# Patent

## Title
Compositions and methods for screening for lyme disease

## Abstract

The invention provides compositions, methods, and kits for the diagnosis or detection of infection by a pathogen that causes Lyme disease in a subject.

## Background
RELATED APPLICATIONS
This application is a divisional application of U.S. Ser. No. 13/583,472, filed Nov. 13, 2012 and issued as U.S. Pat. No. 8,926,989 on Jan. 6, 2015, which is a national stage application filed under 35 U.S.C. §371 of international application no. PCT/US2011/027888, filed Mar. 10, 2011, which claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 61/312,520, filed Mar. 10, 2010, the entire contents of each of which are incorporated herein by reference.


GOVERNMENT SUPPORT
This work was supported by the Intramural Research Program of the National Institutes of Health, the National Institute of Dental and Craniofacial Research, the NIH Clinical Center, and the National Institute for Allergy and Infectious Disease. The Government has certain rights to this invention.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 28, 2014, is named 85313US(47992)_SL.txt and is 33,555 bytes in size.
BACKGROUND
Lyme disease is caused by the spirochete Borrelia burgdorferi (Bb) in North America and predominantly by Borrelia afzelii and Borrelia garinii in Eurasia. The pathogen is transmitted by the bite of a tick (Ixodes sp.), deer tick or western black-legged tick in North America. One of the typical first signs of Borrelia sp. infection is erythema migrans (EM), a bull's eye-like skin lesion, which arises within a few days of the bite. However, the bite may not be painful, and a rash does not develop in all patients. Patients can also experience flu-like symptoms, however, such symptoms may be attributed by the patient to any of a number of other causes.
After infection, the spirochetes can disseminate in the bloodstream to various target tissues. Prompt treatment with antibiotics can typically kill the pathogen and prevent long term ill effects of infection. If the infection is not treated, or not successfully treated, it can result in neurological, rheumatological, and cardiac damage over time. Some common symptoms from long-term Lyme infection include arthritis, facial palsy, and neuroboreliosis. Even after antibiotic treatment of Lyme disease, some individuals show post-Lyme disease syndrome (PLDS) and have lingering symptoms such as fatigue, musculoskeletal pain, and cognitive complaints.
Because of the difficulty in culturing Borrelia bacteria in the laboratory, diagnosis of Lyme disease is typically based on clinical exam findings and a history of exposure to endemic Lyme areas (Ryan K J, Ray C G (editors) 2004. Sherris Medical Microbiology (4th ed.). McGraw Hill. pp. 434-437). The EM rash, which does not occur in all cases, is considered sufficient to establish a diagnosis of Lyme disease even when serologic blood tests are negative (Hofmann et al., 1996, Infection 24: 470-472; Pachner et al., 1989. Rev. Infect. Dis. 11 Suppl 6: S1482-1486). Serological testing can be used to support a clinically suspected case but is not diagnostic by itself (Ryan K J, Ray C G (editors) 2004. Sherris Medical Microbiology (4th ed.). McGraw Hill. pp. 434-437).
SUMMARY OF THE INVENTION
The invention provides compositions, methods, and kits for the detection of infection by a Borrelia sp. pathogen.
The invention provides compositions containing an isolated peptide having an amino acid sequence at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to SEQ ID NO: 1, wherein a 10-fold molar excess of the peptide inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 1 to a sample from a subject suffering from an infection by Borrelia burgdorferi. In certain embodiments, the isolated peptide has the amino acid sequence of SEQ ID NO: 1. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, Borrelia garinii, and/or Borrelia valaisiana can be evaluated using these compositions in routine diagnostic methods such as those provided herein. In embodiments, the subject is suffering from Borrelia burgdorferi. 
The invention provides compositions that include the mixtures of the antigenic components of SEQ ID NO: 1. Such compositions according to the invention contain one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc) isolated peptides, wherein the peptides include amino acid sequences of SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 9. The mixtures can include separate peptides having the sequences of SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 9. The peptides can have sequences of SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 9 joined, for example, by covalent linkage, such as a peptide bond or a peptide linker. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, and/or Borrelia garinii can be evaluated using these compositions in routine diagnostic methods such as those provided herein. In embodiments, the subject is suffering from Borrelia burgdorferi. 
The invention provides compositions containing an isolated peptide having an amino acid sequence at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to SEQ ID NO: 3, wherein a 10-fold molar excess of the peptide inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 3 to a sample from a subject suffering from an infection by Borrelia afzelii. In certain embodiments, the isolated peptide has the amino acid sequence of SEQ ID NO: 3. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, Borrelia garinii, and/or Borrelia valaisiana can be evaluated using these compositions in routine diagnostic methods such as those provided herein. In embodiments, the subject is suffering from Borrelia afzelii. 
The invention provides compositions that include the mixtures of the antigenic components of SEQ ID NO: 3. Such compositions according to the invention contain one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc) isolated peptides, wherein the peptides include amino acid sequences of SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9. The mixtures can include separate peptides having the sequences of SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9. The peptides can have sequences of SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9 joined, for example, by covalent linkage, such as a peptide bond or a peptide linker. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, Borrelia garinii, and/or Borrelia valaisiana can be evaluated using these compositions in routine diagnostic methods such as those provided herein. In embodiments, the subject is suffering from Borrelia afzelii. 
The invention provides compositions containing an isolated peptide having an amino acid sequence at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to SEQ ID NO: 2, wherein a 10-fold molar excess of the peptide inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 2 to a sample from a subject suffering from an infection by Borrelia garinii. In certain embodiments, the isolated peptide has the amino acid sequence of SEQ ID NO: 2. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, Borrelia garinii, and/or Borrelia valaisiana can be evaluated using these compositions in routine diagnostic methods such as those provided herein. In embodiments, the subject is suffering from Borrelia garinii. 
The invention provides compositions that include the mixtures of the antigenic components of SEQ ID NO: 2. Such compositions according to the invention contain one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc) isolated peptides, wherein the peptides include amino acid sequences of SEQ ID NO: 6 and SEQ ID NO: 9. The mixtures can include separate peptides having the sequences of SEQ ID NO: 6 and SEQ ID NO: 9. The peptides can have sequences of SEQ ID NO: 6 and SEQ ID NO: 9 joined, for example, by covalent linkage, such as a peptide bond or a peptide linker. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, and/or Borrelia garinii can be evaluated using these compositions in routine diagnostic methods such as those provided herein. In embodiments, the subject is suffering from Borrelia garinii. 
The invention provides compositions that include the mixtures of the antigenic peptide sequences provided herein. Such compositions according to the invention contain one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc) isolated peptides, wherein the peptides include amino acid sequences of SEQ ID NO: 1-9. The mixtures can include separate peptides having the sequences of SEQ ID NO: 1-9. The peptides can have sequences of SEQ ID NO: 1-9 joined, for example, by covalent linkage, such as a peptide bond or a peptide linker. A sample from a subject suffering from infection by Borrelia burgdorferi, Borrelia afzelii, Borrelia garinii, and/or Borrelia valaisiana can be evaluated using these compositions in routine diagnostic methods such as those provided herein.
The isolated peptides can further be linked to other polypeptide sequences by linkages well-known in the art, including but not limited to, chemical linkers, peptide bonds, and peptide linkers. For example, peptides of the invention can be linked to one or more of reporter polypeptide sequences and/or an epitope tag sequences. In certain embodiments, one of the peptides of SEQ ID NO: 1-9 is joined to a reporter polypeptide sequence(s) and/or an epitope tag sequence(s). In certain embodiments, 2, 3, 4, 5, 6, 7, 8, or 9 of peptides having the sequence of SEQ ID NO: 1-9 are joined to a reporter polypeptide sequence(s) and/or an epitope tag sequence(s).
The invention provides nucleic acids encoding one or more of the peptides (1, 2, 3, 4, 5, 6, 7, 8, or 9) of the invention, alone or in a mixture with other nucleic acids encoding one or more polypeptides of the invention. In certain embodiments, each of the peptides is encoded by a separate nucleic acid expression construct. In certain embodiments, more than one peptide is encoded by a single nucleic acid expression construct.
The invention provides methods for diagnosing infection by Borrelia sp. in a subject including the steps of:
a) obtaining a sample from a subject,
b) contacting the sample with the peptide composition of any one of the antigenic peptide compositions of the invention, and
c) detecting binding of the peptide to an antibody in the sample, wherein binding is indicative of infection of the subject by Borrelia sp.
The invention also provides methods for monitoring therapeutic treatment response in a subject having a Borrelia sp. infection including the steps of:
a) obtaining a sample from a subject after therapeutic treatment,
b) contacting the sample with the peptide composition of any one of the antigenic peptide compositions of the invention, and
c) detecting binding of the peptide to an antibody in the sample, and
d) correlating binding with the treatment response of the subject, thereby evaluating the therapeutic treatment response of the subject. In embodiments, the therapeutic treatment involves the administration of an immunogenic composition (e.g., a vaccine).
The invention also provides methods for selecting a treatment regimen for a subject having a Borrelia sp. infection including the steps of:
a) administering an agent to a subject,
b) obtaining a sample from the subject,
c) contacting the sample with the peptide composition of any one of the antigenic peptide compositions of the invention, and
d) detecting binding of the peptide to an antibody in the sample, wherein decreased binding is indicative that the subject is susceptible to treatment with the agent, and wherein the treatment regimen comprises administering the agent to the subject if the subject is determined to be susceptible to treatment with the agent.
In the above aspects of the invention, detection of binding of the peptide and the antibody can be assayed for by any method well-known in the art. In embodiments, detection includes detection of an enzymatic reaction. Enzymatic reactions can be catalyzed by an enzyme, for example, luciferase, alkaline phosphatase, or beta-galactosidase. In certain embodiments, the methods include isolating the antibody-antigen complex from the sample, for example by binding the antigen-antibody complex to a solid substrate. In certain embodiments, the antibody-antigen complex is formed in solution. In embodiments, the assay is an immunoassay Immunoassays include, but are not limited to, competitive and non-competitive assay systems using techniques such as LIPS, BIAcore analysis, FACS analysis, immunofluorescence, immunocytochemistry, Western blots, radioimmunoassays, ELISA, “sandwich” immunoassays, immunoprecipitation assays, precipitation reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, and protein A immunoassays. See Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York, which is hereby incorporated by reference.
In the above aspects of the invention, the sample can be any body fluid or tissue from the subject. Samples can be obtained from the subject using any method well-known in the art. In embodiments, the sample is blood, plasma, or serum. In embodiments, the sample is donated blood, tissue, or organ.
The invention provides kits including one or more peptides of the invention. The invention also provides kits including one or more nucleic acids for encoding one or more peptides of the invention. In embodiments, the kits further include instructions for using the peptides and/or nucleic acids in any of the methods described herein.
The invention further provides other embodiments that are provided herein.



