Patent Application
20200172878
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Feb. 8, 2020, is named CHEN_P12766_seq_ST25.txt and is 20,480 bytes in size.
The present invention is directed to novel immunogenic compositions that protect swine from disease caused by porcine Sapelovirus (PSV).
Porcine Sapelovirus (PSV) is characterized by a wide range of symptoms, including diarrhea, skin lesions, myelitis, polioencephalomyelitis with ataxia and eventual limb paralysis, reproductive failure (SMEDI syndrome), atypical neurologic disease and has a common mortality rate of 1-3% and occasionally up to 10 on affected farms. The causative agent, porcine Sapelovirus (PSV), is a single stranded, positive sense polyadenylated and nonenveloped RNA virus belonging to the Sapelovirus genus of the family Picornaviridae. PSV has a total genome size of approximately 7.5 kb to 8.3 kb and contains 1 open reading frame encoding four structural proteins (VP1, VP2, VP3, and VP4) and seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C, and 3D). The Sapelovirus genus is closely related to the genus Enterovirus and includes three known species, Avian Sapelovirus, Sapelovirus A (porcine Sapelovirus), and Sapelovirus B (simian Sapelovirus), with a single serotype. There is currently no commercially available vaccine or immunization for PSV, and little is known about cross-protection between strains.
Incidence of PSV increased dramatically in 2017. It has been isolated in many countries around the world, including the United States of America, China, Japan, India, South Korea, Brazil, Germany, the United Kingdom, and Spain. Current treatments include isolating herd specific strains and then generating herd custom vaccines to use against an already infected population of animals.
PSV generally ruptures cells in culture, and there is a need to identify strains that are appropriate for the culturing of sufficient virus for commercial vaccine preparation. Additionally, there is a need to develop vaccines that provide effective cross protection against known isolates of PSV, and which are expected to provide effective cross protection against evolving PSV strains worldwide.
The present invention encompasses immunogenic compositions comprising variant PSV strains passaged from prototype strains. The prototype strains were isolated from the brain or spinal cords of swine showing front limp ataxia, without gross lesions in the spinal cords, muscles, or bone of the spinal columns, and showing nonsuppurative myelitis in spinal cord as histological lesions. They were then serial passaged to create a culture stable variant strain. The U.S. PSV variant strain US/ISU26908B/18 is genetically different in the polyprotein open reading frame (ORF) from the sample isolated strain by a 3-nt insertion at position 3,006, and several single nucleotide polymorphs (SNPs) at positions 1,318, 2,360, 2,793, 4,154, and 6,115.
Thus, the invention comprises an immunogenic composition, suitable to be used as a vaccine, which comprises a variant PSV strain of the invention, preferably live and attenuated, or an immunogenic fragment thereof, one or more adjuvants, and optionally one or more excipients, in an amount effective to elicit production of neutralizing antibodies in swine. The adjuvant preferably provides an oil-in-water emulsion with additional components. The immunogenic compositions of the invention protect swine from infection by PSV, and are effective in single doses, in two-dose programs, or in vaccination programs involving multiple doses, which may be spread apart by at least a week, and optionally at greater intervals of time, such as one to several months. It should be noted that depending on the level of epidemic threat in a particular swine population, the vaccine dose program of one, two, or multiple doses may be repeated, from time to time, as a precautionary measure. Additionally, it should be noted that vaccinating a mother sow during pregnancy will provide protection to a young piglet, via maternal transfer of antibodies and T-cells in colostrum and milk, although such protection may need to be followed up with additional vaccination doses to the piglet. Vaccination of all swine, including piglets and adults is contemplated.
The present invention includes novel nucleotide and amino acid sequences of PSV, including novel genotypes thereof, all of which are useful in the preparation of vaccines for treating and preventing diseases in swine and other animals. Vaccines provided according to the practice of the invention are effective against multiple swine PSV genotypes and isolates. Diagnostic and therapeutic polyclonal and monoclonal antibodies are also a feature of the present invention, as are infectious clones useful in the propagation of the virus and in the preparation of vaccines. Of particular importance, there are disclosed vaccines that comprise, as antigen, a whole virus (live or attenuated) or a single antigenic protein of a PSV open reading frame, most particularly from the first 2.7 kb of the ORF, more particularly the region encoding the structural genes, and also fragments of the full-length sequence encoding the PSV proteins. The invention also provides the full-length genomic sequences of PSV strains at different passages in cell culture that can replicate efficiently in host animals and tissue culture.
The present invention provides a method of treating or preventing a disease or disorder in an animal caused by infection with PSV, including disease states that are directly caused by PSV, and disease states contributed to or potentiated by PSV. Disease states in swine that may be potentiated by PSV, and which may also be treated or prevented according to the practice of the invention, include those caused by or associated with Enterovirus.
The present invention also includes the option to administer a combination vaccine, that is, a bivalent or multivalent combination of antigens, which may include live, modified live, or inactivated antigens against the non-PSV pathogen, with appropriate choice of adjuvant.
Based in part upon the unique PSV sequences as disclosed herein, the present invention also provides a diagnostic kit for differentiating between porcine animals vaccinated with the above described PSV vaccines and porcine animals infected with field strains of PSV.
Representative embodiments of the invention include an isolated polynucleotide sequence that includes a genomic polynucleotide which encodes variant PSV proteins which are attenuated and may be used as an immunogenic composition. This can include whole genome sequences selected from the group consisting of:
(a) SEQ ID NOS 1 or 2 or an immunogenic fragment thereof that encodes the PSV virus variants;
(b) the complement of any sequence in (a);
(c) a polynucleotide that hybridizes with a sequence of (a) or (b) under stringent conditions defined as hybridizing to filter bound DNA in 0.5M NaHPO4, 7% SDS, 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C.
(d) a polynucleotide that is at least 70% identical to the polynucleotide of (a) or (b);
(e) a polynucleotide that is at least 80% identical to the polynucleotide of (a) or (b);
(f) a polynucleotide that is at least 90% identical to the polynucleotide of (a) or (b); and
(g) a polynucleotide that is at least 95% identical to the polynucleotide of (a) or (b)
Preferably in combination with a second heterologous sequence.
The invention further provides RNA and DNA molecules, their complements, fragments and vectors and plasmids for the expression of any such RNA or DNA polynucleotides, and for PSV virus that is expressed from such nucleotide sequences, wherein said virus is live, or fully or partially attenuated.
The invention also provides a vaccine that comprises a polynucleotide sequence as aforementioned, and corresponding nucleotide sequences that may function as infectious clones.
The invention further provides nucleic acid sequences and resultant protein variants that have amino acid substitutions, and which reduce virulence, cause attenuation and allow the compositions to be used safely as immunogenic compositions and as vaccines.
In a further embodiment the invention includes vaccine compositions comprising a live attenuated variant strain PSV, and a carrier, wherein said composition is capable of protecting swine from challenge by both variant and prototype strains of PSV and preventing or treating one or more of symptoms associated with PSV infection, and wherein achievement of protection is determined by an endpoint selected from the group consisting of prevention or control of any of the PSV infection symptoms of diarrhea, skin lesions, myelitis, polioencephalomyelitis with ataxia and eventual limb paralysis, reproductive failure (SMEDI syndrome), atypical neurologic disease, and mortality.
The invention further includes passages and amino acid substitution from passaging the prototype virus.
In a further embodiment the invention includes vaccine compositions comprising a live attenuated variant strain PSV, and a carrier, wherein said composition is capable of protecting swine from challenge by both variant and prototype strains of PSV and preventing or treating one or more of symptoms associated with PSV infection, and wherein achievement of protection is determined by an endpoint selected from the group consisting of prevention or control of any of the PSV infection symptoms, wherein said strain encodes proteins with a substitution of proteins encoded by SEQ ID NO: 2 and their conservative variants and proteins with the specific substitutions and 99% homology to the remainder of the sequences.
It is within the scope of the invention to make additional modifications in any PSV passages described herein, wherein said modifications include introducing mutations of another passage described herein using known methods according to one of skill in the art, for example, homologous recombination.
GenBank® is the recognized United States-NIH genetic sequence database, comprising an annotated collection of publicly available DNA sequences, and which further incorporates submissions from the European Molecular Biology Laboratory (EMBL) and the DNA DataBank of Japan (DDBJ), see Nucleic Acids Research, January 2013, v 41(D1) D36-42 for discussion.
The following drawings form part of the specification and are included to further demonstrate certain embodiments or various aspects of the invention. In some instances, embodiments of the invention can be best understood by referring to the accompanying drawings in combination with the detailed description presented herein. The description and accompanying drawings may highlight a certain specific example, or a certain aspect of the invention. However, one skilled in the art will understand that portions of the example or aspect may be used in combination with other examples or aspects of the invention.
The following definitions and introductory matters are applicable in the specification.
The singular terms “a”, “an”, and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicate otherwise. The word “or” means any one member of a particular list and also includes any combination of members of that list.
