# Patent

## Title
Method and device for improved restriction fragment length polymorphism

## Abstract

A chromosomal gene of Borrelia burgdorferi which encodes a conserved antigen of approximately 79 kD has been isolated and sequenced. The chromosomal gene, the gene product, and antibodies to the gene product may be used in diagnostic methods for the detection of Borrelia burgdorferi infection. The antigen and fragments thereof are suitable for use in vaccine compositions and methods.

## Background
1. Field of the Invention

Lyme disease was first described in the late 1970's as a unique grouping of arthritic symptoms in patients from Lyme, Connecticut. Subsequent investigation demonstrated that the disease is caused by infection with Borrelia burgdorferi, a spirochete, following exposure to deer (ixodid) ticks. It is now known that lyme disease in humans is a multi-systemic disorder characterized by dermatologic, rheumatologic, cardiac, and neurologic manifestations.

While several isolates of B. burgdorferi from North America and Europe have been characterized at both the genetic and antigenic level, the unequivocal diagnosis of lyme disease remains problematic. Isolation and cultivation of borrelia from infected patients is difficult and not practical for routine diagnosis. Immunological and genetic detection methods have not become generally available, at least in part because the known major antigens of B. burgdorferi have previously been thought to be coded on linear plasmid and have demonstrated significant antigenic variation with regard to the level of expression and molecular weight. There have also been reports of serological cross-reactivity with related human pathogens, such as B. hermsii (the causative agent of tick-born relapsing fever) and Treponema pallidum (the causative agent of syphilis).

It would therefore be desirable to provide improved methods for diagnosing lyme disease and in particular for unequivocally determining the presence of B. burgdorferi in patient samples. To provide such methods, it would be desirable to identify genetic and antigenic information which is widely conserved among B. burgdorferi strains and which can be used in a variety of detection protocols. More specifically, it would be desirable to identify a conserved chromosomal gene which encodes a major antigenic protein, where the gene can serve as the basis for genetic screening assays and the antigen can serve as the basis for immunologic screening assays.

2. Description of the Background Art

Immunochemical analyses of B. burgdorferi have revealed the presence of several immunodominant antigens that are recognized during the described stages of human infection. (Craft, et al. (1986). Clin. Invest. 78:934-938; Grodzicki, et al. (1988) J. Infect. Dis. 157:790-797; Nadal, et al. (1989) Pediatr. Res. 26:377-382) One of the immunodominant antigens was reported to have a molecular weight of approximately 83 kD. No description or characterization of the gene encoding this antigen had been reported prior to the work which is the subject of the present application. The data included in the Experimental section hereinafter was reported in LeFebvre et al. (1990) J. Clin. Microbiol. 28:1673-1675 and in Perng et al. (1991) Infect. Immun. 59:2070-2074.

The methods and compositions of the present invention are based on the discovery that an approximately 79 kilodalton (kD) immunodominant antigen of Borrelia burgdorferi is encoded by a chromosomal gene which is widely conserved among strains throughout Europe and North America. Based on this discovery, the present invention provides screening assays for Borrelia burgdorferi infection, where the assays detect the presence of the chromosomal gene, the gene product (79 kD antigen), or antibodies to the 79 kD antigen, in a patient sample.

The present invention also provides isolated polynucleotides which encode the approximately 79 kD antigen or fragments thereof, as well as oligonucleotides capable of hybridizing under stringent conditions to the chromosomal gene. The oligonucleotides may be labeled for use in hybridization assays or may be present as primer pairs for use in polymerase chain reaction assays.

The present invention further provides diagnostic kits which contain a reagent capable of binding to the gene, gene product (antigen), or antibodies to the antigen under conditions which permit detection of binding. The kits will further contain instructions which set forth the corresponding detection protocol, such as hybridization assays, polymerase chain reaction assay, or immunoassay.

The present invention still further comprises isolated and optionally purified polypeptides which comprise a sequence analogous to at least six contiguous amino acids of the approximately 79 kD antigen. Such polypeptides may be produced by expression of a heterologous gene in cultured cells and will usually be reactive with antibodies produced by a host in response to infection by Borrelia burgdorferi. Preferably, the polypeptides will be capable of eliciting a protective immunity when administered to a susceptible host.

Vaccine compositions according to the present invention will comprise a polypeptide which is immunologically cross-reactive with the conserved 79 kD immunodominant antigen. The polypeptide will be present in a physiologically acceptable carrier in an amount effective to elicit protective immunity when administered to a susceptible host. The polypeptide may comprise substantially the entire 79 kD antigen, or may be a portion thereof. Frequently, the polypeptide will be produced by expression in a heterologous gene in cultured cells.

The present invention further comprises monospecific antibodies for the conserved 79kD antigen of Borrelia burgdorferi. The monospecific antibodies may be monoclonal or polyclonal.

FIG. 1 is an immunoblot demonstrating the reactivity of the approximately 79 kD antigen to rabbit antiserum raised against whole-cell Borrelia burgdorferi.

FIG. 2 is an immunoblot demonstrating the reactivity of the approximately 79 kD antigen to human serum from seropositive Lyme borreliosis patients.

FIG. 3A is a polyacrylamide gel of whole-cell Borrelia burgdorferi. FIG. 3B is a Southern blot of the gel in FIG. 3A.

FIG. 4 is an autoradiograph of whole cell DNA from B. burgdorferi digested with ClaI and probed with a labeled fragment of the 79.8 kD gene.

FIG. 5 is an immunoblot of whole cell lysates of representative strains of B. burgdorferi reacted with antisera raised against the 79.8 kD antigen.

The present invention provides novel compositions and methods for diagnosing, treating, and vaccinating against infection by Borrelia burgdorferi, the spirochete which causes Lyme disease in humans. The invention is based, in part, on the discovery of a widely conserved approximately 79 kilodalton (kD) immunodominant antigen which is encoded by a chromosomal gene. As discussed above, the existence of the chromosomal gene encoding an immunodominant antigen is surprising since previous genes encoding major antigene of Borrelia burgdorferi were believed to be located on linear plasmids, and would therefore not be expected to be as widely conserved as chromosomal genes.

The present invention provides a complete sequence of the chromosomal gene encoding the 79 kD antigen as well as the corresponding amino acid sequence of the antigen itself. The sequence of the polynucleotide encoding the antigen is set forth in SEQ ID NO:1, and the amino acid sequence of the antigen is set forth in both SEQ ID NO:1 and SEQ ID NO:2 thereto. The 79 kD antigen gene is contained within a 2.5 kilobase pair (kbp) FoKI fragment of the chromosomal DNA of Borrelia burgdorferi reference strain B31, which is available from the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Maryland 20852, under the designation ATCC 35210.

It will be appreciated that the DNA sequence set forth in SEQ ID NO:1 represents the particular allele which is present in the reference strain B31 and that other alleles will exist in nature. The compositions of the present invention may be derived from such other alleles and from the nucleic acid and amino acid sequences of such alleles according to the general methods as described hereinafter.

In accordance with the present invention, nucleic acid sequences encoding the conserved 79 kD antigen have been isolated and characterized. An isolated nucleic acid is one which has been removed from its natural chromosomal location. Isolated nucleic acids may be produced by excision from the chromosomal DNA of cultured Borrelia burgdorferi cells, e.g., using restriction enzymes. Alternatively, the isolated nucleic acids may be produced by the synthesis techniques set forth hereinbelow.

Isolated nucleic acid sequences, including polynucleotides and oligonucleotides, encoding the antigen and portions thereof may be expressed in cultured cells to provide isolatable quantities of polypeptides displaying biological (e.g. immunological) properties of the naturally occurring 79 kD antigen. Other useful nucleic acids are substantially homologous to the sequences encoding the antigen, can be either natural or synthetic. Such homologous nucleic acids may find use as probes or primers for locating or characterizing natural or synthetic nucleic acids encoding the 79 kD antigen.