BRIEF DESCRIPTION OF THE FIGURES
FIGS. 1A-1F include scatter plots showing the antibody titers resulting from VlsE-Δ1 (FIG. 1A), DbpB (FIG. 1B), DbpA (FIG. 1C), p39 (BMP) (FIG. 1D), Fla (FIG. 1E) and OspC (FIG. 1F) tested by LIPS. The serum samples included 11 EM (erythema migrans), 8 multiple erythema migrans (MEM), 2 Lyme palsy, 6 Lyme arthritis, 1 late Lyme neuroborreliosis, post-Lyme disease syndrome (PLDS) patient samples and 8 uninfected control samples. Each symbol represents a serum sample from an individual patient. The geometric mean is shown as the bar. The cut-off value for calculating sensitivity and specificity is shown by the dotted line and is derived from the mean plus 5 standard deviation (SD) of the 8 uninfected controls.
FIG. 2 includes a scatter plot of the antibody responses from the LIPS VOVO test. Shown are results from 11 EM, 8 multiple erythema migrans (MEM), 2 Lyme palsy, 6 Lyme arthritis, 1 late Lyme neuroborreliosis, post-Lyme disease syndrome (PLDS) patient samples and 8 uninfected control samples. Each symbol represents a serum sample from an individual patient. The geometric mean is shown as the bar.
FIGS. 3A-3B show that the VOVO antigen has 94% sensitivity and 100% specificity. FIG. 3A includes a scatter plot showing the results from 141 serum samples from patients with confirmed Lyme disease, and 59 control serum samples. Each symbol represents a serum sample from an individual patient. Using the cut-off based on the mean plus 5 SD shown by the solid line, the VOVO LIPS test showed 94% sensitivity and 100% specificity. The C6 ELISA on these same samples showed 76% sensitivity and 96% specificity FIG. 3B includes a plot showing the correlation between the titer values obtained from LIPS and C6 ELISA. The LIPS titer values were first log10 transformed and then analyzed using a Speraman rank correlation. These results showed rs=0.778.
FIGS. 4A-4C include sequences from Borrelia sp. FIG. 4A includes sequences showing three exemplary VOVO antigens for Borrelia burgdorferi (Bb, SEQ ID NO: 1), Borrelia garinii (Bg, SEQ ID NO: 2), and Borrelia afzelii (Ba, SEQ ID NO: 3). FIG. 4B includes sequence alignments of VslE (“V” fragments) peptide sequences from Borrelia burgdorferi (Bb SEQ ID NO: 4 and 5), Borrelia garinii (Bg, SEQ ID NO: 6), and Borrelia afzelii (Ba, SEQ ID NO: 7 and 8). Alignments shows sequence homology within the group of sequences and pairwise homology between pairs of sequences. FIG. 4C includes a sequence fragment of the OspC (“0” fragment) peptide present in Borrelia burgdorferi, Borrelia garinii, and Borrelia afzelii (SEQ ID NO: 9). FIG. 4B discloses SEQ ID NOS 4-8, 4-6, 4-5, 7, 4-5 and 8, respectively, in order of appearance.
FIG. 5 is a schematic of the pREN2 mammalian expression vector. Features indicated are CMV (cytomegalovirus) promoter, the N-terminal FLAG epitope and Ruc. Sequences for Ruc are in bold. cDNAs for tumor antigens were cloned downstream of Ruc between the BamHI-XhoI sites. Sequences of the FLAG-epitope operably linked to luciferase (SEQ ID NO: 10 and 11) and the multiple cloning site (SEQ ID NO: 12 and 13) are provided. (Plasmid is described in Burbelo et al., 2005. BMC Biotechnology. 5:22, which is hereby incorporated by reference).



