Diagnosis, prevention and treatment of calicivirus infection in humans

Abstract

Caliciviruses are herein recognized as potentially important human pathogens, infecting a large percentage (18%) of a sampled human population. A new calicivirus isolate called “San Miguel sea lion virus 5 serotype Homosapien-1” (SMSV-5 Hom-1) is also disclosed. Compositions and methods are disclosed that allow diagnosis, prevention and treatment of calicivirus (including SMSV-5 Hom-1) infection in humans.

Description

FIELD OF THE INVENTION

[0001] The invention relates to caliciviruses, which are newly recognized as potentially important human pathogens. In a population of adult blood donors from Oregon, 18% were found to exhibit caliciviruses-specific antibodies.

BACKGROUND

[0002] Viruses of the family Caliciviridae are non-enveloped single stranded positive sense RNA viruses having a genome of about 8 Kbs in size. The capsid protein is a single molecular species of about 60 KDa and forms 22 cups or calyxs on the viral surface thereby providing the morphologic basis for the name Caliciviridae. Viruses of the calicivirus family have been known to be pathogenic in mammals since at least 1932 when they were shown to be the causative agent of vesicular exanthema of swine (VES). Subsequently, caliciviruses have been shown to be pathogens for cats and marine mammals, such as sea lions.

[0003] The family of Caliciviridae is divided into four taxonomic genera: Norwalk viruses and Sapporo viruses (both of which are gastrointestinal pathogens in humans), rabbit hemorrhagic disease viruses and vesiviruses. The first three of these genera all have proven refractory to in vitro cell culture replication. The fourth genus, the vesiviruses, may be replicated in cell culture, for instance using Vero cells. Despite the fact that caliciviruses have been known for many years as pathogens of mammals, cultivatable caliciviruses have not been found to be of clinical significance in the human population. In particular, vesiviruses have not shown to be significant infectious agents for humans.

[0004] Serologic evidence can suggest that animal viruses are also human pathogens and occasionally this is confirmed by a single case as was reported for Cache Valley virus [3]. Other times, with no prior warning, a single case signals the arrival of a new zoonotic disease as occurred with the death of a horse trainer in Australia infected with a previously unknown morbillivirus [4]. Such events can occur when shifts in ecologic relationships cause intermixing of species and result in increased “viral traffic” [5]. In turn, “viral traffic” encourages adaptive shifts in viral genomes and host-parasite relationships which can result in emerging new diseases, especially zoonoses [5]. An increase in viral traffic for one calicivirus has been deliberate in Australia, where hemorrhagic virus of rabbits [6, 7, 8] has been spread as a biologic control agent, resulting in a continent-wide calicivirus challenge of naive and diverse populations.

[0005] The early detection of, and appropriate responses to, emerging viral diseases that may result from events that heighten viral traffic require preventive programs involving research, early diagnosis, public health awareness and reporting.

SUMMARY

[0006] The invention concerns reagents and methods of detecting calicivirus in humans. The invention also provides calicivirus nucleic acid sequences and amino acid sequences that are useful for developing immunostimulatory polypeptides. As will be made clear by the specification, calicivirus infection is linked to human diseases, reproductive dysfunctions, and moreover calicivirus in humans may be transmitted via blood.

[0007] It has been discovered that caliciviruses are common infective agents in humans and can cause a serious vesicular disease characterized by fever, generalized myalgia and painful blistering of the hands and feet and a new strain of calicivirus (belonging to the vesivirus genus), that is called “San Miguel sea lion virus 5 serotype Homosapien-1” (SMSV-5 Hom-1) has been discovered and isolated. This disclosure is directed towards methods of detecting an infective agent in a sample from a human comprising detecting calicivirus antigens and/or anti-calicivirus antibodies; to methods of stimulating immune responses in human subjects against caliciviruses; and to SMSV-5 Hom-1, its polynucleotides and polypeptides.

[0008] One aspect of the present invention is a method of detecting a past (or present) infection of a human by an infectious viral agent comprising detecting anti-calicivirus antibodies in a sample from the putatively infected human subject. Another aspect of the present invention is a method of detecting a present viral infection of a human comprising detecting one or more calicivirus antigens and/or calicivirus genomic segments in a sample taken from the putatively infected human subject. A further aspect of the present invention is the provision of a protective vaccine against caliciviruses comprising inoculating a human subject with a vaccine comprising at least one calicivirus antigen or its cDNA sequence with a vector comprising a recombinant caliciviral polynucleotide wherein the viral vector expresses at least one calicivirus antigen.

[0009] Another aspect relates to nucleotides of SMSV-5 Hom-1, some of which may be used as probes or primers, for instance for use in detecting or amplifying viral polynucleotides. Yet another aspect relates to proteins of SMSV-5 Hom-1, which may be antigenic, some of which may be used in diagnostic and immune stimulatory applications such as the creation of vaccines. The invention also relates to antibodies specific for SMSV-5 Hom-1, which in certain embodiments may be monoclonal antibodies. Also included are assays to detect antigens of SMSV-5 Hom-1. Additionally, the invention includes assays to detect antibodies specific for SMSV-5 Hom-1. A further aspect of the invention relates to vaccines against SMSV-5 Hom-1 infection. All these different embodiments are discussed in detail below.

Sequence Listings

[0010] The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three-letter code for amino acids. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood to be included by any reference to the displayed strand.

[0011] SEQ ID NO: 1 shows the nucleic acid sequence of the SMSV-5 Hom-1 RNA polymerase region.

[0012] SEQ ID NO: 2 shows the amino acid sequence of the SMSV-5 Hom-1 RNA polymerase region.

[0013] SEQ ID NO: 3 shows the nucleic acid sequence (1671 bases) of the p5RT73 genomic segment of SMSV-5.

[0014] SEQ ID NO: 4 shows a cDNA that encodes an amino acid sequence that is useful for detecting caliciviral specific binding agents.

[0015] SEQ ID NO: 5 shows the amino acid sequence encoded by the cDNA of SEQ ID NO: 4.

[0016] SEQ ID NOS: 6-10 show PCR primers.

[0017] SEQ ID NOS: 11-13 show the three possible ORFs of the nucleic acid sequence shown in SEQ ID NO: 3.

[0018] SEQ ID NO: 14 shows the nucleic acid sequence of a 300 bp probe that can be used to detect a broad range of caliciviruses.

BRIEF DESCRIPTION OF THE DRAWINGS

[0019] FIG. 1 is a photograph showing hand lesions from which SMSV-5 Hom-1 was isolated.

[0020] FIG. 2 is a flipper lesions on Northern fur seals from which the prototype strain (205) of SMSV-5 was isolated. Solid arrows show intact vesicles particularly around the vestigial claws and “e” shows erosions left by denuded vesicular lesions.

[0021] FIG. 3 is an electronphoto micrograph using phosphotungstic acid negative stain. One of several clusters of virus-like particles from human vesicular fluid having morphology characteristic of the caliciviruses (bar=50 nm).

[0022] FIG. 4 is a graph comparing the nucleotide and predicted amino acid sequences of prototype SMSV-5 (SEQ ID NO: 2), PCV Pan-1 and SMSV-5 Hom-1 in the RNA polymerase gene region. SMSV-5 Hom-1 has 97% nucleotide and 96% amino acid identity with the prototype SMSV-5 and 85% nucleotide and 92% amino acid sequence identity with Pan-1 in this most highly conserved region of calicivirus genomes. These differences are consistent with the SMSV-5 Hom-1 's designation as a strain of SMSV-5 [11]. The following GenBank accession numbers have been assigned to these sequences: SMSV-5 [U52093], SMSV-5 Hom-1 [U62327], and Pan-1 [U52086].

[0023] FIG. 5 is a graph showing the distribution of optical density values among adult blood donors in Portland, Oreg. in an ELISA for antibody to SMSV caliciviruses. 18% of 300 blood donor sera collected over a six-month period show high levels of reactivity at OD value >0.20 (8% at OD>0.50).

[0024] FIG. 6 is a list showing the cDNA sequence (SEQ ID NO: 3) of the p5RT73 genomic segment shown in FIG. 9.

[0025] FIG. 7 is a list showing the translation in three forward reading frames of the nucleic acid sequence shown in FIG. 6 (SEQ ID NOS: 11-13).

[0026] FIG. 8 is a list showing the cDNA sequence and amino acid sequence for group reactive caliciviral antigen for antibody detection 6 (SEQ ID NOS: 4-5).

[0027] FIG. 9 is a list showing the genomic location and size of p5RT73 within the calicivirus genome, as well as the restriction map and location of the 5RT73xr-300 probe used in the hybridization experiments. The 3C-like cysteine protease region (3C) and the RNA-dependent RNA polymerase region (GDD) are also indicated.

[0028] FIG. 10 is a list showing the translated amino acid sequence comparison of SMSV-5 to other published calicivirus amino acid sequences within the 3C-like cysteine protease region of the non-structural protein of caliciviruses. SMSV-5 was compared to: FCV, feline calicivirus (155); RHDV, rabbit hemorrhagic disease virus (145); and SV, Southampton virus, a Norwalk-like virus, (122). Carats (−) above amino acid residues represent the putative catalytic sites of the protein. Asterisks (*) under the sequences represent the number of caliciviruses which have identical amino acid residues to SMSV-5.

[0029] FIG. 11 is a list showing the translated amino acid sequence comparison of SMSV-5 (SEQ ID NO: 2) to other published calicivirus amino acid sequences within the RNA-dependent RNA polymerase region of the non-structural protein of caliciviruses. The symbols, and origin of comparison sequences are as in FIG. 10.

[0030] FIG. 12 is a table showing monoclonal antibodies used to identify neutralizing epitopes for vaccines.

[0031] FIG. 13 is a table showing monoclonal antibodies reactive with nearly all variants of the vesicular genus.

[0032] FIG. 14 is a table that shows the reactivity of polyclonal antibody sera with various antigen pools. The virus types for each pool are shown at the bottom of the corresponding column.

DETAILED DESCRIPTION

Overall Description of Various Embodiments

[0033] Caliciviruses are common infective agents in the human population (18% of the population sampled) and these infective viruses may be important in producing human disease. A human disease caused by calicivirus is characterized by fever, generalized myalgia and painful blistering of the hands and feet. Because of the prevalence of caliciviruses in the human population and their ability to produce disease, it would be desirable to have compositions and methods that would allow for the detection of calicivirus antigen and/or calicivirus antibody in a sample from a human. It would also be desirable to produce a vaccine that would protect a human against a caliciviral infection.