Substantial homology of a nucleic acid sequence means either that (a) there is greater than about 65%, typically greater than about 75%, more typically greater than about 85%, preferably greater than about 95%, and more preferably greater than about 98% homology with a compared segment of at least about 10 contiguous nucleotides or (b) the homologous nucleic acid sequence will hybridize to the compared sequence or its complementary strand under stringent conditions of the temperature and salt concentration. These stringent conditions will generally be a temperature greater than about 22.degree. C., usually greater than about 30.degree. C. and more usually greater than about 45.degree., and a salt concentration generally less than about 1 M, usually less than about 500 mM, and preferably less than about 200 mM. The combination of temperature and salt concentration is more important in defining stringency than either the temperature or the salt concentration alone. Other conditions which affect stringency include GC content of the compared sequence, extent of complementarity of the sequences, and length of the sequences involved in the hybridization, as well as the composition of buffer solution(s) used in the hybridization mixture. These and other factors affecting stringency are well described in the scientific and patent literature.

Nucleic acids according to the present invention can be synthesized based on the DNA sequence set forth in SEQ ID NO:1 using well known synthesis techniques. For example, short, single-stranded DNA fragments (oligonucleotides) may be prepared by the phosphoramadite method described by Beaucage and Carruthers (1981) Tett. Lett. 22:1859-1862. A double-stranded fragment may then be obtained by either synthesizing the complementary strand and annealing the strands together under appropriate conditions or by adding the complementary strand using DNA polymerase and an appropriate primer sequence.

Polymerase chain reaction techniques may also be used for the production of probes and/or the amplification of polynucleotides for synthetic purposes. Suitable primer pairs for use in polymerase chain reaction techniques may be obtained based on the DNA sequence of SEQ ID NO:1. See, Innis et al., Ed., PCR Protocols, Academic Press, New York, 1990, the disclosure of which is incorporated herein by reference.

Natural or synthetic DNA fragment encoding the 79 kD antigen or portions thereof may be incorporated in DNA constructs, usually self-replicating construct, capable of introduction to and expression in in vitro cell culture. Usually, the DNA constructs will be capable of replication in a unicellular host, such as bacteria or yeast, but may also be intended for introduction to and the integration within the genome of cultured mammalian or other eukaryotic cell lines. DNA constructs prepared for introduction into bacteria usually include replication system recognized by the host, the desired coding sequence for the 79 kD antigen or a portion thereof, transcriptional and translational initiation regulatory sequences joined to the 5'-end of the antigen coding sequence, and transcriptional and translational termination regulatory sequences drawing to the 3'-end of the antigen coding sequence. The transcriptional regulatory sequences will typically include a heterologous promoter which is recognized by the host. Conveniently, available expression vectors which include the replication system and transcriptional and translational regulatory sequences together with an insertion site for the antigen coating region may be employed.

The present invention further provides polypeptides which correspond to the 79 kD antigen or a fragment thereof. The polypeptides will usually be either haptenic or antigenic, typically including at least six amino acids, usually including at least nine amino acids, and more usually at least twelve amino acids found contiguously within a natural form of the 79 kD antigen. The contiguous amino acids may be located within any regions of the antigen. Longer peptides up to and including substantially the full length of the natural protein, and larger, may also find use.

Usually, the polypeptides will define or correspond to at least one determinant site (also known as epitopic site) which is characteristic of a naturally-occurring 79 kD antigen of Borrelia burgdorferi. By characteristic, it is meant that the determinant site will allow immunologic detection of the exposed polypeptide segment in a biological sample with reasonable assurance, in most cases allowing the Borrelia burgdorferi to be immunologically distinguished from other related organisms, particularly pathogenic organisms.

The polypeptides will be useful as a reagents for use in diagnostic methods and kits, for preparing polyclonal and monoclonal antibodies, and for use as the immunogenic component in vaccine compositions. Each of these uses will be described in more detail hereinafter.

In a preferred aspect, the polypeptides of the present invention will be identical to or equivalent to at least a portion of the amino acid sequence set forth in SEQ ID NO:2. By equivalent, it is meant that a substantial identity of amino acids exist over a series of at least 10 contiguous residues, or that each position of the corresponding sequences is either identical to or has conservative substitution in at least about 60% of the residues, preferably at least about 70% of the residues, and more preferably at least about 80% of the residues. The polypeptide sequences, however, may be modified by occasional deletions, additions, or replacements in accordance with known methods for comparison. See, for example, Sequence Analysis Software Package, University of Wisconsin Biotechnology Center, Madison, Wisc. Conservative substitutions or replacements within the groups (a) gly, ala; (b) val, ile, leu; (c) asp, glu; (d) asn, gln; (e) set, thr; (f) lys, arg; and (g) phe, tyr.

Synthetic polypeptides which are immunologically cross-reactive with a natural 79 kD antigen may be produced by either of at least two general approaches. First, polypeptides having fewer than about 100 amino acids, more usually having fewer than about 50 amino acids, can be synthesized by the Merrifeld solid-phase synthesis method where amino acids sequentially added to a growing chain. See, Merrifield (1963) Journal of the American Chemical Society J. Am. Chem. Soc. 85:2149-2146. Conveniently, the amino acid sequences may be taken directly from the listing in FIG. 4. Equipment for automatically synthesizing polypeptides is commercially available from suppliers such as Applied Biosystems, Inc., Foster City, California; DuPont Company, Biotechnology Systems, Wilmington, Delaware; and MilliGen/Biosearch, a division of Millipore, Burlington, Mass.

An alternative for synthesizing polypeptides of the present invention involves the expression in cultured cells of recombinant DNA molecules encoding the 79 kD antigen or a desired portion thereof. The gene itself may be natural or synthetic, as described above. The natural gene is obtainable from cDNA or genomic libraries using standard techniques. In particular, probes synthesized based on the nucleotide sequence of SEQ ID NO:1 may be used to identify and isolate genes representing other alleles of the 79 kD antigen gene using well known methods.

To be useful in the detection and therapeutic methods of the present invention, the polypeptides are usually obtained in substantially pure form. That is, the polypeptides will be at least about 50% pure by weight and be substantially free of interfering proteins and contaminants. Preferably, the polypeptides of the present invention will be isolated or synthesized to a purity of at least about 80% by weight, more preferably being at least about 95% by weight or greater. Using conventional protein purification techniques, homogeneous polypeptide compositions of at least 99% by weight can be obtained. For example, the polypeptides may be purified by use of the antibodies described hereinafter in affinity chromatography procedures, Such affinity chromatography is performed by first linking antibodies to a solid support and then contacting the solid support with the source of the polypeptides, e.g. lysates of the Borrelia burgdorferi which naturally produce the 79 kD antigen or lysates of cultured cells in which the 79 kD antigen or fragment thereof have been recombinantly produced.

Production of antibodies to the approximately 79 kD antigen of Borrelia burgdorferi or antigenic portions thereof may be accomplished using the purified or synthetic polypeptides of the present invention. Once a sufficient quantity of the polypeptide has been obtained by any of the methods described above, polyclonal antibodies specific for the determinant regions may be produced in in vivo or in vitro techniques. In vivo techniques rely on the exposure of antigenic polypeptides or fragments to any of a wide variety of vertebrates, suitable vertebrates are typically non-human, such as mice, rats, rabbits, sheep, goats, and the like. Polypeptides having at least about 5 amino acids, usually at least about 30 amino acids, and preferably at least about 50 amino acids may serve directly as immunogene. If the polypeptide is smaller than about 10 kD, particularly smaller than about 6 kD, it may be necessary to join the polypeptide to a larger molecule to elicit the desired immune response. The immunogens are then injected into the animal host according to a predetermined schedule, and the animals are bled periodically, with successive bleeds generally having improved titer and specificity. Such antisera will then be purified in order to produce the desired monospecific antibodies of the present invention. Conveniently, purification can be accomplished by affinity chromatography using the polypeptides of the present invention coupled to a suitable solid phase. Such affinity chromatography for the purification of antibodies is well described in the patent and scientific literature. See, for example, Hudson and Hay, Practical Immunology, Blackwell Scientific Publications, Oxford, 1980, the relevant portions of which are incorporated herein by reference. Suitable in vitro techniques for producing the monospecific antibodies of the present invention involve the in vitro exposure of lymphocytes to the antigenic polypeptides corresponding the 79 kD antigen of Borrelia burgdorferi. Such techniques produce monoclonal antibodies and are described in Huse et al. (1989) Science 246:1275-1281; and Ward et al. (1989) Nature 341:544-546, both of which are incorporated herein by reference.