DEFINITIONS
“Antigenic fragment” and the like are understood as at least that portion of an antigen capable of being recognized and specifically bound by an antibody present in a subject having or suspected of having an infection, particularly a Borrelia sp., particularly when the antigen includes a partial sequence of consecutive amino acids of at least one of VslE and OspC antigens. When the antigen is a polypeptide, epitopes can be formed both from contiguous amino acids and noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained upon protein denaturing, whereas epitopes formed by tertiary folding are typically lost upon protein denaturing. Typically, antigenic fragments include at least 3, and more usually, at least 4, 5, 6, 7, 8, or 10 amino acids in a unique spatial conformation. Moreover, common epitopes for antigens have been mapped and can be used as antigenic fragments in the compositions and methods provided herein. Antigenic fragments can include deletions of the amino acid sequence from the N-terminus or the C-terminus, or both. For example, an antigenic fragment can have an N- and/or a C-terminal deletion of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, or more amino acids. Antigenic fragments can also include one or more internal deletions of the same exemplary lengths. Antigenic fragments can also include one or more point mutations, particularly conservative point mutations. In addition, an antigenic fragment (e.g., a protein) can include the full length, wild-type sequence of the antigen. An antigenic fragment can include more than one potential antibody binding site.
As used herein, “binding” is understood as having at least a 102 or more, 103 or more, preferably 104 or more, preferably 105 or more, preferably 106 or more preference for binding to a specific binding partner as compared to a non-specific binding partner (e.g., binding an antigen to a sample known to contain the cognate antibody). That an antibody “specifically binds” to an antigen, epitope or protein means that the antibody reacts or associates more frequently, more rapidly, with greater duration, with greater affinity, or with some combination of the above to an antigen, epitope or protein than with alternative substances, including unrelated proteins.
As used herein, “Borrelia sp.” is understood as any Borrelia species known to cause Lyme disease, for example, Borrelia burgdorferi (Bb), Borrelia afzelii, Borrelia garinii, and Borrelia valaisiana. 
As used herein, “changed as compared to a control” sample or subject is understood as having a level of the analyte or diagnostic or therapeutic indicator to be detected at a level that is statistically different than a sample from a normal, untreated, or control sample. Control samples include, for example, cells in culture, one or more laboratory test animals, or one or more human subjects. Methods to select and test control samples are within the ability of those in the art. An analyte can be a naturally occurring substance that is characteristically expressed or produced by the cell or organism (e.g., an antibody, a protein) or a substance produced by a reporter construct (e.g, β-galactosidase or luciferase). Depending on the method used for detection the amount and measurement of the change can vary. Changed as compared to a control reference sample can also include a change in one or more signs or symptoms associated with or diagnostic of Borrelia sp. infection. Determination of statistical significance is within the ability of those skilled in the art, e.g., the number of standard deviations from the mean that constitute a positive result.
As used herein, the terms “comprises,” “comprising,” “containing,” “having” and the like can have the meaning ascribed to them in U.S. patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments. As used herein in reference to antigenic polypeptides, “consisting essentially of” is understood as an antigenic polypeptide sequence including the claimed sequence, and optionally further containing other elements or optionally having shorter amino acid sequences than presented that do not materially affect the basic and novel characteristics of the antigenic polypeptide. That is, other elements or deletion of sequences that neither substantially inhibit or enhance binding of the peptide to cognate antibodies in a subject sample, or decrease the specificity of the binding of the antigen to a subject sample. In certain embodiments, antigenic fragments of longer polypeptides can be expressed to include an initiator methionine, a signal sequence for translocation of the protein, or may include sequences at the N- or C-terminus after cleavage with a protease not present in the native sequence. As used herein, a polypeptide consisting essentially of an antigenic fragment can be linked covalently (e.g., by a peptide bond or other linkage) to a second polypeptide, for example a reporter polypeptide, or an epitope tag (e.g., a FLAG tag). In an antigen with multiple domains or binding sites, the antigenic domains can be covalently linked by any type of linkage that does not disrupt binding to the antigenic site, e.g., through any of a number of chemical covalent linkages (e.g., cross-linking reagents commercially available from Pierce, a part of Thermo Fisher Scientific, and other sources), or through peptide bonds, including peptide sequences typically referred to as linker sequences or peptide linkers.
“Contiguous” is understood as touching or connected to through an unbroken sequence.
“Detect” refers to identifying the presence, absence or amount of the analyte to be detected.
By “diagnosing” and the like as used herein refers to a clinical or other assessment of the condition of a subject based on observation, testing, or circumstances for identifying a subject having a disease, disorder, or condition based on the presence of at least one indicator, such as a sign or symptom of the disease, disorder, or condition. Typically, diagnosing using the method of the invention includes the observation of the subject for multiple indicators of the disease, disorder, or condition in conjunction with the methods provided herein. A diagnostic methods provide an indicator that a disease is or is not present. A single diagnostic test typically may not provide a definitive conclusion regarding the disease state of the subject being tested.
As used herein, “epitope tag” is understood as a peptide sequence unrelated to the peptide to which it is attached that provides a specific antigen (e.g., myc tag, HAI tag, FLAG tag) or binding site (e.g., GST, 6×His (SEQ ID NO: 14)) for which a commercially available reagent (e.g., monoclonal antibody, affinity matrix) is available to facilitate isolation of a molecule including the epitope tag.
As used herein, the terms “identity” or “percent identity”, refers to the subunit sequence similarity between two polymeric molecules, e.g., two polynucleotides or two polypeptides. When a subunit position in both of the two molecules is occupied by the same monomeric subunit, e.g., if a position in each of two peptides is occupied by serine, then they are identical at that position. The identity between two sequences is a direct function of the number of matching or identical positions, e.g., if half (e.g., 5 positions in a polymer 10 subunits in length), of the positions in two peptide or compound sequences are identical, then the two sequences are 50% identical; if 90% of the positions, e.g., 9 of 10 are matched, the two sequences share 90% sequence identity. The identity between two sequences is a direct function of the number of matching or identical positions. Thus, if a portion of the reference sequence is deleted in a particular peptide, that deleted section is not counted for purposes of calculating sequence identity. Identity is often measured using sequence analysis software e.g., BLASTN or BLASTP (available at www.ncbi.nih.gov/BLAST). Additional, computer programs for determining identity are well-known in the art.
As used herein, “immunoassay” includes any of a number of antibody based assays including LIPS, ELISA, RIA, immunoprecipitation assay, dot blot, slot blot, immunofluorescence, and immunohistochemistry. In certain embodiments, immunoassay does not include western blots.
As used herein, “isolated” or “purified” when used in reference to a polypeptide or nucleic acid means that a naturally occurring polypeptide or nucleic acid has been removed from its normal physiological environment (e.g., protein isolated from plasma or tissue, optionally bound to another protein) or is synthesized in a non-natural environment (e.g., artificially synthesized in an in vitro transcription or translation system or using chemical synthesis, fragments amplified by PCR and/or generated by restriction digest). Thus, an “isolated” or “purified” polypeptide can be in a cell-free solution or placed in a different cellular environment (e.g., expressed in a heterologous cell type). The term “purified” does not imply that the polypeptide is the only polypeptide present, but that it is essentially free (about 90-95%, up to 99-100% pure) of cellular or organismal material naturally associated with it, and thus is distinguished from naturally occurring polypeptide. Similarly, an isolated nucleic acid is removed from its normal physiological environment. “Isolated” when used in reference to a cell means the cell is in culture (i.e., not in an animal), either cell culture or organ culture, of a primary cell or cell line. Cells can be isolated from a normal animal, a transgenic animal, an animal having spontaneously occurring genetic changes, and/or an animal having a genetic and/or induced disease or condition. An isolated virus or viral vector is a virus that is removed from the cells, typically in culture, in which the virus was produced.
By “agent” is meant any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragments thereof.
As used herein, “kits” are understood to contain at least one non-standard laboratory reagent for use in the methods of the invention in appropriate packaging, optionally containing instructions for use. The kit can further include any other components required to practice the method of the invention, as dry powders, concentrated solutions, or ready to use solutions. In some embodiments, the kit comprises one or more containers that contain reagents for use in the methods of the invention; such containers can be boxes, ampules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding reagents.
As used herein, a “nucleic acid encoding a polypeptide” is understood as any possible nucleic acid that upon (transcription and) translation would result in a polypeptide of the desired sequence. The degeneracy of the nucleic acid code is well understood. Further, it is well-known that various organisms have preferred codon usage, etc. Determination of a nucleic acid sequence to encode any polypeptide is well within the ability of those of skill in the art.
As used herein, “operably linked” is understood as joined, preferably by a covalent linkage, e.g., joining an amino-terminus of one peptide; expressing an enzyme to a carboxy terminus of another peptide; expressing a signal sequence to target the protein to a specific cellular compartment; or joining a promoter sequence with a protein coding sequence, in a manner that the two or more components that are operably linked either retain their original activity, or gain an activity upon joining such that the activity of the operably linked portions can be assayed and have detectable activity, e.g., enzymatic activity or protein expression activity.
As used herein, “plurality” is understood to mean more than one. For example, a plurality refers to at least two, three, four, five, or more.
As used herein, “peptide linker” and the like are understood to be amino acid sequences of essentially any length (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acids) and are relatively non-antigenic. Peptide linker sequences can be encoded by nucleic acid sequences between nucleic acid sequences encoding functional components of the peptide, e.g., antigenic peptide sequences, reporter peptide sequences, epitope tag sequences, etc. Alternatively, peptide linkers can be short peptide sequences including reactive groups, typically at the termini of the peptide that can be used to join the linker sequences to peptides to allow them to be covalently linked.
A “polypeptide” or “peptide” as used herein is understood as two or more independently selected natural or non-natural amino acids joined by a peptide bond. A peptide can include 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more natural or non-natural amino acids joined by peptide bonds. Polypeptides as described herein include full length proteins (e.g., fully processed proteins), shorter amino acids sequences (e.g., fragments of naturally occurring proteins or synthetic polypeptide fragments), or artificial peptide sequences composed of naturally occurring and/or non-naturally occurring peptide sequences.
As used herein, a “reporter protein” or a “reporter polypeptide” is understood as a polypeptide that can be readily detected, preferably quantitatively detected, either directly or indirectly. A reporter polypeptide typically has an enzymatic activity, luciferase activity, alkaline phosphatase activity, beta-galactosidase activity, acetyl transferase activity, or the like, wherein catalysis of a reaction with a substrate by the enzyme results in the production of a product, e.g., light, that can be detected at a specific wavelength of light, radioactivity, or the like, such that the amount of the reporter peptide can be determined in the sample, either as a relative amount, or as an absolute amount by comparison to control samples.
A “sample” as used herein refers to a biological material that is isolated from its environment (e.g., blood or tissue from an animal, cells, or conditioned media from tissue culture) and is suspected of containing, or known to contain an analyte, such as an antibody. A sample can also be a partially purified fraction of a tissue or bodily fluid (e.g., serum or plasma). A reference sample or a control sample can be a sample from a donor not having the disease or condition, including fluid or tissue from a subject. A reference or control sample can also be from an untreated donor or cell culture not treated with an active agent (e.g., no treatment or administration of vehicle only). A reference or control sample can also be taken at a time point prior to contacting the cell or subject with an agent or therapeutic intervention to be tested or at the start of a prospective study.
“Sensitivity and specificity” are statistical measures of the performance of a binary classification test. The sensitivity (also called recall rate in some fields) measures the proportion of actual positives which are correctly identified as such (e.g., the percentage of sick people who are identified as having the condition); and the specificity measures the proportion of negatives which are correctly identified (e.g., the percentage of well people who are identified as not having the condition). They are closely related to the concepts of type I and type II errors. A theoretical, optimal prediction can achieve 100% sensitivity (i.e., predict all people from the sick group as sick) and 100% specificity (i.e., not predict anyone from the healthy group as sick).
The concepts are expressed mathematically as follows:

