WO2008083432A1 - Recombinant antibodies - Google Patents

Abstract

A recombinant antibody fragment having a binding specificity for an FMDV antigenic determinant.

Description

RECOMBINANT ANTIBODIES

Field of the Invention

The present invention relates to the field of recombinant antibodies, and more particularly to the generation and screening of recombinant antibodies generated against foot-and-mouth disease virus (FMDV). The present invention also provides various means by which a wide range of FMDV recombinant antibody- based therapeutics, prophylactics and diagnostic reagents may be developed.

Background

Foot-and-mouth disease virus (FMDV) is a positive-sense, single stranded RNA virus belonging to the aphthovirus genus of the family Picornaviridae. Foot and mouth disease (FMD) is a highly contagious viral disease that affects pigs, cattle, sheep, goats and deer. It is spread rapidly by contact with infected animals, transmission on clothing and vehicles, and through the air. The virus multiplies to such an extent in infected animals that their expired air is virtually a cloud of virus.

Economically, foot-and-mouth disease (FMD) is the most important viral disease of livestock worldwide. This was demonstrated by the large FMDV outbreak experienced in the United Kingdom in 2001. This outbreak had devastating effects on the country's livestock and tourism industries costing, according to some estimates, billions of pounds sterling. Many lessons were learned from this large outbreak of FMD and as a result the control and eradication programs for FMD now reflect a global change in culture compared with the mass culling of animals to control an outbreak. The new program requires alternatives that do not involve such a loss of animals and incorporates a combination of exclusion, slaughter and vaccination strategies. Vaccination strategies have been used to help outbreaks; however the key to better use of this approach will be the ability to accurately and reliably differentiate vaccinated from infected animals, which would then allow the option to vaccinate the animals to keep them alive.

Control programmes that use vaccination for viral outbreaks and infections must have an effective system to monitor for continued presence of viral infection within the population. However, vaccination complicates large scale surveillance for the spread of the infection by serological means, as both vaccinated and exposed subjects produce antibody specific to the virus. The antigenic similarity between the infecting virulent field strain of the virus and the viral vaccine (particularly if killed virus is used as a vaccine) hampers the discrimination between infected and vaccinated subjects as vaccination results in the occurrence and persistence of antibodies that are indistinguishable between infected and vaccinated subjects. There are many viral diseases including Foot and Mouth Disease, Avian Influenza (Al), Newcastle disease, West Nile virus and feline immunodeficiency virus (FIV), where monitoring of disease outbreaks and spread is hampered by the inability to distinguish infected from vaccinated subjects.

There is increasing world interest in DIVA (differentiating infected and vaccinated animals) vaccination strategies. Current methods of monitoring include physical tagging of vaccinated animals, the use of sentinel animals, virological testing and the use of recombinant heterologous vaccines. However, these current methods have a number of limitations.

The physical tagging of vaccinated animals involves the individual identification of vaccinated subjects by physical means such as ear tags, leg bands or wing tags. However, these methods are difficult to apply on a large scale due to logistical and economic reasons. The use of unvaccinated sentinel animals is also logistically and economically difficult in many affected countries that have small scale village stocks of at-risk animals, such as poultry flocks or individual cattle. Furthermore, there is also a risk that if sentinels become infected with the virus there is increased risk of spread to humans.

Virological testing of individuals via screening and detection of live virus or RT- PCR surveillance testing is a very expensive and infrastructure heavy process, which is unsuitable for many countries, particularly poorer countries, where diseases such as foot and mouth disease are well established. The methods also suffer from scale-up problems. Furthermore, Virology for detection of virus and RT-PCR testing only provides information relating to the current infection of an individual subject, and does not allow analysis of the infection and/or vaccination history of that subject.

Recently, a number of recombinant heterologous vaccines termed "differentiating infected from vaccinated animals" or DIVA vaccines have been developed. After vaccination with such recombinant vaccines, vaccinated animals produce a different antibody response than for naturally infected animals. Differentiating antibody tests are then used to determine if the subject has been infected with the wild-type virus or the recombinant virus

There is currently a need for improved diagnostic and or therapeutic agents effective against FMDV. In particular there is a need for diagnostics that are capable of differentiating FMDV strains that might be used to track the incursion of exotic strains of FMDV into a particular country and or for differentiating FMDV strains very similar to vaccine FMDV strains from circulating field strains. In addition, there is a need to differentiate between an immune response induced by FMDV vaccines from that induced by field strains. There is also strong demand for new therapeutics capable of combating this devastating disease.

Summary of the Invention

The present invention provides at least a recombinant antibody fragment against FMDV. More particularly, the recombinant antibody fragment will have specificity for an FMDV antigenic determinant and comprise a variable region having a heavy chain (VH) region and or a light chain (V_L) region.

The subject invention also provides polynucleotides encoding specific recombinant antibody fragments as described herein. In a preferred form, the invention provides nucleic acid molecules encoding V_H or V_L regions or single chain antibody fragments comprising VH and V_L regions linked together via a linker.

The present invention also provides a process for identifying recombinant antibody fragments, which process comprises the steps:

(i) amplifying nucleotide sequences comprising VH and VL chains from lymphocytes from a host which has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof;

(ii) generating a library comprising amplified nucleotide sequences from step (i), which library is capable of being screened to identify VH and or VL regions reactive with at least FMDV or an FMDV polypeptide or a fragment thereof; and - A -

(iii) screening said library and selecting at least a recombinant antibody fragment that has an affinity for FMDV or an FMDV polypeptide or a fragment thereof.

Such a method is particularly useful for identifying recombinant FMDV antibodies that may serve as immunodiagnostic and or immunotherapeutic agents that may for example serve as candidate antagonists of FMDV biological activity.

The present invention also provides recombinant FMDV antibodies and methods for identifying recombinant FMDV antibodies that have specificity for binding to the FMDV non-structural protein 3ABC or components or fragments of the FMDV non-structural protein 3ABC. The binding is serotype-independent. These antibodies can be utilised for serotype independent detection of FMDV and for differentiation of infected from vaccinated animals (DIVA) and used in DIVA assays.

The invention also provides a method for detecting the presence of FMDV in a sample comprising contacting said sample with a recombinant FMDV antibody which specifically binds to an FMDV antigen, comprising a variable region having a heavy chain region and a light chain region, and determining binding of said antibody to FMDV antigen in said sample as a determination of FMDV infection in said sample.

Further, the invention provides therapeutic, pharmaceutical or diagnostic compositions as herein described comprising: a recombinant antibody fragment according to the invention, optionally, in combination with a pharmaceutically acceptable excipient, diluent or carrier.

BRIEF DESCRIPTION OF DRAWINGS

The Figures are described as follows:

Figure 1 : Nucleotide sequence of the variable regions of the heavy chain (SEQ ID NO.16-18) and light chain (SEQ ID NO:19-21 ) genes of scFV clones and of single chain antibody fragments comprising VH and VL regions linked together via a linker (for example SEQ ID NO: 22-24.) Figure 2: Deduced amino acid sequences of the variable regions of the heavy (SEQ ID NO: 1-3) and light (SEQ ID NO: 4-6) chain of scFv clones. Deduced amino acid sequences of recombinant antibody fragment selected from combinations of heavy and light chains linked by linker sequence (SEQ ID NO:7 to SEQ ID NO:15).

Figure 3: Amino acid sequence alignment of scFvs CRAb-FM26, -FM27 and - FM29. Sequences identical to the consensus are indicated by dotted lines. Variable heavy (V_H), linker and variable light (V_L) regions are indicated. Immunoglobulin framework regions 1 - 4 (FR1 , FR2, FR3 and FR4) and complementary determining regions 1 - 3 (CDR1 , CDR2 and CDR3) are indicated. CDR regions are highlighted.

Figure 4: Western blot analysis of the binding specificity of three scFvs. Similar quantities of E. coli expressed recombinant proteins FMDV-3A, -3B, -3C, -3ABC and a non-related protein (NRP) were separated on a 12% SDS-PAGE. The membrane was probed with soluble forms of CRAb-FM26, -FM27 and -FM29.

Figure 5: Comparison of CRAb-FM26 and -FM27 in C-ELISA in combination with A) FMDV-3ABC or B) FMDV-3B as the coating antigen. Four positive bovine sera from animals infected with serotypes O1-Manisa, Asiai -India, A22-lraq and C- Oberbayern and two negative sera pools of pre-bleeds obtained from the O/Asia1 and A22/C infected animals were assessed. Sera dilutions of 1/10-1/640 are shown along the x-axis.

Figure 6: Differentiation of infected from naϊve or vaccinated animals by C-ELISA using recombinant reagents. Panels of bovine (six naive, six known positives, and six vaccinates), porcine (six naϊve, four known positives, and six vaccinates) sera were assessed using E. coli expressed FMDV-3ABC as the coating antigen and E. coli expressed CRAb-FM27 as the competing antibody. Detailed Description of the Invention

General

Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in the specification, individually or collectively, and any and all combinations or any two or more of the steps or features.

The present invention is not to be limited in scope by the specific embodiments described herein, which are intended for the purpose of exemplification only. Functionally equivalent products, compositions and methods are clearly within the scope of the invention as described herein.

The entire disclosures of all publications (including patents, patent applications, journal articles, laboratory manuals, books, or other documents) cited herein are hereby incorporated by reference. No admission is made that any of the references constitute prior art or are part of the common general knowledge of those working in the field to which this invention relates.

As used herein the term "derived" and "derived from" shall be taken to indicate that a specific integer may be obtained from a particular source albeit not necessarily directly from that source.

Throughout this specification, unless the context requires otherwise, the word "comprise", or variations such as "comprises" or "comprising", will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.

Other definitions for selected terms used herein may be found within the detailed description of the invention and apply throughout. Unless otherwise defined, all other scientific and technical terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which the invention belongs. Description

The present invention provides novel, recombinant antibody fragments specific for FMDV. The invention also provides methods for the production of these antibody fragments as well as methods for their use in the diagnosis and treatment of FMDV disease. In a highly preferred form of the invention the recombinant antibody fragments comprise: a V_H region selected from the group consisting of SEQ ID NOS:1 to 3, or a homologue of any one of these sequences and or a VL region selected from the group consisting of SEQ ID NOS:4 to 6, or a homologue of any one of these sequences.

The term "recombinant antibody fragment" is used herein to denote any antibody fragment produced using recombinant means or in vitro protein synthesis techniques, and excludes monoclonal antibodies produced by traditional monoclonal antibody techniques. Preferably, such fragments are initially derived from nucleotide sequences encoding heavy and light chain variable regions produced in B-lymphocytes from a host that has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof.

The term "antibody" as used herein, unless indicated otherwise, is used broadly to refer to, for example, Fv fragments, single-chain Fv fragments (scFv), Fab¹ fragments, and F(ab')2 fragments, diabodies, individual V_L chains, individual VH chains, chimeric fusions between VH and or V_L chains and other molecules, and the like.

A homologous sequence is taken to include an amino acid sequence which is at least 60, 70, 80 or 90% identical, preferably at least 95 or 98% identical at the amino acid level over at least 20, 50 or 100 amino acids against which that sequence is compared and will possess FMDV related immunological properties. Homology should typically be considered with respect to those regions of the sequence known to be essential for the function of the protein rather than nonessential neighbouring sequences. Thus, for example, homology comparisons are preferably made over V_H and V_L chain regions and more particularly over those regions of the VH and VL chains that are essential for antigen binding. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express homology in terms of sequence identity. Homology comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate % homology between two or more sequences.

Recombinant antibody fragments including substitutions, deletions and modifications within the scope of the present invention include those antibodies that have binding affinity for at least an FMDV strain. In most instances such antibodies will recognise more than one FMDV strain, however, where binding is specific to a single FMDV strain that recombinant antibody fragment may provide a means to differentially identify that strain.