Monoclonal antibodies may also be prepared by the now classic technique of Kohler and Milstein, as well as by improvements on their basic technique. Briefly, these methods rely on preparing immortalized cell lines capable of producing antibodies having the desired specificity, i.e., reactivity with the determinant regions of the 79 kD antigen. Such immortalized cell lines may be produced by a variety of techniques. Conveniently, a small vertebrate, such as mouse, is hyperimmunized with the desired antigen by the method just described in connection with the preparation of polyclonal antibodies. The vertebrate is then killed, usually several days after the final immunization, the spleen removed, and the spleen cells immortalized. The manner of immortalization is not critical. Presently, the most common technique is fusion with a myeloma cell fusion partner, as first described by Kohler and Milstein (1976) Eur. J. Immunol. 6:511-519. Other techniques include EVB transformation, transformation with bare DNA, e.g., oncogenes, retroviruses, and the like, and any other method which provides for the stable maintenance of the cell line and production of monoclonal antibodies. Common techniques are described in Lane and Harlow, Antibodies: A Laboratory Manual, Cold Spring Harbor Press, New York, 1988; and Goding, Monoclonal Antibodies: Principles and Practice, 2nd Edition, Academic Press, New York, 1986, both of which are incorporated herein by reference.

When employing fusion with a fusion partner, the manner of fusion is usually not critical and various techniques may be employed. Conveniently, the spleen cells and myeloma cells are combined in the presence of a nonionic detergent, usually polyethylene glycol, and other additives such as Dulbecco's Modified Eagle's Medium, for a few minutes. At the end of the fusion, the nonionic detergent is rapidly moved by washing the cells. The fused cells are promptly dispensed in small culture wells (usually in a microtiter plate) at relatively low density, ranging from about 1 to 5.times.10.sup.5 per well, in a selective medium chosen to support growth of the hybrid cells while being lethal to the myeloma cells. Usually, the myeloma cell line has been mutated to be sensitive to a lethal agent, typically being HAT sensitive. After a sufficient time, usually from about 1 to 2 weeks, colonies of hybrids are observed and plates containing hybrid positive wells are identified. The plates and wells having only one colony per well are selected, and supernatants from these wells are tested for binding activity against the desired 79 kD antigen or isolated portion thereof. Once positive hybridomas are identified, the cell line can be maintained as a viable culture and/or by lyophilization and frozen storage.

Depending on the desired use for the antibodies, further screening of the hybridomas may be desirable. Hybridomas providing high titers are desirable. Furthermore, cytotoxic antibodies, e.g., IgG.sub.2 b, IgG.sub.3 and IgM, may be selected for use in therapeutic treatment of Borrelia burgdorferi infection. For use in immunodiagnostic assays as described in more detail hereinbelow, antibodies having very high specificity for corresponding determinants are desirable.

Once the desired hybridomas have been selected, monoclonal antibodies may be isolated from the supernatants of the growing colonies. The yield of antibodies obtained, however, is usually low. The yield may be enhanced by various techniques, such as injection of the hybridoma cell line into the peritoneal cavity of a vertebrate host which will accept the cells. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Proteinaceous and other contaminants will usually be removed from the monoclonal antibodies prior to use by conventional techniques, e.g., chromatography, gel filtration, precipitation, extraction, or the like.

By properly selecting the polypeptides used as the immunogen, antibodies having high specificity and affinity for the desired 79 kD antigen epitope can be obtained. The polypeptide selected should represent one or more epitopic sites which are unique to the antigen protein and which can distinguish Borrelia burgdorferi from closely related pathogene and other potentially cross-reactive proteins. Such unique epitopes are found on polypeptides expressed by cells containing sequences disclosed in SEQ ID NO:2.

The polypeptides and antibodies of the present invention may be used with or without modification. Frequently, the polypeptides and antibodies will be labeled by joining, either covalently or non-covalently, a substance which provides for a detectable signal. A wide variety of labels and conjugation techniques are known and are reported extensively in both the scientific and patent literature. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescers, chemiluminescers, magnetic particles, biotin, and the like. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241, the disclosures of which are incorporated herein by reference.

Antibodies and polypeptides prepared as described above can be used in various immunological

techniques for detecting the 79 KD antigen of Borrelia burgdorferi in biological specimens, particularly body fluid samples, including blood, plasma, serum, urine, stool, and the like as well as cell samples, such as tissue biopsy samples. The use of blood, plasma and serum samples will preferably be preferred.

A first type of immunoassay will involve combining the patient sample with monospecific antibody, either polyclonal or monoclonal, which is capable of specifically binding to the 79 kD antigen in the sample. The antibody will usually be labeled or immobilized, as described above, and detection of binding between the antibody and antigen will be indicative of the presence of Borrelia burgdorferi in the sample. Numerous specific protocols are available for performing such antibody-based immunoassays and are well described in the scientific and patent literature. Such protocols can generally be classified as heterogeneous (requiring separation of the antigen from a sample) or homogenous (not requiring separation); competitive or noncompetitive; and the like.

A second type of immunoassays relies on the combination of the patient sample with the isolated 79 kD antigen polypeptide or a fragment thereof. The polypeptide will be able to bind to a patient antibody which has been produced in response to infection with Borrelia burgdorferi. The specific protocols for detecting patient antibody with the polypeptides will generally rely on use of immobilized polypeptide to capture and remove the antibody from the sample. The captured antibody can be detected in using labeled anti-human antibody in a sandwich technique or using a labeled polypeptide in a semi-competitive technique.

An exemplary polypeptide-based assay for detecting infection by Borrelia burgdorferi is an enzyme linked immunosorbent assay (ELISA) where the polypeptide is immobilized on a solid phase, usually a test well in a microtiter plate, although polystyrene beads, glass beads, agarose beads, and other solid phases may also find use. After exposure to sample and binding of antibody (if one is present) the solid phase is exposed to labeled antibody directed against the patient antibody, e.g. labeled anti-human antibody. The label is an enzyme which may be detected by exposure to appropriate substrates. Such ELISA techniques are amply described in the patent and scientific literature.

Of course, numerous other assay protocols exist which may combine use of the polypeptide antigene and antibodies of the present invention. The above descriptions of polypeptide-based and antibody-based assays are intended to be exemplary only.

In addition to immunoassays, the presence of Borrelia burgdorferi in a patient sample may be detected using nucleic acid hybridization probes prepared as described hereinabove. The samples will be treated to release chromosomal DNA from any Borrelia burgdorferi which may be present in the sample. Optionally, but not necessarily, the patient sample may be cultured to expand the amount of Borrelia burgdorferi present prior to treatment to release the chromosomal DNA. In a first particular protocol, the Borrelia burgdorferi will be lysed to free the chromosomal DNA, and the released DNA fixed on a solid phase support. The DNA is denatured so that single stranded fragments remain on the solid phase, and the solid phase is contacted with the labeled oligonucleotide probes of the present invention under hybridizing conditions. The hybridizing conditions are sufficiently stringent to assure binding specificity. Hybridization of the nucleic acid probes to the solid phase is thus diagnostic of the presence of the Borrelia burgdorferi. Such nucleic acid hybridization methods are described in U.S. Pat. No. 4,358,535, the disclosure of which is incorporated herein by reference.

An alternative protocol permits the Borrelia burgdorferi to be lysed in a liquid phase without prior culturing to expand the amount of the microorganisms present. Lysing is effected using a detergent to free the nucleic acids under denaturing conditions. The lysed solution is then contacted with the solid phase which selectively binds a single strand of nucleic acids which may then be detected using the oligonucleotide probes of the present invention. Such an alternative protocol described in PCT Application 86/00139, the disclosure of which is incorporated herein by reference. Methods for performing such nucleic acid hybridization assays are described in general in Hanes and Higgins, Nucleic Acid Hybridization: A Practical Approach, IRL Press, 1985, the disclosure of which is incorporated herein by reference.