sensitivity=# true positives/# true positives+# false negatives

specificity=# true negatives/# true negatives+# false positives.

A “subject” as used herein refers to an organism. In certain embodiments, the organism is an animal. In certain embodiments, the subject is a living organism. In certain embodiments, the subject is a cadaver organism. In certain preferred embodiments, the subject is a mammal. In certain embodiments, the subject is a domesticated mammal or a primate including a non-human primate. In certain preferred embodiments, the subject is a mammal that is capable of being infected by a sp. Borrelia pathogen. Examples of subjects include humans, monkeys, dogs, cats, mice, rats, cows, horses, goats, and sheep. A human subject may also be referred to as a patient.
A “subject sample” can be a sample obtained from any subject, typically a blood or serum sample, however the method contemplates the use of any body fluid or tissue from a subject. The sample may be obtained, for example, for diagnosis of a specific individual for the presence or absence of sp. Borrelia pathogen infection. In certain embodiments, a subject sample can be a sample for screening of a subject tissue (solubilized or treated to release antibodies) or body fluid (e.g., blood, serum, plasma) prior to transplant or transfusion into a recipient.
A subject “suffering from,” “suspected of suffering from,” or “having” a specific disease, condition, or syndrome has a sufficient number of risk factors or presents with a sufficient number or combination of signs or symptoms of the disease, condition, or syndrome such that a competent individual would diagnose or suspect that the subject has the disease, condition, or syndrome. Methods for identification of subjects suffering from or suspected of suffering from conditions such as sp. Borrelia pathogen infection is within the ability of those in the art. Subjects suffering from, and suspected of suffering from, a specific disease, condition, or syndrome are not necessarily two distinct groups.
As used herein, “susceptible to” or “prone to” or “predisposed to” a specific disease or condition and the like refers to an individual who based on genetic, environmental, health, and/or other risk factors is more likely to develop a disease or condition than the general population. An increase in likelihood of developing a disease may be an increase of about 10%, 20%, 50%, 100%, 150%, 200%, or more.
As used herein, a “VOVO antigen” is understood as an antigen that includes isolated peptides having sequences of at least one of SEQ ID NO: 4-8 and SEQ ID NO: 9. The peptides can be separate peptides. The peptides can be linked directly by a covalent linkage such as a peptide bond. The peptides can be linked by a peptide linker sequence. Peptide sequences of SEQ ID NO: 4-9 are identical to or significantly identical to portions of the VlsE C6 and OspC peptides of a Borrelia sp. bacteria, particularly one of Borrelia burgdorferi (Bb), Borrelia garinii (Bg), Borrelia afzelii (Ba), and Borrelia valaisiana. The VOVO antigens provided herein are based on protein sequences of one of the Borrelia sp. However, VOVO antigens can include sequences from more than one Borrelia sp. An exemplary Borrelia burgdorferi VOVO antigen composition includes at least the peptide sequences amino acids 1-26 of SEQ ID NO: 1 (i.e., SEQ ID NO: 4), a fragment corresponding to the VlsE-Δ1 protein; amino acids 30-40 of SEQ ID NO: 1 (i.e., SEQ ID NO: 5), a fragment corresponding to the OspC protein; and amino acids 41-65 of SEQ ID NO: 1 (i.e., SEQ ID NO: 9), a fragment corresponding to the VlsE-Δ2 protein; and/or a composition that has a peptide sequence that is at least 80%, optionally at least 85% identical, at least 90% identical, or at least 95% identical to SEQ ID NO: 1, wherein a 10-fold molar excess of the peptide or a combination of the peptide sequences, inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 1 to a sample from a subject suffering from an infection by a Borrelia burgdorferi pathogen. Competition assays can be performed using any method known in the art, for example, using a BIACORE device.
Similarly, an exemplary Borrelia garinii (Bg) VOVO antigen can include isolated peptide sequences SEQ ID NO: 6 and SEQ ID NO: 9; and/or a composition that has a peptide sequence that is at least 80%, optionally at least 85% identical, at least 90% identical, or at least 95% identical to SEQ ID NO: 2, wherein a 10-fold molar excess of the peptide or a combination of the peptide sequences, inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 2 to a sample from a subject suffering from an infection by a Borrelia garinii pathogen.
Similarly, an exemplary Borrelia afzelii (Ba) VOVO antigen can include isolated peptide sequences SEQ ID NO: 7 or 8 and SEQ ID NO: 9; and/or a composition that has a peptide sequence that is at least 80%, optionally at least 85% identical, at least 90% identical, or at least 95% identical to SEQ ID NO: 3, wherein a 10-fold molar excess of the peptide or a combination of the peptide sequences, inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 3 to a sample from a subject suffering from an infection by a Borrelia afzelii pathogen.
A VOVO antigen can also be generated for detection of Borrelia sp. infection from any combination of Borrelia burgdorferi, Borrelia afzelii, Borrelia garinii, and Borrelia valaisiana for the detection of Lyme disease. The VOVO antigen can be a mixed VOVO antigen including a mixture of any combination of peptides having at least 80% sequence identity to each of SEQ ID NO: 1, 2, or 3, wherein a 10-fold molar excess of the peptide inhibits binding of at least 50% of a peptide comprising the corresponding amino acid sequence of SEQ ID NO: 1, 2, or 3 to a sample from a subject suffering from an infection by the corresponding species of Borrelia. In certain embodiments, a generic Borrelia sp. VOVO antigen can be prepared using a combination of isolated peptide sequences of at least one of SEQ ID NO: 4 or 5; SEQ ID NO: 6; at least one of SEQ ID NO: 7 or 8; and SEQ ID NO: 9, wherein a 10-fold molar excess of the peptide or a combination of the three peptide sequences, inhibits binding of at least 50% of a peptide comprising the amino acid sequence of SEQ ID NO: 1, 2, or 3 to a sample from a subject suffering from an infection by a Borrelia burgdorferi (Bb) pathogen, Borrelia garinii (Bg) pathogen, or a Borrelia afzelii (Ba) pathogen, respectively.
The VOVO antigen can be a mixture of peptides, optionally wherein the peptides are covalently linked to each other (e.g., peptide bond). In certain embodiments, the mixed VOVO antigen is expressed from a single nucleic acid. A mixed VOVO antigen need not be designed for use in the diagnosis of all Borrelia sp. infections. In certain embodiments, the mixed VOVO antigen can be an antigen for detection of both Borrelia sp. present in Eurasia (Borrelia afzelii and Borrelia garinii). A subject will typically know if a potential Lyme infection was picked up in the US or Eurasia. However, a single test to detect antibodies to any of the species of Borrelia known to cause Lyme disease could allow for the use of a single test internationally.
The fragments corresponding to each of the VlsE and OspC peptides can be mixed together and used in an immunoassay. When the peptides are expressed separately, preferred assay methods include those in which the antigen is bound to a solid surface prior to contacting the antigen with a serum sample (e.g., ELISA assay). The combination of the sequences in close proximity to each other allows for the binding of the polyclonal antibodies produced in an immune response to bind to more than one site on the surface on which the antigens are coated, increasing the apparent affinity of the antibodies. When binding of the antigens to the antibodies present in serum is performed in solution (e.g., in an immunoprecipitation assay such as a LIPS assay), it is preferred that the peptide sequences are covalently linked to each other. A peptide including all of the fragments can be easily produced using an expression construct in which the three sequences corresponding to a fragment of each of the VlsE-Δ1, VlsE-Δ2, and OspC from the desired Borrelia sp. joined in frame, optionally by linker sequences, and operably linked to a promoter sequence appropriate for the system in which the protein is to be expressed. Although the VOVO peptide exemplified in the instant application includes domains in the following order: VlsE-Δ1, OspC, VlsE-Δ2, and OspC, it is understood that any combination or order of the fragments of the protein sequences is possible, e.g., VlsE-Δ1-VlsE-Δ21-OspC; VlsE-Δ1-OspC-VlsE-Δ2; OspC-VlsE-Δ1-VlsE-Δ2; VlsE-Δ2-VlsE-Δ1-OspC; VlsE-Δ2-OspC-VlsE-Δ1; OspC-VlsE-Δ2-VlsE-Δ1; etc. Analogous combinations can be made based on the sequences SEQ ID NO: 6 and 9. Analogous combinations can be made based on the sequences SEQ ID NO: 7, 8, and 9. It is understood that more than three fragments can be joined together (e.g., 4, 5, 6, 7, 8, 9, 10, etc.), e.g., to facilitate expression of the peptide sequences, provide desired stoichiometry and/or relative positions of the fragments, etc. It is understood that VlsE-Δ1, VslE Δ2, and OspC fragments from different Borrelia sp. can be mixed or joined together. It is further understood that VOVO antigens can be linked to other protein sequences, e.g., reporter constructs, epitope tags, etc.