[0034] One aspect of the present invention is a method of detecting a past (or present) infection of a human by an infectious viral agent comprising detecting anti-calicivirus antibodies in a sample from the putatively infected human subject. Calicivirus antigens (recombinant or otherwise) can be used as substrate reagents in immunoassays to identify antibodies to caliciviruses in a sample, e.g., blood, as one means of determining if the sampled individual has been exposed to (or is currently infected with) a calicivirus, and to determine the concentration of the antibodies in the sample. The immunoassays in which such antigens can be used include, but are not limited to, radioimmunoassay, competition immunoprecipitation, enzyme-linked immunoadsorbent assay, virus neutralization, immunofluorescence assay and the like. The antigens used in such assays may comprise whole infective, attenuated or killed viral particles, or one or more native or recombinant caliciviral epitopes, antigenic subunits or haptens. Hapten molecules may be combined with a carrier molecule to produce antigenicity. The caliciviral antigens may be used in assay compositions in a concentration sufficient to form a detectable complex with specific antibodies. The caliciviral antigens can be mixed with or attached to a suitable matrix (support) or carrier, such as a latex particle or plastic microtiter plate or the like. They can also be conjugated with an enzyme, dye, radio-labeled or the like, depending upon what immunological method is used. The details of conducting various types of immunoassays is well known in the art and also described in Antibodies which is a A Laboratory Manual by Harlow and Lane, Cold Spring Harbor Laboratory (1988).

[0035] Another aspect of the invention is a method of detecting a present viral infection of a human by detecting one or more calicivirus antigens in a sample taken from the putatively infected human subject. Anti-calicivirus antibodies may be made and purified by conventional methods (Antibodies may be produced using standard procedures described in a number of texts, including Antibodies, A Laboratory Manual by Harlow and Lane, Cold Spring Harbor Laboratory, 1988) and may be polyclonal or monoclonal antibodies. Such antibodies may be used in quantitative and qualitative assays for antigens wherein the antibodies are contacted with a sample that putatively contains calicivirus antigens, wherein the antigens and the antibodies specifically bind to each other, and wherein the amount of antibody-antigen conjugate is then detected and measured.

[0036] A further aspect of the present invention is the provision of a protective vaccine against caliciviruses comprising inoculating a human subject with a vaccine comprising at least one calicivirus antigen or with a viral vector comprising a recombinant caliciviral polynucleotide wherein the viral vector, when inoculated into a human, expresses at least one calicivirus antigen. The methods of preparing such vaccines and vaccine vectors is more thoroughly discussed below in relation to SMSV-5 Hom-1, and methods discussed in relation to SMSV-5 Hom-1 vaccines are equally applicable to any calicivirus vaccine.

[0037] With reference to SMSV-5, the invention encompasses isolated polynucleotides derived from SMSV-5 genome, a 1671 base pair portion of which is shown in FIG. 6 (SEQ ID NO: 3), and the identified ORFs (open reading frames; SEQ ID NOS: 11-13) of this genome (for example 5rt73 bp 1-300 (SEQ ID NO: 14) and 300-1671). Also included within the invention are oligonucleotides comprising at least 15, 20, 30, 40, 50, 70, 100 and 150 consecutive nucleotides of the sequence as shown in FIG. 6.

[0038] The invention further includes nucleic acids encoding SMSV-5 Hom-1 amino acid sequences, such as those amino acid sequences shown in FIG. 7, as well as recombinant nucleic acids that may include a promoter operably linked to a nucleic acid that encodes an SMSV-5 Hom-1 amino acid sequence.

[0039] Additionally included are isolated nucleic acid molecules of various defined lengths that show at least 50%, 60%, 70%, 80%, 90%, 95% or 99% sequence identity with at least a part of the nucleotide sequence as shown in FIG. 6 when compared using the BLASTN™ software (further discussed herein) using default parameters.

[0040] The invention also includes isolated nucleic acid molecules of various defined lengths that hybridize with at least a part of the nucleic acid sequence as shown in FIG. 6 (SEQ ID NO: 3). Generally, hybridization conditions are classified into categories, for example very high stringency, high stringency, and low stringency. The conditions for probes that are about 600 base pairs or more in length are provided below in three corresponding categories.

[0041] Very High Stringency (detects sequences that share 90% sequence identity)

Hybridization in	SSC at	65° C.	16 hours
Wash twice in	SSC at	room temp.	15 minutes each
Wash twice in	SSC at	65° C.	20 minutes each

[0042] High Stringency (detects sequences that share 80% sequence identity or greater)

Hybridization in	SSC at	65° C.-70° C.	16-20 hours
Wash twice in	SSC at	room temp.	5-20 minutes each
Wash twice in	SSC at	55° C.-70° C.	30 minutes each

[0043] Low Stringency (detects sequences that share greater than 50% sequence identity)

Hybridization in	SSC at	room temp.	16-20 hours
		−55° C.
Wash twice in	SSC at	room temp.	20-30 minutes each
		−55° C.

[0044] Methods for preparing and using probes and primers are described in the references, for example Sambrook et al. Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, NY, 1989; Ausubel et al. Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley-Intersciences, 1987; and Innis et al., PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc., San Diego, Calif. 1990. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.).

[0045] Also within the invention are cells and virions that contain the nucleic acid molecules as described above. Such nucleic acids may be present in recombinant form, for instance, cloned into an expression vector. Cells may be transformed with a cloned recombinant nucleic acid of the invention in order to facilitate expression of a particular protein, such as that shown in FIG. 8 (SEQ ID NO: 5). Various vector systems are discussed below under “Cloning and Expression of SMSV-5 Hom-1 Nucleotides.” Viruses may be engineered to contain the nucleic acids of the invention in order to produce a vaccine. Such viral vectors are discussed below under “Therapeutic Uses of SMSV-5 Hom-1 Nucleic Acids and Proteins.”

[0046] Recombinant molecules are also encompassed within the bounds of the invention, and include, for instance, a nucleic acid molecule encoding a polypeptide as shown in FIG. 8 (SEQ ID NO: 4) linked to a non-native nucleic acid sequence such as a promoter. The nucleic acid molecule linked to the promoter may be all or part of an ORF as shown in FIG. 7 (SEQ ID NOS: 11-13; and 8 (SEQ ID NO: 5), or may be one or more fragments of a DNA sequence as shown in FIG. 6 (SEQ ID NO: 3).

[0047] Purified proteins (also called polypeptides) and fragments thereof are also included within the invention. These proteins may be proteins encoded by any of the claimed nucleic acid sequences, or may be the protein or a fragment of the proteins shown in FIGS. 7 and 8 (SEQ ID NOS: 11-13 and 5). Proteins and protein fragments of the invention may be of various sizes, for instance 5, 10, 15, 20, 30, 40, 50, 60 or even 100 amino acids or more in length.

[0048] The scope of the invention also encompasses Immunogenic polypeptides (also referred to as immunogenic (or antigenic) amino acid sequences) that are derived from SMSV-5 Hom-1 and that promote an immunological response when introduced into a mammal under suitable conditions for eliciting such a response (Better and Horowitz, 1990, Advances in Gene technology: The Molecular Biology of Immune Disease & the Immune Response (ICSU Short Reports); and Better et al., 1989, Methods in Enzymology 178:176-496). In one embodiment, the present invention is directed to a vaccine composition comprising a pharmaceutically acceptable vehicle and at least one SMSV-5 Hom-1 antigen, which antigen may be any SMSV-5 Hom-1 antigen including, for example a recombinant subunit antigen e.g., those epitopes bound specifically by cross reactive monoclonal neutralizing antibodies (FIG. 12). Alternatively, whole attenuated SMSV-5 Hom-1 virus particles may be used in a vaccine composition. A recombinant subunit antigen may comprise one or more neutralizing epitopes of a SMSV-5 Hom-1 protein or glycoprotein. The protein may be selected from the group consisting of, for example either structural or non structural caliciviral proteins.

[0049] In one embodiment, the invention comprises assays for the detection of anti-SMSV-5 Hom-1 antibodies. SMSV-5 Hom-1 virus antigens or recombinant antigens of SMSV-5 Hom-1 can be used as substrate reagents in immunoassays to identify antibodies to SMSV-5 Hom-1 in a sample, e.g., blood, as one means of determining if the sampled individual has been exposed to (or is currently infected with) SMSV-5 Hom-1 and to determine the concentration of the antibodies in the sample. The immunoassays in which such antigens can be used include, but are not limited to, radioimmunoassay, competition immunoprecipitation, enzyme-linked immunoadsorbent assay, immunofluorescence assay and the like. The antigens of SMSV-5 Hom-1 for example those shown in FIGS. 4 (SEQ ID NO: 2) and 6-8 (SEQ ID NOS: 5 and 11-13) or derived from SMSV-5 Hom 1 may be used in assay compositions in a concentration sufficient to form a detectable complex with specific antibodies. The SMSV-5 Hom-1 antigens can be mixed with or attached to a suitable matrix (support) or carrier, such as a latex particle or plastic microtiter plate or the like. They can also be conjugated with an enzyme, dye, radio-labeled or the like, depending upon what immunological method is used. The details of conducting various types of immunoassays is well known in the art and also described in Antibodies. A Laboratory Manual by Harlow and Lane, Cold Spring Harbor Laboratory (1988), the disclosures of which are incorporated by reference.

[0050] Accordingly, the invention includes a method for determining the presence or absence of or concentration of antibodies for SMSV-5 Hom-1 in a sample by employing an immunoassay, the immunoassay characterized by using one or more non-recombinant or recombinant antigenic SMSV-5 Hom-1 polypeptides (FIG. 5) that bind with anti-SMSV-5 Hom-1 antibodies as a reagent in the immunoassay, whereby a complex of the anti-SMSV-5 Hom-1 antibodies and the SMSV-5 Hom-1 antigens is formed, and determining the presence or absence of or concentration of the complex formed as indicative of the presence or absence of or concentration of the antibodies.

[0051] In one embodiment, the invention comprises assays for detection of SMSV-5 Hom-1 antigens by using anti-SMSV-5 Hom-1 antibodies (for example FIG. 13). Anti-SMSV-5 Hom-1 antibodies may be made and purified by conventional methods (Antibodies may be produced using standard procedures described in a number of texts, including Antibodies, A Laboratory Manual by Harlow and Lane, Cold Spring Harbor Laboratory, 1988) and may be polyclonal or monoclonal antibodies. Such antibodies may be used in quantitative and qualitative assays for antigens wherein the antibodies are contacted with a sample that putatively contains SMSV-5 Hom-1 antigens, wherein the antigens and the antibodies specifically bind to each other, and wherein the amount of antibody-antigen conjugate is then detected and measured.

Definitions

[0052] The following terms are used herein to have the meanings noted below.

