 25 30Gly Arg Ala Met Gly Lys Ala Leu Lys Lys Ala Met Phe Leu Gly Arg 35 40 45Ile Tyr Arg Lys Lys Arg Arg Leu Pro Leu Ser Pro Leu His Ser Pro 50 55 60Pro Lys Ala Arg Lys Leu Leu Arg Gly Met Trp Arg Pro Pro Thr Gln65 70 75 80Asn Val Ser Gly Gln Glu Arg Ser Trp Tyr Asp Ser Val Phe Tyr Ser 85 90 95His Ala Ala Phe Cys Gly Cys Gly Asp Cys Val Gly His Leu Ser Tyr 100 105 110Leu Ala Thr His Leu Gly Arg Pro Pro Ser Ala Gln Pro Pro Pro Gln 115 120 125Leu Gln Pro Pro Val Ile Arg Arg Leu Pro Ala Leu Pro Ala Pro Pro 130 135 140Asn Pro Ser Gly Asp Arg Ala Ala145 1504949PRTartificial sequencetorque teno virus 49Met Ala Glu Phe Ser Thr Pro Val Arg Ser Glu Gly Ala Thr Glu Gly1 5 10 15Ile Pro Asn Val Pro Arg Ala Gly Ala Gly Gly Glu Phe Thr His Arg 20 25 30Ser Gln Gly Ala Ile Arg Ala Arg Asp Trp Pro Gly Tyr Gly Gln Gly 35 40 45Ser

Claims

1. An isolated TT virus polynucleic acid comprising (a) a nucleotide sequence consisting of SEQ ID NOS: 1-4; (b) a nucleotide sequence which shows 70% identity to a nucleotide sequence of (a) and is capable of replicating autonomously; (c) a fragment of a nucleotide sequence of (a) or (b) which is capable of replicating autonomously; (d) a nucleotide sequence which is the complement of the nucleotide sequence of (a), (b), or (c); or (e) a nucleotide sequence which is redundant as a result of the degeneracy of the genetic code compared to any of the above-given nucleotide sequences.

2. The TT virus polynucleic acid of claim 1 comprising (a) a nucleotide sequence consisting of SEQ ID NOS: 1-4; (b) a nucleotide sequence which shows 70% identity to a nucleotide sequence of (a) and is capable of replicating autonomously; (c) a fragment of a nucleotide sequence of (a) or (b) which is capable of replicating autonomously; (d) a nucleotide sequence which is the complement of a nucleotide sequence of (a), (b), or (c); or (e) a nucleotide sequence which is redundant as a result of the degeneracy of the genetic code compared to any of the above-given nucleotide sequences.

3. The TT virus polynucleic acid of claim 1 which is present as a single- or double-stranded extrachromosomal episome.

4. The TT virus polynucleic acid of claim 1 which is a single-stranded DNA.

5. The TT virus polynucleic acid of claim 4 which is linked to a host cell DNA.

6. The TT virus polynucleic acid of claim 5 having at least one of the following properties: (a) growth-stimulation; (b) oncogene function; (c) tumor suppressor gene-like function; or (d) stimulation of autoimmune reactions.

7. The TT virus polynucleic acid of claim 1 comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 5-7, 13, 18-19, 26-27, 28-29 and 30-31.

8. An oligonucleotide primer comprising part of a polynucleic acid according to claim 1, with said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid.

9. The oligonucleotide primer of claim 8 having a nucleotide sequence selected from the group consisting of SEQ ID NOS: 20-25.

10. An oligonucleotide probe comprising part of a polynucleic acid according to claim 1, wherein said probe can specifically hybridize to said polynucleic acid.

11. The oligonucleotide probe of claim 10 having a nucleotide sequence selected from the group consisting of SEQ ID NOS: 13, 18 and 19.

12. The oligonucleotide probe of claim 10, which is detectably labelled or attached to a solid support.

13. The oligonucleotide primer of claim 8 having a length of at least 13 bases.

14. An expression vector comprising a TT virus polynucleic acid of claim 1 operably linked to prokaryotic, eukaryotic or viral transcription and translation control elements.

15. An artificial chromosome comprising the expression vector of claim 14.

16. A host cell transformed with an expression vector according to claim 14.

17. A polypeptide being encoded by a TT virus polynucleic acid of claim 1.

18. An antibody or fragment thereof specifically binding to a polypeptide of claim 17.

19. The antibody or fragment thereof of claim 18, wherein said antibody or fragment is detectably labelled.

20. A diagnostic kit for use in determining the presence of a TT virus polynucleic acid of claim 1, said kit comprising an oligonucleotide primer comprising part of said polynucleic acids, with said primer being able to act as a primer for specifically sequencing or specifically amplifying said polynucleic acid; or an oligonucleotide probe comprising part of said polynucleic acid, wherein said probe can specifically hybridize to said polynucleic acid.