In an alternative embodiment, the “V” and/or “O” fragments can be expressed with an epitope tag, e.g., a 6×His tag (SEQ ID NO: 14), and coated onto a bead for binding to antibodies present in sera.
In an alternative embodiment, the “V” and/or “O” fragments can be joined using any of a number of commercially available cross-linking reagents. The fragments can be joined in any order or any orientation as long as the linking agents do not disrupt binding of the antibodies to the antigen.
Other methods for joining the “V” and/or “O” fragments are well-known to those of skill in the art.
Ranges provided herein are understood to be shorthand for all of the values within the range. This includes all individual sequences when a range of SEQ ID NOs is provided. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive.
Unless specifically stated or obvious from context, as used herein, the terms “a”, “an”, and “the” are understood to be singular or plural.
Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein can be modified by the term about.
The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.
DETAILED DESCRIPTION OF THE INVENTION
Currently, there is a need for sensitive and specific testing to identify and monitor Lyme-infected individuals. A variety of immunoassays, including immunofluorescence assays, Western blot, and ELISAs have been employed to detect antibodies to Bb proteins. One of the most useful approaches employs defined short peptides derived from VslE and OspC for testing (Bacon, et al., 2003. J Infect Dis 187:1187-99; Embers, et al., 2007. Clin Vaccine Immunol 14:931-6; Liang, et al., 1999. J Immunol 163:5566-73; and Liang, et al., 1999. J Clin Microbiol 37:3990-6). For example, the most sensitive ELISA using the C6 peptide of VslE, matches the 2-tiered Western blotting in sensitivity and specificity. While there is an interest in using the C6 ELISA and other serological tests for monitoring antibiotic therapy of Lyme infected patients, these studies are hampered by the limited dynamic range of these solid phase immunoassays and the need for time consuming and cumbersome serum dilutions to obtain values in the linear range (Fleming, et al., 2004. Eur J Clin Microbiol Infect Dis 23:615-8; Levy, et al., 2008. Clin Vaccine Immunol 15:115-9; Philipp, et al., 2003. J Clin Microbiol 41:4955-60; and Philipp, et al., 2005. Clin Diagn Lab Immunol 12:1069-74).
The serological laboratory tests most widely available and employed are the Western blot and ELISA. A two-tiered protocol is recommended by the CDC: the sensitive ELISA test is performed first, and if it is positive or equivocal then the more specific Western blot is run (Wilske et al. 2005. Ann. Med. 37: 568-79). However, Western blots are cumbersome, rarely used in clinical laboratories making the tests more inconvenient, and are not adaptable to high throughput methods. The reliability of testing in diagnosis remains controversial, however, studies show that the IgM Western blot has a specificity of 94-96% for patients with clinical symptoms of early Lyme disease. The initial ELISA test has a sensitivity of about 70%, and in two tiered testing, the overall sensitivity is only 64% although this rises to 100% in a subset of people with disseminated symptoms, such as arthritis.
Luciferase Immunoprecipitation System (LIPS) is a highly sensitive immunoprecipitation technology that utilizes mammalian cell-produced, recombinant fusion protein antigens for efficiently evaluating antibody responses (see US Patent Publication 2007/0259336 and Burbelo et al. 2005. BMC Biotechnol. 5:22, which are hereby incorporated by reference). LIPS shows strong diagnostic performance for detecting antibodies to infectious agents (e.g., HCV, HIV, HTLV-I, and filarial infectious agents) and provides new tools to monitor drug treatment and sub-stratify disease states. LIPS is highly useful for profiling autoimmunity and in one study showed several advantages over a highly sensitive radioactive in vitro transcription/translation assay for detecting anti-IA2 autoantibodies associated with type I diabetes.
LIPS is based on fusing protein antigens to a light emitting enzyme reporter, Renilla luciferase (Ruc), and then using these antigens in immunoprecipitation assays with sera samples and Protein A/G beads. Following washing, light production is measured yielding highly quantitative antibody titers. While LIPS has already shown high sensitivity for detecting fungal, helminthic, filarial, and a variety of viral infection agents, its utility to accurately evaluate humoral responses to bacterial pathogen antigens has not been assessed. As described below, LIPS was used to evaluate antibody responses to a panel of Bb antigens for the serological diagnosis of Lyme disease. Following the evaluation of the training set, several antigens including VslE, DbpA, Dbp-B, BMP, and FlaB, showed high performance. Nevertheless, the antigen with the greatest dynamic range of detection and highest sensitivity and specificity was composed of a synthetic gene (designated VOVO) containing 2 alternating copies of immunoreactive peptides derived from VslE and OspC antigens. Analysis of an independent validation serum set with VOVO showed 94% sensitivity and 100% specificity, and markedly out-performed the C6 ELISA. Without serum dilution, LIPS also showed a wide dynamic range of detection making it a practical tool for accurately quantifying anti-Lyme antibodies. These results demonstrate that an immunoassay based on the VOVO antigen, preferably LIPS screening with VOVO antigen, optionally with other Borrelia sp. proteins (e.g., VslE-Δ1 (Accession No: GU182319), VslE-Δ2 (Accession No: GU182320); Fla (GenBank AAC66541); Bmp (GenBank NP_212517); Dbp (GenBank AAC70025), DBpA (GenBank YP002455347), OspC2-Δ1 (GenBank NP_047005)) or fragments therefrom, is an efficient high-throughput method for accurately determining anti-Lyme patient antibody responses, including without serum dilution.
The test can be used as part of a routine screening panel for sp. Borrelia pathogen progression or regression in a subject by detecting binding of antibodies to VOVO antigens.
Further, the method can be used for monitoring donated blood, organs, and/or tissues for the presence of sp. Borrelia pathogen infection.
EXAMPLES
It should be appreciated that the invention should not be construed to be limited to the examples that are now described; rather, the invention should be construed to include any and all applications provided herein and all equivalent variations within the skill of the ordinary artisan.
Example 1
Material and Methods
Patient Sera.
Serum was obtained from patients or volunteers under institutional review board approved protocols at the Clinical Center, National Institute of Allergy and Infectious Diseases, NIH. The initial training set (n=46) included serum from 11 EM, 8 multiple erythema migrans (MEM), 2 Lyme palsy, 6 Lyme arthritis, 1 late Lyme neuroborreliosis, 10 post-Lyme disease syndrome (PLDS) subject samples, and 8 uninfected control sera subject samples were analyzed. Testing of the validation set consisted of 225 coded serum samples. This validation cohort consisted of 59 control sera and 141 samples from patients with established Lyme disease. The codes for the validation cohort was broken only after titers were established and categorization of Lyme infection status had been made. The antibody titer results for the validation cohort obtained by LIPS was also compared with the C6 ELISA. Of note, an additional 40 samples with uncertain diagnosis for Lyme disease were also analyzed by LIPS and the C6 ELISA, but were not used in calculation of sensitivity and specificity.