The term “adjuvant” refers to a compound that enhances the effectiveness of the vaccine and may be added to the formulation that includes the immunizing agent. Adjuvants provide enhanced immune response even after administration of only a single dose of the vaccine. Adjuvants may include, for example, muramyl dipeptides, pyridine, aluminum hydroxide, dimethyldioctadecyl ammonium bromide (DDA), oils, oil-in-water emulsions, saponins, cytokines, and other substances known in the art. Examples of suitable adjuvants are described in U.S. Patent Application Publication No. US2004/0213817 A1. “Adjuvanted” refers to a composition that incorporates or is combined with an adjuvant.
“Antibodies” refers to polyclonal and monoclonal antibodies, chimeric, and single chain antibodies, as well as Fab fragments, including the products of a Fab or other immunoglobulin expression library. With respect to antibodies, the term, “immunologically specific” refers to antibodies that bind to one or more epitopes of a protein of interest, but which do not substantially recognize and bind other molecules in a sample containing a mixed population of antigenic biological molecules.
An “attenuated” PSV as used herein refers to a PSV which is capable of infecting and/or replicating in a susceptible host but is non-pathogenic or less-pathogenic to the susceptible host. For example, the attenuated virus may cause no observable/detectable clinical manifestations, or less clinical manifestations, or less severe clinical manifestations, or exhibit a reduction in virus replication efficiency and/or infectivity, as compared with the related field isolated strains. The clinical manifestations of PSV infection can include, without limitation, clinical diarrhea, vomiting, lethargy, loss of condition and dehydration.
An “epitope” is an antigenic determinant that is immunologically active in the sense that once administered to the host, it is able to evoke an immune response of the humoral (B cells) and/or cellular type (T cells). These are particular chemical groups or peptide sequences on a molecule that are antigenic. An antibody specifically binds a particular antigenic epitope on a polypeptide. In the animal most antigens will present several or even many antigenic determinants simultaneously. Such a polypeptide may also be qualified as an immunogenic polypeptide and the epitope may be identified as described further.
The term “immunogenic fragment” as used herein refers to a polypeptide or a fragment of a polypeptide, or a nucleotide sequence encoding the same which comprises an allele-specific motif, an epitope or other sequence such that the polypeptide or the fragment will bind a major histocompatibility complex (MHC) molecule and induce a cytotoxic T lymphocyte (“CTL”) response, and/or a B cell response (for example, antibody production), and/or T-helper lymphocyte response, and/or a delayed type hypersensitivity (DTH) response against the antigen from which the immunogenic polypeptide or the immunogenic fragment is derived. A DTH response is an immune reaction in which T cell-dependent macrophage activation and inflammation cause tissue injury. A DTH reaction to the subcutaneous injection of antigen is often used as an assay for cell-mediated immunity.
With the term “induction of an immunoprotective response” is meant a (humoral and/or cellular) immune response that reduces or eliminates one or more of the symptoms of disease, i.e. clinical signs, lesions, bacterial excretion and bacterial replication in tissues in the infected subject compared to a healthy control. Preferably said reduction in symptoms is statistically significant when compared to a control.
An “infectious DNA molecule”, for purposes of the present invention, is a DNA molecule that encodes the necessary elements for viral replication, transcription, and translation into a functional virion in a suitable host cell.
The term “isolated” is used to indicate that a cell, peptide or nucleic acid is separated from its native environment. Isolated peptides and nucleic acids may be substantially pure, i.e. essentially free of other substances with which they may bound in nature.
For purposes of the present invention, the nucleotide sequence of a second polynucleotide molecule (either RNA or DNA) is “homologous” to the nucleotide sequence of a first polynucleotide molecule, or has “identity” to said first polynucleotide molecule, where the nucleotide sequence of the second polynucleotide molecule encodes the same polyaminoacid as the nucleotide sequence of the first polynucleotide molecule as based on the degeneracy of the genetic code, or when it encodes a polyaminoacid that is sufficiently similar to the polyaminoacid encoded by the nucleotide sequence of the first polynucleotide molecule so as to be useful in practicing the present invention. Homologous polynucleotide sequences also refers to sense and anti-sense strands, and in all cases to the complement of any such strands. For purposes of the present invention, a polynucleotide molecule is useful in practicing the present invention, and is therefore homologous or has identity, where it can be used as a diagnostic probe to detect the presence of PSV or viral polynucleotide in a fluid or tissue sample of an infected pig, e.g. by standard hybridization or amplification techniques. Generally, the nucleotide sequence of a second polynucleotide molecule is homologous to the nucleotide sequence of a first polynucleotide molecule if it has at least about 70% nucleotide sequence identity to the nucleotide sequence of the first polynucleotide molecule as based on the BLASTN algorithm (National Center for Biotechnology Information, otherwise known as NCBI, (Bethesda, Md., USA) of the United States National Institute of Health). In a specific example for calculations according to the practice of the present invention, reference is made to BLASTP 2.2.6 [Tatusova T A and T L Madden, “BLAST 2 sequences—a new tool for comparing protein and nucleotide sequences.” (1999) FEMS Microbiol Lett. 174:247-2501 Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 0.1, and the “blosum62” scoring matrix of Henikoff and Henikoff (Proc. Nat. Acad. Sci. USA 325 89:10915-10919. 1992). The percent identity is then calculated as: Total number of identical matches×100/divided by the length of the longer sequence+number of gaps introduced into the longer sequence to align the two sequences.
Preferably, a homologous nucleotide sequence has at least about 75% nucleotide sequence identity, even more preferably at least about 80%, 85%, 90% and 95% nucleotide sequence identity. Since the genetic code is degenerate, a homologous nucleotide sequence can include any number of “silent” base changes, i.e. nucleotide substitutions that nonetheless encode the same amino acid.
A homologous nucleotide sequence can further contain non-silent mutations, i.e. base substitutions, deletions, or additions resulting in amino acid differences in the encoded polyaminoacid, so long as the sequence remains at least about 70% identical to the polyaminoacid encoded by the first nucleotide sequence or otherwise is useful for practicing the present invention. In this regard, certain conservative amino acid substitutions may be made which are generally recognized not to inactivate overall protein function: such as in regard of positively charged amino acids (and vice versa), lysine, arginine and histidine; in regard of negatively charged amino acids (and vice versa), aspartic acid and glutamic acid; and in regard of certain groups of neutrally charged amino acids (and in all cases, also vice versa), (1) alanine and serine, (2) asparagine, glutamine, and histidine, (3) cysteine and serine, (4) glycine and proline, (5) isoleucine, leucine and valine, (6) methionine, leucine and isoleucine, (7) phenylalanine, methionine, leucine, and tyrosine, (8) serine and threonine, (9) tryptophan and tyrosine, (10) and for example tyrosine, tyrptophan and phenylalanine. Amino acids can be classified according to physical properties and contribution to secondary and tertiary protein structure. A conservative substitution is thus recognized in the art as a substitution of one amino acid for another amino acid that has similar properties, and exemplary conservative substitutions may be found in WO 97/09433, page 10, published Mar. 13, 1997 (PCT/GB96/02197, filed Sep. 6, 1996. Alternatively, conservative amino acids can be grouped as described in Lehninger, (Biochemistry, Second Edition; Worth Publishers, Inc. NY:N.Y. (1975), pp. 71-77). Protein sequences can be aligned using both Vector NTI Advance 11.5 and CLUSTAL 2.1 multiple sequence alignment. As used herein the recitation of a particular amino acid or nucleotide sequence shall include all silent mutations with respect to nucleic acid sequence and any and all conservatively modified variants with respect to amino acid sequences.
Homologous nucleotide sequences can be determined by comparison of nucleotide sequences, for example by using BLASTN, above. Alternatively, homologous nucleotide sequences can be determined by hybridization under selected conditions. For example, the nucleotide sequence of a second polynucleotide molecule is homologous to SEQ ID NO:1 (or any other particular polynucleotide sequence) if it hybridizes to the complement of SEQ ID NO:1 under moderately stringent conditions, e.g., hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65° C., and washing in 0.2×SSC/0.1% SDS at 42° C. (see Ausubel et al editors, Protocols in Molecular Biology, Wiley and Sons, 1994, pp. 6.0.3 to 6.4.10), or conditions which will otherwise result in hybridization of sequences that encode a PSV virus as defined below. Modifications in hybridization conditions can be empirically determined or precisely calculated based on the length and percentage of guanosine/cytosine (GC) base pairing of the probe. The hybridization conditions can be calculated as described in Sambrook, et al., (Eds.), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y. (1989), pp. 9.47 to 9.51.
In another embodiment, a second nucleotide sequence is homologous to SEQ ID NO: 1 (or any other sequence of the invention) if it hybridizes to the complement of SEQ ID NO: 1 under highly stringent conditions, e.g. hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% SDS, 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C., as is known in the art.
It is furthermore to be understood that the isolated polynucleotide molecules and the isolated RNA molecules of the present invention include both synthetic molecules and molecules obtained through recombinant techniques, such as by in vitro cloning and transcription.