Deriving recombinant antibody fragments from domestic chickens offers technical advantages over antibodies from other mammalian hosts like mice as the variable region genes in domestic chickens are flanked by constant regions and can easily be amplified using techniques such as polymerase chain reaction (PCR), using a single primer set.

It should be appreciated that the FMDV related recombinant antibody fragment(s) described herein can take a variety of forms. Preferably, the recombinant antibody fragment(s) are scFv fragments, though may also be Fv or Fab¹ fragments that have an affinity for FMDV.

According to the invention the V_H domain and the VL domain within the recombinant antibody fragment may be linked in a single chain to produce a single chain Fv fragment or bound by one or more covalent bonds such as disulphide bonds. Where the recombinant antibody fragment is prepared as a scFv fragment, the V_H domain and the VL domain are preferably linked by a short peptide spacer (usually 15-20 amino acids long) that is introduced at the genetic level during the construction of the scFv. Linkage of VH and V_L regions may be achieved by any method known in the art. For example, a synthetic linker such as a flexible glycine-serine linker may be used. An example of a linker that is illustrated in the Examples herein is (GIy₄Se^. - Ji lt will be appreciated that any VH SEQ ID NOS:1 to 3 may be linked to any V_L region. By pairing different V_H and VL regions to produce recombinant antibody fragments it is possible to change the immunological profile of these fragments. Thus, when referring to the sequences exemplified in this application any of SEQ ID NOS:1 to 3 may be linked to any of SEQ ID NOS:4 to 6. Preferably, however, the sequences are linked via a synthetic linker like (Gly₄Ser)3 in the following order:

SEQ ID NO:1 linked to SEQ ID NO:4; [SEQ ID NO:7] SEQ ID NO:1 linked to SEQ ID NO:5; [SEQ ID NO:8] SEQ ID NO:1 linked to SEQ ID NO:6; [SEQ ID NO:9] SEQ ID NO:2 linked to SEQ ID NO:4; [SEQ ID NO:10] SEQ ID NO:2 linked to SEQ ID NO:5; [SEQ ID NO:11] SEQ ID NO:2 linked to SEQ ID NO:6; [SEQ ID NO:12] SEQ ID NO:3 linked to SEQ ID NO:4; [SEQ ID NO:13] SEQ ID NO:3 linked to SEQ ID NO:5; [SEQ ID NO: 14]

SEQ ID NO:3 linked to SEQ ID NO:6; [SEQ ID NO: 15]

In a preferred embodiment of the invention the recombinant antibody fragment is selected from the group consisting of SEQ ID NO:7 to SEQ ID NO:15, or is a homologue of any of these sequences. In a highly preferred embodiment, the present invention provides recombinant antibody fragments selected from the group consiting of SEQ ID NO:7 (CRAb-FM26), SEQ ID NO: 11 (CRAb-FM27) and SEQ ID NO:15 (CRAb-FM29).

It will be appreciated that the amino acid sequences for V_H and VL regions described herein may also be modified in any manner or form that does not extinguish and more preferably substantially alter the affinity of VH and V_L regions to an FMDV antigen. Such modifications may be naturally and non-naturally occurring. By way of example, the modifications may include, deletions, additions, substitutions, glycosylates, acetylations, phosphorylations, and the like. Examples of amino acid sequence substitution modifications that may be made to recombinant antibody fragments include: (a) one or more aspartic acid residues is substituted with glutamic acid; (b) one or more isoleucine residues is substituted with leucine; (c) one or more glycine or valine residues is substituted with alanine; (d) one or more arginine residues is substituted with histidine; or (e) one or more tyrosine or phenylalanine residues is substituted with tryptophan.

Recombinant antibody fragments in lacking glycosylation and the regions comprising the binding sites for complement and Fc-receptors also lack the natural effector function associated with these regions. Several strategies have been developed to reintroduce these natural effector functions into recombinant antibodies, e.g. the generation of bi-specific antibody fragments for recruitment of effector molecules and cells. For example, FMDV related recombinant antibody fragments may be fused with polypeptide sequences expressing different effector functions, like toxins, enzymes, cytokines, reporter genes (for diagnostic and imaging applications) and the like. Such fragments are not only useful for FMDV diagnosis, but find much greater applications in FMDV immunotherapy and gene therapy. For FMDV therapy, an advantage of recombinant antibody fragments is their small size (the size of a scFv is only about 25 kD), facilitating tissue penetration, bio-distribution and blood clearance. However, it has been shown that somewhat larger fragments (50-80 kD) show in some cases even better pharmacokinetics and that di- or multivalent fragments increase the functional affinity and thereby tissue targeting. Recombinant antibody fragments can furthermore be easily used as building blocks for genetic engineering of new effector mechanisms, affinity maturation, and humanisation.

Therefore, according to another embodiment in the invention the recombinant antibody fragments described may be conjugated with, or attached to other antibodies (or parts thereof) such as monoclonal antibodies. These other antibodies may be reactive with other markers (epitopes) characteristic for the disease against which the antibodies of the invention are directed or may have different specificities chosen, for example, to recruit fragments or cells of the animals immune system to the diseased cells. The antibodies of the invention (or parts thereof) may be linked to such antibodies by conventional chemical or by molecular biological methods.

According to a further aspect of the invention there is provided a multivalent monospecific recombinant antibody fragment comprising two, three, four or more single chain antibody fragments or fragments thereof bound to each other by a connecting structure which protein is not a natural immunoglobulin, each of said recombinant antibody fragments or fragments having a specificity for an FMDV epitope said protein being optionally conjugated with an effector or reporter fragment.

FMDV related recombinant antibody polynucleotide sequences

Determination of the amino acid sequence for a recombinant antibody fragment will reveal information about the likely nucleotide sequence encoding that fragment. Using that information the nucleotide sequence for the recombinant fragment may be obtained. Once the nucleotide sequence for a recombinant antibody fragment has been identified its DNA sequences may be synthesised completely or in part using standard oligonucleotide synthesis techniques. Site- directed mutagenesis and polymerase chain reaction (PCR) techniques may be used as appropriate to modify and or amplify such sequences.

Thus, the subject invention provides also polynucleotides encoding specific recombinant antibody fragments as described herein. The subject polypeptides may be encoded by a wide variety of sequences because of the degeneracy of the genetic code. A person of ordinary skill in the art may readily change a given polynucleotide sequence encoding an FMDV specific antibody into a different polynucleotide encoding the same FMDV specific antibody embodiment. The polynucleotide sequence encoding the antibody may be varied to take into account factors affecting expression such as codon frequency, RNA secondary structure, and the like.

According to the invention there is provided a nucleic acid fragment encoding an isolated recombinant antibody fragment or an allelic variant or analogue or fragments thereof, which is capable of specifically binding FMDV. Specifically, provided are DNA molecules encoding VH or VL regions (for example SEQ ID NO: 16-21 ) or single chain antibody fragments comprising VH and VL regions linked together via a linker (for example SEQ ID NO: 22-24. Most preferably, the nucleotide sequences are selected from the group consisting of (a) DNA molecules set out in SEQ ID NO: 16 to 24 or fragments thereof; (b) DNA molecules that hybridise to the DNA molecules define in (a) or hybridisable fragments thereof; and (c) DNA molecules that encode expression for the amino acid sequence encoded by any of the foregoing DNA molecules.

A polynucleotide is said to "encode" a polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, it can be transcribed and/or translated to produce the mRNA for and/or the polypeptide or a fragment thereof. The anti-sense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced there from.

An "isolated" or "substantially pure" nucleic acid (e.g., RNA, DNA or a mixed polymer) is one which is substantially separated from other cellular components which naturally accompany a native animal sequence or protein, e.g., ribosomes, polymerases, many other animal genome sequences and proteins. The term embraces a nucleic acid sequence or protein that has been removed from its naturally occurring environment, and includes recombinant or cloned DNA isolates and chemically synthesized analogues or analogues biologically synthesized by heterologous systems.

A nucleic acid or fragment thereof is "substantially homologous" ("or substantially similar") to another if, when optimally aligned (with appropriate nucleotide insertions or deletions) with the other nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 60% of the nucleotide bases, usually at least about 70%, more usually at least about 80%, preferably at least about 90%, and more preferably at least about 95-98% of the nucleotide bases.

Alternatively, substantial homology or (identity) exists when a nucleic acid or fragment thereof will hybridise to another nucleic acid (or a complementary strand thereof) under selective hybridisation conditions, to a strand, or to its complement. Selectivity of hybridisation exists when hybridisation that is substantially more selective than total lack of specificity occurs. Typically, selective hybridisation will occur when there is at least about 55% identity over a stretch of at least about 14 nucleotides, preferably at least about 65%, more preferably at least about 75%, and most preferably at least about 90%. The length of homology comparison, as described, may be over longer stretches, and in certain embodiments will often be over a stretch of at least about nine nucleotides, usually at least about 20 nucleotides, more usually at least about 24 nucleotides, typically at least about 28 nucleotides, more typically at least about 32 nucleotides, and preferably at least about 36 or more nucleotides.

Thus, polynucleotides of the invention preferably have at least 75%, more preferably at least 85%, more preferably at least 90% homology to the sequences shown in the sequence listings herein. More preferably there is at least 95%, more preferably at least 98%, homology. Nucleotide homology comparisons may be conducted as described below for polypeptides. A preferred sequence comparison program is the GCG Wisconsin Bestfit program. The default scoring matrix has a match value of 10 for each identical nucleotide and -9 for each mismatch. The default gap creation penalty is -50 and the default gap extension penalty is -3 for each nucleotide.

In the context of the present invention, a homologous sequence is taken to include a nucleotide sequence which is at least 60, 70, 80 or 90% identical, preferably at least 95 or 98% identical at the amino acid level over at least 20, 50, 100, 200, or 300 nucleotides with the nucleotides sequences set out in SEQ ID NOS: 16 to 21.

Generally, the shorter the length of the polynucleotide, the greater the homology required to obtain selective hybridisation. Consequently, where a polynucleotide of the invention consists of less than about 30 nucleotides, it is preferred that the % identity is greater than 75%, preferably greater than 90% or 95% compared with the recombinant antibody fragment nucleotide sequences set out in the sequence listings herein. Conversely, where a polynucleotide of the invention consists of, for example, greater than 50 or 100 nucleotides, the % identity compared with the nucleotide sequences set out in the sequence listings herein may be lower, for example greater than 50%, preferably greater than 60 or 75%.

Nucleic acid hybridisation will be affected by such conditions as salt concentration, temperature, or organic solvents, in addition to the base composition, length of the complementary strands, and the number of nucleotide base mismatches between the hybridising nucleic acids, as will be readily appreciated by those skilled in the art. Stringent temperature conditions will generally include temperatures in excess of 30 degrees C, typically in excess of 37 degrees C, and preferably in excess of 45 degrees C. Stringent salt conditions will ordinarily be less than 1000 mM, typically less than 500 mM, and preferably less than 200 mM. However, the combination of parameters is much more important than the measure of any single parameter. An example of stringent hybridisation conditions is 65⁰C and O.ixSSC (IxSSC = 0.15 M NaCI, 0.015 M sodium citrate pH 7.0).

The "polynucleotide" of this invention include RNA, cDNA, genomic DNA, synthetic forms, and mixed polymers, both sense and antisense strands, and may be chemically or biochemically modified or may contain non-natural or derivatised nucleotide bases, as will be readily appreciated by those skilled in the art. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analogue, internucleotide modifications such as uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.), charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, etc.). Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of the molecule.