Generation of Ruc-Antigen Fusion Constructs.
pREN2, a mammalian Renilla luciferase (Ruc) expression vector, was used to generate all plasmids (FIG. 3). Bb genes were amplified by PCR specific linker-primer adapters using synthetic cDNA templates assembled in the investigators laboratory or obtained from Blue Heron Biotechnology (Seattle, Wash.). Gene-specific primers were then used in PCR amplifications for generating cDNA sequences for cloning as C-terminal fusions of Ruc. For each C-terminal fusion, a stop codon was included at the end of the coding sequence. The nucleotide and protein sequence for VOVO has GenBank Accession number GU134803. The peptide encoded by VOVO is MKKDDQIAAAIALRGMAKDGKFAVKELTSPVVA ESPKKPMKKDDQIAAAMVLRGMAKDGQFALKPVVAESPKKP (SEQ ID NO: 15), in which the peptide sequence from VslE is underlined and the peptide sequence from OspC is in italics. Two constructs, VslE-Δ1 and VslE-Δ2, containing the VslE peptide sequences have GenBank Accession sequences GU182319 and GU182320 were also tested. DNA sequencing was used to confirm the integrity of all the DNA constructs. Plasmid DNA was then prepared from the different pREN2 expression vectors using a Qiagen Midi preparation kit.
LIPS Analysis.
Following transfection of mammalian expression vectors, crude protein extracts were obtained as described in Burbelo, et al. 2008. Biochem Biophys Res Commun 366:1-7, which is hereby incorporated by reference. A detailed protocol of the LIPS assay is now available along with a corresponding technical video from the Journal of Visualized Experiments (Burbelo et al., 2009, J. Vis. Exp. www.jove.com/index/Details.stp?ID=1549).
Data Analysis.
The GraphPad Prism software (San Diego, Calif.) was used for statistical analysis. Results for qualitative antibody titers between the controls and Bb-infected individuals are reported as the mean+5 standard deviation (SD). Mann-Whitney U tests were used to compare the antibody titers among the groups.
Example 2
LIPS Detection of Antibody Responses to a Panel of Bb Antigens
Previous studies from various laboratories have identified a large number of Bb antigens useful for serological screening of Lyme disease. Fifteen different Bb antigens including FlaB, BMP, Dbp-A, DbpB, OspC, OspA, Bbk and 2 different VlsE constructs were initially synthetically assembled and constructed as C-terminal fusion with Ruc. LIPS evaluation of these different antigens began by testing a small cohort of serum samples (n=44) consisting of serum from 11 EM, 8 MEM, 2 Lyme palsy, 6 Lyme arthritis, 1 late Lyme neuroborreliosis, 10 PLDS subjects, and 8 uninfected control subject serum samples. To easily visualize the differing immunoreactivity to this large antigen panel, we employed our previously described heat map analysis to graphically display the antibody responses using a login scale to the most informative antigens (FIG. 1A). From these tests, 6 of these Bb proteins showed weak or non-existent antibody signals (BBk, OspA, OspF, Crasp, OspC, DbpA (with signal peptide), while 7 others (VlsE-Δ1, VlsE-Δ2; Fla; Bmp; DbpA without signal peptide, DbpB without signal peptide, OspC2-Δ1 without signal peptide) showed high levels of immunoreactivity with over 50% of the Lyme samples (FIG. 1A). Based on the mean plus 5 standard deviations, the most informative antigen in the initial panel was VlsE-Δ1 and was followed by VslE-Δ2. Other antigens such as DbpA and Dbp-B showed nearly identical serological activity but were less sensitive.
Next, a new synthetic antigen was generated and tested. This new antigen was synthetically assembled in one recombinant protein. The new antigen was designated VOVO and contained 2 alternating copies of immunoreactive peptides derived from VslE and OspC antigens. The rational behind VOVO's design was that the repeated antigenic peptides from the 2 different proteins might increase the valency, and thereby apparent affinity, and capture low affinity antibodies. From LIPS testing, VOVO appeared to be an effective antigen. Without wishing to be bound by mechanism, it is suggested that the use of the fragments provided herein allows for the unmasking of hidden or cryptic immunodominant antigen sequences to allow for binding of serum antibodies. The mean anti-VOVO antibody titer in the 38 Lyme samples was 1,716,000 LU and was over 1000-fold higher than antibody titer of 1,395 LU in the controls (Mann Whitney U test, P<0.0017). Using a cut-off derived from the mean plus 3 SD of the controls, 84% of the Lyme samples were VOVO positive and all the sera from uninfected controls were negative (FIG. 1B), Only a few serum samples including 1 PLDS and 4 EM samples were seronegative for anti-VOVO antibodies, which were also negative by C6 ELISA. These promising results indicate that VOVO is a highly useful antigen for LIPS screening of Lyme sera, including in the early stage after infection, e.g., within 1-2 weeks of infection.
Example 3
Using VOVO with a New Independent Validation Cohort
To test the effectiveness of VOVO and compare it with the C6 ELISA, a new validation cohort of 225 blinded sera were evaluated. Following breaking the code, the LIPS antibody titer data were analyzed. Similar to the training set, the mean anti-VOVO antibody titer in the 141 Lyme samples was 589,200 LU and was markedly higher than antibody titer of 537 LU in the 59 controls (Mann Whitney U test, P<0.0017). In order to determine the sensitivity and specificity, a diagnostic cut-off 5 value of LU based on the mean plus 5 SD of the control samples was used. Using this cut-off, the VOVO LIPS test showed 94% sensitivity and 100% specificity with these samples (FIG. 2A). The C6 ELISA had a markedly lower diagnostic performance of 76% sensitivity and 98% specificity. ROC analysis showed that the area under the curves for antibodies to LIPS and C6 ELISA were statistically different (p=0.005). The VOVO LIPS tests also had a markedly greater dynamic range of detection (FIG. 2A) and did not require dilution. However, as shown in FIG. 2B, correlation of log10 transformed LIPS values with the C6 ELISA values showed that both assays tracked each other (rs=0.82, p<0.00001).
Example 4
Generation of a VOVO Antigen for Detection of Antibodies to Other Borrelia Sp
Based on the analysis performed for antigens of Bb, antigens were selected based on homology with the VslE sequences selected above from other Borrelia sp. See FIG. 4A-B. Alignments of the Bb VslE-Δ1 and VslE-Δ2 antigen sequences against sequences from VslE proteins from one B. garinii and two B. afzelii sequences are shown in FIG. 4B. The OspC fragment sequence in the Bb VOVO antigen has the same sequence as is found in B. garinii and two B. afzelii. As such, these sequence alignments indicate that B. garinii and B. afzelii can be useful in the context of a VOVO antigen for detection of infection with a pathogen from those species.
Upon generation of VOVO antigens for B. garinii and B. afzelii, the antigens are validated using the method provided in the example above. A set of samples from subjects known to have been infected with either B. garinii or B. afzelii are analyzed for binding to the VOVO antigen. The samples are then unblinded the sensitivity and specificity of the test are analyzed. In addition, an assay to detect infection by B. garinii or B. afzelii using the VOVO antigen containing Bb sequences can be tested to determine if there is sufficient cross-reactivity to allow the antigens to be used cross-species.
Alternatively, other proteins from B. garinii and B. afzelii are tested for their utility as diagnostic antigens. For example, full length proteins and fragments of B. garinii and B. afzelii proteins FlaB, BMP, Dbp-A, DbpB, OspC (FIG. 4C), OspA, Bbk, and VslE are tested for their utility as antigens for detection of infection with B. garinii or B. afzelii. 
All references, patents, patent applications, and GenBank numbers as of the date of filing of the instant application are hereby incorporated by reference as if they were each incorporated individually.