It should be noted that many of the vaccine-capable attenuated PSV viruses of the present invention contain substantial deletions of ORF3 protein, resulting from attenuating mutations in the ORF3 nucleotide sequence, that cause substantial internal deletions and/or most typically the appearance of truncated translation resultant from frameshifting and the appearance of stop codons. It should therefore be noted that within the practice of the present invention, alignment and percent identity calculations and stated identity results (whether or nucleotide or amino acid sequences) can be calculated with or without reference to deleted ORF3 sequences.
“Mammals” include any warm-blooded vertebrates of the Mammalia class, including humans.
A “pharmaceutically acceptable carrier” means any conventional pharmaceutically acceptable carrier, vehicle, or excipient that is used in the art for production and administration of vaccines. Pharmaceutically acceptable carriers are typically non-toxic, inert, solid or liquid carriers.
The terms “porcine” and “swine” are used interchangeably herein and refer to any animal that is a member of the family Suidae such as, for example, a pig.
A “susceptible” host as used herein refers to a cell or an animal that can be infected by PSV. When introduced to a susceptible animal, an attenuated PSV may also induce an immunological response against the PSV or its antigen, and thereby render the animal immunity against PSV infection.
The term “vaccine” refers to an antigenic preparation used to produce immunity to a disease, in order to prevent or ameliorate the effects of infection. Vaccines are typically prepared using a combination of an immunologically effective amount of an immunogen together with an adjuvant effective for enhancing the immune response of the vaccinated subject against the immunogen.
Vaccine formulations will contain a “therapeutically effective amount” of the active ingredient, that is, an amount capable of eliciting an induction of an immunoprotective response in a subject to which the composition is administered. In the treatment and prevention of PSV disease, for example, a “therapeutically effective amount” would preferably be an amount that enhances resistance of the vaccinated subject to new infection and/or reduces the clinical severity of the disease. Such protection will be demonstrated by either a reduction or lack of symptoms normally displayed by a subject infected with PSV, a quicker recovery time and/or a lowered count of virus particles. Vaccines can be administered prior to infection, as a preventative measure against PSV. Alternatively, vaccines can be administered after the subject already has contracted a disease. Vaccines given after exposure to PSV may be able to attenuate the disease, triggering a superior immune response than the natural infection itself.
For the purpose of the practice of all aspects of the invention, it is well known to those skilled in the art that there is no absolute immunological boundary in immunological assays in regard of animals that are seronegative for exposure to a particular antigen or pathogen, and those that are seropositive (having been exposed to a vaccine or pathogen). Nonetheless, those skilled in the art would recognize that in serum neutralization assays, seropositive animals would generally be detected at least up to a 1:1000 serum dilution, whereas a seronegative animal would be expected not to neutralize at a higher dilution that about 1:20 or 1:10.
The invention also relates to an immunogenic composition, suitable to be used as a vaccine, which comprises a variant PSV strain according to the invention. The immunogenic compositions according to the invention elicit a specific humoral immune response toward the PSV comprising neutralizing antibodies.
The preferred immunogenic compositions based upon the variant strains disclosed herein can provide live, attenuated viruses which exhibit high immunogenicity while at the same time not producing dangerous pathogenic or lethal effects.
The immunogenic compositions of this invention are not, however, restricted to any particular type or method of preparation. These include, but are not limited to, infectious DNA vaccines (i.e., using plasmids, vectors or other conventional carriers to directly inject DNA into pigs), live vaccines, modified live vaccines, inactivated vaccines, subunit vaccines, attenuated vaccines, genetically engineered vaccines, etc. These vaccines are prepared by standard methods known in the art.
The present invention preferably includes vaccine compositions comprising a live, attenuated variant PSV of the invention and a pharmaceutically acceptable carrier. As used herein, the expression “live, attenuated PSV of the invention” encompasses any live, attenuated PSV strain that includes one or more of the variations described herein. The pharmaceutically acceptable carrier can be, e.g., water, a stabilizer, a preservative, culture medium, or a buffer. Vaccine formulations comprising the attenuated PSV of the invention can be prepared in the form of a suspension or in a lyophilized form or, alternatively, in a frozen form. If frozen, glycerol or other similar agents may be added to enhance stability when frozen. The advantages of live attenuated vaccines, in general, include the presentation of all the relevant immunogenic determinants of an infectious agent in its natural form to the host's immune system, and the need for relatively small amounts of the immunizing agent due to the ability of the agent to multiply in the vaccinated host.
Attenuation of the virus for a live vaccine, so that it is insufficiently pathogenic to substantially harm the vaccinated target animal, may be accomplished by known procedures, including preferably by serial passaging. The following references provide various general methods for attenuation of coronaviruses, and are suitable for attenuation or further attenuation of any of the strains useful in the practice of the present invention: B. Neuman et al., Journal of Virology, vol. 79, No. 15, pp. 9665-9676, 2005; J. Netland et al., Virology, v 399(1), pp. 120-128, 2010; Y-P Huang et al., “Sequence changes of infectious bronchitis virus isolates in the 3′ 7.3 kb of the genome after attenuating passage in embryonated eggs, Avian Pathology, v. 36 (1), (Abstract), 2007; and S. Hingley et al., Virology, v. 200(1) 1994, pp. 1-10; see U.S. Pat. No. 3,914,408; and Ortego et al., Virology, vol. 308 (1), pp. 13-22, 2003.
Additional genetically engineered vaccines, which are desirable in the present invention, are produced by techniques known in the art. Such techniques involve, but are not limited to, further manipulation of recombinant DNA, modification of or substitutions to the amino acid sequences of the recombinant proteins and the like.
Genetically engineered vaccines based on recombinant DNA technology are made, for instance, by identifying alternative portions of the viral gene encoding proteins responsible for inducing a stronger immune or protective response in pigs (e.g., proteins derived from VP1, VP2, VP3, VP4, etc.). Various subtypes or isolates of the viral protein genes can be subjected to the DNA-shuffling method. The resulting heterogeneous chimeric viral proteins can be used as broad protecting subunit vaccines. Alternatively, such chimeric viral genes or immuno-dominant fragments can be cloned into standard protein expression vectors, such as the baculovirus vector, and used to infect appropriate host cells (see, for example, O'Reilly et al., “Baculovirus Expression Vectors: A Lab Manual,” Freeman & Co., 1992). The host cells are cultured, thus expressing the desired vaccine proteins, which can be purified to the desired extent and formulated into a suitable vaccine product.
If the clones retain any undesirable natural abilities of causing disease, it is also possible to pinpoint the nucleotide sequences in the viral genome responsible for any residual virulence, and genetically engineer the virus avirulent through, for example, site-directed mutagenesis. Site-directed mutagenesis is able to add, delete or change one or more nucleotides (see, for instance, Zoller et al., DNA 3:479-488, 1984). An oligonucleotide is synthesized containing the desired mutation and annealed to a portion of single stranded viral DNA. The hybrid molecule, which results from that procedure, is employed to transform bacteria. Then double-stranded DNA, which is isolated containing the appropriate mutation, is used to produce full-length DNA by ligation to a restriction fragment of the latter that is subsequently transfected into a suitable cell culture. Ligation of the genome into the suitable vector for transfer may be accomplished through any standard technique known to those of ordinary skill in the art. Transfection of the vector into host cells for the production of viral progeny may be done using any of the conventional methods such as calcium-phosphate or DEAE-dextran mediated transfection, electroporation, protoplast fusion and other well-known techniques (e.g., Sambrook et al., “Molecular Cloning: A Laboratory Manual,” Cold Spring Harbor Laboratory Press, 1989). The cloned virus then exhibits the desired mutation. Alternatively, two oligonucleotides can be synthesized which contain the appropriate mutation. These may be annealed to form double-stranded DNA that can be inserted in the viral DNA to produce full-length DNA.
An immunologically effective amount of the vaccines of the present invention is administered to a pig in need of protection against viral infection. The immunologically effective amount or the immunogenic amount that inoculates the pig can be easily determined or readily titrated by routine testing. An effective amount is one in which a sufficient immunological response to the vaccine is attained to protect the pig exposed to the PSV virus. Preferably, the pig is protected to an extent in which one to all of the adverse physiological symptoms or effects of the viral disease are significantly reduced, ameliorated or totally prevented.
Vaccines of the present invention can be formulated following accepted convention to include acceptable carriers for animals, such as standard buffers, stabilizers, diluents, preservatives, and/or solubilizers, and can also be formulated to facilitate sustained release. Diluents include water, saline, dextrose, ethanol, glycerol, and the like. Additives for isotonicity include sodium chloride, dextrose, mannitol, sorbitol, and lactose, among others. Stabilizers include albumin, among others. Other suitable vaccine vehicles and additives, including those that are particularly useful in formulating modified live vaccines, are known or will be apparent to those skilled in the art. See, e.g., Remington's Pharmaceutical Science, 18th ed., 1990, Mack Publishing, which is incorporated herein by reference.