[0053] Calicivirus: The family Caliciviridae comprises a group of morphologically distinct viruses with an unusually diverse host spectrum, both phylogenetically and geographically. Caliciviruses are small (29-37 nm), non-enveloped, icosahedral viruses with T=3 lattice symmetry, that possess unique cup-shaped surface structures which are readily identifiable under the electron microscope. The genome of the caliciviruses is comprised of a single molecule of polyadenylated, single-stranded RNA of positive polarity. These agents have been isolated from, or observed in, a phylogenetically diverse variety of marine and terrestrial organisms, and serotype specific neutralizing antibody titers suggest that many of these agents move freely, over great distances, between ocean and land. Caliciviruses have the potential to cause serious disease in a wide variety of animals, including humans, whenever they are introduced into a susceptible population.

[0054] Vesiviruses: The genus vesivirus is currently made up of the caliciviruses that have been cultivated in-vitro and all have a genomic organization distinct from the other three currently described genera of the family caliciverdae. The vesiviruses (5′ to 3′) have three open reading frames coding (from 5′ to 3′) for non-structural (including polymerase), structural (including capsid) and VPg proteins.

[0055] SMSV-5 Hom-1: San Miguel sea lion virus 5 serotype Homosapien-1, isolated from a human subject (26). SMSV-5 Hom-1 may be grown on Vero cells, as described below, using standard virological techniques.

[0056] Antibodies: include intact antibodies as well as fragments thereof, such as Fab, Fab′, F(ab′)2, and Fv which bind to an AIB1 epitope. These antibody fragments are defined as follows: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab′, the fragment of an antibody molecule obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule; (3) (Fab′)2, the fragment of the antibody obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)2, a dimer of two Fab′ fragments held together by two disulfide bonds; (4) Fv, a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (5) single chain antibody (“SCA”), a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule. Methods of making these fragments are routine.

[0057] An antigen: refers to a molecule containing one or more epitopes that, when introduced into a host, will stimulate a host's immune system to make a humoral and/or cellular antigen-specific response. The term is also used interchangeably with “immunogen.”

[0058] A subunit antigen: an antigen entity separate and discrete from a whole virus (live or killed). Thus, an antigen contained in a cell free extract would constitute a “subunit antigen” as would a substantially purified antigen.

[0059] An epitope: the site on an antigen or hapten to which a specific antibody molecule binds. The term is also used interchangeably with “antigenic determinant” or “antigenic determinant site.”

[0060] A hapten: a molecule containing one or more epitopes that does not stimulate a host's immune system to make a humoral or cellular response unless linked to a carrier.

[0061] An immunological response: the development in the host of a cellular and/or antibody-mediated immune response to a composition or vaccine of interest. Usually, such a response consists of the subject producing antibodies, B cells, helper T cells, suppressor T cells, and/or cytotoxic T cells directed specifically to an antigen or antigens included in the composition or vaccine of interest.

[0062] Immunogenic polypeptide (or immunogenic amino acid sequence): refers to a polypeptide or amino acid sequence, respectively, which elicit antibodies that can participate in neutralizing viral infectivity, and/or mediate antibody-complement or antibody dependent cell cytotoxicity to provide protection of an immunized host.

[0063] The activity of the immunogenic polypeptide can be assayed using one of many assay that are well know in the art. Hence, the DNA sequences provided by this invention encode polypeptides that can stimulate T-cells to produce INF-γ. That is, these polypeptides act as epitopes for CD4 T-cells in the immune system. Studies have demonstrated that polypeptides isolated from an infectious agent and which are shown to be T-cell epitopes can protect against the disease caused by that agent when administered as a vaccine, Mougneau et al., Science 268:536-566, 1995 and Jardim et al., J. Exp. Med. 172:645-648, 1990. For example, T-cell epitopes from the parasite Leishmania major have been shown to be effective when administered as a vaccine, Jardim et al., J. Exp. Med. 172:645-648, 1990; Mougneau et al., Science 268:536-566, 1995; and Yang et al., J. Immunology 145:2281-2285, 1990. Therefore, the immunostimulatory polypeptides (T-cell epitopes) encoded by the DNA sequences according to the invention may be used, in purified form, as a vaccine.

[0064] An “immunogenic polypeptide” as used herein, includes the full length (or near full length) sequence of the desired protein (for instance, those eliciting a neutralizing antibody response (FIG. 12) or an immunogenic fragment thereof. By “immunogenic fragment” is meant a fragment of a polypeptide that includes one or more epitopes and thus elicits antibodies that neutralize viral infectivity, and/or mediates antibody-complement or antibody dependent cell cytotoxicity to provide protection of an immunized host. Such fragments will usually be at least about 5 amino acids in length, and preferably at least about 10 to 15 amino acids in length. There is no critical upper limit to the length of the fragment, which could comprise up to the full length of a protein sequence, or even a fusion protein comprising fragments of two or more subunit antigens.

[0065] Transformed: a transformed cell is a cell into which has been introduced a nucleic acid molecule by molecular biology techniques. The term encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transfection with viral vectors, transformation with plasmid vectors, and introduction of naked DNA by electroporation, lipofection, and particle gun acceleration.

[0066] Purified: the term purified does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified protein preparation is one in which the subject protein or other substance is more pure than in its natural environment within a cell. Generally, a protein preparation is purified such that the protein represents at least 50% of the total protein content of the preparation.

[0067] Specific binding agent: a molecule that binds substantially only to a protein of interest when assessed using the methods described below.

[0068] For instance, a molecule that binds specifically- to a protein derived from SMSV-5 Hom-1 is said to be a specific binding protein for the SMSV-5 Hom-1 protein. Such specific binding agents include antibodies that specifically bind to a protein of the present invention, as well as immunologically effective portions (fragments) thereof. These include, for instance, antibodies that bind specifically to the proteins shown in FIG. 8 (SEQ ID NO: 5). Specific binding agents that are capable of specifically binding to a protein of the invention may include polyclonal antibodies, monoclonal antibodies (including humanized monoclonal antibodies) and fragments of monoclonal antibodies such as Fab, F(ab′)2 and Fv fragments, as well as any other agent capable of specifically binding to a protein of interest. For a review, see Better and Horowitz, 1990, Advances in Gene technology: The Molecular Biology of Immune Disease & the Immune Response (ICSU Short Reports). Antibodies may be produced using standard procedures described in a number of texts, including Antibodies, A Laboratory Manual by Harlow and Lane, Cold Spring Harbor Laboratory (1988).

[0069] Antibodies of the present invention may include humanized antibodies. Methods of making humanized monoclonal antibodies are well known, and include those described in U.S. Pat. No. 5,585,089 (Humanized Immunoglobulins), U.S. Pat. No. 5,565,332 (Production of Chimeric Antibodies—A Combinatorial Approach), U.S. Pat. No. 5,225,539 (Recombinant Altered Antibodies And Methods Of Making Altered Antibodies), U.S. Pat. No. 5,693,761 (Polynucleotides encoding Improved Humanized Immunoglobulins), U.S. Pat. No. 5,693,762 (Humanized Immunoglobulins), U.S. Pat. No. 5,585,089 (Humanized Immunoglobulins), and U.S. Pat. No. 5,530,101 (Humanized Immunoglobulins), and references cited therein.

[0070] Similarly, methods of making and using immunologically effective portions of monoclonal antibodies, also referred to as antibody fragments, are well known and include those described in Better and Horowitz, 1990, Advances in Gene technology: The Molecular Biology of Immune Disease & the Immune Response (ICSU Short Reports); and Better et al., 1989, Methods in Enzymology 178:176-496.; and U.S. Pat. No. 5,648,237 (Expression of Functional Antibody Fragments), U.S. Pat. No. 4,946,778 (Single Polypeptide Chain Binding Molecules), and U.S. Pat. No. 5,455,030 (Immunotherapy Using Single Chain Polypeptide Binding Molecules), and references cited therein.

[0071] Virion: a complete viral particle including envelope (if any), capsid, and nucleic acid elements.

[0072] Isolated: an isolated nucleic acid has been substantially separated or purified away from other nucleic acid sequences in the cell of the organism in which the nucleic acid naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA. The term “isolated” thus encompasses nucleic acids purified by standard nucleic acid purification methods. The term also embraces nucleic acids prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.

[0073] ORF: open reading frame. An ORF is a contiguous series of nucleotide triplets coding for amino acids. These sequences are usually translatable into a polypeptide.

[0074] Homologs: two nucleotide or amino acid sequences that share a common ancestral sequence and diverged when a species carrying that ancestral sequence split into two species. Homologs frequently show a substantial degree of sequence identity.

[0075] Nucleic acid sequence identity: refers to the degree to which two polynucleotide sequences possess identical nucleotides when compared using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to achieve a more meaningful comparison of the two sequences. The higher the percentage sequence identity between two sequences, the more similar the two sequences are said to be. Such similarity is frequently an indication of homology (i.e.: evolutionary relatedness).

[0076] A commonly used and freely available sequence comparison algorithm is the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul et al., 1990), which is available from several sources, including the NBCI, Bethesda, Md. and on the Internet, for use in connection with the sequence analysis programs blastp (for proteins), blastn (for nucleotides), blastx, tblastn and tblastx. These tools are commonly used with gap and other parameters set to default settings. BLAST can be accessed at http//www.ncbi.nim.nih.gov/BLAST.

[0077] A pair of nucleic acids being compared, for instance from two evolutionarily related sequences, may have at least 50% sequence identity counted over the length of one of the nucleic acids (the reference nucleic acid) using the NCBI Blast 2.0.6, gapped blastn set to default parameters. Such a pair of nucleic acids may show, for example, at least 50%, 60%, 70%, 80%, 90%, 92%, 94, 95% or even 98% sequence identity.

[0078] Two nucleic acid sequences that show 50% or greater sequence identity will often encode polypolypeptides that are immunologically cross reactive with each other, i.e., antisera raised against one protein will cross react with antigens from the other protein.

[0079] Nucleic acids being compared may be of various lengths, for example, not less than 15, 25, 35, 45, 55, 65, 75 or 100 nucleotides in length. In some cases, entire genes may be compared, and in some cases, nucleotide fragments being compared may contain multiple genes and be hundreds or thousands of nucleotides in length.

[0080] Nucleic acid hybridization: Another indication that two nucleic acid sequences share a high degree of similarity, for example, 50% or greater, is that the two molecules hybridize to each other under defined hybridization conditions. The defined hybridization conditions may be more or less stringent, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched.

[0081] Because the degree to which two nucleic acids will bind is dependent upon their sequences, stringency is sequence dependent. Generally, stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out. Generally, such wash temperatures are selected to be about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating T. and conditions for nucleic acid hybridization is well known and can be found in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor, N.Y.; specifically see volume 2, chapter 9.