The present invention provides recombinant nucleic acids comprising all or part of anyone of SEQ ID NOS:16 to 24. The recombinant construct may be capable of replicating autonomously in a host cell. Alternatively, the recombinant construct may become integrated into the chromosomal DNA of the host cell. Such a recombinant polynucleotide comprises a polynucleotide of genomic, cDNA, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation, 1 ) is not associated with all or a portion of a polynucleotide with which it is associated in nature; 2) is linked to a polynucleotide other than that to which it is linked in nature; or 3) does not occur in nature.

Therefore, recombinant nucleic acids comprising sequences otherwise not naturally occurring are provided by this invention. Although the wild-type sequence may be employed, it will often be altered, e.g., by deletion, substitution or insertion.

A "Recombinant nucleic acid" is a nucleic acid that is not naturally occurring, or which is made by the artificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by either chemical syntheses means, or by the artificial manipulation of isolated segments of nucleic acids, by genetic engineering techniques. Such is usually done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions.

cDNA or genomic libraries generated from lymphocytes caused to be infected with FMDV may be screened as natural sources of the nucleic acids of the present invention, or such nucleic acids may be provided by amplification of sequences resident in genomic DNA or other natural sources, e.g., by PCR. The choice of cDNA libraries normally corresponds to a tissue source that is abundant in mRNA for the desired proteins. Phage libraries are normally preferred, but other types of libraries may be used. Clones of a library are spread onto plates, transferred to a substrate for screening, denatured and probed for the presence of desired sequences.

Techniques for nucleic acid manipulation are described generally, for example, in Sambrook et al., (1989) "Molecular Cloning: a laboratory manual". Sambrook, J., Fritsch, E. F. and Maniatis, T. (eds) (1989). Coldspring Harbour Laboratory Press, Coldspring Harbour, NY or Ausubel et al., (1992) "Current Protocols in Molecular Biology". Ausubel, F. M., Brent, R., Kingston, R.E., Moore, D. D., Seidman, J. G., Smith, J.G. and Struhl, K. (1987). John Wiley and Sons, NY. Reagents useful in applying such techniques, such as restriction enzymes and the like, are widely known in the art and commercially available from such vendors as New England BioLabs, Boehringer Mannheim, Amersham, Promega Biotec, U.S. Biochemicals, New England Nuclear, and a number of other sources. The recombinant nucleic acid sequences used to produce fusion proteins of the present invention may be derived from natural or synthetic sequences. Many natural gene sequences are obtainable from various cDNA or from genomic libraries using appropriate probes. See, GenBank, National Institutes of Health.

Portions of the polynucleotide sequence having at least about eight nucleotides, usually at least about 15 nucleotides, and fewer than about 6 kb, usually fewer than about 1.0 kb, from a polynucleotide sequence encoding FMDV related antibody recombinant fragments are preferred as probes. The probes may also be used to determine whether mRNA encoding antibody recombinant fragments is present in a cell or tissue and whether the genomic organisation of the constituent parts of the antibody recombinant fragments are deleted or otherwise damaged.

In further aspects, the invention also includes cloning and expression vectors containing these DNA sequences, host cells transformed with these DNA sequences and processes for producing the heavy or light chains and antibody fragments comprising expressing these DNA sequences in a transformed host cell.

Identification of recombinant FMDV antibodies

According to a further aspect the invention provides a process for identifying recombinant antibody fragments, which process comprises the steps:

(i) amplifying nucleotide sequences comprising VH and VL chains from lymphocytes from a host which has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof; (ii) generating a library comprising amplified nucleotide sequences from step

(i), which library is capable of being screened to identify V_H and or V_L regions reactive with at least FMDV or an FMDV polypeptide or a fragment thereof; and (iii) screening said library and selecting at least a recombinant antibody fragment that has an affinity for FMDV or an FMDV polypeptide or a fragment thereof.

According to this method nucleotide sequences encoding V_H and V_L region fragments are derived from B-lymphocytes from a host, which has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof. Selecting such nucleotide sequences and using them to generate recombinant antibody fragments generates a level of certainty that the VH and V_L chains will be specific for the FMDV agent that provoked the antibody production in the B-lymphocyte. Moreover, by selecting B-lymphocytes infected with a particular virus as the source for nucleotide sequences for generating recombinant antibody fragments, problems attendant with differential antigen presentation and hence differential immune responses between different animal species may be ameliorated.

Any system capable of generating a library comprising amplified nucleotide sequences from step (i), which library is capable of being screened to identify VH and V_L chains reactive with at least FMDV or an FMDV polypeptide or a fragment thereof may be used in the described method. Preferably, phage display technology is used to generate and screen the library such technology.

Phage displayed recombinant antibody libraries offer a number of advantages over other systems in that they allow expression of conformational epitopes and enable the use of strong selection procedures for the isolation of strain specific antibodies. The isolation of FMDV specific recombinant antibody fragments from chickens has the advantage of obtaining antibodies from the normal host. In addition, they offer technical advantages over antibodies from other mammalian hosts like mouse as the V region genes in chickens are flanked by constant regions and can easily be amplified by PCR using a single primer set. Large libraries of diverse antibody combining sites can be expressed in E.coli by bacteriophage and can be easily screened.

Phage display is a technique for the expression or ^'display¹ of a peptide or protein on the surface of a filamentous phage. This is accomplished by the insertion of a gene or gene fragment in a phage surface protein gene. Provided that the reading frame is correct and that the insert does not interfere with the essential functions of the surface protein, the insert will result in a fusion protein on the phage surface. If the peptide is well exposed on the phage surface it will be available to act as a ligand, enzyme, immunogen or otherwise actively participate in a biochemical process. The insertion of random oligonucleotide sequences such as those derived from B-lymphocytes from a host, which has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof, provides a means of constructing extensive peptide libraries that may be screened to select peptides with specific affinities or activities against FMDV molecules.

Separation of phage particles expressing different peptide inserts in the phage

_* surface protein may be accomplished by any method known in the art. One such method of affinity selection is a method called panning. This strategy allows one to test a myriad of structures for optimal function without detailed information about the relationship between the function and the structure.

Filamentous phage are ideal as in vitro selection vehicles because they have small genomes in which large libraries, consisting of a number of different genes or gene fragments, are easily constructed. The viral particles (virions) are stable to potential elution conditions such as low pH and they accumulate to high titers (10¹² ml^"1) so that every clone in a gene library can be well represented. Some commonly used phage particles are M13, fd, and f1. The phage have ten different genes of which the two that have been used in phage display are gene III (gill) and gene VIII (gVIII). Gene III encodes a protein at the proximal end of the phage, protein III (pill). Protein III is required for infection of E. coli and binds to the end of the pili of the bacteria. Gene VIII encodes a major coat protein, protein VIII (pVIII), and is therefore present in approximately 2700 copies in comparison with gene III that is present in 3-5 copies depending on the phage used.

Phage display technology can be performed in two different ways, polyvalent phage display and monovalent phage display. In both methods the insertion is usually done near the amino-terminal end between the amino- and carboxy- terminal domains. In polyvalent phage display, small foreign DNA fragments are inserted into the phage surface protein gene. In this method the peptide is expressed in multiple copies on the phage produced, i.e. the peptide is expressed in all copies of the gene product. In polyvalent display the fusion using pill cannot have a too large insert since it will affect the infectivity of the phage. Fusion using pVIII is even more limited by the size of the insert, since larger peptides than 6-10 amino acids will probably interfere with the packaging process. For monovalent phage display, the gene fusion is constructed in a phagemid where DNA fragments of varying sizes are inserted in the phage surface protein gene. A phagemid is a plasmid with the intergenic sequence from the phage that is used and the phage origin of replication, but it lacks all other phage genes and can therefore not give rise to new phage. The intergenic sequence contains the packing sequence used for phage construction. The virions are produced after infection of the cells harbouring the phagemid with a helper phage. The helper phage provide for those functions and genes the phagemid lacks and also contains the wild type gene for the surface protein. The helper phage is packaging-deficient, meaning that the intergenic region of the genome is not as efficient as in the phagemid. The phagemid is then transferred into a bacterial host (eg E. coli). Selection by antibiotic resistance will result in only bacteria that have acquired the phagemid growing. The number of clones that are required to cover the whole genome is dependent of the size of the gene insert. While the helper phage supplies wild-type protein in large excess, only approximately 10 % of the phagemid population will display one copy of the fusion protein. This system removes the problem of a protein fusion affecting the phage packing properties and functions in the case where all of the proteins have an insertion. Insertion of the amber stop codon TAG is commonly interposed between the foreign gene and the gene used for the fusion. The stop codon is suppressed in suitable strains to allow phage production and allows for easy production of soluble protein by transfer to a non-suppressor strain.

According to a highly preferred form of the method described herein the library is generated using a phagemid system. The efficacy of such a system is largely dependant on the phagemid vector selected and used. Numerous phagemid vectors are commercially available: Amersham Pharmacia Biotech, Sweden; Maxim Biotech, USA; Mediators Diagnostika, Austria; Mobitec, Germany; New England Biolabs, USA; Stratagene, USA. Desirably, however, the selected vector enables the direct sequential ligation of heavy and or light chain nucleotide sequences. By using such a vector, a higher diversity of recombinant antibodies may be generated.

A particularly preferred phagemid vector that may be used in the described method is pCANTAB-link. This vector is based on pCANTAB 5E. However, it encodes a polypeptide linker region (Gly4Ser)3 flanked by two multiple cloning regions. PCR fragments for V_H or VL can be sequentially ligated into unique restriction sites upstream (Sfil, Ncol, Ascl, Pstl and Xbal) or downstream (Sail, EcoRV and Notl) of the linker. This vector eliminates the inefficient and problematic PCR assembly step, replacing it with sequential ligation of V_H and V_L chains directly into the vector. Using this vector much higher diversities of recombinant antibody scFv libraries can be generated by sequential ligation of VH and V_L PCR fragments into pCANTAB-link vector than by using pCANTAB 5E. The presence of unique restriction sites between the polypeptide linker and the variable fragments also offers the option for easy downstream modifications of libraries/clones such as convenient shuffling of V_H and VL fragments or the exchange of different polypeptide linkers (for generation of diabodies etc.). The vector can be used for the construction of scFv libraries of any animal species.

Advantages of the highly efficient pCANTAB-link vector for libraries of high diversity compared with pCANTAB 5E may be summarised as follows:

(i) Compatible with pCANTAB 5E system.

(ii) Option of two different cloning strategies:

(a) either direct sequential ligation of V_H and VL PCR fragments

(b) or ligation of PCR assembly products (used like pCANTAB 5E). (iii) Contains additional unique restriction enzyme sites for subcloning and screening.

(iv) Contains region for polypeptide linker (G₄S)₃ (vector without linker is also available).

(v) Facilitates easy replacement of different polypeptide linkers or shuffling of VH and V_L chains to generate new combinatorial libraries.

(vi) Can be used to construct scFv libraries of any species.

Therefore, in a preferred form of the above method the recombinant FMDV antibody fragment is identified according to the following method:

(i) lymphocytes are obtained from the spleen of chickens immunised against an infectious bursal disease strain;

(ii) mRNA is extracted from those Lymphocytes and transcribed into cDNA;

(iii) VH and V_L chain genes are then amplified and purified;

(iv) purified VH and V_L chains are then joined together via the use of a synthetic linker to yield scFv fragments; (v) the scFv fragments are then cloned into an expression vector and transformed into a suitable host;

(vi) with the aid of a helper phage, recombinant phage specific for FMDV are selected by panning against a plate coated with FMDV antigens; and

(vii) Phage specific for FMDV antigens are eluted off and grown up individually.