21-34. (canceled)

35. A diagnostic kit for use in determining the presence of a TT virus polypeptide, said kit comprising an antibody or fragment thereof specifically binding to a polypeptide being encoded by a TT virus polynucleic acid of claim 1.

36. A diagnostic composition for the diagnosis of a predisposition or an early stage of cancer or an autoimmune disease said composition comprising an oligonucleotide primer comprising part of a TT virus polynucleic acid according to claim 1, with said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid; or an oligonucleotide probe comprising part of a polynucleic acid, wherein said probe can specifically hybridize to said polynucleic acid; or an antibody or fragment thereof specifically binding to a polypeptide being encoded by said TT virus polynucleic acid.

37. A method for the detection of a TTV polynucleic acid according to claim 1 in a biological sample, comprising: (a) optionally extracting a polynucleic acid from said biological sample, (b) amplifying said polynucleic acid with at least one optionally labelled primer comprising part of said polynucleic acid, with said primer being able to act as primer for specifically sequencing or specifically amplifying said polynucleic acid and (c) detecting the amplified polynucleic acid.

38. A method for the detection of a TTV polynucleic acid which is present as a single- or double-stranded extrachromosomal episome in a biological sample, comprising: (a) optionally extracting a polynucleic acid from said biological sample, (b) hybridizing the polynucleic acid as described above with at least one optionally labelled probe comprising part of a polynucleic acid according to claim 1, wherein said probe can specifically hybridize to said polynucleic acid and (c) detecting the hybridized polynucleic acid.

39. A method for detecting a polypeptide being encoded by a TT virus polynucleic acid of claim 1 present in a biological sample, comprising: (a) contacting the biological sample for the presence of such polypeptide with an antibody against a polypeptide being encoded by said TT virus polynucleic acid, and (b) detecting the immunological complex formed between said antibody and said polypeptide.

40. A method for detecting an antibody against a polypeptide being encoded by a TT virus polynucleic acid of claim 1 present in a biological sample, comprising: (a) contacting the biological sample for the presence of said antibody with a polypeptide being encoded by said TT virus polynucleic acid, and (b) detecting the immunological complex formed between said antibody and said polypeptide.

41. An antisense oligonucleotide reducing or inhibiting the expression of the TT virus polynucleic acid of claim 1.

42. A pharmaceutical composition comprising the antibody of claim 18 and a suitable pharmaceutical carrier.

43. A pharmaceutical composition comprising the antisense oligonucleotide of claim 41 and a suitable pharmaceutical carrier.

44. A method of preventing or treating cancer or an autoimmune disease or early stages thereof comprising administering to a subject with such disorder a therapeutically effective amount of the antibody or fragment of claim 18.

45. A method of preventing or treating cancer or an autoimmune disease or early stages thereof comprising administering to a subject with such disorder a therapeutically effective amount of the antisense oligonucleotide of claim 41.

46. The method according to claim 44, wherein said autoimmune disease is multiple sclerosis (MS), asthma, polyarthritis, juvenile diabetes, Lupus erythematodes, Colitis ulcerosa, or Crohn's disease; and wherein said cancer is breast cancer, colorectal cancer, pancreatic cancer, cervical cancer, Hodgkin's lymphoma, B-lymphoma, acute lymphocytic leukaemia, or Burkitt's lymphoma.

47. A vaccine comprising a TT virus polynucleic acid of claim 1, or a polypeptide being encoded by said TT virus polynucleic acid.

48. A method of immunizing a mammal against a TT virus infection wherein an effective amount of the vaccine of claim 47 is administered to said mammal.

49. A method for the generation of a database for determining the risk to develop cancer or an autoimmune disease, comprising the following steps (a) determining the nucleotide sequence of a host cell DNA linked to TT virus polynucleic acids according to claim 5 and being present in episomal form, if present, in a sample from a patient suffering from at least one of said diseases; and (b) compiling sequences determined in step (a) associated with said diseases in a database.

50. A method for evaluating the risk to develop cancer or an autoimmune disease of a patient suspected of being at risk of developing such disease, comprising the following steps (a) determining the nucleotide sequence of a host cell DNA linked to TT virus polynucleic acids and being present in episomal form, in a sample from said patient; and (b) comparing sequences determined in step (a) with the sequences compiled in the database generated to the method of claim 49 wherein the absence of a host cell DNA linked to a TT virus polynucleic acid or the presence only of host cell DNA linked to a TT virus polynucleic acid not represented in said database indicates that the risk of developing such disease is decreased or absent.

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