The use of hybridization assays may be combined with polymerase chain reaction techniques to amplify any amount of a gene encoding the 79 kD antigen which may be present in the patient sample. Polymerase chain reaction employ pairs of nucleotides, usually from about 10 to 50 nucleotides in length, and which are spaced from about 50 to 500 nucleotides apart on either of the two complementary strands of the 79 kD gene. Specimen preparation will include cellular lysis, typically followed by separation of the released nucleic acids on a solid phase, usually for example, glass beads or silicone particles such as those employed in the commercial kit GENECLEAN, available from Bio101, La Jolla, Calif. After the single stranded nucleic acids are bound to the solid phase, they can be amplified by thermal cycling in the presence of the nucleotide primers and DNA polymerase. Typically, the temperature will be cycled between about 98.degree. C. and 60.degree. C., for time periods as short as 1 or 2 minutes per cycle. Cycling can be continued for as long as the desire to achieve amplification of a portion of the gene bounded by the two primers. The amplified gene fragment may then be detected using labeled oligonucleotide probes generally as described above.

Vaccines against Borrelia burgdorferi infections may be prepared using the compositions of the present invention. These vaccines may be passive, consisting of Ig supplementation which interferes with Borrelia burgdorferi growth or toxicity. Alternatively, vaccines may be active producing a humoral and/or cellular response providing protective immunity by active suppression of Borrelia burgdorferi infections.

A vaccine prepared utilizing the 79 kD polypeptide antigen or immunogenic equivalents will usually comprise: (a) fixed cells either recombinantly altered to produce these antigen proteins or cells from the Borrelia burgdorferi itself; (b) a crude cell extract; or (c) a partially or completely purified antigen preparation. Fusion proteins combining a segment of the 79 kD antigen will be readily prepared. In some embodiments, a multiple vaccination may be achieved by fusing these antigene with other target antigene on a single protein, inducing protection against multiple infectant vectors. Alternatively, a "cocktail" of different immunogene may be simultaneously administered or inoculated. These immunogene can be prepared in vaccine dose form by well-known procedures. These vaccines can be in the form of an injectable dose and may be administered intramuscularly, intravenously, or subcutaneously. These vaccines can also be administered intranasally by aspiration, or orally by mixing the active components with food or water, providing a tablet form, and the like. Means for administering, or more typically inoculating, these vaccines should be apparent to those skilled in the art from the teachings herein; accordingly, the scope of the invention is not limited any particular delivery form.

For parenteral administration, such as subcutaneous injection, these immunogene can be combined with a suitable physiologically acceptable carrier, for example, it can be administered in water, saline, alcohol, fats, waxes, or buffered vehicles with or without various adjuvants or immunomodulating agents. Suitable immunological adjuvants or agents include, but are not limited to, aluminum hydroxide, aluminum phosphate, aluminum potassium sulfate (alum), beryllium sulfate, silica, kaolin, carbon, water-in-oil emulsions, oil-in-water emulsions, muramyl dipeptide, bacterial endotoxin, lipid X, Corynebacterium parrum (Proplonobacterium acnes), Bordetolla pertussis, polyribonucleotides, sodium alginate, lanolin, lysolecithin, vitamin A, saponin, liposomes, levamisole, DEAE-dextran, blocked copolymers or other synthetic adjuvants. Such adjuvants are available commercially from various sources, for example, Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.) or Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Michigan). Other suitable adjuvants are Amphigen (oil-in--water), Alhydrogel (aluminum hydroxide), or a mixture of Amphigen and Alhydrogel.

The proportion of immunogen and adjuvant can be varied over a broad range so long as both are present in effective amounts. On a per-dose basis, the amount of the immunogen can range broadly from about 1.0 pg to about 100 mg per kg of host, usually at least about 10 pg, typically at least about 100 pg, and preferably at least about 1 ng per kg of host weight, and usually less than about 1 mg, typically less than about 10 .mu.g, and more typically less than about 1 .mu.g, and preferably less than about 100 ng per kg of host. A preferable range is from about 10 pg to about 100 ng per dose. A suitable dose size will usually be between about 0.01 and 5 ml, preferably about 0.5 ml for a 20-59 kg organism. Comparable dose forms can also be prepared for parenteral administration to smaller or larger patients but the amount of immunogen per dose will usually be smaller, for a smaller patients.

For the initial vaccination of immunologically naive patients, a regiment of between 1 and 4 doses can be used with the injections spaced out over a 2 to 6-week period. Typically, a two-dose regimen is used. The second dose of the vaccine then should be administered some weeks after the first dose, for example, about 2 to 4 weeks later. Patients that have been previously exposed to Borrelia burgdorferi.

The vaccine may also be combined with other vaccines for other diseases to produce multivalent vaccines. It may also be combined with other medicaments, for example, antibiotics. A pharmaceutically effective amount of the vaccine can be employed with a pharmaceutically acceptable carrier such as viral capsid protein complex or diluent understood to be useful for the vaccination of animals.

The following examples are offered by way of illustration, not by way of limitation.

Bacterial strains. The isolates used in this study were chosen to represent a wide geographical distribution of B. burgdorferi strains. The B. burgdorferi isolates Son 335, Son 188, Hum 3336, and Ala 410 were received from M. Biesett (California Department of Public Health, Berkeley, Calif.). Isolates RSL20, CA2, and CA3 were received from R.S. Lane (Department of Entomological Sciences, U.C. Berkeley, Calif.). The B. burgdorferi isolates B31 (Bb), B35 (At), Wisconsin, Mass., 297, B914, and K48, B. hermsii, B. coriaceae and B. duttonii strains were supplied by R. C. Johnson (University of Minnesota, Minneapolis, Minn.). Strain PGU was received from V. Preac-Mursic (University of Munich, Munich). The B56 isolate was received from A. Schonberg (Institute fur Veterinarmedizin des Bundesgesundheitsamtes, West Germany), B. anserina strain was obtained from R. Walker (U.C. Davis, Davis, Calif.) (see Table 1). The spirochetes were maintained in BSKII (Barbour-Stoenner-Kelly) medium (Barbour (1984) Yale J. Biol. Med. 57:521-525) at 33.degree. C. The cells were harvested at mid-logphase of growth (10.sup.8 /ml), washed in PBS, and prepared for DNA or protein analysis as described below. ______________________________________ Description of Organisms Isolate      Source         Location ______________________________________ B. burgdorferi B31 ATCC35210 Ixodes dammini New York Wis          human skin isolate Wisconsin Ma           human skin isolate Massachusetts B35 reference strain ATCC35211    Ixodes ricinus Switzerland K48          Ixodes ricinus Czechoslovakia V297         human cerebral Connecticut spinal fluid B56          Ixodes ricinus Germany B914         Ixodes ricinus Germany P/GU         human skin isolate Germany California isolates         county Son335       Ixodes pacificus Sonoma Son188       Ixodes pacificus Sonoma Hum3336      Ixodes pacificus Humboldt Ala410       Ixodes pacificus Alameda CA2          Ixodes neotomae Mendocino CA3          Ixodes pacificus Marin RSL20        Ixodes pacificus Marin B. coriaceae ATCC         Ornithodoros coriaceae California 43381 (B.c.) B. hermsii ATCC         Ornithodoros hermsii Washington 35209 (B.h.) B. anserina  poultry        California B. duttonii  mouse          Minnesota ______________________________________