[0082] Conditions for hybridization between nucleotides of the present invention (e.g., between two nucleotides showing substantial similarity) include wash conditions of 70° C. and about 0.2×SSC for 1 hour, or alternatively, 65° C., 60° C., or 55° C. and about 0.2 to 2×SSC (with, for instance, about 0.1% SDS) for 1 hour. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, salmon sperm DNA. Hybridization, particularly under highly stringent conditions (e.g., wash temperatures of 60° C. or more and SSC concentrations of 0.2×) is suggestive of evolutionary similarity between the nucleotides. Such similarity (whether produced by convergent or divergent evolution) is strongly indicative of a similar role for the nucleotides and their resultant proteins.

[0083] Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequence that all encode substantially the same protein. The length of nucleic acids being hybridized may vary widely and either the hybridization probe or the target sequence or both may be as short as 15 nucleotides or as long as several thousand nucleotides. Such nucleic acids are described, for example, under “Nucleic Acid Sequence Identity” above.

[0084] Sequence similarity: The similarity between two nucleic acids or two amino acid sequences is expressed in terms of percentage sequence identity. The higher the percentage sequence identity between two sequences, the more similar the two sequences are.

[0085] In the case of protein alignments, similarity is measured not only in terms of percentage identity, but also takes into account conservative amino acid substitutions. Such conservative substitutions generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded protein. The computer programs used to calculate protein similarity employ standardized algorithms that, when used with standardized settings, allow the meaningful comparison of similarities between different pairs of proteins.

[0086] Sequences are aligned, with allowances for gaps in alignment, and regions of identity are quantified using a computerized algorithm. Default parameters of the computer program are commonly used to set gap allowances and other variables.

[0087] Methods of alignment of sequences for comparison are well-known in the art. Various programs and alignment algorithms are described by Pearson et al., Methods in Molecular Biology 24: 307-331, 1994, and in Altschul et al., Nature Genet. 6:119-129, 1994. Altschul et al. presents a detailed consideration of sequence alignment methods and homology calculations.

[0088] The NCBI Basic Local Alignment Search Tool (BLAST™) (Altschul et al., J. Mol. Biol. 215:403-410, 1990 is available from several sources, including the National Center for Biotechnology Information (NBCI, Bethesda, Md.) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. BLAST™ can be accessed at htp://www.ncbi.nim.nih.gov/BLAST/. A description of how to determine sequence identity using this program is available at the web site. As used herein, sequence identity is commonly determined with the BLAST™ software set to default parameters. For instance, blastn (version 2.0) software may be used to determine sequence identity between two nucleic acid sequences using default parameters (expect=10, matrix=BLOSUM62, filter=DUST (Tatusov and Lipmann, in preparation as of Dec. 1, 1999; and Hancock and Armstrong, Comput. Appl. Biosci. 10:67-70, 1994), gap existence cost=11, per residue gap cost=1, and lambda ratio=0.85). For comparison of two polypeptides, blastp (version 2.0) software may be used with default parameters (expect 10, filter=SEG (Wootton and Federhen, Computers in Chemistry 17:149-163, 1993), matrix=BLOSUM62, gap existence cost=11, per residue gap cost=1, lambda=0.85).

[0089] When aligning short polypeptides (fewer than around 30 amino acids), the alignment should be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties).

[0090] An alternative alignment tool is the ALIGN Global Optimal Alignment tool (version 3.0) available from Biology Workbench at http://biology.ncsa.uiuc.edu. This tool may be used with settings set to default parameters to align two known sequences. References for this tool include Meyers and Miller, CABIOS 4:11-17, 1989.

[0091] Conservative amino acid substitutions: are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.

Original Residue Conservative Substitution
ala              ser
arg              lys
asn              gln, his
asp              glu
cys              ser
gln              asn
glu              asp
gly              pro
his              asn, gln
ile              leu, val
leu              ile, val
lys              arg, gln, glu
met              leu, ile
phe              met, leu, tyr
ser              thr
thr              ser
trp              tyr
tyr              trp, phe
val              ile, leu

[0092] Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.

[0093] The substitutions which in general are expected to produce the greatest changes in protein properties will be non-conservative, for instance changes in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histadyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

[0094] Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in the same reading frame.

[0095] Probe: An isolated nucleic acid attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes.

[0096] Antisense, Sense, and Antigene: Double-stranded DNA (dsDNA) has two strands, a 5′->3′ strand, referred to as the plus strand, and a 3′->5′ strand, referred to as the minus strand. Because RNA polymerase adds nucleic acids in a 5′->3′ direction, the minus strand of the DNA serves as the template for the RNA during transcription. Thus, the RNA formed will have a sequence complementary to the minus strand, and identical to the plus strand (except that U is substituted for T).

[0097] Antisense molecules are molecules that are specifically hybridizable or specifically complementary to either RNA or the plus strand of DNA. Sense molecules are molecules that are specifically hybridizable or specifically complementary to the minus strand of DNA. Antigene molecules are either antisense or sense molecules directed to a dsDNA target.

[0098] In the context viral genomes that are RNA the strand that encodes the polypeptide is considered the “plus-strand” and the non-coding strand, if present, is considered the minus strand. Thus, antisense molecules and/or antigene molecules can be designed to hybridize to either the “plus-strand” or the “minus-strand” of the viral nucleic acid.

[0099] Therapeutically effective calicivirus oligonucleotides and oligonucleotide Analogs: “Therapeutically effective oligonucleotides and oligonucleotide analogs” are characterized by their ability to inhibit the viral replication. Complete inhibition, however, is not necessary for therapeutic effectiveness. Therapeutically effective oligonucleotides and oligonucleotide analogs are characterized by their ability to inhibit viral replication. Inhibition can be measured by adding the oligonucleotides to cultured cells that have been or are subsequently infected with calicivirus. The level of viral replication can then be determined via northern blotting or ELISA. The results from the sample treated with the oligonucleotides can then be compared to the results from a control non-infected cell culture. The oligonucleotide is considered “therapeutically effective” if it inhibits viral replication when compared to the control. Additionally, some oligonucleotides will be capable of inhibiting the viral replication by at least 15%, 30%, 40%, 50%, 60%, or 70%.

[0100] Therapeutically effective oligonucleotides and oligonucleotide analogs are additionally characterized by being sufficiently complementary to a viral nucleic acid sequence. Sufficient complementary means that the therapeutically effective oligonucleotide or oligonucleotide analog can specifically disrupt viral replication.

[0101] Primers: Short nucleic acids, preferably DNA oligonucleotides 10 nucleotides or more in length, which are annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods known in the art.

[0102] Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or 150 consecutive nucleotides of the disclosed nucleic acid sequences.

[0103] Methods for preparing and using probes and primers are described in the references, for example Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor, N.Y.; Ausubel et al., 1987, Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences; Innis et al., 1990, PCR Protocols, A guide to Methods and Applications. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.).

[0104] Recombinant nucleic acid: a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook et al. (1989). The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector, used to transform a cell.

[0105] Alternatively, such a recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.

Methods

[0106] General Methods

[0107] The present invention utilizes standard laboratory practices for the cloning, manipulation and sequencing of nucleic acids, purification and analysis of proteins and other molecular biological and biochemical techniques, unless otherwise stipulated. Such techniques are explained in detail in standard laboratory manuals such as Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor, N.Y.; and Ausubel et al., 1987, Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences.

[0108] Preparation of SMSV-5 Horn-1 Nucleic Acid Sequences

[0109] A. Obtaining the Viral Genome

[0110] The SMSV-5 Hom-1 genome of the invention may be procured by de-novo isolation from a viral culture. A biological sample of the virus (accession number ______) may be obtained from the ATCC in Manassas, Va. This virus may be grown in vitro using Vero cell monolayers as described in the Examples below. The virus may be harvested from the culture supernatant and infected Vero cells. Cellular debris may be removed by centrifugation and intracellular virus particles may be released by sonication followed by centrifugation to pellet debris. The virus may then be pelleted by centrifugation and further purified through a CsCl gradient. The band containing the virus may be collected and the virus then pelleted by centrifugation. Viral RNA may be isolated by extraction with Trizol reagent (GIBCO-BRL, Gaithersburg, Mass.).

[0111] B. Obtaining Selected Polynucleotides from the Viral Genome

[0112] The isolated viral genome may be used as a source of polynucleotides as identified by the sequences disclosed herein (FIGS. 4, 6-8; and SEQ ID NOS: 1, 3 and 4). The reverse-transcriptase polymerase chain reaction (RT-PCR) may be used to amplify any polynucleotide selected from the known viral sequence using the viral genome as a source of template RNA. The template RNA may also be provided in the form of the complete viral genome or one or more cosmids that contain fragments of the viral genome for example the clone with 5rt73 (FIG. 6; and SEQ ID NO: 3). Actual RT-PCR amplifications of cDNA sequences have been carried out using primers, for example from a primate calicivirus as described below in the examples and FIG. 4.

[0113] The selection of PCR primers may be made according to the portions of the genome to be amplified. Primers may be chosen to amplify small fragments of the genome, ORFs or fragments including many contiguous genes from the genome. Variations in amplification conditions may be required to accommodate primers of differing lengths, and such considerations are well known in the art and are discussed in Innes at al, 1990, Sambrook et al, 1989, and Ausubel et al, 1987. For example, the ORF corresponding to that shown in FIG. 4 may be amplified from an SMSV-5 Hom-1 genomic (or appropriate cosmid) template using the following pair of primers (these primers correspond to nucleotide sequences outside of that shown in FIG. 4 (SEQ ID NO: 1):

[0114] 5′-CGGGTCGGTTTCAGACCAAAC-3′ (SEQ ID NO: 6)

[0115] 5′-ATCCAAGTTGGCATCAAA-3′ (SEQ ID NO: 7)

[0116] For the RT step, 5 μl of extracted nucleic acid was added to 0.2 μg primer and 10 units of avian myeloblastosis virus reverse transcriptase (Amersham Corp., Arlington Heights, Ill.) and the 50 μl reaction mixture was incubated for 1 h at 42° C. Next, 0.2 μg of the second primer and 5 units of Taq polymerase (Perkin-Elmer Cetus, Norwalk, CO) were added to the mixture to produce a final volume of 100 μl. Forty cycles of 1 min of denaturation at 94° C., 1 min of annealing at 37° C., and 1 min of primer extension at 72° C. were performed in thermal cycler (programmable Thermal Controller, M.J. Research, Inc., Cambridge, Mass.). Annealing temperatures were raised to obtain some products. The RT-PCR products were visualized by agarose gel electrophoresis.

[0117] Such primers are illustrative only and it will be readily appreciated by one of ordinary skill in the art that many different primers may be selected from the sequence disclosed and used in PCR amplification reactions to amplify cDNA sequences of interest from the SMSV-5 Hom-1 genome.