In an even more preferred form of the invention, steps (iv) and (v) are combined and a pCANTAB-link vector is used as the expression vector. Thus Purified V_H and V_L chains are ligated directly into a pCANTAB-link vector which contains a synthetic linker to yield scFv fragments. The vector is then transformed into a suitable host.

After, the nucleotide sequences of V_H and V_L chains are cloned into the vector a library of recombinant antibody fragments is generated. Techniques for inserting such vectors into cells are conventional, for example, transformation, electroporation, protoplast fusion and transfection are examples of well-known methods. The host cells that may be used for this step in the method may be bacterial (for example E. coli), fungi, algae, mammalian cells or any other prokaryote or eukaryotic cell. Desirably the host cell is E. coli.

The recombinant antibody fragments of interest can be selected by techniques known to persons skilled in the art. Such techniques include those based on affinity interaction. Standard procedures use either antigens coated directly or indirectly (e.g using streptavidin) onto plastic surfaces (plates or immunotubes) or antigens that are biotinylated and coupled to strepavidin-coated paramagnetic beads. Selections can be carried out with whole cells or even living organisms. Usually, the antigens are incubated with phage display libraries and specifically bound phage are eluted after each round. Desirably, the antibody of interest is detected by the technique of panning, which is known to persons skilled in the art.

Preparation of recombinant or chemically synthesized FMDV related recombinant antibody nucleic acids; vectors, transformation, host cells

Once the amino acid constitution for a recombinant antibody fragment is known, that fragment may be reproduced by any means known in the recombinant DNA art. It should be appreciated that one of the significant advantages of using recombinant antibody fragments over traditional antibody preparation techniques is that such antibodies can be produced in large volume using standard protein production techniques.

Any FMDV related recombinant antibody nucleic acid specimen, in purified or non-purified form, can be utilised as the starting nucleic acid or acids for the preparation of recombinant antibody fragment(s).

Functional gene fragments utilised herein may be extracted as mRNA from any tissue sample, such as blood, tissue material (eg B lymphocytes) and the like and converted to cDNA by reverse transcription by a variety of techniques such as that described by Maniatis, et. al. in Molecular Cloning:A Laboratory Manual, Cold Spring Harbor, N.Y., p 280-281 , 1982). If the extracted sample has not been purified, it may be treated before amplification with an amount of a reagent effective to open the cells, or animal cell membranes of the sample, and to expose and/or separate the strand(s) of the nucleic acid(s). This lysing and nucleic acid denaturing step to expose and separate the strands will allow amplification to occur much more readily.

PCR is one such process that may be used to amplify FMDV related recombinant antibody gene sequences. This technique may amplify, for example, DNA or RNA, including messenger RNA, wherein DNA or RNA may be single stranded or double stranded. In the event that RNA is to be used as a template, enzymes, and/or conditions optimal for reverse transcribing the template to DNA would be utilised. In addition, a DNA-RNA hybrid that contains one strand of each may be utilised. A mixture of nucleic acids may also be employed, or the nucleic acids produced in a previous amplification reaction described herein, using the same or different primers may be so utilised.

The specific nucleic acid sequence to be amplified, i.e., the polymorphic gene sequence, may be a fraction of a larger molecule or can be present initially as a discrete molecule, so that the specific sequence constitutes the entire nucleic acid. It is not necessary that the sequence to be amplified is present initially in a pure form; it may be a minor fraction of a complex mixture, such as contained in whole human DNA. A double-stranded fragment may be obtained from the single-stranded product of chemical synthesis either by synthesizing the complementary strand and annealing the strands together under appropriate conditions or by adding the complementary strand using DNA polymerase with an appropriate primer sequence.

Large amounts of the polynucleotides of the present invention may also be produced by replication in a suitable host cell. Natural or synthetic polynucleotide fragments coding for a desired fragment will be incorporated into recombinant polynucleotide constructs, usually DNA constructs, capable of introduction into and replication in a prokaryotic or eucaryotic cell. Usually the polynucleotide constructs will be suitable for replication in a unicellular host, such as yeast or bacteria, but may also be intended for introduction to (with and without integration within the genome) cultured mammalian or plant or other eucaryotic cell lines.

Polynucleotides of the invention may be incorporated into a recombinant replicable vector for introduction into a prokaryotic or eucaryotic host. Such vectors may typically comprise a replication system recognized by the host, including the intended polynucleotide fragment encoding the desired polypeptide, and will preferably also include transcription and translational initiation regulatory sequences operably linked to the polypeptide encoding segment. Expression vectors may include, for example, an origin of replication or autonomously replicating sequence (ARS) and expression control sequences, a promoter, an enhancer and necessary processing information sites, such as ribosome-binding sites, RNA splice sites, polyadenylation sites, transcriptional terminator sequences, and mRNA stabilizing sequences. Secretion signals may also be included where appropriate, which allow the protein to cross and/or lodge in cell membranes, and thus attain its functional topology, or be secreted from the cell. For example, a recombinant antibody fragment may be expressed with a bacterial leader sequence at the N-terminus capable of driving export of the protein to the periplasmic space. There, the various domains of the recombinant antibody molecules may fold into functionally active proteins. Such vectors may be prepared by means of standard recombinant techniques well known in the art and discussed, for example, in Sambrook et al., 1989 supra or Ausubel et al. 1992 supra.

An appropriate promoter and other necessary vector sequences will be selected so as to be functional in the host. Examples of workable combinations of cell lines and expression vectors are described in Sambrook et al., 1989 or Ausubel et al., 1992. Many useful vectors are known in the art and may be obtained from such vendors as Stratagene, New England Biolabs, Promega Biotech, and others. Promoters such as the trp, lac and phage promoters, tRNA promoters and glycolytic enzyme promoters may be used in prokaryotic hosts. Useful yeast promoters include promoter regions for metallothionein, 3-phosphoglycerate kinase or other glycolytic enzymes such as enolase or glyceraldehyde-3- phosphate dehydrogenase, enzymes responsible for maltose and galactose utilization, and others. Vectors and promoters suitable for use in yeast expression are further described in Hitzeman et al., EP 73.675A. Appropriate non-native mammalian promoters might include the early and late promoters from SV40 or promoters derived from murine Moloney leukaemia virus, mouse tumour virus, avian sarcoma viruses, adenovirus II, bovine papilloma virus or polyoma. In addition, the construct may be joined to an amplifiable gene (e.g., DHFR) so that multiple copies of the gene may be made. For appropriate enhancer and other expression control sequences.

While such expression vectors may replicate autonomously, they may also replicate by being inserted into the genome of the host cell, by methods well known in the art.

Expression and cloning vectors will likely contain a selectable marker, a gene encoding a protein necessary for survival or growth of a host cell transformed with the vector. The presence of this gene ensures growth of only those host cells that express the inserts. Typical selection genes encode proteins that a) confer resistance to antibiotics or other toxic substances, e.g. ampicillin, neomycin, methotrexate, etc.; b) complement auxotrophic deficiencies, or c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli. The choice of the proper selectable marker will depend on the host cell, and appropriate markers for different hosts are well known in the art.

The vectors containing the nucleic acids of interest can be transcribed in vitro, and the resulting RNA introduced into the host cell by well-known methods, e.g., by injection, or the vectors can be introduced directly into host cells by methods well known in the art, which vary depending on the type of cellular host, including electroporation; transfection employing calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other substances; microprojectile bombardment; lipofection; infection (where the vector is an infectious agent, such as a retroviral genome); and other methods. The introduction of the polynucleotides into the host cell by any method known in the art, including, inter alia, those described above, will be referred to herein as "transformation." The cells into which have been introduced nucleic acids described above are meant to also include the progeny of such cells.

Thus the present invention provides host cells transformed or transfected with a nucleic acid molecule of the invention. Preferred host cells include bacteria, yeast, mammalian cells, plant cells, insect cells, and human cells in tissue culture. Illustratively, such host cells are selected from the group consisting of E. coli, Pseudomonas, Bacillus, Streptomyces, yeast, CHO, R1.1 , B-W, L-M, COS 1. COS 7, BSC1 , BSC40, BMT10, and Sf9 cells.

Also provided are mammalian cells containing an FMDV antibody polypeptide encoding DNA sequence and modified in vitro to permit higher expression of FMDV related antibody polypeptides by means of a homologous recombinational event.

The general methods for construction of the vector of the invention, transfection of cells to produce the host cell of the invention, culture of cells to produce the antibody of the invention are all conventional molecular biology methods. Likewise, once produced, the recombinant antibody fragments of the invention may be purified by standard procedures of the art, including cross-flow filtration, ammonium sulphate precipitation, affinity column chromatography, gel electrophoresis and the like. Thus, the present invention also provides methods for preparing an FMDV related antibody polypeptide comprising: (a) culturing a cell as described above under conditions that provide for expression of the FMDV related antibody polypeptide; and (b) recovering the expressed FMDV related antibody polypeptide. This procedure can also be accompanied by the steps of: (c) chromatographing the polypeptide using any suitable means known in the art; and (d) purifying the polypeptide by for example gel filtration.

The present invention also provides for host cells transformed with two or more expression vectors of the invention, the first vector containing an operon encoding a VH chain derived polypeptide and the second containing an operon encoding a VL chain derived polypeptide. The two vectors may contain different selectable markers but, with the exception of the V_H and V_L chain coding sequences, are preferably identical. This procedure provides for equal expression of V_H and V_L chain polypeptides. Alternatively, a single vector may be used which encodes both VH and V_L chain polypeptides. The coding sequences for the VH and V_L chains may comprise cDNA or genomic DNA or both. In a preferred embodiment of this aspect of the invention at both vectors provide leader sequences capable of directing the expressed proteins out of the cell, most preferably into the periplasm where disulphide bond formations may occur.

Many uses for antibodies, which have been produced using the disclosed methods, are contemplated, including diagnostic and therapeutic uses.

Diagnostic use and detection of FMDV

The present invention also provides the above antibody fragments, detectably labeled, as described below, for use in diagnostic methods for in vitro or in vivo detection of FMDV.

(i) FMDV related recombinant antibody polypeptide fragments

The recombinant antibody fragments of the present invention may be employed in any known antibody associated assay method. For example, the recombinant antibody fragments of the present invention are useful for immunoassays that detect or quantitate FMDV in a sample. For example they may be employed in competitive binding assays, direct and indirect sandwich assays, or immune-precipitation assays and immunohistochemistry assays.

An immunoassay for FMDV will typically comprise incubating a biological sample in the presence of a detectably labeled recombinant antibody fragment capable of binding to FMDV and detecting the labeled antibody which is bound in a sample. Various clinical immunoassay procedures are described in Immunoassays for the 80s, A. Voller eds, University Park, 1981.

Thus in an embodiment of the diagnostic uses of FMDV related recombinant antibody fragments, the antibody fragment or a biological sample may be added to nitrocellulose, or other solid support that is capable of immobilizing cells, cell particles or soluble proteins. The support may then be washed with suitable buffers followed by treatment with the detectably labeled recombinant antibody fragment. The solid phase support may then be washed with the buffer a second time to remove unbound antibody fragments. The amount of bound label on said solid support may then be detected by conventional means.

By "solid phase support" or "carrier" is intended any support capable of binding antigen or antibodies. Well-known supports or carriers, include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, agaroses, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to FMDV or. Thus, the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod.

Alternatively, the surface may be flat such as a sheet, test strip, etc. Preferred supports include polystyrene beads. Those skilled in the art will know many other suitable carriers for binding recombinant antibody fragments or antigen, or will be able to ascertain the same by use of routine experimentation.

For diagnostic applications, the recombinant antibody fragment typically will be labelled directly or indirectly with a detectable moiety. The detectable moiety can be any one, which is capable of producing, either directly or indirectly, a detectable signal. Any method known in the art for separately conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature 144:945 (1962); David et al., Biochemistry 13:1014 (1974); Pain et al., J. Immunol. Meth. 40:219 (1981); and Nygren, J. Histochem. and Cytochem. 30:407 (1982).