Cloning of the chromosomal DNA from strain B31. Chromosomal DNA was isolated as follows. A 20-ml portion of logarithmic-growth-phase cells was washed three times in phosphate-buffered saline (pH 7.2) plus 5 mM MgCl.sub.2. The pellets were suspended in 100 .mu.l of 15% sucrose in 50 mM Tris hydrochloride, pH 8.0-50 mM EDTA, to which an equal volume of 5 M NaC1 was added. To this solution was added 1/10 volume (20 .mu.l ) of 1% sodium deoxycholate. The solution was placed on ice for 20 minutes, followed by centrifugation in a microcentrifuge for 5 min. (The supernatant fluid, containing the plasmid DNA, was saved for other studies.) The pellet, containing the chromosomal DNA, was suspended in 100 .mu.l of 15% sucrose in 50 mM Tris hydrochloride, pH 8.0-50 mM EDTA. To this was added 50 .mu.l of 100% sodium dodecyl sulfate and 25 .mu.l of  20 mg of proteinase K per ml. The solution was incubated for 30 min at 37.degree. C., followed by phenol extraction and ethanol precipitation. The chromosomal DNA was digested with ClaI and ligated into a ClaI and ligated into a ClaI-digested Pev-Vrf expression vector (Crowl et al. (1985) Gene 38: 31-38). E. coli RRI (.lambda. cI857) was transformed with the recombinant plasmids. Expression of cloned genes into this vector was controlled by heat shock (42.degree. C. for 2 h). Recombinant colonies were screened for expression of B. burgdorferi antigene by colony blot immunoassay (Craft et al. (1986) Clin. Invest. 78:934-938). Positive clones were further characterized by immunoblot assay (Burnett (1981) Anal. Biochem. 112:195-203, Towbin et al. (1979) Proc. Natl. Acad. Sci. USA 76:4350-4354) by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (12% gels) (Laemmli (1970) Nature 227:680-685). Recombinant plasmids from clones identified to be expressing B. burgdorferi antigene were purified (Birnbolm (1983) J. Clin. Microbiol. 25:2296-2301), radiolabeled (Feinberg et al. (1983) Anal. Biochem. 132:6-13, Maniatis et al. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.), and used to probe Southern blots (Southern (1975) J. Mol. Biol. 98:503-518) of pulsed-field gels (Schwartz et al. (1984) Cell 37:67-75 containing undigested, whole-cell B. burgdorferi DNA. The electrophoresis was performed as previously described (LeFebvre et al. (1989) J. Clin. Microbiol. 27:389-393.

Subcloning and sequencing. The gene expressing the 25 79.8 kD antigen (LeFebvre et al. (1990) J. Clin. Microbiol. 28:1673-1675) was determined to be contained within a 2.5 kbp FoKI fragment of the original 6.5 kbp ClaI insert in the pLPI plasmid based on DNA sequence analysis. This fragment was subcloned into a pUC19 plasmid according to standard procedures (Maniatis et al. (1982) supra.) and was designated pLP4. The gene was sequenced according to standard procedures (Sanger et al. (1977) Proc. Natl. Acad. Sci. USA 74:5463-5467). Within this 2.5 kbp fragment were several HindIII sites. A 500 bp HindIII fragment of the gene was subcloned, radiolabeled (Feinberg et al. (1983) Anal. Biochem. 132:6-13, Maniatis (1982) supra.), and used as a probe to determine the presence and configuration of the gene in other B. burgdorferi isolates from North America and Europe as well as other Borrelia spp.

Amino acid sequence and analysis of the antigen. The amino acid sequence of the antigen, hydrophobic and hydrophilic domains, and codon usage were derived from the nucleic acid sequence using the Genetics Computer Group (GCG) software (Devereux (1989) Version 6.0, Genetics Computer Group, University of Wisconsin, Biotechnology Center, Madison, Wisc.).

Detection of the chromosomal gene expressing the 79.8 kD antigen in North American and European isolates. Whole cell DNA from the Borrelia spp. was isolated as previously described (Anderson et al. (1989) J. Olin. Microbiol. 27:13-20). The purified DNA was digested with ClaI (the restriction enzyme used initially to clone the 79.8 kD gene (LeFebvre et al. (1990) supra.) according to the manufacturer's specifications (BRL). The digested fragments were fractionated in a 0.7% agarose gel at 60V for 15.5 hr in Tris-Borate buffer (TBE, 0.089M Tris, 0,089M boric acid, 0.002M EDTA, pH8.0). The gel was stained with ethidium bromide and photographed under ultraviolet illumination. The DNA was transferred to a nylon membrane by the method of Southern (Southern (1975) J. Mol. Biol. 47:61-66). The hybridization and subsequent washes were carried out under stringent conditions according to standard procedures (Maniatis (1982) supra.).

Immunoblot analysis for expression of the 79.8 kD antigen in North American and European isolates. Expression of the 79.8 kD antigem in the B. burgdorferi isolates and Borrelia spp. was determined. Sodium-dodecyl-sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed as previously described (Laemmli (1970) Nature 227:680-685, Maniatis et al. (1982) supra.). Approximately 20 .mu.g of whole cell lysates of each isolate was added to a 12% gel. The gel was run at 60 mA constant current for 4.5-5 hr. Transfer of the electrophoresed proteins to nitrocellulose membranes was performed with a Pharmacia/LKB semi-dry transfer system according to manufacturer's specifications (Pharmacia, Uppsala, Sweden). The membrane was blocked and probed by standard procedures (Maniatis et al. (1982) supra.). Rabbit antiserum raised against B. burgdorferi (titered at 1:10,000 by enzyme-linked immunosorbent assay (ELISA)) was used at a dilution of 1:5000 to probe the blot. Biotinylated goat anti-rabbit antibody (Vector Laboratories, Burlingame, California) was added, followed by alkaline phosphatase conjugated to streptavidin (Kirkegaard and Perry Laboratories, Gaithersburg, Maryland). The enzyme substrate for the alkaline phosphatase was 5-bromo-4-chloro-3-indolylphosphate.

Of approximately 10 clones which were identified as expressing B. burgdorferi antigene in E. coli cells, 3 were found to express an 83-kDa protein (later determined to be approximately 79.8 kD), as determined with rabbit polyclonal antiserum raised against whole-cell B. burgdorferi (FIG. 1). The protein had the same molecular size and antigenic reactivity as an 83-kDa antigen in B. burgdorferi cells. Several lower-molecular-weight antigene were also expressed by the clone. These antigene are not discussed further herein.

FIG. 1 is an immunoblot demonstrating the reactivity of the putative 83-kDa antigen to rabbit antiserum raised against whole-cell B. burgdorferi. The whole-cell lysates were fractionated in 12% acrylamide gels prior to transfer to nitrocellulose membranes. Lane 1, B. burgdorferi B31; lane 2, E. coli RRI (.lambda. cI857) (negative control); lane 3, induced E. coli RRI (.lambda. cI857) containing the Pev-Vrf expression vector (negative control); lane 4, E. coli RRI (.lambda. cI857) containing a recombinant Pev-Vrf ligated to a randomly cloned piece of B. burgdorferi chromosomal DNA; lanes 5 to 7, E. coli RRI (.lambda. cI857) induced with recombinants of Pev-Vrf containing B. burgdorferi chromosomal DNA inserts expressing the 83 kDa antigen.

One of the recombinant plasmids expressing the putative 83-kDa antigen, designated pLP1, was further characterized. FIG. 2 represents an immunoblot of lysed whole-cell B. burgdorferi and E. coli cells transformed with either pLP1 or pUC18 plasmids. The blot was exposed to human antisera from two patients presenting with symptoms of Lyme borreliosis and determined to have been exposed to the agent by using enzyme-linked immunosorbent assay (Voller et al. (1980) Manual of Clinical Immunology, 2nd Ed., American Society for Microbiology, Washington, D.C.) with sera diluted 1:200 (data not shown). The 83-kDa antigen expressed in the E. coli cells containing the pLP1 plasmid reacted with the sera from both patients. No reaction at this molecular size was seen in the pUC18 control cells. These results demonstrate the fact that the 83-kDa antigen expressed by the cloned chromosomal gene in E. coli represents a major antigen of B. burgdorferi which induces an immune response in the human host. No reaction to the antigen was observed with antisera from humans who served as negative controls (data not shown).