Vaccines of the present invention may further comprise one or more additional immunomodulatory components such as, e.g., an adjuvant or cytokine, among others. Non-limiting examples of adjuvants that can be used in the vaccine of the present invention include the RIBI adjuvant system (Ribi Inc., Hamilton, Mont.), alum, mineral gels such as aluminum hydroxide gel, oil-in-water emulsions, water-in-oil emulsions such as, e.g., Freund's complete and incomplete adjuvants, Block copolymer (CytRx, Atlanta Ga.), QS-21 (Cambridge Biotech Inc., Cambridge Mass.), SAF-M (Chiron, Emeryville Calif.), AMPHIGEN® adjuvant, saponin, Quil A or other saponin fraction, monophosphoryl lipid A, ionic polysaccharides, and Avridine lipid-amine adjuvant. Non-limiting examples of oil-in-water emulsions useful in the vaccine of the invention include modified SEAM62 and SEAM 1/2 formulations. Modified SEAM62 is an oil-in-water emulsion containing 5% (v/v) squalene (Sigma), 1% (v/v) SPAN® 85 detergent (ICI Surfactants), 0.7% (v/v) TWEEN® 80 detergent (ICI Surfactants), 2.5% (v/v) ethanol, 200 μg/ml Quil A, 100 μg/ml cholesterol, and 0.5% (v/v) lecithin. Modified SEAM 1/2 is an oil-in-water emulsion comprising 5% (v/v) squalene, 1% (v/v) SPAN® 85 detergent, 0.7% (v/v) Tween 80 detergent, 2.5% (v/v) ethanol, 100 μg/ml Quil A, and 50 μg/ml cholesterol. Other immunomodulatory agents that can be included in the vaccine include, e.g., one or more interleukins, interferons, or other known cytokines.
Additional adjuvant systems permit for the combination of both T-helper and B-cell epitopes, resulting in one or more types of covalent T-B epitope linked structures, with may be additionally lipidated, such as those described in WO2006/084319, WO2004/014957, and WO2004/014956.
In a preferred embodiment of the present invention PSV proteins or fragments thereof, is formulated with 5% AMPHIGEN® as discussed hereinafter.
The vaccine compositions of the invention may or may not include adjuvants. In particular, as based on an orally infective virus, the modified live vaccines of the invention may be used adjuvant free, with a sterile carrier. Adjuvants that may be used for oral administration include those based on CT-like immune modulators (rmLT, CT-B, i.e. recombinant-mutant heat labile toxin of E. coli, Cholera toxin-B subunit); or via encapsulation with polymers and alginates, or with mucoadhesives such as chitosan, or via liposomes. A preferred adjuvanted or non adjuvanted vaccine dose at the minimal protective dose through vaccine release may provide between approximately 10 and approximately 106 log10 TCID50 of virus per dose, or higher. “TCID50” refers to “tissue culture infective dose” and is defined as that dilution of a virus required to infect 50% of a given batch of inoculated cell cultures. Various methods may be used to calculate TCID50, including the Spearman-Karber method which is utilized throughout this specification. For a description of the Spearman-Karber method, see B. W. Mahy & H. O. Kangro, Virology Methods Manual, p. 25-46 (1996). Adjuvants, if present, may be provided as emulsions, more commonly if non-oral administration is selected, but should not decrease starting titer by more than 0.7 logs (80% reduction).
In one example, adjuvant components are provided from a combination of lecithin in light mineral oil, and also an aluminum hydroxide component. Details concerning the composition and formulation of Amphigen® (as representative lecithin/mineral oil component) are as follows.
A preferred adjuvanted may be provided as a 2 ML dose in a buffered solution further comprising about 5% (v/v) Rehydragel® (aluminum hydroxide gel) and “20% Amphigen”® at about 25% final (v/v). Amphigen® is generally described in U.S. Pat. No. 5,084,269 and provides de-oiled lecithin (preferably soy) dissolved in a light oil, which is then dispersed into an aqueous solution or suspension of the antigen as an oil-in-water emulsion. Amphigen has been improved according to the protocols of U.S. Pat. No. 6,814,971 (see columns 8-9 thereof) to provide a so-called “20% Amphigen” component for use in the final adjuvanted vaccine compositions of the present invention. Thus, a stock mixture of 10% lecithin and 90% carrier oil (DRAKEOL®, Penreco, Karns City, Pa.) is diluted 1:4 with 0.63% phosphate buffered saline solution, thereby reducing the lecithin and DRAKEOL components to 2% and 18% respectively (i.e. 20% of their original concentrations). Tween 80 and Span 80 surfactants are added to the composition, with representative and preferable final amounts being 5.6% (v/v) Tween 80 and 2.4% (v/v) Span 80, wherein the Span is originally provided in the stock DRAKEOL component, and the Tween is originally provided from the buffered saline component, so that mixture of the saline and DRAKEOL components results in the finally desired surfactant concentrations. Mixture of the DRAKEOL/lecithin and saline solutions can be accomplished using an In-Line Slim Emulsifier apparatus, model 405, Charles Ross and Son, Hauppauge, N.Y., USA.
The vaccine composition also includes Rehydragel® LV (about 2% aluminum hydroxide content in the stock material), as additional adjuvant component (available from Reheis, N.J., USA, and ChemTrade Logistics, USA). With further dilution using 0.63% PBS, the final vaccine composition contains the following compositional amounts per 2 ML dose; 5% (v/v) Rehydragel® LV; 25% (v/v) of “20% Amphigen”, i.e. it is further 4-fold diluted); and 0.01% (w/v) of merthiolate.
As is understood in the art, the order of addition of components can be varied to provide the equivalent final vaccine composition. For example, an appropriate dilution of virus in buffer can be prepared. An appropriate amount of Rehydragel® LV (about 2% aluminum hydroxide content) stock solution can then be added, with blending, in order to permit the desired 5% (v/v) concentration of Rehydragel® LV in the actual final product. Once prepared, this intermediate stock material is combined with an appropriate amount of “20% Amphigen” stock (as generally described above, and already containing necessary amounts of Tween 80 and Span 80) to again achieve a final product having 25% (v/v) of “20% Amphigen”. An appropriate amount of 10% merthiolate can finally be added.
The vaccinate compositions of the invention permit variation in all of the ingredients, such that the total dose of antigen may be varied preferably by a factor of 100 (up or down) compared to the antigen dose stated above, and most preferably by a factor of 10 or less (up or down). Similarly, surfactant concentrations (whether Tween or Span) may be varied by up to a factor of 10, independently of each other, or they may be deleted entirely, with replacement by appropriate concentrations of similar materials, as is well understood in the art.
Rehydragel® concentrations in the final product may be varied, first by the use of equivalent materials available from many other manufacturers (i.e. Alhydrogel®, Brenntag; Denmark), or by use of additional variations in the Rehydragel® line of products such as CG, HPA or HS. Using LV as an example, final useful concentrations thereof including from 0% to 20%, with 2-12% being more preferred, and 4-8% being most preferred, Similarly, the although the final concentration of Amphigen (expressed as % of “20% Amphigen”) is preferably 25%, this amount may vary from 5-50%, preferably 20-30% and is most preferably about 24-26%.
According to the practice of the invention, the oil used in the adjuvant formulations of the instant invention is preferably a mineral oil. As used herein, the term “mineral oil” refers to a mixture of liquid hydrocarbons obtained from petrolatum via a distillation technique. The term is synonymous with “liquefied paraffin”, “liquid petrolatum” and “white mineral oil.” The term is also intended to include “light mineral oil,” i.e., oil which is similarly obtained by distillation of petrolatum, but which has a slightly lower specific gravity than white mineral oil. See, e.g., Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pa.: Mack Publishing Company, 1990, at pages 788 and 1323). Mineral oil can be obtained from various commercial sources, for example, J. T. Baker (Phillipsburg, Pa.), USB Corporation (Cleveland, Ohio). Preferred mineral oil is light mineral oil commercially available under the name DRAKEOL®.
Typically, the oily phase is present in an amount from 50% to 95% by volume; preferably, in an amount of greater than 50% to 85%; more preferably, in an amount from greater than 50% to 60%, and more preferably in the amount of greater than 50-52% v/v of the vaccine composition. The oily phase includes oil and emulsifiers (e.g., SPAN® 80, TWEEN® 80 etc), if any such emulsifiers are present.
Non-natural, synthetic emulsifiers suitable for use in the adjuvant formulations of the present invention also include sorbitan-based non-ionic surfactants, e.g. fatty-acid-substituted sorbitan surfactants (commercially available under the name SPAN® or ARLACEL®), fatty acid esters of polyethoxylated sorbitol (TWEEN®), polyethylene glycol esters of fatty acids from sources such as castor oil (EMULFOR®); polyethoxylated fatty acid (e.g., stearic acid available under the name SIMULSOL® M-53), polyethoxylated isooctylphenol/formaldehyde polymer (TYLOXAPOL®), polyoxyethylene fatty alcohol ethers (BRIJ®); polyoxyethylene nonphenyl ethers (TRITON® N), polyoxyethylene isooctylphenyl ethers (TRITON® X). Preferred synthetic surfactants are the surfactants available under the name SPAN® and TWEEN®, such as TWEEN®-80 (Polyoxyethylene (20) sorbitan monooleate) and SPAN®-80 (sorbitan monooleate). Generally speaking, the emulsifier(s) may be present in the vaccine composition in an amount of 0.01% to 40% by volume, preferably, 0.1% to 15%, more preferably 2% to 10%.