The recombinant antibody fragment can be fused to a short immunogenic peptide sequence which is detected by an antibody directed against it.

Enzymes which can be used to detectably label the FMDV-specific antibodies of the present invention include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5-steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-6- phosphate dehydrogenase, giucoamylase and acetylcholinesterase.

By radioactively labeling the recombinant antibody fragments, it is possible to detect FMDV through the use of a radioimmunoassay (RIA) (see, for example, Work, T.S., et al., Laboratory Techniques and Biochemisty in Molecular Biology, North Holland Publishing Company, N.Y. (1978). The radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography. Isotopes which are particularly useful for the purpose of the present invention are: ³H, ¹⁴C, ³²P, ³⁵S, ¹²⁵I or ¹³¹I and preferably, ¹²⁵I .

It is also possible to label the recombinant antibody fragments with a fluorescent compound. When the fluorescent labeled recombinant antibody fragment is exposed to light of the proper wave length, its presence can then be detected due to fluorescence. Among the most commonly used fluorescent labelling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, 2-phthaldehyde and fluorescamine.

The recombinant antibody fragments can also be detectably labeled using fluorescence-emitting metals such as ¹⁵²Eu, or others of the lanthanide series. These metals can be attached to the MF-specific antibody using such metal chelating groups as diethylenetriaminepentaacetic acid or ethylenediamine- tetraacetic acid.

The recombinant antibodies also can be detectably labeled by coupling to a chemiluminescent compound. The presence of the chemiluminescently labeled antibody is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are isoluminol, theromatic acridinium ester, imidazole, acridinii salt and oxalate ester.

Likewise, a bioluminescent compound may be used to label the recombinant antibody of the present invention. Bioluminescence is a type of chemiluminescence found in biological systems in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin.

Detection of the recombinant antibody may be accomplished by a scintillation counter, for example, if the detectable label is a radioactive gamma emitter, or by a fluorometer, for example, if the label is a fluorescent material. In the case of an enzyme label, the detection can be accomplished by colorometric methods which employ a substrate for the enzyme. Detection may also be accomplished by visual comparison of the extent of enzymatic reaction of a substrate in comparison with similarly prepared standards.

For the purposes of the present invention, FMDV which is detected by the above assays may be present in a biological sample. Any sample containing FMDV can be used. Preferably, the sample is a tissue extract or homogenate, allantoic fluid, or any biological fluid such as, for example, blood, serum, lymph, urine, inflammatory exudate, cerebrospinal fluid, and the like and fixed tissue (like in formalin fixed and paraffin embedded blocks) and tissue impression smears. However, the invention is not limited to assays using only these samples, it being possible for one of ordinary skill in the art to determine suitable conditions which allow the use of other samples. In situ detection may be accomplished by removing a histological specimen from a patient, and providing the combination of labeled antibodies of the present invention to such a specimen. The antibody (or fragment) is preferably provided by applying or by overlaying the labeled antibody (or fragment) to a biological sample.

Therefore according to an embodiment of the invention there is provided a method for detecting presence of FMDV in a sample comprising contacting said sample with a recombinant antibody fragment which specifically binds to an FMDV antigen, comprising a VR region and a V_L region, said VH region having an amino acid sequence selected from the group consisting of SEQ ID NOS:1 to 3, and said V_L region having an amino acid sequence selected from the group consisting of SEQ ID NOS:4 to 6, and determining binding of said recombinant antibody fragments to FMDV antigen in said sample as a determination of FMDV presence in said sample.

It will be appreciated that by varying the VH and V_L regions employed in the antibody fragments it is possible to alter the affinity and hence possible use to which said antibodies may be put. For example, SEQ ID NO:7 to SEQ ID NO: 15 show varying degrees of specificity for FMDV strains. Thus different fragments may be employed in differing diagnostic applications. Such fragments may be employed to identify the presence of FMDV in a sample and those that react strongly with denatured FMDV samples may be used as diagnostic reagents on fixed and/or denatured diagnostic samples such as in immunohistochemistry of fixed infected tissue and in protein blotting applications.

The recombinant antibodies, for example such as described in the example herein SEQ ID NO:1 to SEQ ID NO:15 can be packaged into diagnostic kits. Diagnostic kits include the recombinant antibodies which may be labelled; alternatively, the recombinant antibodies may be unlabeled and the ingredients for labelling may be included in the kit. The kit may also contain other suitably packaged reagents and materials needed for the particular antigen or antibody detection, for example, standards, as well as instructions for conducting the test. Recombinant antibody fragments are also useful for the affinity purification of FMDV from recombinant cell culture or natural sources. (ii) FMDV related recombinant antibody polynucleotide fragments

Polynucleotides encoding recombinant antibody fragments may also be used to provide diagnostic analysis. For example, allele specific oligonucleotide primers derived from FMDV related recombinant antibody gene sequences, particular those gene sequences encoding FMDV neutralising recombinant antibodies described herein may be useful in determining whether an animal is at risk of suffering from an FMDV ailment. Alternatively by detecting changes in the transcription of and or translation of polynucleotide sequences described herein it will be possible to identify whether a particular host is suffering from a particular FMDV ailment. Therefore through the use of such a procedure, it is possible to determine not only the presence of FMDV but also the distribution of FMDV in the examined tissue.

According to one detection system recombinant antibody polynucleotides may be identified using PCR related technologies. Many different PCR related technologies suitable for such use are known in the field. Such methodologies are broadly described in Ausubel, F., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J. G., Smith, J.A., Struhl, K. Current protocols in molecular biology. Greene Publishing Associates/Wiley Intersciences, New York and are incorporated herein by reference.

Primers used in any diagnostic assays derived from the present invention should be of sufficient length and appropriate sequence to provide initiation of polymerisation. Environmental conditions conducive to synthesis include the presence of nucleoside triphosphates and an agent for polymerisation, such as DNA polymerase, and a suitable temperature and pH.

Primers are preferably single stranded for maximum efficiency in amplification, but may be double stranded. If double stranded, primers may be first treated to separate the strands before being used to prepare extension products. Primers should be sufficiently long to prime the synthesis of extension products in the presence of the inducing agent for polymerisation. The exact length of a primer will depend on many factors, including temperature, buffer, and nucleotide composition. Oligonucleotide primers will typically contain 12-20 or more nucleotides, although they may contain fewer nucleotides. The deoxyribonucleotide triphosphates dATP, dCTP, dGTP and dTTP are added to the synthesis mixture, either separately or together with the primers, in adequate amounts and the resulting solution is heated to about 90 - 100⁰C from about 1 to 10 minutes, preferably from 1 to 4 minutes. After this heating period, the solution is allowed to cool, which is preferable for the primer hybridisation. To the cooled mixture is added an appropriate agent for effecting the primer extension reaction (called herein "agent for polymerisation"), and the reaction is allowed to occur under conditions known in the art. The agent for polymerisation may also be added together with the other reagents if it is heat stable. This synthesis (or amplification) reaction may occur at room temperature up to a temperature above which the agent for polymerisation no longer functions. Thus, for example, if DNA polymerase is used as the agent, the temperature is generally no greater than about 40⁰C. Most conveniently the reaction occurs at room temperature.

Some other useful diagnostic techniques for detecting the presence of particular fragments and or mutations to the fragment genes that encode recombinant antibody fragments of particular interest include, but are not limited to: 1) allele- specific PCR; 2) single stranded conformation analysis (SSCA); 3) denaturing gradient gel electrophoresis (DGGE); 4) RNase protection assays; 5) the use of proteins which recognize nucleotide mismatches, such as the E. coli mutS protein; 6) allele-specific oligonucleotides (ASOs); and 7) fluorescent in situ hybridisation (FISH). Other approaches based on the detection of mismatches between the two complementary DNA strands include clamped denaturing gel electrophoresis (CDGE), heteroduplex analysis (HA) and chemical mismatch cleavage (CMC).

In addition to the above methods recombinant antibody fragment genes and mutants thereof may be detected using conventional probe technology. Using the disclosed portions of the isolated FMDV related recombinant antibody polynucleotide fragments as a basis oligomers of approximately 8 nucleotides or more can be prepared, either by excision or synthetically, which hybridise with the FMDV related recombinant antibody polynucleotides.

The probes for FMDV related recombinant antibody polynucleotides (natural or derived) are a preferably of a length which allows the detection of these unique sequences. While 6-8 nucleotides may be a workable length, sequences of 10- 12 nucleotides are preferred, and about 20 nucleotides would be optimal. Preferably, these sequences will derive from regions which lack heterogeneity. These probes can be prepared using routine methods, including automated oligonucleotide synthetic methods.

For use as probes, complete complementarity is desirable, though it may be unnecessary as the length of the fragment is increased. For use of such probes as diagnostics, the biological sample to be analysed is treated, if desired, to extract the nucleic acids contained therein. The resulting nucleic acid from the sample may be subjected to gel electrophoresis or other size separation techniques; alternatively, the nucleic acid sample may be dot blotted without size separation.

When probes are used to detect the presence of the target sequences, the biological sample to be analysed, such as tissue homogenate, may be treated, if desired, to extract the nucleic acids. The sample nucleic acid may be prepared in various ways to facilitate detection of the target sequence; e.g. denaturation, restriction digestion, electrophoresis or dot blotting. The targeted region of the sample nucleic acid usually must be at least partially single-stranded to form hybrids with the targeting sequence of the probe. If the sequence is naturally single-stranded, denaturation will not be required. However, if the sequence is double-stranded, the sequence will probably need to be denatured. Denaturation can be carried out by various techniques known in the art.

Sample nucleic acid and probe are incubated under conditions that promote stable hybrid formation of the target sequence in the probe with the putative targeted sequence in the sample. The region of the probes that is used to bind to the sample can be made completely complementary to the targeted region. Therefore, high stringency conditions are desirable in order to prevent false positives. However, conditions of high stringency may be used only if the probes are complementary to regions of the chromosome that are unique in the genome. The stringency of hybridisation is determined by a number of factors during hybridisation and during the washing procedure, including temperature, ionic strength, base composition, probe length, and concentration of formamide. Under certain circumstances, the formation of higher order hybrids, such as triplexes, quadraplexes, etc., may be desired to provide the means of detecting target sequences.

Detection, if any, of the resulting hybrid is usually accomplished by the use of labelled probes. Alternatively, the probe may be unlabeled, but may be detectable by specific binding with a ligand that is labelled, either directly or indirectly. Suitable labels, and methods for labelling probes and ligands are known in the art, and include, for example, radioactive labels which may be incorporated by known methods (e.g., nick translation, random priming or kinasing), biotin, fluorescent groups, chemiluminescent groups (e.g., dioxetanes, particularly triggered dioxetanes), enzymes, antibodies and the like. Variations of this basic scheme are known in the art, and include those variations that facilitate separation of the hybrids to be detected from extraneous materials and/or that amplify the signal from the labelled moiety.

Two detection methodologies that are particularly effective, work on the principle that a small ligand (such as digoxigenin, biotin, or the like) is attached to a nucleic acid probe capable of specifically binding FMDV related antibody polynucleotides. The small ligand is then detected. In one example, the small ligand attached to the nucleic acid probe might be specifically recognized by an antibody-enzyme conjugate. For example, digoxigenin may be attached to the nucleic acid probe. Hybridisation is then detected by an antibody-alkaline phosphatase conjugate that turns over a chemiluminescent substrate. In a second example, the small ligand may be recognized by a second ligand-enzyme conjugate that is capable of specifically complexing to the first ligand. A well-known example is the biotin- avidin type of interactions.