Borrelia afzelii - OspC



(SEQ ID NO: 16)



MKKNTLTAILMTLFLFISCNNSGKVGILTSTNPADESAKGPNLTEISKKITDSNAFVLAVKEVETLVLSIDELAK



 


KAIGQKIDNNNGLAALNNQNGSLLAGAYAISTLITEKLSKLKNLEELKTEIAKAKKCSEEFTNKLKSGHADLGKQ


 


DATDDHAKAAILKTHATTDKGAKEFKDLFESVEGLLKAAQVALTNSVKELTSPVVAESPKKP*


 


Borrelia burgdorferi - OspC


(SEQ ID NO: 17)



MKKNTLSAILMTLFLFISCNNSGKDGNTSANSADESVKGPNLTEISKKITDSNAVLLAVLEVEALLSSIDEIAAK



 


AIGKKIHQNNGLDTENNHNGSLLAGAYAISTLIKQKLDGLKNEGLKEKIDAAKKCSETFTNKLKEKHTDLGKEGV


 


TDADAKEAILKTNGTKTKGAEELGKLFESVEVLSKAAKEMLANSVKELTSPVVAESPKKP*


 


Borrelia garinii - OspC


(SEQ ID NO: 18)



mkkntlsail mtlflfiscn nsggdtastn pdesakgpnl tviskkitds nafvlavkev



 


ealissidel ankaigkvih qnnglnanag qngsllagay aistlitekl sklknseeln


 


kkieeaknhs eaftnrlkgs haqlgvaaat ddhakeailk snptkdkgak elkdlsesve


 


slakaaqeal ansvkeltnp vvaespkkp


 


FlaB (flagellin; p41)


Amino acids 20-336 of B.B. B31 strain (GenBank AAC66541)


(SEQ ID NO: 19)



 20 anlsktqekl ssgyrinras ddaagmgvsg kinaqirgls



 


 61 gasrntskai nfiqttegnl nevekvlvrm kelavqsgng tysdadrgsi qieieqltde


 


121 inriadqaqy nqmhmlsnks asqnvrtaee lgmqpakint paslsgsqas wtlrvhvgan


 


181 qdeaiavniy aanvanlfsg egaqtaqaap vqegvqqega qqpapataps qggvnspvnv


 


241 tttvdantsl akienairmi sdqranlgaf qnrlesikns teyaienlka syaqikdatm


 


301 tdevvaattn siltqsamam iaqanqvpqy vlsllr*336


 


BmpA


Amino acids 26-339 of B.b. B31 strain (GenBank NP_212517)


(SEQ ID NO: 20)



 26 seipk vsliidgtfd dksfnesaln gvkkvkeefk



 


 61 ielvlkesss nsylsdlegl kdagsdliwl igyrfsdvak vaalqnpdmk yaiidpiysn


 


121 dpipanlvgm tfraqegafl tgyiaaklsk tgkigflggi egeivdafry gyeagakyan


 


181 kdikistqyi gsfadleagr svatrmysde idiihhaagl ggigaievak elgsghyiig


 


241 vdedqaylap dnvitsttkd vgralnifts nhlktntfeg gklinyglke gvvgfvrnpk


 


301 misfelekei dnlsskiink eiivpsnkes yekflkefi*339


 


DbpB


amino 25-280 of B.b. sensu lato (GenBank AAC70025)


(SEQ ID NO: 21)



 25 alesss kdlknkilki kkdatgkgvl feaftglktg



 


 61 skvtsgglal reakvqaive tgkflkiiee ealklketgn sgqflamfdl mlevvesled


 


121 vgiiglkarv leesknnpin taerllaaka qienqlkvvk ekqniengge kknnkskkkk*


 


DbpA


amino 33-194 of B.b. of Zs7 strain (GenBank YP_002455347)


(SEQ ID NO: 22)



 33 etkiiler sakdiidein kikkdaadnn



 


 61 vnfaafkedk tgskvsensf ileakmrgtt vaekfvtaie geatklkktg ssgefsamyn


 


121 mmlevsgple elgvlrmtkt vtdaaeqhpt ttaegileia ktmktklqrv htknycalkk


 


181 kenpsftdek cknn*194


 


OspC


amino acids 22-210 of B.b. B31 strain (GenBank NP_047005)


(SEQ ID NO: 23)



 22 sgkdgntsa nsadesvkgp nlteiskkit dsnavllavk



 


 61 eveallssid eiaakaigkk ihqnngldte nnhngsllag ayaistlikq kldglknegl


 


121 kekidaakkc setftnklke khtdlgkegv tdadakeail ktngtktkga eelgklfesv


 


181 evlskaakem lansvkelts pvvaespkkp*210


 


LOCUS GU182319 171 by DNA linear SYN 9 Feb. 2010









DEFINITION
Synthetic construct immunodominant VlsE protein (VslE-d1)




gene, partial cds.


ACCESSION
GU182319


VERSION
GU182319.1 GI:288189225


 








(SEQ ID NO: 24)



translation=“ADAAEQDGKKPEEAKNPIAAAIGDKDGDAEFNQDDMKKDDQIAAAIALRGMAKDGK”



 


ORIGIN


(SEQ ID NO: 25)



  1 gccgacgccg ccgagcagga cggcaagaag cccgaggagg ccaagaaccc catcgccgcc



 


 61 gccatcggcg acaaggacgg cgacgccgag ttcaaccagg acgacatgaa gaaggacgac


 


121 cagatcgccg ccgccatcgc cctgcgcggc atggctaagg atggaaagtg a


 


LOCUS GU182320 483 by DNA linear SYN 9 Feb. 2010









DEFINITION
Synthetic construct immunodominant VlsE protein(Vlse-d2)




gene, partial cds.