In an alternative embodiment of the invention, the final vaccine composition contains SP-Oil® and Rehydragel® LV as adjuvants (or other Rehydragel® or Alhydrogel® products), with preferable amounts being about 5-20% SP-Oil (v/v) and about 5-15% Rehydragel LV (v/v), and with 5% and 12%, respectively, being most preferred amounts. In this regard it is understood that % Rehydragel refers to percent dilution from the stock commercial product. (SP-Oil® is a fluidized oil emulsion with includes a polyoxyethylene-polyoxypropylene block copolymer (Pluronic® L121, BASF Corporation, squalene, polyoxyethylene sorbitan monooleate (Tween®80, ICI Americas) and a buffered salt solution.)
It should be noted that the present invention may also be successfully practiced using wherein the adjuvant component is only Amphigen®.
In another embodiment of the invention, the final vaccine composition contains TXO as an adjuvant; TXO is generally described in WO 2015/042369. All TXO compositions disclosed therein are useful in the preparation of vaccines of the invention. In TXO, the immunostimulatory oligonucleotide (“T”), preferably an ODN, preferably containing a palindromic sequence, and optionally with a modified backbone, is present in the amount of 0.1 to 5 ug per 50 ul of the vaccine composition (e.g., 0.5-3 ug per 50 ul of the composition, or more preferably 0.09-0.11 ug per 50 ul of the composition). A preferred species thereof is SEQ ID NO: 8 as listed (page 17) in the WO2015/042369 publication (PCT/US2014/056512). The polycationic carrier (“X”) is present in the amount of 1-20 ug per 50 ul (e.g., 3-10 ug per 50 ul, or about 5 ug per 50 ul). Light mineral oil (“O”) is also a component of the TXO adjuvant.
In certain embodiments, TXO adjuvants are prepared as follows:
a) Sorbitan monooleate, MPL-A and cholesterol are dissolved in light mineral oil. The resulting oil solution is sterile filtered;
b) The immunostimulatory oligonucleotide, Dextran DEAE and Polyoxyethylene (20) sorbitan monooleate are dissolved in aqueous phase, thus forming the aqueous solution; and
c) The aqueous solution is added to the oil solution under continuous homogenization thus forming the adjuvant formulation TXO.
All the adjuvant compositions of the invention can be used with any of the PSV strains and isolates covered by the present Specification.
Additional adjuvants useful in the practice of the invention include Prezent-A (see generally United States published patent application US20070298053; and “QCDCRT” or “QCDC”-type adjuvants (see generally United States published patent application US20090324641.
The immunogenic and vaccine compositions of the invention can further comprise pharmaceutically acceptable carriers, excipients and/or stabilizers (see e.g. Remington: The Science and practice of Pharmacy, 2005, Lippincott Williams), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations, and may comprise buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as Mercury((o-carboxyphenyl)thio)ethyl sodium salt (THIOMERSAL), octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrans; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g. Zn-protein complexes); and/or non-ionic surfactants such as polyethylene glycol (PEG), TWEEN or PLURONICS.
Vaccines of the present invention can optionally be formulated for sustained release of the virus, infectious DNA molecule, plasmid, or viral vector of the present invention. Examples of such sustained release formulations include virus, infectious DNA molecule, plasmid, or viral vector in combination with composites of biocompatible polymers, such as, e.g., poly (lactic acid), poly (lactic-co-glycolic acid), methylcellulose, hyaluronic acid, collagen and the like. The structure, selection and use of degradable polymers in drug delivery vehicles have been reviewed in several publications, including A. Domb et al., 1992, Polymers for Advanced Technologies 3: 279-292, which is incorporated herein by reference. Additional guidance in selecting and using polymers in pharmaceutical formulations can be found in texts known in the art, for example M. Chasin and R. Langer (eds), 1990, “Biodegradable Polymers as Drug Delivery Systems” in: Drugs and the Pharmaceutical Sciences, Vol. 45, M. Dekker, NY, which is also incorporated herein by reference. Alternatively, or additionally, the virus, plasmid, or viral vector can be microencapsulated to improve administration and efficacy. Methods for microencapsulating antigens are well-known in the art, and include techniques described, e.g., in U.S. Pat. Nos. 3,137,631; 3,959,457; 4,205,060; 4,606,940; 4,744,933; 5,132,117; and International Patent Publication WO 95/28227, all of which are incorporated herein by reference.
Liposomes can also be used to provide for the sustained release of virus, plasmid, viral protein, or viral vector. Details concerning how to make and use liposomal formulations can be found in, among other places, U.S. Pat. Nos. 4,016,100; 4,452,747; 4,921,706; 4,927,637; 4,944,948; 5,008,050; and 5,009,956, all of which are incorporated herein by reference.
An effective amount of any of the above-described vaccines can be determined by conventional means, starting with a low dose of virus, viral protein plasmid or viral vector, and then increasing the dosage while monitoring the effects. An effective amount may be obtained after a single administration of a vaccine or after multiple administrations of a vaccine. Known factors can be taken into consideration when determining an optimal dose per animal. These include the species, size, age and general condition of the animal, the presence of other drugs in the animal, and the like. The actual dosage is preferably chosen after consideration of the results from other animal studies.
One method of detecting whether an adequate immune response has been achieved is to determine seroconversion and antibody titer in the animal after vaccination. The timing of vaccination and the number of boosters, if any, will preferably be determined by a doctor or veterinarian based on analysis of all relevant factors, some of which are described above.
The effective dose amount of virus, protein, infectious nucleotide molecule, plasmid, or viral vector, of the present invention can be determined using known techniques, taking into account factors that can be determined by one of ordinary skill in the art such as the weight of the animal to be vaccinated. The dose amount of virus of the present invention in a vaccine of the present invention preferably ranges from about 101 to about 109 pfu (plaque forming units), more preferably from about 102 to about 108 pfu, and most preferably from about 103 to about 107 pfu. The dose amount of a plasmid of the present invention in a vaccine of the present invention preferably ranges from about 0.1 μg to about 100 mg, more preferably from about 1 μg to about 10 mg, even more preferably from about 10 μg to about 1 mg. The dose amount of an infectious DNA molecule of the present invention in a vaccine of the present invention preferably ranges from about 0.1 μg to about 100 mg, more preferably from about 1 μg to about 10 mg, even more preferably from about 10 μg to about 1 mg. The dose amount of a viral vector of the present invention in a vaccine of the present invention preferably ranges from about 101 pfu to about 109 pfu, more preferably from about 102 pfu to about 108 pfu, and even more preferably from about 103 to about 107 pfu. A suitable dosage size ranges from about 0.5 ml to about 10 ml, and more preferably from about 1 ml to about 5 ml.
Suitable doses for viral protein or peptide vaccines according to the practice of the present invention range generally from 1 to 50 micrograms per dose, or higher amounts as may be determined by standard methods, with the amount of adjuvant to be determined by recognized methods in regard of each such substance. In a preferred example of the invention relating to vaccination of swine, an optimum age target for the animals is between about 1 and 21 days, which at pre-weening, may also correspond with other scheduled vaccinations such as against Mycoplasma hyopneumoniae. Additionally, a preferred schedule of vaccination for breeding sows would include similar doses, with an annual revaccination schedule.
A preferred clinical indication is for treatment, control and prevention in both breeding sows and gilts pre-farrowing, followed by vaccination of piglets. In a representative example (applicable to both sows and gilts), two 2-ML doses of vaccine will be used, although of course, actual volume of the dose is a function of how the vaccine is formulated, with actual dosing amounts ranging from 0.1 to 5 ML, taking also into account the size of the animals. Single dose vaccination is also appropriate.
The first dose may be administered as early as pre-breeding to 5-weeks pre-farrowing, with the second dose administered preferably at about 1-3 weeks pre-farrowing. Doses vaccine preferably provide an amount of viral material that corresponds to a TCID50 (tissue culture infective dose) of between about 106 and 108, more preferably between about 107 and 5×107, and can be further varied, as is recognized in the art. Booster doses can be given two to four weeks prior to any subsequent farrowings. Intramuscular vaccination (all doses) is preferred, although one or more of the doses could be given subcutaneously. Oral administration is also preferred. Vaccination may also be effective in naïve animals, and non-naïve animals as accomplished by planned or natural infections.
In a further preferred example, the sow or gilt is vaccinated intramuscularly or orally at 5-weeks pre-farrowing and then 2-weeks pre-farrowing. Under these conditions, a protective immune response can be demonstrated in PSV-negative vaccinated sows in that they developed antibodies (measured via fluorescent focal neutralization titer from serum samples) with neutralizing activity, and these antibodies were passively transferred to their piglets. The protocols of the invention are also applicable to the treatment of already seropositive sows and gilts, and also piglets and boars. Booster vaccinations can also be given, and these may be via a different route of administration. Although it is preferred to re-vaccinate a mother sow prior to any subsequent farrowings, the vaccine compositions of the invention nonetheless can still provide protection to piglets via ongoing passive transfer of antibodies, even if the mother sow was only vaccinated in association with a previous farrowing.