It is also contemplated within the scope of this invention that the nucleic acid probe assays of this invention will employ a cocktail of nucleic acid probes capable of detecting FMDV related antibody polynucleotides. Thus, in one example to detect the presence of FMDV related antibody polynucleotides in a cell sample, more than one probe complementary to FMDV related antibody polynucleotides is employed and in particular the number of different probes is alternatively 2, 3, or 5 different nucleic acid probe sequences. In another example, to detect the presence of mutations in the FMDV related antibody polynucleotides gene sequence in an animal, more than one probe complementary to FMDV related antibody polynucleotides is employed where the cocktail includes probes capable of binding to an allele-specific mutation identified in populations of animals with alterations in FMDV related antibody polynucleotides. In this embodiment, any number of probes can be used, and will preferably include probes corresponding to the major gene mutations identified as predisposing an animal to the FMDV infection.

In a highly preferred embodiment, screening techniques based on hybridisation to probes, particularly a plurality of probes that correspond to allele-specific mutations use probes immobilized to solid substrates as described above, for example in the form of DNA arrays on silicon substrates (DNA chips).

The probes or primers described herein can be packaged into diagnostic kits. Diagnostic kits include the probe DNA, which may be labelled; alternatively, the probe DNA may be unlabeled and the ingredients for labelling may be included in the kit. The kit may also contain other suitably packaged reagents and materials needed for the particular hybridisation protocol, for example, standards, as well as instructions for conducting the test.

Diagnostic use in Differentiating Infected from Vaccinated Animals (DIVA)

The present invention also provides recombinant FMDV antibodies and methods for identifying recombinant FMDV antibodies that have specificity for binding to the FMDV non-structural protein 3ABC or components or fragments of the FMDV non-structural protein 3ABC. The binding is serotype-independent. These antibodies can be utilised for serotype independent detection of FMDV and for differentiation of infected from vaccinated animals (DIVA) and used in DIVA assays.

Differentiating antibody tests are then used to determine if the subject has been infected with the wild-type virus or the recombinant virus and can form part of a diagnostic assay in order to determine infected animals from those vaccinated animals. Therapeutic use

The present invention also provides therapeutic, pharmaceutical or prophylactic compositions, which may take any suitable form, for administration to an animal to treat that animal against FMDV related ailments. It also provides methods for the administration of the antibodies fragments, either labelled or unlabelled, to an animal.

Where the recombinant antibody fragment(s) is to be administered to an animal it is preferably in a form suitable for administration e.g. by injection or infusion, for example by bolus injection or continuous infusion. Where the product is for injection or infusion, it may take the form of a suspension, solution or emulsion in an oily or aqueous vehicle and it may contain adjuvants and or formulatory agents such as acceptable carriers, excipients or stabilizers.

The term "adjuvant" refers to a compound or mixture that enhances the immune response to an antigen. An adjuvant can serve as a tissue depot that slowly releases the immunogen and also as a lymphoid system activator that non- specifically enhances the immune response [Hood et al., in Immunology, p. 384, Second Ed., Benjamin/Cummings, Menlo Park, California (1984)].

Acceptable carriers, excipients or stabilizers are non-toxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as Tween, Pluronics or polyethylene glycol (PEG).

Therapeutic formulations of the recombinant antibody fragments may be prepared for by mixing the recombinant antibody fragments having the desired degree of purity with optional physiologically acceptable carriers, excipients, or stabilizers (Remington's Pharmaceutical Sciences, 16th edition, Osol, A., Ed., [1980]), in the form of lyophilised cake or aqueous solutions.

The recombinant antibody fragments may also be administered either as individual therapeutic agents or in combination with other therapeutic agents. For example the recombinant antibody fragments of this invention my be utilized in combination with other monoclonal antibodies or other antibody fragments and regions or with lymphokines or hemopoietic growth factors, etc., which serve to increase the number or activity of effector cells which interact with the antibodies.

An example of therapeutic application of recombinant antibodies is when the recombinant antibody is complexed with either live vaccine, or virus. Such CRAb. FMDV complex for example can be given to any mammal as an alternative vaccination approach by variety of means. Recombinant antibodies can also be complexed with an antigen such a peptide or protein or a whole inactivated virus, or other biologically active molecules. Such CRAb.antigen complex for example can be administered to animals to induce higher immune responses; or for delivery to a particular site to achieve a variable biological effect.

The fragments may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization (for example, hydroxymethylcellulose or gelatin-microcapsules and poly-[methylmethacylate] microcapsules, respectively), in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules), or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, supra.

The fragments to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution. The fragments ordinarily will be stored in lyophilized form or in solution.

Therapeutic fragment compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierce-able by a hypodermic injection needle. The route of fragment administration will accord with known methods, e.g., injection or infusion by intravenous, intraperitoneal, intracerebral, intramuscular, intraocular, intraarterial, or intralesional routes, or by sustained release systems as noted below. The fragments may also be administered continuously by infusion or by bolus injection.

Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the protein, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels [e.g., poly(2- hydroxyethyl-methacrylate) as described by Langer et al., J. Biomed. Mater. Res. 15:167-277 (1981) and Langer, Chem. Tech. 12:98-105 (1982) or poly(vinylalcohol)], polylactides (U.S. Pat. No. 3,773,919, EP 58,481), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman et al., Biopolymers 22:547-556 [1983]), non-degradable ethylene-vinyl acetate (Langer et al., supra), degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT.TM. (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3-hydroxybutyric acid (EP 133,988).

While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated antibodies remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37°C, resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for antibody stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.

Sustained-release fragment compositions also include liposomally entrapped fragments. Liposomes containing the antibody are prepared by methods known per se: DE 3,218,121 ; Epstein et al., Proc. Natl. Acad. Sci. USA 82:3688-3692 (1985); Hwang et al., Proc. Natl. Acad. Sci. USA 77:4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949; EP 142,641 ; Japanese patent application 83-118008; U.S. Pat. Nos. 4,485,045 and 4,544,545; and EP 102,324. Ordinarily the liposomes are of the small (about 200-800 Angstroms) unilamellar type in which the lipid content is greater than about 30 mol. % cholesterol, the selected proportion being adjusted for the optimal antibody therapy.

An effective amount of antibody to be employed therapeutically will depend, for example, upon the therapeutic objectives, the route of administration, and the condition of the animal. Accordingly, it will be necessary for the therapist to titer the dosage and modify the route of administration as required to obtain the optimal therapeutic effect. A typical daily dosage might range from about 1 mg/kg to up to 10 mg/kg or more, depending on the factors mentioned above. Typically, the clinician will administer fragments until a dosage is reached that achieves the desired effect. The progress of this therapy is easily monitored by conventional assays.

The present invention further provides the use of a polypeptide or polynucleotide of the invention, which polypeptide or polynucleotide is, or encode, biologically active in gene therapy. Thus the invention provides a method of treating a FMDV disease which method comprises administering to said cells a functional recombinant antibody polypeptide or polynucleotide encoding said polypeptide fragment to suppress FMDV proliferation in a host.

Thus a recombinant antibody fragment polynucleotide sequence may be introduced into the cell or host (or live animal) in a vector or as naked DNA such that the polynucleotide sequence remains extrachromosomal. In such a situation, the polynucleotide sequence will be expressed by the cell from the extrachromosomal location. If a polynucleotide sequence is introduced and expressed in a cell carrying a mutant FMDV related antibody encoding polynucleotide sequence, the polynucleotide sequence should encode an FMDV related antibody protein that is capable of disturbing FMDV proliferation. More preferred is the situation where the wild-type polynucleotide sequence is introduced into the mutant cell in such a way that it recombines with the endogenous mutant polynucleotide sequence present in the cell. Such recombination requires a double recombination event that results in the correction of the polynucleotide sequence mutation.

Vectors for introduction of genes both for recombination and for extrachromosomal maintenance are known in the art, and any suitable vector may be used. However, replication-incompetent retroviral vectors have proved safe and effective in recent trials and most of the approved human gene therapy trials to date rely on retroviral vectors. Thus it is preferred to use retroviral vectors, such as lentiviral vectors, comprising a polynucleotide of the invention and capable of expressing a polypeptide of the invention. Other viral vector systems include adenoviral vectors and herpes virus vectors.

Methods for introducing DNA into cells such as electroporation, calcium phosphate co-precipitation and viral transduction are known in the art, and the choice of method is within the competence of the person skilled in the art. A further gene transfer technique that has been approved by the FDA is the transfer of plasmid DNA in liposomes. Suitable liposome compositions include Lipofectin™.

Gene therapy would be carried out according to generally accepted methods. Cells from an animal would be first analysed by the diagnostic methods described above, to ascertain the production of FMDV related recombinant antibody fragment in a host. A virus or plasmid vector (see further details below), containing a copy of an FMDV related recombinant antibody fragment polynucleotide sequence linked to expression control elements and capable of replicating inside preferably a lymphocyte, is prepared. Suitable vectors are known, such as disclosed in U.S. Pat. No. 5,252,479 and PCT published application WO 93/07282. The vector is then injected into the patient, either locally or systemically. If the transfected gene is not permanently incorporated into the genome of each of the targeted cells, the treatment may have to be repeated periodically.

Gene transfer systems known in the art may be useful in the practice of the gene therapy methods of the present invention. These include viral and ήonviral transfer methods. A number of viruses have been used as gene transfer vectors, including papovaviruses, e.g., SV40, adenovirus, vaccinia virus, adeno-associated virus, herpesviruses including HSV and EBV, and retroviruses of avian, murine, and human origin. Most gene therapy protocols have been based on disabled murine retroviruses.

Nonviral gene transfer methods known in the art include chemical techniques such as calcium phosphate co-precipitation; mechanical techniques, for example microinjection; membrane fusion-mediated transfer via liposomes; and direct DNA uptake and receptor-mediated DNA transfer. Viral-mediated gene transfer can be combined with direct in vivo gene transfer using liposome delivery, allowing one to specifically direct the viral vectors to the cells of interest. Alternatively, the retroviral vector producer cell line can be injected into the lymphocytes. Injection of producer cells would then provide a continuous source of vector particles.

In an approach which combines biological and physical gene transfer methods, plasmid DNA of any size is combined with a polylysine-conjugated antibody specific to the adenovirus hexon protein, and the resulting complex is bound to an adenovirus vector. The trimolecular complex is then used to infect cells. The adenovirus vector permits efficient binding, internalisation, and degradation of the endosome before the coupled DNA is damaged.

Liposome/DNA complexes have been shown to be capable of mediating direct in vivo gene transfer. While in standard liposome preparations the gene transfer process is non-specific, localised in vivo uptake and expression have been reported in some tumour deposits, for example, following direct in situ administration.

Best Mode(s) for Carrying Out the Invention

Further features of the present invention are more fully described in the following non-limiting Figures, Tables and Example. It is to be understood, however, that this description is included solely for the purposes of exemplifying the present invention. It should not be understood in any way as a restriction on the broad description of the invention as set out above.

EXAMPLES Methods of molecular biology that are not explicitly described in the following examples are reported in the literature and are known by those skilled in the art. General texts that described conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art, included, for example: Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989); Glover ed., DMA Cloning: A Practical Approach, Volumes I and II, MRL Press, Ltd., Oxford, U.K. (1985); and Ausubel, F., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., Struhl, K. Current protocols in molecular biology. Greene Publishing Associates/Wiley Intersciences, New York. McCafferty, J., Hoogenboom, H. R. and Chiswell, D.J. (eds.), Antibody engineering, a practical approach (1996), Oxford University Press.