[0118] Polynucleotides that may be obtained by the above methods include, for example those shown in FIG. 4 (SEQ ID NO: 1). It is readily apparent that fragments of any length may be made using the above methods and information.

[0119] C. Cloning and Expression of SMSV-5 Hom-1 Nucleotides

[0120] Fragments amplified as described herein can be cloned into standard cloning vectors and expressed in commonly used expression systems consisting of a cloning vector and a cell system in which the vector is replicated and expressed.

[0121] Since calicivirus is a virus isolated from a mammal, eukaryotic vectors may be well suited to the expression of calicivirus derived genes, although prokaryotic vectors may also be used and may be well suited for high protein expression. A number of commercial protein expression and purification systems are widely available and may be used for expression and purification of calicivirus proteins.

[0122] Various yeast strains and yeast-derived vectors are commonly used for expressing and purifying proteins, for example, Pichia pastoris expression systems are available from Invitrogen (Carlsbad, Calif.). Such systems include suitable Pichia pastoris strains, vectors, reagents, transformants, sequencing primers and media. Available strains include a GS115 his 4 deficient strain, a KM71 aox1 deficient strain, a GS115 His+ Mut− strain for extracellular expression and a His+Mut− strain for intracellular expression, all of which are available commercially from Invitrogen (Carlsbad, Calif.).

[0123] Non-yeast eukaryotic vectors may also be used for expression of the calicivirus proteins. Examples of such systems are the well known Baculovirus system, the Ecdysone-inducible mammalian expression system that uses regulatory elements from Drosophila melanogaster to allow control of gene expression, and the Sindbis viral expression system that allows high level expression in a variety of mammalian cell lines. These expression systems are also available from Invitrogen.

[0124] Standard prokaryotic cloning vectors may also be used, for example pBR322, pUC18 or pUC19 as described in Sambrook et al, 1989. Nucleic acids of calicivirus may be cloned into such vectors which may then be transformed into bacteria such as Escherischia coli (E. coli) which may then be cultured so as to express the protein of interest. Other prokaryotic expression systems include, for instance, the arabinose-induced pBAD expression system that allows tightly controlled regulation of expression, the IPTG-induced pRSET system that facilitates rapid purification of recombinant proteins and the IPTG-induced pSE402 system that has been constructed for optimal translation of eukaryotic genes. These three systems are available commercially from Invitrogen and, when used according to the manufacturer's instructions, allow routine expression and purification of proteins.

[0125] The cloned expression vector may then be transformed into a particular cell type and the nucleotide expressed. Many different types of cell may be used to express the modified nucleic acid molecules. Examples of such cells include cells of yeasts, fungi, insects and humans and plants, including transformed and non-transformed cells. For instance, common mammalian cells that could be used for the invention include human HeLa cells, SW-527 human cells (ATCC deposit #7940), WISH cells (ATCC deposit #CCL-25), Daudi cells (ATCC deposit #CCL-213), Mandin-Darby bovine kidney cells (ATCC deposit #CCL-22) and Chinese Hamster ovary cells (ATCC deposit #CRL-2092). Common yeast cells include Pichia pastoris (ATCC deposit #201178) and Saccharomyces cerevisiae (ATCC deposit #46024). Insect cells include cells from Drosophila melanogaster (ATCC deposit #CRL-10191), the cotton boilworm (ATCC deposit #CRL-9281) and from Trichoplusia ni egg cell homoflagelates. Fish cells that may be used include those from rainbow trout (ATCC deposit #CLL-55), salmon (ATCC deposit #CRL-1681) and Zebrafish (ATCC deposit #CRL-2147). Amphibian cells that may be used include those of the Bullfrog, Rana catesbelana (ATCC deposit #CLL-41). Reptile cells that may be used include those from Russell's Viper (ATCC deposit #CCL-140>. Plant cells that could be used include Chlamydomonas cells (ATCC deposit #30485), Arabidopsis cells (ATCC deposit #54069) and tomato plant cells (ATCC deposit #54003). Many of these cell types are commonly used and are available from the ATCC as well as from commercial suppliers such as PHARMACIA™ and INVITROGEN™.

[0126] Expressed protein may be accumulated within a cell or may be secreted from the cell. Such expressed protein may then be collected and purified. This protein may then be characterized for activity and heat stability and may be used to practice the methods of the invention.

[0127] Production of an Antibody to Calicivirus Proteins

[0128] Antibodies may be produced to a calicivirus protein. Optimally, antibodies raised against the calicivirus protein will specifically detect (bind specifically with) the calicivirus protein and would not substantially recognize or bind to other proteins. The determination that an antibody specifically detects a SMSV-5 Hom-1 protein is made by any one of a number of standard immunoassay methods; e.g., the Western blotting technique (Sambrook et al., 1989). An antibody that is specific for a calicivirus protein will bind substantially only to the calicivirus protein on a Western blot, and will not show significant binding to unrelated proteins (e.g., from serum albumin). Antibodies that are capable of specifically binding to an calicivirus protein may include polyclonal antibodies, monoclonal antibodies (including humanized monoclonal antibodies) and fragments of monoclonal antibodies such as Fab, F(ab′)2 and Fv fragments, as well as any other agent capable of specifically binding to an SMSV-5 Hom-1 protein.

[0129] Substantially pure calicivirus protein suitable for use as an immunogen may be obtained using an expression system as described above. Concentration of protein in the final preparation is adjusted, for example, by concentration on an Amicon filter device, to the level of a few micrograms per milliliter. Monoclonal or polyclonal antibody to the protein can then be prepared as described by Harlow and Lane, 1988, Antibodies, A Laboratory Manual, Cold Spring Harbor Press.

[0130] Alternatively, antibodies may be raised against synthetic calicivirus polypeptides synthesized on a commercially available polypeptide synthesizer based upon the predicted amino acid sequence of the SMSV-5 Hom-1 protein (Harlow and Lane, 1988).

[0131] Another method of raising antibodies against calicivirus proteins is by subcutaneous injection of a DNA vector which expresses the calicivirus protein into laboratory animals, such as mice. Delivery of the recombinant vector into the animals may be achieved using a hand-held form of the Biolistic system (Sanford et al., 1987, Particulate Sci. Technol. 5:27-37) as described by Tang et al. 1992, Nature (London) 356:152-154. Expression vectors suitable for this purpose may include those which express one or more calicivirus proteins under the transcriptional control of either the human β-actin promoter or the cytomegalovirus (CMV) promoter.

[0132] Antibody preparations prepared according to these protocols are useful in quantitative immunoassays which determine concentrations of antigen-bearing substances in biological samples; they are also used semi-quantitatively or qualitatively to identify the presence of antigen in a biological sample. FIG. 13 provides examples of monoclonal antibodies for such purposes and FIG. 14 provides polyclonal antibody examples.

[0133] Diagnostic Uses of SMSV-5 Hom-1 Proteins

[0134] Whole virus (CsCl purified) can be used as caliciviral specific protein for antibody detection (26) as can selected subgenomic expression products (FIG. 8; SEQ ID NO: 4).

[0135] The nucleic acid sequence (SEQ ID NO: 4) and the corresponding amino acid sequence (SEQ ID NO: 5) have been shown to be useful for detecting specific binding agents that bind to different calicivirus isolates. Therefore, the polypeptide shown in SEQ ID NO: 5, or fragments thereof, may be useful for screening samples from subjects that are thought to have been exposed to calicivirus.

[0136] Diagnostic Uses of SMSV-5 Hom-1 Antibodies

[0137] Type specific neutralizing antibodies can be used to identify specific virus isolates (26), polyclonal and monoclonal antibodies can serve as group specific test (FIGS. 13 & 14) for viral presence or for histochemical probes to detect virus in tissues or bodily samples.

[0138] Those reagents having utility for diagnosing and preventing vesiviral diseases and their application in humans as described in this disclosure would be expected to also have application for use in detecting and preventing vesivirus infections in animal species where these animals may be or may become reservoirs of vesiviruses posing a threat to human health. For instance, the vesivirus designated SMSV-17 which can be expected to have approximately 90% nucleotide homology with SMSV-5 Hom-1, has been isolated from edible shellfish (a marine mussel) and also from an aborted mammalian fetus (see Poet SE Detection and Isolation of Calicivirus from a Bivalve Mollusk [Mytilus californianus] Collected from Rocks Adjacent to Pinniped Rookeries Ph.D. Thesis, Oregon State University (1994) pages 77-98). In all, over 20 species of domestic animals, wildlife, zoologic species and poikilotherms such as fish, frogs and snakes have yielded vesivirus isolates that are now expected to pose a human health challenge either as food safety threats or by contact.

[0139] Therapeutic Uses of Calicivirus Nucleic Acids and Proteins

[0140] The calicivirus virus may be used to produce a vaccine that provides a protective immune response against calicivirus infection. Such vaccines may be monovalent or polyvalent. Such a vaccine may include whole virus particles that may be attenuated or killed by, for example chemical or heat treatment. Such a vaccine may also comprise immunogenic subunit antigens (epitopes) derived from calicivirus using whole attenuated live virus given by injection, nasal spray or orally or by other means to insure processing of appropriate antigens by immunocytic tissues. Attenuated viruses are those that have been adapted to alternate hosts and thus lose their disease causing properties yet retain some replicative ability in the target host. Examples would be chick embryo adapted vaccines for rabies. Alternatively whole virus inactivated but delivered properly and in sufficient quantities to stimulate immune response could be carried out as could selected antigenic components (subunits) of the virus delivered as “killed” vaccine. Subunits can also be rendered immunogenic by incorporating them into live vector systems (for example vaccinia virus) where the replicating vaccinia virus produces the desired recombinant antigen, for example a Sindbis virus neutralizing antibody producing epitope or epitopes was expressed by vaccinia virus in cattle and in turn they elicited antibody that neutralized Sindbis virus (*See Franke et al “Immunization of cattle with a recombinant Togavirus-vaccinia virus strain.” Res Vet Sci 1985 39:113-115). A second example is the rabies vaccines administered as live vaccinia virus recombinants to wildlife. Another example of viral vectors for live virus vaccines are the herpesviruses and there are others. Yet other systems include insect viruses (for example, Baculovirus) used for producing large quantities of protein from a recombinant insert. Expressed protein is then purified and used as a vaccine. Finally, so-called DNA vaccines could be developed where cDNA is incorporated into tissues of the target host, these cells express foreign protein that the host recognizes as foreign and builds antibodies to these.