It should be noted that piglets may then be vaccinated as early as Day 1 of life. For example, piglets can be vaccinated at Day 1, with or without a booster dose at 3 weeks of age, particularly if the parent sow, although vaccinated pre-breeding, was not vaccinated pre-farrowing. Piglet vaccination may also be effective if the parent sow was previously not naïve either due to natural or planned infection. Vaccination of piglets when the mother has neither been previously exposed to the virus, nor vaccinated pre-farrowing may also effective. Boars (typically kept for breeding purposes) should be vaccinated once every 6 months. Variation of the dose amounts is well within the practice of the art. It should be noted that the vaccines of the present invention are safe for use in pregnant animals (all trimesters) and neonatal swine. The vaccines of the invention are attenuated to a level of safety (i.e. no mortality, only transient mild clinical signs or signs normal to neonatal swine) that is acceptable for even the most sensitive animals again including neonatal pigs. Of course, from a standpoint of protecting swine herds both from PSV epidemics and persistent low-level PSV occurrence, programs of sustained sow vaccination are of great importance. It will be appreciated that sows or gilts immunized with PSV modified live virus (MLV) will passively transfer immunity to piglets, including PSV-specific IgA, which will protect piglets from PSV associated disease and mortality. Generally, pigs that are immunized with PSV MLV will have a decrease in amount and/or duration or be protected from shedding PSV in their feces, and further, pigs that are immunized with PSV MLV will be protected from weight loss and failure to gain weight due to PSV, and further, PSV MLV will aid in stopping or controlling the PSV transmission cycle.
It should also be noted that animals vaccinated with the vaccines of the invention are also immediately safe for human consumption, without any significant slaughter withhold, such as 21 days or less.
When provided therapeutically, the vaccine is provided in an effective amount upon the detection of a sign of actual infection. Suitable dose amounts for treatment of an existing infection include between about 101 and about 106 log10 TCID50, or higher, of virus per dose (minimum immunizing dose to vaccine release). A composition is said to be “pharmacologically acceptable” if its administration can be tolerated by a recipient. Such a composition is said to be administered in a “therapeutically or prophylactically effective amount” if the amount administered is physiologically significant.
At least one vaccine or immunogenic composition of the present invention can be administered by any means that achieve the intended purpose, using a pharmaceutical composition as described herein. For example, route of administration of such a composition can be by parenteral, oral, oronasal, intranasal, intratracheal, topical, subcutaneous, intramuscular, transcutaneous, intradermal, intraperitoneal, intraocular, and intravenous administration. In one embodiment of the present invention, the composition is administered by intramuscularly. Parenteral administration can be by bolus injection or by gradual perfusion over time. Any suitable device may be used to administer the compositions, including syringes, droppers, needleless injection devices, patches, and the like. The route and device selected for use will depend on the composition of the adjuvant, the antigen, and the subject, and such are well known to the skilled artisan. Administration that is oral, or alternatively, subcutaneous, is preferred. Oral administration may be direct, via water, or via feed (solid or liquid feed). When provided in liquid form, the vaccine may be lyophilized with reconstitution, pr provided as a paste, for direct addition to feed (mix in or top dress) or otherwise added to water or liquid feed.
Viruses of the invention may be grown in various cell stocks, such as but not limited to ST or IPEC-1 cell stocks. To generate safe and approved cell stock, a vial of cells may be subject to additional passaging. The cells may be passed one or more times in the appropriate medium, such as but not limited to MEM or more completely media such as but not limited to PMEM w/wheat to produce a Master Cell Stock (MCS). The MCS may be tested in accordance with 9 CFR & EP requirements in PGM-Biological Quality Control; Lincoln, Nebr. The MCS may be tested for satisfactory results in sterility, freedom from mycoplasmas, and extraneous agents.
As a nonlimiting example, seed origin and passage may be as follows. A frozen Pre-master Cell stock of cells is thawed. Cell stock may be prepared by growing the thawed cells in MEM or PMEM bovine serum and L-glutamine. The Pre-master cell stock may then be passaged a number of times, for example from about 1 to about 50 times, from about 10 to about 40 times, or from about 20 to about 30 times. All cultures may be grown in flacks, such as 25, 75, or 150 cm2 T-Flasks. The flasks may be incubated in about 5.0% CO2 at about 36° C. for about 5 days, for about 6 days, for about 7, for about 8 days, or more and then expanded. After flasks reach about 80%, about 90%, or about 100% confluency, the cultures may be passed into larger, such as 850 cm2, roller bottles. Rollers may be incubated at about 36° C. at about 0.125 to about 0.250 rpm without CO2. After a final passage, cryopreservation may be completed by adding about 8%, about 9%, about 10%, about 11% or about 12% bovine calf serum and about 8%, about 9%, about 10%, about 11%, or about 12% dimethyl sulfoxide (DMSO) to the condensed cell suspension. Containers containing about 4 ml of cells may then be placed into a controlled rate freezer and then transferred into liquid nitrogen tank for long term storage at vapor phase. Antibiotics may be used to produce the MCS.
Sterility Testing of the Master Cell Stock may be tested as per 9 CFR (026-ST0) and EP 2.6.1 to determine if the MCS is free of bacterial and fungal contamination.
Mycoplasma Testing and Extraneous Testing were accomplished of the MCS may be tested as per 9 CFR (028-PU0) and EP 2.6.7. Extraneous testing may also be completed as per 9 CFR 113.52 using NL-BT-2 (Bovine), Vero, NL-ED-5 (Equine), NL-ST-1 (Porcine), NL-DK (Canine), or NL-FK (Feline) cells. The MCS may be checked to determine if it is negative for MGG, CPE and HAd and tested by FA for BVD, BRSV, BPV, BAV-1, BAV-5, Rabies, Reo, BTV, ERV, Equine arteritis, PPV, TGE, PAV, HEV, CD, CPV, FPL and FIP. The MCS may further be tested by ELISA for other contaminates such as, but not limited to, FIV. Additionally, the MCS may be tested for BCV, BVDV, CSF, HPS, IAV, IBRV, HMP, MHR, MHS, PCV, PDCV, PEDV, PRCV, PRRSV, PRV, or SVA.
EP extraneous testing was as per 5.2.4 (52-2002) for extraneous testing may use Bovine NL-BT-2 and EBK (Primary), Vero, NL-ED-5 (Equine), NL-ST-1 (Porcine), MARC MA 104, NL-DK (Canine) NL-FK (Feline) cells to test for for MGG, CPE, HAd and tested by FA for BVD, BPV, BAV-1, BAV-5, Bovine corona, Bovine rotavirus, BHV-3, PI3, IBR, BRSV and BEV-1, Reo, BTV, ERV, Equine arteritis, PPV, PRV, TGE, HEV, PAV, P. rota A1, rota A2, PRRSV, CD, CPI, CAV-2, Measles, C. rota, Rabies, CCV, FP, FCV, FVR, FIP and FeLV.
Representative embodiments of the invention include an isolated polynucleotide sequence that comprises a polynucleotide selected from the group consisting of: (a) SEQ ID NOs: 1, 2; or a fragment thereof; (b) the complement of any sequence in (a); (c) a polynucleotide that hybridizes with a sequence of (a) or (b) under stringent conditions defined as hybridizing to filter bound DNA in 0.5M NaHPO4, 7% SDS, 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C.; (d) a polynucleotide that is at least 70% identical to the polynucleotide of (a) or (b); (e) a polynucleotide that is at least 80% identical to the polynucleotide of (a) or (b); (f) a polynucleotide that is at least 90% identical to the polynucleotide of (a) or (b); and (g) a polynucleotide that is at least 95% identical to the polynucleotide of (a) or (b). In a preferred embodiment the polynucleotide includes a second heterologous polynucleotide sequence.
The invention also provides a polypeptide encoded by the open reading frames of the genotype of SEQ ID NOs: 1, 2, combinations thereof, or a polypeptide that is at least 90% identical thereto, domains thereof, or to a fragment thereof, including the option that additional otherwise identical amino acids are replaced by conservative substitutions.
The invention also provides a polypeptide encoded by the open reading frame of the variant PSV strain of the invention or a polypeptide that is at least 90% identical thereto, or to a fragment thereof, including the option that additional otherwise identical amino acids are replaced by conservative substitutions.
In a further preferred embodiment, there are further provided PSV polypeptide-based vaccines wherein the antigen is defined by: a protein encoded by the open reading frame of SEQ ID NOs: 1, 2, combinations thereof, or an immunogenic fragment thereof.
The polynucleotide and amino acid sequence information provided by the present invention also makes possible the systematic analysis of the structure and function of the viral genes and their encoded gene products. Knowledge of a polynucleotide encoding a viral gene product of the invention also makes available anti-sense polynucleotides which recognize and hybridize to polynucleotides encoding a polypeptide of the invention, or a fragment thereof. Full length and fragment anti-sense polynucleotides are useful in this respect. The worker of ordinary skill will appreciate that fragment anti-sense molecules of the invention include (i) those which specifically recognize and hybridize to a specific RNA (as determined by sequence comparison of DNA encoding a viral polypeptide of the invention as well as (ii) those which recognize and hybridize to RNA encoding variants of the encoded proteins. Antisense polynucleotides that hybridize to RNA/DNA encoding other PSV peptides are also identifiable through sequence comparison to identify characteristic, or signature sequences for the family of molecules, further of use in the study of antigenic domains in PSV polypeptides, and may also be used to distinguish between infection of a host animal with remotely related non-PSV members of the Picornaviridae.