The immunoblot of FIG. 2 demonstrates the reactivity of the putative 83-kDa antigen to human serum from seropositive Lyme borreliosis patients. Lanes 1 to 3 were reacted with serum from patient A, and lanes 4 and 5 were reacted with patient B antiserum. Lane 1, B. burgdorferi B31 whole cells; lanes 2 and 4, E. coli RRI (.lambda.c1857) induced with the Pev-Vrf expression vector (negative control); lanes 3 and 5, E. coli RRI (.lambda.c1857) transformed with the recombinant plasmid pLP1 expressing the 83-kDa antigen.

FIG. 3A is a photograph of an ethidium bromide-stained pulsed-field gel illuminated by UV irradiation. Several bands, representing linear and circular plasmids as well as chromosomal DNA, are evident. Of importance in this figure is the largest band which entered the gel (-1.c.) and the DNA remaining in the loading well. These two regions represent broken or linearized chromosomal DNA and intact circular chromosomal DNA, respectively. As demonstrated hereinafter, both of these bands represent chromosomal DNA of B. burgdorferi. FIG. 3B is an autoradiograph demonstrating the results of a Southern blot hybridization of this gel. The probe used in lane 1 was labeled whole-cell B31 DNA. Radiolabeled recombinant plasmid pLP1 (Maniatis et al. (1982) supra.) was used as the probe in lane 2. The pLP1 probe hybridized specifically and exclusively to the two bands representing B. burgdorferi chromosomal DNA, as described above. Thus, pLP1 represents the first description of a chromosomal gene expressing an antigen in B. burgdorferi. Only B. coriaceae has been shown to encode major antigene in chromosomal DNA (Perng et al. (1990) Infect. Immun. 58:1744-1748). All other reports describing antigen expression in Borrelia species have located the genes on linear plasmids (Barbour (1988) J. Clin. Microbiol. 26:475-478; Barbour et al. (1987) Science 237:409-411; Howe et al. (1986) Infect. Immun. 54:207-212; Howe et al. (1984) Science 227:645-646; Meier et al. (1985) Cell 41:403-409; and Plasterk et al. (1985) Nature 318:257-262) .

FIG. 3A is an ethidium bromide-stained pulsed-field gel of whole-cell B. burgdorferi B31 DNA, cc., Circular chromosomal DNA which did not enter the gel; l.c. broken or linearized chromosomal DNA. FIG. 3B is a Southern blot of the gel in FIG. 3A. Lane 1 was probed with radiolabeled whole-cell B31 DNA. Lane 2 was probed with the recombinant plasmid pLP1 containing the 83-kDa antigen gene.

DNA and amino acid sequence. The gene expressing the 79.8 kD antigen was determined to be contained within the 2.5 kbp ClaI fragment in the original pLP1 clone. The gene was sequenced and a functional TATA box (Pribnow Box) and ribosome binding site (Shine Dalgarno sequence) were identified (SEQ ID NO:1). SEQ ID NO:1 lists the DNA sequence of the gene, and SEQ ID NO:2 lists the amino acid sequence of the expressed antigen. The hydrophobicity profile revealed that the 79.8 kD protein is a hydrophilic protein (78%). Two large hydrophobic domains were identified; one located at the carboxy-terminal portion (about 30 amino acid residues), and the other at the amino terminal portion (about 20 amino acid residues). The central domain of the protein consisted of hydrophilic amino acids (about 350 amino acid residues). On the basis of its amino acid composition, the 79.8 kD protein is an acidic protein with an isoelectric point of 4.92. The calculated molecular mass (79.8 kD) was somewhat lower than the molecular mass estimated from SDS-PAGE (83 kD). No cysteine residues, two tryptophan residues, and three histidine residues were found in the deduced amino acid sequence. In a comparison with previously published protein sequences from a search of a protein data base, a low degree of homology (<15%) was observed. Table 2 lists the codon frequency and amino acid usage for the antigen. ______________________________________ Codon frequency and amino acid usage in the B31 79.8kDa antigen gene. A.A..sup.a Codon    Number.sup.b A.A.  Codon  Number ______________________________________ Gly    GGG      3         Thr   ACG    0 Gly    GGA      8         Thr   ACA    11 Gly    GGT      10        Thr   ACT    13 Gly    GGC      4         Thr   ACC    2 Glu    GAG      23        Tyr   TAT    19 Glu    GAA      40        Tyr   TAC    0 Asp    GAT      60        Leu   TTG    14 Asp    GAC      8         Leu   TTA    31 Val    GTG      5         Phe   TTT    23 Val    GTA      6         Phe   TTC    2 Val    GTT      30        Ser   TCG    0 Val    GTC      0         Ser   TCA    9 Ala    GCG      0         Ser   TCT    23 Ala    GCA      11        Ser   TCC    3 Ala    GCT      13        Arg   CGG    1 Ala    GCC      3         Arg   CGA    1 Ala    GCC      3         Arg   CGA    1 Arg    AGG      5         Arg   CGT    1 Arg    AGA      12        Arg   CGC    0 Ser    AGT      22        Gln   CAG    12 Ser    AGC      9         Gln   CAA    18 Lys    AAG      28        His   CAT    3 Lys    AAA      63        His   CAC    0 ASN    AAT      40        Leu   CTG    1 Asn    AAC      5         Leu   CTA    1 Met    ATA      9         Leu   CTT    21 Ile    ATA      11        Leu   CTC    0 Ile    ATT      40        Pro   CCG    2 Ile    ATC      2         Pro   CCA    3 Cys    TGT      0         Pro   CCT    11 Cys    TGC      0         Pro   CCC    0 End    TAG      0         Trp   TGG    2 End    TAA      1         End   TGA    0 ______________________________________ .sup.a A.A.: amino acid. .sup.b Number indicates the sum usage of a codon in the 79.8kD antigen gene.

Detection of the 79.8 kD antigen gone in B. burgdorferi isolates and Borrelia spp. Whole cells DNA, digested with ClaI, was electrophoresed, blotted, and probed with the labeled 500bp subclone of the 79.8 kD protein gone. FIG. 4 displays an autoradiograph of the ClaI digested whole cell DNA hybridized to the probe. A single major band of approximately 6.5 kb was seen in B31, the strain from which the gone was cloned. A single major band of the same size was also observed in the Wisc, 297, MA, Son188, RSL20, AT, and CA2 B. burgdorferi isolates and in B. anserina.

The B914, B56, and K48 strains were similar to each other in that they revealed 2 major band which hybridized to the probe. The weaker of these 2 bands resolved at 20 kb and the stronger resolved at 3 kb. The P/Gu strain demonstrated 4 band which hybridized to the probe at 6.8, 4.1, 2.1, and 1.0 kbp. The B. coriaceae, B. Hermsii, B. duttoni did not hybridize to the probe. Immunoassay of B. burgdorferi strains and Borrelia spp. for expression of the 79.8 kD antigen in vitro. FIG. 5 is an immunoblot of whole cell lyeares of representative strains of the B. burgdorferi isolates and other Borrelia spp. discussed in Table 1. It is apparent from FIG. 5 that the 79.8 kD antigen is a commonly expressed antigen amongst B. burgdorferi isolates. All of the strains assayed exhibited a reacting antigen at approximately 79.8 kD. Previous reports have also identified the presence of this antigen in other B. burgdorferi isolates (Craft et al. (1986) supra.; LeFebvre et al. (1990) supra.; LeFebvre et al. (1990) J. Clin. Microbiol. 28:700-707; Maniatis et al. (1982) supra.; Muhlemann et al. (1982) Lancet i:553-554; and Nadal et al. (1989) Pediatr. Res. 26:377-382). The B914 strain exhibited a slightly higher molecular weight antigen. Of the non-B. burgdorferi spp., only B. anserina expressed a reacting antigen at 79.8 kD. In Coomassie blue or silver stained gels of B. burgdorferi the 79.8 kD protein could not be visualized (data not shown) thus suggesting that it is expressed at low levels within the cells. This finding, in turn, indicates that the protein is a potent immunogen based on its low level of expression within B. burgdorferi isolates and its strong reactivity to anti-B. burgdorferi immune sera.