ACCESSION
GU182320


 








(SEQ ID NO: 26)



translation=“GAGKLFGKAGAAAHGDSEAASKAAGAVSAVSGEQILSAIVTAAD



 


AAEQDGKKPEEAKNPIAAAIGDKDGGAEFGQDEMKKDDQIAAAIALRGMAKDGKFAVK


 


DGEKEKAEGAIKGAAESAVRKVLGAITGLIGDAVSSGLRKVGDSVKAASKETPPALNK”


 


ORIGIN


(SEQ ID NO: 27)



  1 ggtgccggta agttgttcgg taaggctggt gccgcagcac acggtgatag tgaagccgcc



 


 61 tccaaggctg ccggtgctgt aagcgctgtc tccggtgaac aaatcttgtc cgctatagtt


 


121 accgctgccg atgcagctga acaagatggt aaaaagccag aagaagcaaa gaatcccatt


 


181 gctgctgcaa ttggtgataa ggatggtggt gccgaatttg gtcaagatga aatgaaaaag


 


241 gatgatcaaa tcgcagccgc catcgccctt cgcggtatgg ccaaagatgg taaatttgca


 


301 gttaaggatg gtgaaaaaga aaaagctgaa ggcgcaatta agggtgccgc tgaaagcgcc


 


361 gtacgcaagg tactcggtgc aattacgggt ctcattggtg atgcagtgag ctcaggtctg


 


421 cgcaaggtgg gtgatagtgt gaaagctgcc agcaaagaaa caccccccgc cctcaacaag


 


481 tag


 


LOCUS ADA82861 192 aa linear BCT 27 Jan. 2010









DEFINITION
VlsE [Borrelia burgdorferi].



ACCESSION
ADA82861


VERSION
ADA82861.1 GI:282555520


DBSOURCE
accession GQ506415.1


KEYWORDS
.


SOURCE
Borrelia burgdorferi (Lyme disease spirochete)


 








(SEQ ID NO: 28)



  1 egaikevsel ldklvkavkt aegassgtaa igevvadada akvadkasvk giakgikeiv



 


 61 eaaggseklk avaaakgenn kgagklfgka gaaahagdse aaskaagavs avsgeqilsa


 


121 ivtaadaaeq egkkpaeakn piaaaignkd ggaefgqdem kkddqiaaai alrgmakdgk


 


181 favkednkkg ka


 


(SEQ ID NO: 29)



  1 gagggggcta ttaaggaagt tagcgagttg ttggataagc tggtaaaagc tgtaaagaca



 


 61 gctgaggggg cttcaagtgg tactgctgca attggagaag ttgtggctga tgctgatgct


 


121 gcaaaggttg ctgataaggc gagtgtgaag gggattgcta aggggataaa ggagattgtt


 


181 gaagctgctg gggggagtga aaagctgaaa gctgttgctg ctgctaaagg ggagaataat


 


241 aaaggggcag ggaagttgtt tgggaaggct ggtgctgctg ctcatgctgg ggacagtgag


 


301 gctgctagca aggcggctgg tgctgttagt gctgttagtg gggagcagat attaagtgcg


 


361 attgttacgg ctgctgatgc ggctgagcag gagggaaaga agcctgcaga ggctaaaaat


 


421 ccgattgctg ctgctattgg gaataaagat gggggtgcgg agtttggtca ggatgagatg


 


481 aagaaggatg atcagattgc tgctgctatt gctttgaggg ggatggctaa ggatggaaag


 


541 tttgctgtga aggaggataa taagaaaggg aaggct


 


LOCUS AAN87831 174 aa linear BCT 7 Apr. 2003









DEFINITION
vls recombination cassette Vls7 [Borrelia garinii].



ACCESSION
AAN87831


VERSION
AAN87831.1 GI:29075690


DBSOURCE
accession AY100633.1


SOURCE
Borrelia garinii


 








ORIGIN



(SEQ ID NO: 30)



  1 asaatgnaai gdvvngdvak akggdaasvn giakgikgiv daaekadake gklnaagaeg



 


 61 ttnadagklf vknagnvgge agdagkaaaa vaavsgeqil kaivdaakdg gekqgkkaad


 


121 atnpidaaig gtndndaaaa fatmkkddqi aaamvlrgma kdgqfalkda aaah


 


ORIGIN


(SEQ ID NO: 31)



  1 gcaagtgctg ctactggtaa tgcagcgatt ggagatgttg ttaatggtga tgtggcaaaa



 


 61 gcaaaaggtg gtgatgcggc gagtgttaat gggattgcta aggggataaa ggggattgtt


 


121 gatgctgctg agaaggctga tgcgaaggaa gggaagttga atgctgctgg tgctgagggt


 


181 acgactaacg cggatgctgg gaagttgttt gtgaagaatg ctggtaatgt gggtggtgaa


 


241 gcaggtgatg ctgggaaggc tgctgctgcg gttgctgctg ttagtgggga gcagatatta


 


301 aaagcgattg ttgatgctgc taaggatggt ggtgagaagc agggtaagaa ggctgcggat


 


361 gctacaaatc cgattgacgc ggctattggg ggtacaaatg ataatgatgc tgctgcggcg


 


421 tttgctacta tgaagaagga tgatcagatt gctgctgcta tggttctgag gggaatggct


 


481 aaggatgggc aatttgcttt gaaggatgct gctgctgctc at


 


LOCUS AY100628 606 by DNA linear BCT 18 Mar. 2003









DEFINITION
Borrelia afzelii strain ACAI vls recombination silent




cassette locus, complete sequence.


ACCESSION
AY100628 REGION: 1..606


 








(SEQ ID NO: 32)



translation=“ESAVDGVSKWLEEMIKAAKEAATKGGTGGGSEKIGDVGAANNQG



 


AVADKDSVKGIAKGIKGIVDAAGKAFGKDGNALTGVKEVADEAGANEDAGKLFAGNAG


 


NAAAADIAKAAGAVTAVSGEQILKAIVDGAGGAAQDGKKAAEAKNPIAAAIGADAAGA


 


DFGDDMKKSDKIAAAIVLRGVAKSGKFAVANAAKKESVKSAV”


 


ORIGIN


(SEQ ID NO: 33)



  1 gagagtgctg ttgatggggt tagcaagtgg ttagaagaga tgataaaagc tgctaaggag



 


 61 gctgctacaa agggtggtac tggtggtggt agcgaaaaga ttggggatgt tggtgctgct


 


121 aataatcagg gtgctgtagc tgataaggac agtgttaagg ggattgcgaa ggggataaag


 


181 gggattgttg atgctgctgg gaaggctttt ggtaaggatg gtaatgcgct gacaggtgta


 


241 aaagaagttg ctgatgaggc tggggctaac gaggatgcgg ggaagttgtt tgctggtaat


 


301 gctggtaatg ctgctgctgc tgacattgcg aaggcggctg gtgctgttac tgcggttagt


 


361 ggggagcaga tactgaaagc tattgttgat ggtgctggtg gtgcggctca agatggtaaa


 


421 aaggctgcgg aggctaagaa tccgattgca gctgcgattg gggctgatgc tgctggtgcg


 


481 gattttggtg atgatatgaa gaagagtgat aagattgctg cggctattgt tttgaggggg


 


541 gtggctaaga gtggaaagtt tgctgttgct aatgctgcta agaaggagag tgtgaagagt


 


601 gctgtg

## Claims

1. A method of diagnosing an infection by Borrelia sp. in a subject comprising:
a) obtaining a sample from a subject,
b) contacting the sample with a composition comprising an isolated peptide, wherein said isolated peptide comprises SEQ ID NO: 1, and
c) detecting binding of the isolated peptide to an antibody in the sample, wherein the binding between the peptide and the antibody is indicative that the subject has an infection with a Borrelia sp.,
wherein the Borrelia sp. is selected from B. burgdorferii, B. garinii and B. afzelii.

2. The method of claim 1, wherein the method further comprises isolating the antibody peptide complex from the sample.

3. The method of claim 1, wherein the isolated peptide consists of SEQ ID NO: 1.

4. The method of claim 1, wherein the composition further comprises a reporter polypeptide covalently linked to the isolated peptide.