Antigens for Immunisation, panning and ELISA

Plasmid pMF14C, containing the 3ABC gene fragment (nt 4988-6298), from the FMDV strain 01 K was used for construction of expression clones. The full length 3ABC gene was subcloned from pMF14C using Kpn I and Hind III into the same sites of pRSETb vector (Invitrogen) giving pRSETb-3ABC. Expression plasmids containing the coding regions for 3A, 3B, and 3C were constructed by PCR from pMF14C template and subcloned into a modified pRSETb vector. DNA sequencing confirmed the integrity of the constructs.

E. coli BL21 (DE3) (Novagen) containing recombinant plasmid was cultured in 2 ml of LB-Amp broth (Lauria-Beriani broth containing ampicillil at 50μg/ml) at 37⁰C with shaking overnight. The cultures were diluted 1 :100 and incubated at 37⁰C for 2h before induction of protein expression by the addition of 1mM isopropyl-beta- D-thiogalactoside (IPTG). After 4 h incubation at 37°C cells were harvested by centrifugation at 10,000 x g for 5 min. The cell pellet was resuspended in lysis buffer (500 mM NaCI, 50 mM phosphate buffer, pH 7.8) and lysed by sonication. The insoluble protein fraction was collected by centrifugation at 10,000 x g for 20 min, and solubilised in 8 M urea in phosphate buffered saline (PBS). Recombinant 3ABC was purified by preparative sodium dodecyl sulphate- polyacrylamide gel electrophoresis (SDS-PAGE) using conventional methods (Sambrook et al., 1989). Protein was eluted from gel fragments in PBS containing 0.1 % SDS for 16 h at room temperature. The purity and quantity of recombinant 3ABC was determined by SDS-PAGE and Western blot.

Immunisation of chickens

Immunisation of chickens was performed using a DNA prime/protein boost strategy. Two five-week-old specific pathogen-free (SPF) chickens were immunised by intra-muscular inoculation of 100 μg of plasmid pClneo-3ABC, which has the full length 3ABC gene cloned into the eukaryotic expression vector pClneo (Promega), emulsified with 50 μl of Lipofectin (Invitrogen) in a total volume of 500 μl. The same inoculation was repeated 21 days later. The third (21 days post second DNA inoculation) and fourth inoculations (35 days post second DNA inoculation) consisted of 100 μg of FMDV-3ABC protein emulsified with an equal volume of montanide ISA50V adjuvant (SEPPIC, France) in a total volume of 200 μl. Six days post fourth inoculation, chickens were euthanised and spleens removed for purification of lymphocytes. Serum was collected before each immunisation and the presence of antibody confirmed by Western blot analysis.

Preparation of mRNA and cDNA

Spleens from chickens were pooled and minced through a stainless steel mesh screen in cold PBS and layered onto an equal volume of Histopaque (Sigma Chemical Co., St. Louis, MO, U.S.A.). White blood cells were separated by centrifugation for 20 min at 700 x g and total RNA extracted using Qiagen RNeasy midi kit (Qiagen, Hilden, Germany). Complementary DNA (cDNA) was synthesized using a Qiagen Omniscript cDNA synthesis kit (Qiagen), approximately 30 μg of RNA was primed with random hexamers in a total volume of 100 μl.

PCR amplification of heavy and light chain variable domain genes

PCR was performed in a total volume of 100 μl containing 10 μl of cDNA, 50 μl of 2 x Hotstar master mix (Qiagen), 2 μl (6 ng) of each forward and reverse primer (Table 1 ). The following thermal cycle program, 15 min at 95°C followed by 30 cycles consisting of: 45 sec at 94⁰C; 45 sec at 50⁰C; 2 min at 72°C, followed by a final extension of 10 min at 72°C, was performed on an Applied Biosystems 9700 thermocycler. A total of 15 separate PCR's were performed for VH and VL and the products pooled respectively. VL and V_H PCR products of approximately 350 and 390 bp (respectively) were gel purified using a 1.2% agarose gel, and DNA of the expected molecular weight extracted using a QIAquick gel extraction kit (Qiagen).

Library Construction

Phagemid vector pCANTAB-link (Sapats et al., 2003) and gel purified VL gene fragments were digested with restriction enzymes Sal [/Not I, and ligated to form an "intermediate library" (pCANTAB-link-V_L). After propagation of this library in E coli XL-1 blue cells (Stragene CA, USA), gel purified V_H gene fragments were digested with restriction enzymes Asc \JXba I and cloned into the Asc \IXba I site of the pooled pCANTAB-link-V_L, to form a "full library" (pCANTAB-V_H-link-V_L). The ligated DNA was electroporated into electrocompetent E. coli XL-1 blue cells. An aliquot was taken to determine the library size and cultured on SOB agar plates containing 100 μg/ml ampicillin and 2% glucose (SOBAG). The remaining culture was plated out onto 60 SOBAG agar plates and incubated overnight at 30⁰C. The resulting lawns of bacterial cells were scraped into 5 ml 2YT per plate, 1.0 ml of this was infected with 6 x 10¹⁰ plaque forming units (PFU) of helper phage M13KO7 (Amersham Pharmacia Biotech). After 2 h shaking at 37°C the cells were harvested by centrifugation at 1400 x g for 15 min and resuspended in 10 ml 2YT containing 100 μg/ml ampicillin and 50 μg/ml kanamycin (2YT-AK) and incubated overnight with shaking at 37°C. Cells were pelleted at 1400 x g for 15 min and the supernatant, containing phage, was filtered through a 0.45 μm filter. Phage particles were concentrated from the supernatant by polyethylene glycol (PEG) precipitation (Sapats et al., 2003).

Selection by panning

Maxisorp lmmunotubes (Nunc, Roskilde, Denmark) were coated overnight at 4°C with 15 μg of FMDV-3ABC antigen per tube in 4 ml sodium carbonate buffer, pH 9.6. The immunotubes were washed three times with PBS containing 0.1 % Tween 20 (PBS-T) and blocked for 1 h with PBS-T containing 5% skim milk (Blotto). Panning was carried out by diluting 1.0 ml of the PEG precipitated phage with 3.0 ml of Blotto in the blocked tubes, followed by incubation at 37°C for 2 h. The tubes were then washed three times with PBS, followed by three washes with PBS-T. Phage was eluted from the immunotubes by adding 100 μl of 100 mM triethylamine (Sigma) and incubation at room temperature for 15 min. The triethylamine was Positive phagemid clones identified in the above ELISA screening were used to electroporate a non-suppressor strain of E. coli (HB2151, Stratagene). Individual colonies (one per clone) were selected to inoculate 50 ml of 2YT-AG and incubated overnight at 3O⁰C. Sixteen ml aliquots of overnight culture were diluted into 400 ml of fresh 2YT-AG (1/25 dilution) and incubated 1 h at 30⁰C shaking. Cells were centrifuged and resuspended in the same volume of fresh 2YT containing 100 μg/ml ampicillin and 1 mM IPTG and shaken for 4 h at 30⁰C to induce expression of soluble scFv protein (Sab). Cells were collected by centrifugation at 1400 x g for 10 min and resuspended in 25 ml PBS. The soluble antibodies were harvested by cell lysis using a French press and the cell lysate centrifuged at 5000 x g for 20 min to remove cellular debris.

Characterization of scFvs by direct ELISA and DNA sequencing

A Nunc Maxisorb ELISA plate (Nunc) was coated overnight at 4°C with 0.25 μg of FMDV-3ABC per well in 100 μl of sodium carbonate buffer, pH 9.6. The plate was then blocked for 1 h at room temperature with 100 μl of Blotto. Phage-bound or soluble forms of scFvs were diluted 1/5 volume in Blotto. The binding of scFv was detected with a mouse monoclonal anti-E Tag/HRP conjugate (Pharmacia). TMB One solution (Promega) was used to develop the colour reaction, which was stopped after 10 min with 2M sulphuric acid and the absorbance read at 450 nm. The non-specific binding of scFvs was evaluated using the same ELISA conditions, but with a non-related His-tagged protein expressed from the same vector system and purified using SDS-PAGE as before.

Genotypes of positive scFvs clones were determined by direct sequencing of phagemid DNA using primers listed in Table 1. Sequence analyses were performed using SeqMan and MegAlign programs (DNA Star Inc.). Further alignments of the deduced amino acid sequence of selected clones were performed using CLUSTAL W program (Thompson et al., 1994) in BioManager by ANGIS (http://www.anqis.orq.au). Table i: PCR primers for recombinant antibody library construction and DNA sequencing.

Restriction enzyme sites used for cloning are shown underlined

Competition ELISA

Optimal concentrations of coating antigen (3ABC and 3B) and recombinant antibodies CRAb-FM26 and -FM27 were determined by serial dilutions. Maxisorb ELISA plates (Nunc) were coated overnight at 4°C with 3ABC (31.25 ng/well) or 3B (125 ng/well), respectively, in sodium carbonate buffer (pH 9.6) at 100 μl per well. The plates were washed five times with phosphate buffered saline containing 0.05% Tween 20 (PBS-T) and then blocked with Blotto for 1h at 37°C with shaking. Various dilutions of test sera in Blotto were added at 30 μl per well and incubated for 30 min at 37°C with shaking, immediately followed by the addition of CRAb-FM26 (1 :80 dilution) or CRAb-FM27 (1 :1600) in blotto at 30 μl per well and incubated for a further 1h at 37°C with shaking. Plates were washed as before, followed by the addition of 50 μl of anti-E Tag/HRP conjugate (Pharmacia) diluted at 1 :10 000 in Blotto. Colour development and plate reading was carried out as above. Each serum was tested in duplicate and each plate included a control that consisted of all test reagents but no test serum for the calculation of the maximum optical density. Percentage inhibition (Pl) = 100 - (OD test sera)/(max OD) x 100. Results were expressed as mean percentage inhibition of test wells as compared with the maximum OD where there was no competition.

Experimental Sera

The following panels of sera were used in C-ELISA evaluation. The cattle sera represented 4 different FMDV serotypes of importance to Australia and were kindly provided by Dr. Alan R. Samuel, Institute for Animal Health, Pirbright, UK. lnfected pig sera were generated against serotype A24 and were kindly provided by J. Lubroth, Plum Island Animal Disease Center, N.Y. Naϊve pig sera were obtained in-house at AAHL. The vaccinated pig sera were kindly provided by Dr. Dong Manh Hoa, Regional Animal Health Center Ho Chi Minh city, Vietnam. Two FMDV-infected sheep sera were generated from infection with O-UKG kindly provided by Dr. Bob Armstrong, Institute for Animal Health, Pirbright, UK and one with experimental infection with 01 -Tunisia, A5, A10, 01 -BFS and C1-Detmold and was kindly provided by Dr. Aldo Dekker, Central Institute for Animal Disease Control, Lelystad, The Netherlands. The naϊve or pre-bleed sera and vaccinated sheep sera were generated from the O, A or Asiai serotype vaccine and were kindly provided by Dr. Jef Hammond, AAHL.

Results

Expression and purification of recombinant NSP proteins

All recombinant FMDV NSPs expressed in E. coli BL21 (DE3) were largely insoluble and present in inclusion bodies. Protein from inclusion bodies was purified by preparative SDS-PAGE, followed by passive elution. The purity, size and antigenicity of the recombinant proteins were determined by SDS-PAGE and Western blot. The purity of all recombinant proteins was 95% or above (data not shown).

Isolation and characterisation of 3ABC-specific phage antibody clones

After ligation and transformation of E. coli, a library of approximately 1 x 10⁷ ampicillin-resistant colonies was obtained. Following super-infection with M13K07 and after 4 rounds of panning, individual phage clones were analysed for specific binding to 3ABC. From a total of 96 randomly selected clones, approximately 33% (32 clones) demonstrated significant binding to 3ABC by ELISA. The specificity of these clones was further assessed by ELISA using a non-related protein expressed from the same vector, and the results indicated that these phage bound antibodies had either no binding or low binding affinity to the non-related protein.