Although the foregoing invention has been described in detail for purposes of clarity of understanding, it will be obvious that certain modifications may be practiced within the scope of the appended claims. SEQUENCE LISTING (1) GENERAL INFORMATION: (iii) NUMBER OF SEQUENCES: 2 (2) INFORMATION FOR SEQ ID NO:1: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2258 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: (A ) NAME/KEY: CDS (B) LOCATION: 51..2151 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: ATTTAGTTGGTAAGGTAGATTATAATTAAATTTATAGGAGAATTTCTTTTATGAAA56 MetLys 1 AAAATGTTACTAATCTTTAGTTTTTTTCTTATTTTCTTGAATGGATTT104 LysMetLeuLeuIlePheSerPhePheLeuIlePheLeuAsnGlyPhe 5 1015 CCTGTTAGTGCAAGAGAAGTTGATAGGGAAAAATTAAAGGACTTTGTT152 ProValSerAlaArgGluValAspArgGluLysLeuLysAspPheVal 2025 30 AATATGGATCTTGAGTTTGTAAATTATAAAGGCCCTTATGATTCTACA200 AsnMetAspLeuGluPheValAsnTyrLysGlyProTyrAspSerThr 3540 4550 AATACATATGAACAAATAGTGGGTATTGGGGAGTTTTTAGCAAGACCG248 AsnThrTyrGluGlnIleValGlyIleGlyGluPheLeuAlaArgPro 55 6065 TTGACCAATTCCAATAGCAACTCAAGTTATTATGGTAAATATTTTATT296 LeuThrAsnSerAsnSerAsnSerSerTyrTyrGlyLysTyrPheIle 707 580 AATAGATTTATTGATGATCAAGATAAAAAAGCAAGCGTTGATGTTTTT344 AsnArgPheIleAspAspGlnAspLysLysAlaSerValAspValPhe 8590 95 TCTATTGGTAGTAAGTCAGAGCTTGACAGTATATTGAATTTAAGAAGA392 SerIleGlySerLysSerGluLeuAspSerIleLeuAsnLeuArgArg 100105 110 ATTCTTACAGGGTATTTAATAAAGTCTTTCGATTATGACAGGTCTAGT440 IleLeuThrGlyTyrLeuIleLysSerPheAspTyrAspArgSerSer 115120125 130 GCAGAATTAATTGCTAAGGTTATTACAATATATAATGCTGTTTATAGA488 AlaGluLeuIleAlaLysValIleThrIleTyrAsnAlaValTyrArg 135140 145 GGAGATTTGGATTATTATAAAGGGTTTTATATTGAGGCTGCTTTAAAG536 GlyAspLeuAspTyrTyrLysGlyPheTyrIleGluAlaAlaLeuLys 150155 160 TCTTTAAGTAAAGAAAATGCAGGTCTTTCTAGGGTTTATAGTCAGTGG584 SerLeuSerLysGluAsnAlaGlyLeuSerArgValTyrSerGlnTrp 165170175 GCTGGAAAGACACAAATATTTATTCCTCTTAAAAAGGATATTTTGTCT632 AlaGlyLysThrGlnIlePheIleProLeuLysLysAspIleLeuSer 180185190 GGAAATA TTGAGTCTGACATTGATATTGACAGTTTAGTTACAGATAAG680 GlyAsnIleGluSerAspIleAspIleAspSerLeuValThrAspLys 195200205210 GTG GTGGCAGCTCTTTTAAGTGAAAATGAAGCAGGTGTTAACTTTGCA728 ValValAlaAlaLeuLeuSerGluAsnGluAlaGlyValAsnPheAla 215220225 AGA GATATTACAGATATTCAAGGCGAAACTCATAAGGCAGATCAAGAT776 ArgAspIleThrAspIleGlnGlyGluThrHisLysAlaAspGlnAsp 230235240 AAAAT TGATATTGAATTAGACAATATTCATGAAAGTGATTCCAATATA824 LysIleAspIleGluLeuAspAsnIleHisGluSerAspSerAsnIle 245250255 ACAGAAACTA TTGAAAATTTAAGGGATCAGCTTGAAAAAGCTACAGAT872 ThrGluThrIleGluAsnLeuArgAspGlnLeuGluLysAlaThrAsp 260265270 GAAGAGCATAAAAAAGAG ATTGAAAGTCAGGTTGATGCTAAAAAGAAA920 GluGluHisLysLysGluIleGluSerGlnValAspAlaLysLysLys 275280285290 CAAAAGGAAGAGCTA GATAAAAAGGCAATAAATCTTGATAAAGCTCAG968 GlnLysGluGluLeuAspLysLysAlaIleAsnLeuAspLysAlaGln 295300305 CAAAAATTAGATTC TGCTGAAGATAATTTAGATGTTCAAAGAAATACT1016 GlnLysLeuAspSerAlaGluAspAsnLeuAspValGlnArgAsnThr 310315320 GTTAGAGAGAAAATTC AAGAGGATATTAACGAAATTAACAAGGAAAAG1064 ValArgGluLysIleGlnGluAspIleAsnGluIleAsnLysGluLys 325330335 AATTTACCAAAGCCTGGTGAT GTAAGTTCTCCTAAAGTTGATAAGCAA1112 AsnLeuProLysProGlyAspValSerSerProLysValAspLysGln 340345350 CTACAAATAAAAGAGAGCCTGGAAGATTTG CAGGAGCAGCTTAAAGAA1160 LeuGlnIleLysGluSerLeuGluAspLeuGlnGluGlnLeuLysGlu 355360365370 ACTGGTGATGAAAATCAGAAAAGAGA AATTGAAAAGCAAATTGAAATC1208 ThrGlyAspGluAsnGlnLysArgGluIleGluLysGlnIleGluIle 375380385 AAAAAAAGTGATGAAAAGCTTTTAA AAAGTAAAGATGATAAAGCAAGT1256 LysLysSerAspGluLysLeuLeuLysSerLysAspAspLysAlaSer 390395400 AAAGATGGTAAAGCCTTGGATCTTGAT CGAGAATTAAATTCTAAAGCT1304 LysAspGlyLysAlaLeuAspLeuAspArgGluLeuAsnSerLysAla 405410415 TCTAGCAAAGAAAAAAGTAAAGCCAAGGAAGAA GAAATAACCAAGGGT1352 SerSerLysGluLysSerLysAlaLysGluGluGluIleThrLysGly 420425430 AAGTCACAGAAAAGCTTAGGCGATTTGAATAATGATGAAA ATCTTATG1400 LysSerGlnLysSerLeuGlyAspLeuAsnAsnAspGluAsnLeuMet 435440445450 ATGCCAGAAGATCAAAAATTACCTGAGGTTAAAAAAT TAGATAGCAAA1448 MetProGluAspGlnLysLeuProGluValLysLysLeuAspSerLys 455460465 AAAGAATTTAAACCTGTTTCTGAGGTTGAGAAATTA GATAAGATTTTT1496 LysGluPheLysProValSerGluValGluLysLeuAspLysIlePhe 470475480 AAGTCTAATAACAATGTTGGAGAATTATCACCGTTAGAT AAATCTTCT1544 LysSerAsnAsnAsnValGlyGluLeuSerProLeuAspLysSerSer 485490495 TATAAAGACATTGATTCAAAAGAGGAGACAGTTAATAAAGATGT TAAT1592 TyrLysAspIleAspSerLysGluGluThrValAsnLysAspValAsn 500505510 TTGCAAAAGACTAAGCCTCAGGTTAAAGACCAAGTTACTTCTTTGAAT1 640 LeuGlnLysThrLysProGlnValLysAspGlnValThrSerLeuAsn 515520525530 GAAGATTTGACTACTATGTCTATAGATTCCAGTAGTCCTGTATTTTTA 1688 GluAspLeuThrThrMetSerIleAspSerSerSerProValPheLeu 535540545 GAGGTTATTGATCCAATTACAAATTTAGGAACTCTTCAACTTATTGAT 1736 GluValIleAspProIleThrAsnLeuGlyThrLeuGlnLeuIleAsp 550555560 TTAAATACTGGTGTTAGCCTTAAAGAAAGCACTCAGCAAGGCATTCAG 1784 LeuAsnThrGlyValSerLeuLysGluSerThrGlnGlnGlyIleGln 565570575 CGGTATGGAATTTATGAACGTGAAAAAGATTTGGTTGTTATTAAAATG1832 ArgTyrGlyIleTyrGluArgGluLysAspLeuValValIleLysMet 580585590 GATTCAGGAAAAGCTAAGCTTCAGATACTTGATAAACTTGAAAATTTA1880 AspSerGl