Guidance for effective codon optimization for enhanced expression in yeast and E. coli for the constructs of the invention is generally known to those of skill in the art.
Also contemplated by the present invention are anti-PSV antibodies (e.g., monoclonal and polyclonal antibodies, single chain antibodies, chimeric antibodies, humanized, human, porcine, and CDR-grafted antibodies, including compounds which include CDR sequences which specifically recognize a PSV polypeptide of the invention. The term “specific for” indicates that the variable regions of the antibodies of the invention recognize and bind a PSV polypeptide exclusively (i.e., are able to distinguish a single PSV polypeptide from related polypeptides despite sequence identity, homology, or similarity found in the family of polypeptides), and which are permitted (optionally) to interact with other proteins (for example, S. aureus protein A or other antibodies in ELISA techniques) through interactions with sequences outside the variable region of the antibodies, and in particular, in the constant region of the Ab molecule. Screening assays to determine binding specificity of an antibody of the invention are well known and routinely practiced in the art. For a comprehensive discussion of such assays, see Harlow et al. (Eds), Antibodies A Laboratory Manual; Cold Spring Harbor Laboratory; Cold Spring Harbor, N.Y. (1988), Chapter 6. Antibodies that recognize and bind fragments of the PSV polypeptides of the invention are also contemplated, provided that the antibodies are first and foremost specific for, as defined above, a PSV polypeptide of the invention from which the fragment was derived.
For the purposes of clarity, “antibody” refers to an immunoglobulin molecule that can bind to a specific antigen as the result of an immune response to that antigen. Immunoglobulins are serum proteins composed of “light” and “heavy” polypeptide chains having “constant” and “variable” regions and are divided into classes (e.g., IgA, IgD, IgE, IgG, and IgM) based on the composition of the constant regions. Antibodies can exist in a variety of forms including, for example, as, Fv, Fab, F(ab′)2, monospecific Fab2, bispecific Fab2, trispecific Fab3, monovalent IgG, scFv, bispecific diabody, trispecific triabody, scFv-Fc, or minibody, as well as in single chains, and include synthetic polypeptides that contain all or part of one or more antibody single chain polypeptide sequences.
An immunoglobulin or its encoding cDNA may be further modified. Thus, in a further embodiment the method of the present invention comprises any one of the step(s) of producing, for example, a chimeric antibody, porcinized, murinized, or humanized antibody, single-chain antibody, Fab-fragment, bispecific antibody, fusion antibody, labeled antibody or an analog of any one of those. Corresponding methods are known to the person skilled in the art and are described, e.g., in Harlow and Lane “Antibodies, A Laboratory Manual”, CSH Press, Cold Spring Harbor (1988). When derivatives of said antibodies are obtained by the phage display technique, surface plasmon resonance as employed in the BIAcore system can be used to increase the efficiency of phage antibodies which bind to the same epitope as that of any one of the antibodies described herein (Schier, Human Antibodies Hybridomas 7 (1996), 97-105; Malmborg, J. Immunol. Methods 183 (1995), 7-13). The production of chimeric antibodies is described, for example, in international application WO89/09622. Methods for the production of humanized antibodies are described in, e.g., European application EP-A1 0 239 400 and international application WO90/07861. A further source of antibodies to be utilized in accordance with the present invention are so-called xenogeneic antibodies. The general principle for the production of xenogeneic antibodies such as human-like antibodies in mice is described in, e.g., international applications WO91/10741, WO94/02602, WO96/34096 and WO 96/33735. As discussed above, the antibody of the invention may exist in a variety of forms besides complete antibodies; including, for example, Fv, Fab and F(ab)2, as well as in single chains; see e.g. international application WO88/09344.
The present invention also provides diagnostic kits. The kit can be valuable for differentiating between porcine animals naturally infected with a field strain of a PSV virus and porcine animals vaccinated with any of the PSV vaccines described herein. The kits can also be of value because animals potentially infected with field strains of PSV virus can be detected prior to the existence of clinical symptoms and removed from the herd or kept in isolation away from naive or vaccinated animals. The kits include reagents for analyzing a sample from a porcine animal for the presence of antibodies to a particular component of a specified PSV virus. Diagnostic kits of the present invention can include as a component a peptide or peptides from the variant PSV strain of the invention which is present in a field strain but not in a vaccine of interest, or vice versa, and selection of such suitable peptide domains is made possible by the extensive amino acid sequencing. As is known in the art, kits of the present invention can alternatively include as a component a peptide which is provided via a fusion protein. The term “fusion peptide” or “fusion protein” for purposes of the present invention means a single polypeptide chain consisting of at least a portion of a PSV virus protein.
The invention includes the following embodiments. An isolated Porcine Sapelovirus (PSV) encoded by a DNA polynucleotide of a sequence for US/ISU26908B/18.
The virus US/ISU26908B/18 wherein said sequence for US/ISU26908B/18 is defined as a DNA polynucleotide encoding said virus is at least 95%, 98%, 99%, or 99.5% identical, at a full-length nucleotide level, to SEQ ID NO: 2.
A vaccine composition comprising a porcine Sapelovirus (PSV) US/ISU26908B/18, and a carrier, wherein said composition is capable of protecting swine from challenge by both variant and prototype strains of PSV and preventing or treating one or more symptoms associated with PSV infection, and wherein achievement of protection is determined by an endpoint selected from the group consisting of prevention or control of any of the PSV infection symptoms diarrhea, skin lesions, myelitis, polioencephalomyelitis with ataxia and eventual limb paralysis, reproductive failure (SMEDI syndrome), atypical neurologic disease, and mortality.
The vaccine composition wherein the virus is live or killed.
The vaccine composition wherein said carrier is a diluent.
The vaccine composition further comprising an adjuvant.
The vaccine composition wherein said protected swine include any of sows, gilts, boars, hogs, and piglets.
The vaccine composition wherein said vaccine is effective in a single dose program or a two-dose program.
The vaccine composition, wherein the first dose is administered when the piglet is about 1-7 days old, and the second dose is administered when the piglet is 2-5 weeks old.
The vaccine composition, wherein the single dose is administered at about 1-21 days old, preferably at about 1-7 days old.
The vaccine composition, wherein the minimum effective dose is between about 101 and about 106 log10 TCID50.
The vaccine composition wherein the adjuvant is de-oiled lecithin dissolved in an oil, usually light liquid paraffin and aluminum hydroxide, or CpG/DEAE-dextran/mineral oil (TXO).
A method of treating or preventing disease in a piglet caused by PSV, comprising administering to said piglet a first dose of the vaccine composition when said piglet is about 1-7 days old.
The method wherein said administering further includes administering a second dose of said vaccine when the piglet is about 2-5 weeks old.
The method, wherein 2 doses are administered to the piglet, and the parent sow, although vaccinated pre-breeding, was not vaccinated pre-farrowing.
The method, wherein 2 doses are administered to the piglet, and the parent sow is vaccinated pre-farrowing.
A method of treating or preventing disease in a piglet caused by porcine Sapelovirus (PSV), comprising administering to said piglet a single effective dose of the vaccine composition when said piglet is about 1-7 days old, wherein the mother sow is naïve to PSV, and is not, at any time, vaccinated.
A full-length RNA polynucleotide that corresponds to the encoding DNA polynucleotide of US/ISU26908B/18, or the complement thereof.
The RNA polynucleotide that is an infectious clone.
A plasmid or bacterial artificial chromosome that comprises the encoding DNA polynucleotide US/ISU26908B/18.
A live attenuated virus composition, comprising:
a variant strain porcine Sapelovirus (PSV); and
a carrier.
The live attenuated virus composition, wherein said variant strain porcine Sapelovirus (PSV) is US/ISU26908B/18.
The virus US/ISU26908B/18, wherein said sequence for US/ISU26908B/18 is defined as a DNA polynucleotide encoding said virus is at least 95%, 98%, 99%, or 99.5% identical, at a full-length nucleotide level, to SEQ ID NO: 2.
A vaccine composition comprising a live attenuated variant porcine epidemic Sapelovirus (PSV) and a carrier wherein said strain is encoded by a sequence of US/ISU26908B/18, wherein said composition is capable of protecting swine from challenge by both variant and prototype strains of PSV and preventing or treating one or more symptoms associated with PSV infection, and wherein said protection is assessed by an endpoint selected from the group consisting of diarrhea, skin lesions, myelitis, polioencephalomyelitis with ataxia and eventual limb paralysis, reproductive failure (SMEDI syndrome), atypical neurologic disease, and mortality.
The vaccine composition wherein said carrier is a diluent.
The vaccine composition wherein said diluent is a sterile diluent.