EXAMPLES

[0141] Electron Microscopy

[0142] A blister on the patient's hand was cleansed with alcohol and vesicular fluid (approx. 25 mL) was aspirated and placed into 1 mL of sterile distilled water. The sample was vortexed and clarified for 10 minutes at 850×g. The resulting supernatant was transferred to a new tube and centrifuged 20 minutes at 15,000×g. The pellet was resuspended in 10 μL of distilled water and transferred to parafilm. A Formvar-coated, 300-mesh copper grid was floated on the drop for 2 minutes, blotted dry with filter paper, stained with phosphotungstic acid (PTA), and examined at an accelerating voltage of 80 kilovolt (KV) using a Phillips 300 transmission electron microscope (EM). Subsequent to EM examination, the remainder of the sample was processed for virus isolation.

[0143] Virus Propagation

[0144] Isolation of the calicivirus SMSV5 Hom-1 was carried out in Vero cell monolayers inoculated with 0.2 ml of a 1:10 sterile distilled water dilution of vesicular fluid aspirate and then incubated and examined for cytopathic effect and isolates plaque passaged three times, as previously described [1]. For comparisons, the clinical human isolates and prototype SMSV-5 strain 205 originally isolated from an ill pinniped [1] were used for agar gel electrophoresis (SDS-PAGE) capsid protein comparisons. Vero cells were inoculated with a multiplicity of infection (MOI)>10 of the respective viruses, incubated for one hour at 37° C., then rinsed and fed with minimum essential media (MEM) plus 1% fetal bovine sera (FBS) and incubated at 37° C. At 3.5 hours post inoculation, the medium was removed, the cells rinsed once with MEM and then fed for 30 minutes with methionine-free MEM containing actinomycin D at 2 μg/ml. At 4 hours post inoculation, fresh methionine-free medium with 35S-methionine (25 μCi/ml) was added and uptake of labeled methionine was allowed to continue for 30 minutes. The cells then were rinsed once with ice-cold 0.5 M tris-HCl (pH 7.4) and samples collected with lysis buffer (0.05 M tris-HCl and 2% SDS, pH 7.4). Samples were processed for immunoprecipitation and were electrophoresed under reducing conditions.

[0145] Serum Neutralization

[0146] Neutralization for typing and to determine antibody titers in patient sera were completed using Vero cells in 96 well plates and replicates of 4 wells with 2 fold dilution of test serum against 100 tissue culture infective dose (TCID)50 of virus [1]. The human isolate was typed using twenty antibody units of heterologous typing serum from each of 40 calicivirus types including SMSV-5 [26].

[0147] ELISA for Antibody to SMSVs

[0148] Assays were completed using a 96-well microtiter plate (#76-371-04, ICN Biomedicals Inc. Horsham, Pa.) The test antigen consisted of a pool of three CsCl banded caliciviruses (SMSV-5, SMSV-13, and SMSV-17) in 0.1 M carbonate buffer, pH 9.6. The test antigen was adsorbed to the plate for 2 hours at 37° C., then washed 2×with tris buffered saline containing Tween 20 Tris buffered saline in tween (TBST) and blocked overnight at 4° C. with TBST containing 0.25% BSA. After two TBST washes, each serum diluted 1:100 in blocking buffer was added for 2 hours at 37° C., then washed 6×with TBST. Next, anti-human IgG-alkaline phosphatase (SIGMA), diluted 1:40,000 in blocking buffer, was added and incubated 2 hours at 37° C., then the wells were washed 6× with TBST and 2× with TBS without Tween. The chromogenic substrate pnpp (SIGMA) was added (200 μl per well at 1 mg/ml) and incubated overnight at 37° C. Optical densities (OD) were read at 405 nm on an enzyme linked immunosorbent assay (ELISA) plate reader (Titertek Multiskan). The OD value used was the test OD value minus the OD of a serum control well.

[0149] The OD values of control wells were 0.005, and most were 0.000. Values above an OD of 0.2 are considered positive.

[0150] RT-PCR Amplicon Generation

[0151] Amplicons (cDNA amplification products of a specific template RNA sequence) were generated by reverse transcriptase-polymerase chain reaction (RT-PCR) using primers Pr35 and Pr36 based upon the Pan-1 sequence.[9, 10] RT-PCR products were cloned into pGem-T (Promega, Madison, Wis.) and sequenced using “forward” and “reverse” primers and dideoxy chain termination. Primers PrCV35, PrCV36, and PrCV39 were synthesized from the sequence of Pan-1 (Matson D O, Zhong W-M, Jiang X, Smith A W, Unpubl.) PrCV35 and PrCV36 (nucleotides 5200-20 and 4727-45 of the Pan-1 sequence, respectively) and span GLPS and YGDD amino acid motifs characteristic of the presumed viral RNA polymerase. PrCV39 (nucleotides 5622-50 of the Pan-1 sequence) begins 46 nucleotides upstream from the first AUG in the second open reading frame (ORF) of Pan-1, the ORF that encodes the capsid protein. The primer sequences were: PrCV35, 5′-CGGGTCGGTTTCAGACCAAAC-3′ (SEQ ID NO: 8); PrCV36, 5′-ATCCAAGTTGGCATCAAA-3′ (SEQ ID NO: 9), and PrCV39, 5′-GTGGTCGGCCGGGGCTCGTTGGGGAGGTG-3′ (SEQ ID NO:

[0152] 10). Additional internal primers were synthesized for sequencing reactions. The pGEM-T vector system (Promega Corporation, Madison, Wis.) was used to clone RT-PCR products for sequencing. One to two cDNA clones of the predicted size were sequenced with “forward” and “reverse” primers using the 35S-dideoxy nucleotide chain termination procedure (Sequenase kit, United States Biochemical Corporation, Cleveland, Ohio). Internal primers were synthesized to complete the sequencing on both strands of each clone. Radionucleotide-labeled products were resolved in 8% polyacrylamide gels that were exposed overnight to X-AR-2 film (Kodak, Rochester, N.Y.).

[0153] Method of Creating Monoclonal Antibodies that Recognize and/or Neutralize Multiple Serotypes of Vesiviruses

[0154] The goal of creating monoclonal antibodies that recognize and/or neutralize multiple different calicivirus strains was achieved using two different methods of developing antigens. The first method involved a “surface-in” approach wherein the virions were enzymatically degraded for set periods of time and then used as antigens to inoculate mice. The second method involved infecting a cell culture with calicivirus and taking samples at various time intervals with the intent of isolating epitopes that are normally not present on the exterior of the virion. This second method is termed the “inside-out” method. Both methods offer the possibility of generating both a humoral response and a cellular immune response where intracellular calicivirus specific polypeptides of 9-11 amino acids in length could be presented via the Type I histocompatibility complex to killer T cells which in turn would lyse calicivirus infected host cells thereby arresting virus replication.

[0155] A number of epitopes associated with a neutralizing antibody response have been described for the feline calicivirus but all are type specific and between serotype neutralizing activity was not shown (*Tohya et al., 1991, Arch. Virol. 117:173-181). However, highly conserved monoclonal antibody binding epitopes on the capsid protein common to as many as 38 calcivirus serotypes (FIG. 13) has been demonstrated as well as a series of monoclonals antibodies that neutralize multiple serotypes (FIG. 12). Those with neutralizing antibody binding action give strong insight into the specific functional moieties that are present and highly conserved which are critical to caliciviral survival and/or replication. This also suggests that these important functional components are sequestered such that the immune system will preferentially select the more available, but often variable, viral epitopes. It also suggests that if humoral antibody can be successfully targeted for specific, but essential elements that are minor epitopes, then these antibodies should block critical functions and be protective.

[0156] The first method of generating calicivirus epitopes was accomplished by progressively peeling off of major epitopes on the more exposed outer surfaces of the calcivirus coat protein, using progressive digestion with specific proteolytic enzymes. This would be a “surface-in” approach. These digests were stopped at predetermined time intervals established by using direct electron microscopic (EM) examination to determine the degree of capsid degradation. The digestion products were used to produce a series of monoclonal antibodies in mice. Then mouse splenocytes from mice injected with these caliciviral digest preparations were fused with myeloma cells and fusion supernatants examined for cross neutralizing Mab. The positive results are shown in FIG. 12. These Mabs can now be reacted against polypeptides generated from a calcivirus cDNA library cloned into a high efficiency eukaryotic expression vector (pcDNA I). Polypeptides bound by cross-reactive neutralizing Mabs can be further examined as vaccine candidates either singly or in combination.

[0157] The second method of generating calicivirus specific monoclonal antibodies involved working from the inside out, by examining viral polypeptides which occur as the replicative cycle progresses. To do this, samples of a calicivirus-infected cell culture were frozen beginning with 60 minutes after absorption to cell cultures and then every 30 to 60 minutes thereafter up to 8 hours or until replication was complete. Each time interval preparation was used as outlined above for producing mouse monoclonal antibodies that were screened for calicivurs neutralizing activity. The rationale for this “core-out” approach is to examine viral replicative proteins, such as the capsid precursor protein, nonstructural proteins, genome associate protein, and similar functional antigens that might be lost or altered during virus maturation and release. Monoclonal antibodies resulting from these two series of experiments showed the ability to bind up to 38 different calicivirus serotypes (FIG. 13) and to neutralize several calicivirus serotype (FIG. 12).

Results and Discussion

[0158] A. Human Subject with Flu-Like Illness and Blistering

[0159] A 32-year-old male researcher developed a flu-like illness that was followed in two days by an initial blister on the right index finger. Within 12 hours, deep, painful blisters (not unlike hand, foot and mouth disease caused by some enteroviruses) [11] appeared on the palms and fingers of both hands (FIG. 1) and by 24 hours on the soles and toes of both feet.

[0160] In all, several dozen lesions occurred, ranging from small, red, raised areas to fluid-filled blisters 1 cm in diameter. Healing commenced within 1 week and was essentially complete in 2 weeks. The prototype SMSV-5 calicivirus was isolated from similar lesions on the flippers of northern fur seals. (FIG. 2)

[0161] Virus particles having the morphologic characteristics typical of the Caliciviridae were visualized by negative contrast electron microscopy in the aspirated vesicular fluid [12] (FIG. 3), and a calicivirus was isolated in Vero cells. Comparisons of RT-PCR amplicons of SMSV-5 strain 205, [1] and the virus isolate from the hand lesions revealed that these were the same genotype. (FIG. 4) [11] The human isolate, designated strain SMSV-Homosapien-1 (SMSV-5 Hom-1), was neutralized by typing antiserum to SMSV-5 but was not neutralized by typing antisera to 39 other calicivirus serotypes.