yLysAlaLysLeuGlnIleLeuAspLysLeuGluAsnLeu 595600605610 AAAGTGGTATCAGAGTCTAATTTTGAGATTAATAAAAATTCATCTCTT1928 LysV alValSerGluSerAsnPheGluIleAsnLysAsnSerSerLeu 615620625 TATGTTGATTCTAAAATGATTTTAGTAGCTGTTAGGGATAAAGATAGT1976 Tyr ValAspSerLysMetIleLeuValAlaValArgAspLysAspSer 630635640 AGTAATGATTGGAGATTGGCCAAATTTTCTCCTAAAAATTTAGATGAG2024 SerAsn AspTrpArgLeuAlaLysPheSerProLysAsnLeuAspGlu 645650655 TTTATTCTTTCAGAGAATAAAATTATGCCTTTTACTAGCTTTTCTGTG2072 PheIleLeuSe rGluAsnLysIleMetProPheThrSerPheSerVal 660665670 AGAAAAAATTTTATTTATTTGCAAGATGAGTTTAAAAGTCTAGTTATT2120 ArgLysAsnPheIleTyrL euGlnAspGluPheLysSerLeuValIle 675680685690 TTAGATGTAAATACTTTAAAGAAAGTTAAGTAACTTTACAGTTAGATTTAA2171 LeuAspValAsnThr LeuLysLysValLys 695700 TTTGTATAAATCGTTAAAAAACCAAAAAAGCTAAAAACAAAAGTTTTTTGCTTTTTTAAT2231 ATTTTTTCGGGATGGTGGGATTCGAAC 2258 (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 700 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: MetLysLysMetLeuLeuIlePheSerPhePheLeuIlePheLeuAsn 1 51015 GlyPheProValSerAlaArgGluValAspArgGluLysLeuLysAsp 202530 PheValAsnMetAspLeuGlu PheValAsnTyrLysGlyProTyrAsp 354045 SerThrAsnThrTyrGluGlnIleValGlyIleGlyGluPheLeuAla 5055 60 ArgProLeuThrAsnSerAsnSerAsnSerSerTyrTyrGlyLysTyr 65707580 PheIleAsnArgPheIleAspAspGlnAspLysLysAlaSerValAsp 859095 ValPheSerIleGlySerLysSerGluLeuAspSerIleLeuAsnLeu 100105110 ArgArgIleL euThrGlyTyrLeuIleLysSerPheAspTyrAspArg 115120125 SerSerAlaGluLeuIleAlaLysValIleThrIleTyrAsnAlaVal 130135 140 TyrArgGlyAspLeuAspTyrTyrLysGlyPheTyrIleGluAlaAla 145150155160 LeuLysSerLeuSerLysGluAsnAlaGlyLeuSer ArgValTyrSer 165170175 GlnTrpAlaGlyLysThrGlnIlePheIleProLeuLysLysAspIle 180185190 LeuSerGlyAsnIleGluSerAspIleAspIleAspSerLeuValThr 195200205 AspLysValValAlaAlaLeuLeuSerGluAsnGluAlaGlyValAsn 210 215220 PheAlaArgAspIleThrAspIleGlnGlyGluThrHisLysAlaAsp 225230235240 GlnAspLysIleAspIleGluLeu AspAsnIleHisGluSerAspSer 245250255 AsnIleThrGluThrIleGluAsnLeuArgAspGlnLeuGluLysAla 260265 270 ThrAspGluGluHisLysLysGluIleGluSerGlnValAspAlaLys 275280285 LysLysGlnLysGluGluLeuAspLysLysAlaIleAsnLeuAspLys 290295300 AlaGlnGlnLysLeuAspSerAlaGluAspAsnLeuAspValGlnArg 305310315320 AsnThrValArgG luLysIleGlnGluAspIleAsnGluIleAsnLys 325330335 GluLysAsnLeuProLysProGlyAspValSerSerProLysValAsp 340 345350 LysGlnLeuGlnIleLysGluSerLeuGluAspLeuGlnGluGlnLeu 355360365 LysGluThrGlyAspGluAsnGlnLysArgGluIle GluLysGlnIle 370375380 GluIleLysLysSerAspGluLysLeuLeuLysSerLysAspAspLys 385390395400 Al aSerLysAspGlyLysAlaLeuAspLeuAspArgGluLeuAsnSer 405410415 LysAlaSerSerLysGluLysSerLysAlaLysGluGluGluIleThr 420425430 LysGlyLysSerGlnLysSerLeuGlyAspLeuAsnAsnAspGluAsn 435440445 LeuMetMetProGluAspGlnLysL euProGluValLysLysLeuAsp 450455460 SerLysLysGluPheLysProValSerGluValGluLysLeuAspLys 465470475 480 IlePheLysSerAsnAsnAsnValGlyGluLeuSerProLeuAspLys 485490495 SerSerTyrLysAspIleAspSerLysGluGluThrValAsnLys Asp 500505510 ValAsnLeuGlnLysThrLysProGlnValLysAspGlnValThrSer 515520525 LeuAsnGluAspLe uThrThrMetSerIleAspSerSerSerProVal 530535540 PheLeuGluValIleAspProIleThrAsnLeuGlyThrLeuGlnLeu 545550 555560 IleAspLeuAsnThrGlyValSerLeuLysGluSerThrGlnGlnGly 565570575 IleGlnArgTyrGlyIleTyrGluArgGluLysA spLeuValValIle 580585590 LysMetAspSerGlyLysAlaLysLeuGlnIleLeuAspLysLeuGlu 595600605 Asn LeuLysValValSerGluSerAsnPheGluIleAsnLysAsnSer 610615620 SerLeuTyrValAspSerLysMetIleLeuValAlaValArgAspLys 625630 635640 AspSerSerAsnAspTrpArgLeuAlaLysPheSerProLysAsnLeu 645650655 AspGluPheIleLeuSerGluAs nLysIleMetProPheThrSerPhe 660665670 SerValArgLysAsnPheIleTyrLeuGlnAspGluPheLysSerLeu 675680 685 ValIleLeuAspValAsnThrLeuLysLysValLys 690695700

## Claims

1. An assay for identifying in samples suspected of containing Borrelia burgdorferi, the presence of a chromosomal gene of Borrelia burgdorferi which encodes a conserved antigen of approximately 79 kD, comprising contacting the isolate with a nucleic acid probe which binds specifically to the gene, wherein the nucleotide sequence of said gene consists of SEQ ID NO:1, under conditions sufficiently stringent to assure specific binding and detecting said binding as identification of Borrelia burgdorferi.

2. An assay as in claim 1, wherein the contacting step includes contacting the sample with a nucleic acid primer pair which binds specifically to the gene, wherein the nucleotide sequence of said gene consists of SEQ ID NO:1, under conditions sufficiently stringent to assure specific binding, performing polymerase chain reaction and detecting the product of said reaction as identification of Borrelia burgdorferi.

3. A diagnostic kit comprising a labeled nucleic acid probe in a container, wherein the probe binds specifically to a chromosomal gene of Borrelia burgdorferi consisting of SEQ ID NO:1 which encodes a conserved antigen of approximately 80 kD under conditions sufficiently stringent to assure specific binding, and instructions setting forth the detection method of claim 1.