The vaccine composition further comprising an adjuvant.
The vaccine composition wherein said protected swine include any of sows, gilts, boars, hogs, and piglets.
The vaccine composition, which is effective in piglets that are 1 day of age or older.
The vaccine composition wherein said vaccine is effective in a single dose program.
The vaccine composition wherein said vaccine is effective in a two dose program.
The vaccine composition, wherein the first dose is administered when the piglet is about 1-7 days old, and the second dose is administered when the piglet is 2-5 weeks old.
The vaccine composition, wherein the minimum effective dose is between about 101 and about 106 log10 TCID50.
The vaccine composition wherein the adjuvant is de-oiled lecithin dissolved in an oil, usually light liquid paraffin and aluminum hydroxide.
The vaccine composition, wherein said adjuvant is CpG/DEAE-dextran/mineral oil (TXO).
A method of treating or preventing disease in a piglet caused by PSV, comprising administering to said piglet a first dose of the vaccine composition when said piglet is about 1-7 days old, and optionally, administering a second dose of said vaccine when the piglet is about 2-5 weeks old.
The method, wherein 2 doses are administered to the piglet, and the parent sow, although vaccinated pre-breeding, was not vaccinated pre-farrowing.
The method, wherein 1 dose is administered to the piglet, and the parent sow, was vaccinated both pre-breeding and pre-farrowing.
A method of treating or preventing disease in a piglet caused by PSV, comprising first administering the vaccine composition to the sow of said piglet pre-farrowing or pre-breeding, following by administering one or more doses of said vaccine composition to said piglet after birth.
A method of preventing disease in healthy pigs caused by PSV, comprising first vaccinating said pigs with the vaccine composition, followed by annual or pre-farrowing administration of further doses of inactivated PSV vaccine.
The composition wherein said variant indel strain is more virulent in 3 week old pigs, but less virulent in 7 week old pigs.
A method of preventing disease in healthy pigs caused by PSV, comprising first vaccinating said pigs with a prototype attenuated live PSV vaccine composition in 3 week old pigs followed by a second vaccination at week 7 or older pigs with a vaccine composition.
A binding molecule for porcine Sapelovirus (SPV), comprising one or more complementary determining regions (CDRs) recognizing epitopes on one or more polypeptides encoded by a sequence of US/ISU26908B/18 or a fragment thereof.
The binding molecule, wherein said binding molecule is an antibody or a fragment, variant, or derivative thereof.
The antibody fragment, wherein said antibody fragment, variant, or derivative is selected from the group comprising: Fab, F(ab′)2, monospecific Fab2, bispecific Fab2, trispecific Fab3, monovalent IgG, scFv, bispecific diabody, trispecific triabody, scFv-Fc, or minibody.
The antibody, wherein said antibody is porcinized, humanized. murinized, or chimeric.
A polynucleotide encoding the antibody polypeptide.
An expression vector, comprising:
one or more polynucleotides; and
a promoter, wherein said one or more polynucleotides is operantly linked to said promoter.
The promoter, wherein said promoter is an eukaryote promoter.
A bacterial host cell transformed with the expression vector
The promoter wherein said promoter is a heterologous promoter.
The expression vector, wherein said expression vector is a plasmid, phage, virus, or retrovirus.
A host cell, comprising an expression vector.
The host cell, wherein said host cell is mammalian.
A kit for detecting the presence of anti-PSV antibodies, comprising:
one or more PSV polypeptides with at least 90% identity to one or more polypeptides encoded by a sequence of US/ISU26908B/18 or fragment thereof; and
a set of reagents.
The one or more polypeptides, wherein said one or more polypeptides is found in a field strain but not a vaccine.
The one or more polypeptides, wherein said one or more polypeptides is found in a vaccine but not in a field strain.
The kit of 63, wherein the sequence of US/ISU26908B/18 is defined as SEQ ID NO: 2.
The sequence of US/ISU26908B/18, wherein said sequence for US/ISU26908B/18 is defined as a DNA polynucleotide encoding said virus is at least 95%, 98%, 99%, or 99.5% identical, at a full-length nucleotide level, to SEQ ID NO: 2.
The sequence of or protein encoded by US/ISU26908B/18 or fragment thereof of which includes one or more of the following features: a) a TTT inserted at position 3,006; b) a G to A SNP at position 1,318;
c) an A to G SNP at position 2,360; d) a C to T SNP at 2,793; e) an A to G SNP at 4,154; and/or f) a G to A SNP at 6,115.
The following Examples are intended to illustrate the above invention and should not be construed as to narrow its scope. One skilled in the art will readily recognize that the Examples suggest many other ways in which the invention could be practiced. It should be understood that numerous variations and modifications may be made while remaining within the scope of the invention.
As no strain has yet been adopted for a purified cell culture system, prototype strains had to be first isolated. For initial isolation, two, seven-week-old pigs (A and B) exhibiting from limb ataxia were euthanized and spinal cord samples were sent for general diagnostics for gross pathology, histopathology, and ancillary diagnostics using standard diagnostic techniques.
The gross pathology of the spinal cord samples showed no grow lesions along the spinal cords, muscles or bone of submitted spinal columns. The histopathology showed that both pigs A and B had nonsuppurative myelitis. The ancillary diagnostics tests showed both pigs A and B had PSV in both of their spinal cords at clinically relevant levels by real time PCR. Additionally, pig A may have had a low amount of porcine teschovirus (PTV) as determined by real time PCR, while pig B may have had a low amount of Steptococcus suis as determined by culture followed by hematoxylin and eosin assays.
These results indicated that both pig A and B had viral myelitis caused by PSV, making strains isolated from pig A and B good targets for creating an isolate adapted for cell culture.
To create the adapted isolate, six different strains, US/ISU26908B/18; US/ISU20472B; US/ISU61750A; US/ISU61750G; US/ISU61750F; and US/ISU66822, extracted from brain or spinal cord were grown on different cell lines, ST, PK-15, and Vero cells. Each strain was grown on each cell line for a total of 18 combinations.
The combinations were made by prepping each tissue sample, and then filtering 200 μL onto each cell line and incubated at 36° C. in a 5% CO2 atmosphere for four hours. After 4 hours, cell lines were washed and then incubated in 1 mL MEM supplemented with 10% fetal bovine serum (FBS) and L-glutamate. The different strain by cell type combinations were then passaged with just MEM without any supplements. Part of passage 2 was assayed by real time PCR for the presence of strains on each cell type, while the rest was used for future passages.
Strains US/ISU26908B/18 and US/ISU66822 showed presence on each of the cell lines while US/ISU61750A showed a low level of grown on only PK-15 cells. Strain US/ISU26908B/18 showed the highest amount of growth on ST cells. Passage 3 was further tested by real time PCR for the presence of various strains in select cell lines, specifically US/ISU26908B/18 on ST, PK-15, and Vero, US/ISU66822 on ST, PK-15, and Vero. As in passage 2, US/ISU26908B/18 on ST showed the highest growth, with US/ISU66822 on PK-15 showing some growth. No growth was detected on the other combinations. Passage 4 for US/ISU26908B/18 on ST was further tested, with US/ISU26908B/18 detected in the cell line. The ST cell line growing US/ISU26908B/18 was carried out past passage 10, and US/ISU26908B/18 continued to be detected.
In order to ensure the ST cell cultures were free of contaminants, they were tested for possible viral and bacterial contamination. This PSV isolate (ST cell passage 7) is free of rotavirus type A, B, or C, atypical porcine pestivirus (APPV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), Porcine Enterovirus (PEV), Porcine Teschovirus (PTV), senecavirus A (SVA) as confirmed by specific PCRs and high-throughput sequencing
As strain US/ISU26908B/18 showed the best growth in cell culture, it was also tested on IPEC-1 cells. IPEC-1 cells were passaged at least ten times with US/ISU26908B/18, showing positive growth after the tenth passage.
Therefore, US/ISU26908B/18, unlike other strains, is capable of growing on various cell cultures through multiple passages.
As passaging viruses during cell culture may result in changes to their sequence, it is important to determine if after long passages the genomes of the virus remains similar to the genome of the prototype.
The complete genomes of strain US/ISU26908B/18 was determined. The determined genomic sequences of virus passage 7 on ST cells is 7,556 nt in length, which remained 99.9% identical to the virus sequence determined from the original spinal cord tissue. This indicate this virus isolate is genetically stable on ST cell line.
The genome of strain US/ISU26908B/18 at passage 7 varied from the isolated strain throughout the polypeptide. Differences were one insertion and five single nucleotide polymorphisms (SNPs) The insertion was a 3-nt “TTT” at position 3,006. The SNPs include a G to A at position 1,318, an A to G at position 2,360, a C to T at position 2,793, an A to G at position 4,154, and a G to A at position 6,115.
As US/ISU26908B/18 is genetically stable on ST cells, it may be used for further modifications for the creations of immunizations or be used to create antibodies in various species for additional uses.
This application claims priority under 35 U.S.C. § 119 to provisional application Ser. No. 62/774,511, filed Dec. 3, 2018, herein incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 62774511 | Dec 2018 | US |