[0162] The infected individual developed type-specific neutralizing antibodies measured using 100 TCID50 of prototype SMSV-5 of test virus as follows: the pre-exposure serum was negative at a 1:4 serum dilution. On day 4 post infection (PI), the neutralization titer was 1:10 and was 1:80 on days 28 and 180 PI. Convalescent serum (day 28 PI) immunoprecipitated the single capsid protein (60 KDa) of the prototype SMSV-5 and SMSV-5 Hom-1, but not proteins in mock-infected Vero cells. SMSV-5 typing serum also immunoprecipitated the capsid protein of both virus stocks. (Figure not shown) In addition, findings of neutralizing antibody in humans were reported previously.[1, 2]

[0163] The source and route of exposure to SMSV-5 could not be determined with certainty and additional or secondary cases were not seen. However, at the time, the infected individual was routinely processing gradient-purified prototype caliciviruses including serotype SMSV-5, working around the mouths and teeth of calves experimentally infected with SMSV-5 and isolating in cell culture the virus being shed in their oropharyngeal secretions.

[0164] B. Testing Unselected Adult Population for Antibodies to SMSVs

[0165] To determine, whether an unselected adult population had been infected with SMSVs in the past, serum reactivity was measured by ELISA using a calicivirus group antigen test. Eighteen percent of 300 sera collected from adults donating blood in Portland, Oreg. during a 6-month period in 1996 had reactivity (OD value >0.20 or 8% at OD>0.50) in an ELISA using as test antigen three CsCl banded marine calicivirus serotypes including SMSV-5. (FIG. 5). Two of two ELISA-positive samples (OD values 0.884 and 1.690) were confirmed to have antibody to the 60 KDa capsid protein of a marine calicivirus (Strain McAII) by Western blot while one ELISA-negative sample (OD 0.011) was also negative by Western blot. Fourteen serum samples (paired samples, acute and convalescent) from seven individuals with confirmed diagnoses of Norwalk gastroenteritis did not test positive against the SMSV group antigen, and the OD readings of convalescent sera compared to acute showed no detectable rise (Data not shown). For these reasons it is believed that the reactivity to SMSV antigen cannot be discounted as cross reactivity to infection from other human caliciviruses of the Norwalk group and ELISA reactivity to our calicivirus antigen could be eliminated by preadsorbing the sera with calicivirus antigen.

[0166] C. Antibodies Directed to Calicivirus are Detected in the Serum from Patients who Suffered Spontaneous Abortions

[0167] The Elisa assay discussed above was used to test serum samples from cases of spontaneous abortion. 100 samples were tested and 15% of these gave positive responses in the ELISA test. In comparison 5% of 398 samples collected from “normal” subjects were positive. Thus, establishing a link between calicivirus infection and spontaneous abortion.

[0168] D. Calicivirus Hepatitis Agent Transmitted by Blood

[0169] Five serums sets provided by the American Red Cross Regional Testing Laboratory Portland, Oreg. and Chiron Corp., Emeryville, Calif. were tested for the presence of calicivirus antibodies. The ELISA described above using a pooled vesivirus antigen made up of SMSV-5, SMSV-13, and SMSV-17 was used to test the serum. The results from these serum samples were as follows:

GROUPS*	POSITIVE	NEGATIVE	TOTAL	% Positive
Normal Red	19	379	398	5%
Cross Serums*
ALT Elevated	17	181	197	9%
>120 But
Negative For
Hepatitis B And
C As Well As
All Other Viral
Agents
Routinely
Tested For.*
Clinical Cases	2	14	16	13%
Of Hepatitis
That Were
Negative For
Hepatitis A-
G**
Positive	2	8	10	20%
Samples For
Hepatitis B And
C**
Clinical Cases	7	25	32	22%
Of Hepatitis
Following
Transfusion Or
Dialysis**
Chi sq. = 17.1, P = <.001
*samples provided by the American Red Cross
**samples provided by Chiron Corp.

[0170] The above groupings are rank ordered for probable risk for blood transmission (transfusion transmitted) hepatitis and the data provides compelling evidence of a calicivirus hepatitis agent transmitted via blood a P value of <0.001.

[0171] E. Antibodies Directed to Calicivirus are Detected in the Serum from Patients who Suffer from Chronic Fatigue Syndrome

[0172] The ELISA described above, which utilizes SMSV-5,-13, and McA11, to bind to vesivirus specific antibodies was used to test for the presence of vesivirus specific antibodies in serum from patients with Chronic Fatigue Syndrome (CFS). Ten control serum samples were tested and ten CFS samples were tested. The results show that at least 20% of the CFS samples had elevated levels of vesivirus specific antibodies.

	Code	Ser plus	Serum	Corrected
	Number	antrigen	Control	OD
	176-A	Control	.314	.001	.314
	186-B	Control	.014	.002	.012
	191-C	Control	.018	.000	.018
	192-D	Control	.006	.001	.005
	193-E	Control	.012	.002	.010
	194-F	Control	.050	.003	.047
	195-G	Control	.018	.000	.018
	196-H	Control	.045	.001	.044
	197-I	Control	.027	.002	.025
	199-J	Control	.008	.000	.008
	413-K	CFS	.433	.003	.430
	478-L	CFS	.041	.009	.032
	602-M	CFS	.017	.007	.010
	644-N	CFS	.102	.003	.099
	712-O	CFS	.049	.005	.044
	718-P	CFS	.276	.001	.275
	787-Q	CFS	.012	.005	.007
	805-R	CFS	.011	.004	.007
	1184-S	CFS	.036	.012	.024
	1206-T	CFS	.018	.010	.008

[0173] F. Additional Diseases that may be Associated with Calicivirus Infection in Humans

[0174] The discovery that calicivirus is an infectious agent in humans makes it likely that other diseases in humans will be linked to calicivirus infection. Moreover, it is likely that humans may suffer from similar diseases as those that are already known to be caused by calicivirus in other mammals. The following table shows which diseases have previously been shown to be associated calicivirus infections in various species.

SPECIES
DISEASE
CONDITION	SWINE	HORSE	CAT	COW	SHEEP	DOG	PINNIPED	CETACEAN	PRIMATE
Blistering	X		X			X			X
and Erosion
of Mucus
Membranes
Pneumonia			X	X			X
Dairrhea	X			X		X			X
Myocarditis	X						X
Myositis			X
Hepatitis	X
Encephalitis	X						X		X
Abortion	X		X				X
Hemorrhage	X						X
Vesicles	X	X	X	X		X	X	X	X
Thymic							X
Involution
Ten (10) Disease Conditions Expected in Humans By Either Using Extrapolation from Animal Models or Direct Evidence in Either Humans or Primates.

[0175] G. Summary of Results

[0176] SMSV-5 was recovered originally in 1973 from a vesicle on the flipper of a severely affected northern fur seal (Callorhinus ursinus) necropsied on St. Paul Island, Alaska [1] (FIG. 2). Altogether, more than 21 other calicivirus serotypes have been isolated from marine mammals and some of these also have been isolated from domestic livestock [13], further evidence of “viral traffic” between marine and terrestrial species is shown in terrestrial animals by the presence of type specific serum antibodies to a variety of marine calicivirus serotypes[13]. In retrospect, caliciviruses circulating in the 1930's, 1940s, and 1950's in southern California's marine populations are believed to have been the origins of the historic nationwide epizootic of vesicular exanthema of swine (VES) [13, 14]. The feeding of raw or poorly cooked fish products is the recognized mechanism whereby these “ocean” caliciviruses were introduced into terrestrial mammals [13]. Once VES was established in swine, then pork scraps from these infected pigs were discarded into garbage and fed to others thereby initiating a devastating pig-to-pig disease cycle [13, 14]. These historical events involving caliciviruses of ocean origin are not unlike the current Bovine Spongiform Encephalopathy (BSE) cycle in which cattle were thought to have been originally infected by some other species (Scrapie in sheep) and then bovine tissues containing the BSE agent were fed to cows resulting in an epidemic of BSE among cattle [15].

[0177] An animal calicivirus of ocean origin, having ocean reservoirs involving cycles through marine invertebrates, poikilotherms and mammals, now is shown to be a human pathogen. This is a new paradigm for disease occurrence and the history of this previously unknown zoonotic virus cycle is as follows: Caliciviruses of ocean origin were first isolated in primate and human cell lines [1], exposed laboratory workers developed type-specific neutralizing antibodies [2, 13], and the host range of single serotypes included species as phylogenetically diverse as fish, seals, swine and primates therefore suggesting host non specificity that could extend to humans [13]. Three serotypes (SMSV-4, SMSV-5, and VESV-C52) induced vesicular lesions at inoculation sites in monkeys [2]. Primate calicivirus (PCV-Pan-1) is in the marine calicivirus genogroup and was recovered from five species of nonhuman primates, including two species of great apes (pygmy chimpanzee Pan paniscus and lowland gorilla Gorilla gorilla) [10,13,16,17]. In one species (pygmy chimpanzee), the virus was recovered from a herpesvirus-like lip lesion and was excreted in oropharyngeal secretions for at least six months [10]. Another PCV Pan-1 isolate was recovered from the brain of a baby douc langur (Pygathrix nemaeus) which died with encephalitis [16].

[0178] There have been occasional field reports of unusual blistering skin infections among wildlife biologists working with pinnipeds (Personal communication, Robert L. DeLong, National Marine Mammal Laboratory, Sand Point, Seattle, Wash., 1994). One individual who handled diseased Steller sea lions (Eumetopias jubatus) in the Bering Sea required emergency medical treatment for deep, painful blistering of the hard palate, upper lip and facial area. Although the attending physician made a clinical diagnosis of herpesvirus infection, throat washings taken 30 days post onset produced a calicivirus isolate, (currently designated strain McAII). This virus was not neutralized by the 40 different type-specific antisera available at the Laboratory for Calicivirus Studies and will be designated a new calicivirus type. Serum samples were collected at 30, 45 and 60 days post onset. Only the 30-day sample was positive using ELISA with the McAII virus as antigen. Preliminary sequence data indicates this isolate is in the same genogroup as the SMSVs of ocean origin, (Unpublished data, Smith, A W, Skilling, D E, Matson, D O, and Berke, T.) thereby providing evidence of a second, although not fully documented, case of zoonotic calicivirus disease.

[0179] SMSV-5 is one of 40 cultivatable calicivirus serotypes. Subtypes include additional marine and closely related strains isolated from terrestrial animals. All appear to share a common genomic organization [11, 18]. Many serotypes replicate in feline, canine, pig, primate and human cell lines [19] and their similar genomic organization, close sequence identity, and common replicative properties in host animals and cell cultures suggest that SMSV-5 is only one of many calicivirus serotypes in the marine genogroup that could be expected to infect humans if exposure occurs [2]. In fact, the untyped SMSV isolate recovered from the biologist and designated strain McAII, the high levels of neutralizing antibody to serotype SMSV-4 in humans and the presence of antibodies to SMSVs in blood donors living in the pacific rim are three additional pieces of evidence which suggests that this has occurred [2].