Sequence analysis of scFv clones

The complete nucleotide sequence and deduced amino acid sequence of the heavy and light chain variable regions of the 32 clones were determined. Following sequence alignments, three unique genotypes were identified, labeled CRAb-FM26, -FM27 and -FM29. The V_H chain of CRAb-FM26 and -FM27 were very similar in the framework region (FR) with only three amino acid changes and identical in the complementary determining regions (CDR). The major difference between these two clones appeared to be in the amino acid sequence of the VL chain with seven changes present in FR one, and three, and twelve changes evident the in three CDRs. The V_H and V_L chain of CRAb-FM29 differed significantly from CRAb-FM26 and -FM27 in both the CDR and FR regions (data not shown); however clones with this sequence demonstrated some affinity to the non-related protein and were thus excluded from subsequent competition ELISA studies, although the epitopes were still mapped.

Epitope mapping by Western blot

To examine whether the three CRAbs bound to the same or different regions of the 3ABC protein, Western blot analysis was carried out using recombinant 3ABC, 3A, 3B and 3C. A non-related gel purified poly His-tagged protein was included as control. All five proteins were recognized by anti-His-tag antibodies as expected (data not shown). All three antibodies, CRAb-FM26, -FM27 and -FM29, recognised the 3ABC and 3B proteins, but not 3A, 3C nor the non-related protein (Fig. 4). These results suggest that all three CRAbs bind to an epitope or epitopes contained in the 3B region.

C-ELISA lnitial evaluation and optimisation of all recombinant reagents in a C-ELISA format was carried out using a panel of four FMDV-infected and two pre-bleed cattle sera. These were diluted two-fold starting at 1 :10 with a final dilution of 1 :640 (Fig. 5). The cattle sera were obtained from separate animals infected with four FMDV serotypes: O1-Manisa, Asiai -India, A22-lraq and C-Oberbayern, and the two pre- bleed sera were pools of associated naϊve sera from the same animals, O/Asia1 and A22/C, respectively. Under optimised conditions, C-ELISA performed with CRAb-FM27 using 3ABC and 3B as coating antigens and the best discriminating sera dilution of 1 :10, demonstrated a range of inhibition from 85 to 91% and 69 to 88% respectively for the FMDV-positive sera, whereas the negative sera had inhibition levels of 21 to 26% and 34 to 41% respectively. In comparison the C- ELISA with CRAb-FM26 had inhibition levels of 65 to 83% and 45 to 80% respectively with the FMDV-positive sera and inhibition levels of 31 to 37% and 19 to 30% with the negative sera. CRAb-FM27 with 3ABC demonstrated the greatest differentiation between positive and negative sera and was therefore chosen for further evaluation in the C-ELISA.

An expanded panel of sera representing FMDV-negative, FMDV-infected and FMDV-vaccinated cattle, sheep and pigs was used to further evaluate the ability of CRAb-FM27 to discriminate vaccinated from infected animals (Fig. 6). A panel of 18 bovine sera (comprising six known FMDV-positive, six naϊve and six FMDV- vaccinates), 15 ovine sera (comprising three known FMDV-positive, six naϊve and six FMDV-vaccinates) and 16 porcine sera (comprising four known positive, six naϊve and six FMDV-vaccinates) was tested. Of the cattle sera the six naϊve and six FMDV-vaccinated sera demonstrated no inhibition, with the exception of an O1-Manisa vaccinated serum sample which showed an inhibition of 66%. The six FMDV-infected bovine sera, representing O1-Manisa, C-Oberbayern, Asiai -India and three different strains of serotype A (A15, A22-lraq and A24-Cruzeiro), all had an inhibition of greater than 90%. The six naϊve and six FMDV-vaccinated (Serotype O) porcine sera showed an inhibition of less than 15%, with the FMDV- infected porcine sera (serotype A24) demonstrating a range of inhibition from 52 to 80%. For the ovine sera tested, the discrimination between the naϊve, FMDV- vaccinated and FMDV-infected sera was not as clearly defined as those of the cattle and pigs. The infected sera showed inhibition ranging from 60 to 80% and the FMDV-vaccinated ranging from 2 to 30% and naive ovine sera giving inhibition less than 18%.

An additional panel of 47 negative sera from swine (/7=22) and cattle (n=25) were tested by C-ELISA with CRAb-FM27 and showed an average inhibition of less than 20% with a range of 0 to 26% (data not shown).

It is to be understood that the above examples are included solely for the purposes of exemplifying the present invention. They should not be understood in any way as a restriction on the broad description of the invention as set out above.

Claims

THE CLAIMS DEFINING THE INVENTION ARE AS FOLLOWS:

1. A recombinant antibody fragment having a binding specificity for an FMDV antigenic determinant.

2. A recombinant antibody fragment having a binding specificity for an FMDV antigenic determinant, with a variable region comprising at least a light chain region or a heavy chain region.

3. A recombinant antibody fragment having a binding specificity for an FMDV antigenic determinant, which comprises at least a variable region having a heavy chain region and a light chain region.

4. A recombinant antibody fragment comprising a VH region selected from the group consisting of SEQ ID Nos: 1 to 3, or a homologue thereof and or a VL region selected from the group consisting of SEQ ID Nos:4 to 6, or a homologue thereof.

5. A recombinant antibody fragment selected from the group comprising SEQ ID

Nos: 7 to15, or a homologue thereof.

6. A recombinant antibody fragment comprising an amino acid sequence selected from the group consisting of: SEQ ID Nos: 1 to 6, or a homologue thereof, wherein the fragment(s) include a natural or a non-natural modification which does not extinguish the affinity of VH and VL regions to an FMDV antigen.

7. A recombinant antibody fragment comprising an amino acid sequence selected from the group consisting of: SEQ ID Nos: 1 to 6, or a homologue thereof wherein the fragment(s) include a natural or a non-natural modification which does not substantially alter the affinity of V_H and V_L regions to an FMDV antigen.

8. A recombinant antibody fragment according to any one of claims 1 to 3 conjugated with, or attached to other antibodies or parts thereof.

9. A recombinant antibody fragment according to any one of claims 1 to 3 which are multivalent monospecific and comprise at least two single chain antibody fragments bound to each other by a connecting structure which protein is not a natural immunoglobulin and wherein at least one of said recombinant antibody fragments has a specificity for an FMDV antigenic determinant.

10. A recombinant antibody fragment according claim 3 wherein VH domains and the V_L domains are linked.

11. The recombinant antibody fragment(s) according to claim 9 wherein the linker is (Gly₄Ser)₃.

12. A recombinant antibody fragment according to any one of claims 1 to 8 wherein the fragment is capable of distinguishing at least two FMDV strains.

13. A recombinant antibody fragment according to any one of claims 1 to 8 having a differential binding affinity capable of distinguishing at least two FMDV strains.

14. A recombinant antibody fragment according to any one of claims 1 to 3 capable of binding the FMDV strain.

15. A recombinant antibody fragment according to any one of claims 1 to 8 derived from a host that has been caused to produce antibodies against FMDV or an FMDV polypeptide or fragment thereof.

16. A recombinant antibody fragment according to claim 14 wherein the host is a mammal.

17. A recombinant antibody fragment according to claim 14 wherein the host is a maml for example, pigs, cattle, sheep, goats and deer.

18. A nucleic acid molecule encoding an isolated recombinant antibody fragment or an allelic variant or analogue or fragment thereof capable of specifically binding FMDV.

19. Nucleic acid molecules encoding an isolated recombinant antibody fragment having specificity for at least an FMDV antigenic determinant and comprising a variable region having a heavy chain (V_H) region.

20. Nucleic acid molecules encoding an isolated recombinant antibody fragment having specificity for at least an FMDV antigenic determinant and comprising a variable region having a light chain (V_L) region.

21. Nucleic acid molecules encoding an isolated recombinant antibody fragment having specificity for at least an FMDV antigenic determinant and comprising a variable region having a heavy chain (VH) region and a light chain (V_L) region.

22.A process for identifying recombinant antibody fragments, which process comprises the steps:

(i) amplifying nucleotide sequences comprising VH and V_L chains from lymphocytes from a host which has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof;

(ii) generating a library comprising amplified nucleotide sequences from step (i), which library is capable of being screened to identify V_H and or V_L regions reactive with at least FMDV or an FMDV polypeptide or a fragment thereof; and

(iii) screening said library and selecting at least a recombinant antibody fragment that has an affinity for FMDV or an FMDV polypeptide or a fragment thereof.

23.A process according to claim 22 wherein the library generated in step (ii) is prepared using the vector pCANTAB-link.

24. Use of the process according to claim 22 for identifying recombinant FMDV antibodies for use as immunodiagnostic agents.

25. Use of the process according to claim 22 for identifying recombinant FMDV antibodies for use as immunotherapeutic agents.

26. The preparation of agonists against FMDV biological activity prepared by the process according to claim 22.

27.A method for identifying a recombinant FMDV antibody fragment comprising the steps of:

(i) the scFv fragments are then cloned into an expression vector and transformed into a suitable host;

(ii) With the aid of a helper phage, recombinant phage specific for FMDV are selected by panning against a plate coated with FMDV antigens; and

(iii) Phage specific for FMDV antigens are eluted off and grown up individually.

28.A method for detecting the presence of FMDV antibody in a sample comprising:

(i) contacting said sample with a recombinant antibody fragment which specifically binds to an FMDV antigen, comprising a variable region having a heavy chain (VH) region and a light chain (V_L ) region, said VH region having an amino acid sequence selected from the group consisting of SEQ ID Nos: 1 to 3, and VL region having an amino acid sequence selected from the group consisting of SEQ ID Nos: 4 to 6, and

(ii) determining binding of said antibody to FMDV antigen in said sample as a determination of FMDV infection in said sample.

29. Use of the method according to claim 28 for the detection of FMDV in a sample.

30. A vector comprising a nucleic acid sequence according to any one of claims 18 to 21.

31. A recombinant host cell containing a nucleic acid sequence encoding a recombinant antibody fragment according to any one of claims 1 to 8.

32. A method for preparing an FMDV related antibody polypeptide comprising:

(a) culturing a cell under conditions that provide for expression of the FMDV related antibody polypeptide; and

(b) recovering the expressed FMDV related antibody polypeptide

33. A method for preparing an FMDV related antibody polypeptide comprising:

(a) culturing a cell under conditions that provide for expression of the FMDV related antibody polypeptide;

(b) recovering the expressed FMDV related antibody polypeptide;

(c) chromatographing the polypeptide using a suitable means; and

(d) purifying the polypeptide.

34. A kit for diagnosis of FMDV strain comprising an antibody fragment or fragments according to any one of claims 1 to 8.

35. Recombinant antibody fragments according to any one of claims 1 to 8 initially derived from nucleotide sequences encoding heavy and light chain variable regions produced in B-lymphocytes from a host that has been caused to produce antibodies against at least FMDV or an FMDV polypeptide or a fragment thereof.

36. A therapeutic composition comprising at least a recombinant antibody fragment according to any one of claims 1 to 8 and a pharmaceutically acceptable carrier.

37. A method of treating a FMDV disease comprising administering a functional recombinant antibody polypeptide of any one of claims 1 to 8 to suppress FMDV proliferation in a host.

38. A method of treating a FMDV disease comprising administering a polynucleotide of any one of claims 18 to 21 wherein the polynucleotide encodes a functional recombinant antibody polypeptide fragment, to suppress FMDV proliferation in a host.

39. Use of the recombinant antibody fragments according to any one of claims 1 to 9 for the diagnosis of an infection caused by at least one FMDV strain.