[0180] This disclosure describes a newly recognized human disease produced by a novel strain of calicivirus, SMSV-5 Hom-1. The apparent viremia with dissemination of virus to multiple sites of replication on all four extremities mimics the disease observed in pinnipeds and swine infected with the same and related serotypes [1,13, 14, 20]. Pneumonitis, myocarditis, encephalitis, hemorrhagic disease or disseminated intravascular coagulation, gastroenteritis, hepatitis, blistering and reproductive disorders with secondary and cross-species transmission, involving reptiles, amphibians, primates and other mammals, have been described in association with calicivirus infections in animals [2, 13, 19-22]. In humans, caliciviruses are known to cause gastroenteritis and hepatitis and now blistering [23-25]; however, improved diagnostic methods and an understanding of this newly recognized virus cycle should provide insight for the future diagnosis of additional human diseases for which an etiology is currently unknown.

[0181] The above embodiments are set out only as examples and are no way meant to limit the scope of the invention claimed which is to be interpreted only in view of the claims.

[0182] It should be apparent to one skilled in the art that the invention described herein can be modified in arrangement and detail without departing from the scope or spirit of the invention and the claims encompass all such modifications.

REFERENCES

[0183] *1. Smith A W, Prato C M, Skilling D E. Characterization of two new serotypes of San Miguel sea lion virus. Intervirology 1977; 8: 30-36.

[0184] *2. Smith A W, Prato C M, Skilling D E. Caliciviruses infecting monkeys and possibly man. Am J Vet Res 1978; 39: 287-289.

[0185] *3. Sexton D J, Rollin P E, Breitschwerdt E B, Corey G R, et al. Life threatening Cache Valley virus infection. New Eng J of Med 1997;336: 547-549.

[0186] *4. Murray K, Selleck P, Hooper P. et al. A morbillivirus that caused fatal disease in horses and humans. Science 1995; 268, 94-97.

[0187] *5. Morse S S. Examining the origins of emerging viruses. “In” Emerging Viruses, ed. Morse, S. S., Oxford University Press, London, New York 1993; p.10-28.

[0188] *6. Liu S J, Xue H P, Pu B Q, et al. A new viral disease in rabbits Anim Husb Vet Med 1984; 16: 253-255.

[0189] *7. Xu Z J and Chen W X. Viral haemorrhagic disease in rabbits: a review. Vet Res Commun. 1989; 13: 205-212.

[0190] *8. Chasey D, Lucas M H, Westcott D G, et al. Development of a diagnostic approach to the identification of rabbit hemorrhagic disease. Vet Rec Aug. 12, 1995; 137:158-160.

[0191] *9. Smith A W, Skilling D E, Ensley P K, Benirschke K and Lester T L. Calicivirus isolation and persistence in a pygmy chimpanzee (Pan paniscus). Science 221, 79-81.

[0192] *10. Matson D O, Berke T, Dinulos M B; et al. Partial characterization of the genome of nine animal caliciviruses. Archives of Virol 1996; 141, 2443-2456.

[0193] *11. Melnick J L. Enteroviruses—Hand Foot, and Mouth Disease. In: Fields Virology, 2nd ed. Vol. 1. Raven Press, New York, 1990; p.565.

[0194] *12. Skilling D E, Barlough J E, Berry E S and Smith A W. A simple, rapid method for preparation of virus isolates from cell culture for electron microscopy. J. Tissue Cult. Meth. 1985; 9, 217-220.

[0195] *13. Smith A W and Boyt P. Caliciviruses of ocean origin: a review. J of Zoo and Wildlife Medicine 1990; 21, 3-23.

[0196] *14. Bankowski R A. Vesicular exanthema. In: Bankowski, R. A. (Ed.) Advances in Veterinary Science. Academic Press 1965; New York; 23-64.

[0197] *15. Westaway B, Carlson G A and Prusiner S B. On safari with PrP: prion diseases of animals. Trends Microbiol. 1995; 3:141-147.

[0198] *16. Smith A W, Skilling D E, Anderson M P and Benirschke K. Isolation of primate calicivirus Pan paniscus type-1 from a douc langur (Pygathrix nemaesus 1.). J. Wildl. Dis. 1985; 21, 426-428.

[0199] *17. Smith A W, Skilling D E and Benirschke K. Calicivirus isolation from three species of primates: an incidental finding. Am. J. Vet. Res. 1985; 46, 2197-2199.

[0200] *18. Neill J D, Meyer R F and Seal B S. Genetic relatedness of the caliciviruses: San Miguel sea lion and vesicular exanthema of swine viruses constitute a single genotype within the Caliciviridae. J of Virol, 1995; 69, 4484-4488.

[0201] *19. Smith A W, Madin S H, Vedros N A and Bankowski R A. Host range comparisons of five serotypes of caliciviruses. AJVR 1977;38:101-5.

[0202] *20. Smith A W, Skilling D E, Dardiri A H and Latham A B. Calicivirus pathogenic for swine: a new serotype isolated from opaleye Girella nigricans, an ocean fish. Science 1980; 209, 940-941.

[0203] *21. Poet S E, Skilling D E, Megyesi J L, Gilmartin W G and Smith A W. Detection of a non-cultivatable calicivirus from the white tern (Gygis alba rothschildi). J. Wildl. Dis. 1996; 32, 461-467.

[0204] *22. Smith A W, Akers T G, Madin S H and Vedros N A. San Miguel sea lion virus isolation, preliminary characterization and relationship to vesicular exanthema of swine virus. Nature 1973; 244, 108-110.

[0205] *23. Waxham M N and Wolinsky J S. Immunochemical identification of rubella virus hemagglutin. Virology 1983; 126, 194-203.

[0206] *24. Matson D O, Zhong W M, Nakata S, et al. Molecular characterization of a human calicivirus with closer genetic relationship to feline caliciviruse than other human caliciviruses J. Med. Virol. 1995; 45, 215-222.

[0207] *25. Bradley D W. Hepatitis E virus: a brief review of the biology, molecular virology, and immunology of a novel virus. J. Hepatol. 1995; 22, 140-145.

[0208] *26. Smith A W, Berry E S, Skilling D E, Barlough J E, Poet S E, Berke J, and Maston D O. In vitro isolation and characterization of a calicivirus causing a vesicular disease of the hands and feet. Clinical Infectious Diseases 1998; 26: 434-439.

[0209] The references that are preceded by an asterisk * are herein incorporated by reference.

Claims

1. A purified protein isolated from calicivirus, and comprising an amino acid sequence selected from the group consisting of: (a) an amino acid sequence selected from the group consisting of SEQ ID NOS: 5, 11, 12, and 13; (b) amino acid sequence that differ from those specified in (a) by one or more conservative amino acid substitutions; and (c) amino acid sequences having at least 80% sequence identity to the sequences specified in (a) or (b).

2. An isolated nucleic acid molecule encoding a protein according to claim 1.

3. An isolated nucleic acid molecule according to claim 2, wherein the molecule comprises a sequence selected from the group consisting of: (a) SEQ ID NO: 3; (b) SEQ ID NO: 4; and (c) at least 15 consecutive nucleotides of the sequences provided in (a) or (b).

4. An isolated nucleic acid molecule that hybridizes under high stringency conditions with the nucleic acid molecule of claim 3.

5. A recombinant nucleic acid molecule comprising a promoter sequence operably linked to a nucleic acid sequence according to claim 2.

6. A cell transformed with a recombinant nucleic acid molecule according to claim 5.

7. An immunostimulatory polypeptide comprising at least one polypeptide selected from the group consisting of SEQ ID NO: 5, 11, 12, 13, and fragments thereof.

8. A method of detecting calicivirus in a tissue sample from a human, the method comprising: contacting the tissue sample with a calicivirus specific binding agent wherein the calicivirus specific binding agent binds at least two different calicivirus serotypes; and detecting calicivirus or portions of calicivirus that are bound to the specific binding agent.

9. The method of claim 8 wherein the human is at risk of having a spontaneous abortion.

10. The method of claim 8 wherein the human is at risk of having calicivirus hepatitis.

11. The method of claim 8 wherein the human is at risk of having chronic fatigue syndrome.

12. The method of claim 8 wherein the human is at risk of having a disorder selected from the group consisting of diarrhea, myocarditis, myositis, encephalitis, hemorrhage, vesicles, pneumonia, blistering and erosion of mucosal membranes, and thymic involution.

13. A method of generating monoclonal antibodies specific for multiple serotypes of calicivirus, the method comprising; infecting a cell culture specimen with at least one strain of calicivirus; allowing the calicivirus to initiate replication; lysing the cell cutlure; using the lysate to immunize a subject; harvesting at least one cell from the subject; fusing the cell from the subject to a myeloma partner; and identifying hybridomas producing antibodies which bind to at least two different strains of calicivirus.

14. A hybridoma produced by the method of claim 13.

15. A method of detecting calicivirus antibodies in a human, the method comprising: contacting a tissue sample from the human with at least one calicivirus epitope; and detecting antibody bound to the epitope.

16. The method of claim 15, wherein the human has had a spontaneous abortion.

17. The method of claim 15, wherein the human has hepititis symptoms.

18. The method of claim 15, wherein the human has chronic fatigue syndrome.

19. The method of claim 15, wherein the human has a disorder selected from the group consisting of diarrhea, myocarditis, myositis, encephalitis, hemorrhage, vesicles, pneumonia, blistering and erosion of mucosal membranes and thymic involution.

20. The method of claim 15, wherein the epitope is found in SMSV-5 Hom-1 (ATCC No. PTA-4762).

21. The method of claim 15, wherein the calicivirus epitope is selected from the group consisting of the polypeptide shown in SEQ ID NO: 5, and fragments thereof.

22. An isolated polypeptide comprising the amino acid sequence shown in SEQ ID NO: 5.

23. An isolated calicivirus comprising, the SMSV-5 Hom-1 isolate (ATCC No. PTA-4762).

24. An isolated nucleic acid sequence comprising the nucleic acid sequence shown in SEQ ID NO: 14.

25. A method of detecting calicivirus nucleic acid sequences in a human tissue sample, the method comprising: contacting the human tissue sample with the nucleic acid sequence shown is SEQ ID NO:1 and fragments thereof; and detecting calicivirus nucleic acid sequences bound to the nucleic acid sequence.

26. A method of inhibiting caliciviral replication, comprising: contacting a cell with a therapeutically effective amount of an antisense or antigene molecule, wherein the antisense or antigene molecule comprises a sequences selected from the group consisting of SEQ ID NOS: 1, 3, 4, and fragments thereof.