# Patent

## Title
Rotavirus subunit vaccines and methods of making and use thereof

## Abstract

The present invention provides Rotavirus antigenic polypeptides or antigens that elicit an immune response in animal or human against rotavirus, compositions comprising said rotavirus polypeptides, methods of vaccination against rotavirus, and kits for use with such methods and compositions. The invention further provide novel expression vectors for producing the vaccine antigenic polypeptides.

## Background
This application claims priority to U.S. provisional patent application Ser. No. 61/598,624, filed on Feb. 14, 2012, and herein incorporated by reference in its entirety.


FIELD OF THE INVENTION
The present invention relates generally to subunit vaccines, particularly those comprising rotavirus peptides that have been engineered to be genetically and antigenically nearly identical to those expressed by viruses infecting a target population of animals. Plasmids expressing antigenic peptides or subunit protein(s) are maintained in the bacterial cell population by way of toxin/antidote selection system. The bacterial cells produce a toxic protein, which is counteracted by antidote protein encoded by the plasmid carrying the peptides, rendering non-transformed cells non-viable.
BACKGROUND
Rotavirus is the most common cause of severe diarrhea among infants and young children (Dennehy P H, 2000), and is one of several viruses that cause infections often called stomach flu, despite having no relation to influenza. It is a genus of double-stranded RNA virus in the family Reoviridae. There are five species of this virus, referred to as A, B, C, D, and E (ICTV Virus Taxonomy: 2009 Release). Table 1 provides a summary of known rotaviral proteins. Rotavirus A, the most common, causes more than 90% of infections in humans. The virus is transmitted by the fecal-oral route, and infects and damages the cells that line the small intestine and causes gastroenteritis. In addition to its impact on human health, rotavirus also infects animals, and is a pathogen of livestock (Dubovi E J, 2010).
For example, according to a recent study, rotavirus was commonly found (65%) in the feces or intestinal contents from pigs with diarrhea. The majority of animals were infected by single group (A, B, C) although concurrent infection by more than one rotavirus group does occur (Yoon, K J, Epidemiology of rotaviruses, ISUVDL submissions, 2010-2011, Iowa State). Nearly one-third of animals were infected by at least Group C Rotavirus. Until now, prevention of rotavirus in porcines had involved rather arcane practices, such as feeding infected piglet tissue to healthy pigs. This practice was necessitated because Group C rotavirus cannot be grown in vitro, thus preventing the production of conventional inactivated/attenuated whole-virus vaccines. Thus, there is a clear and urgent need for safer and more effective preventative measures.







TABLE 1







Rotavirus protein summary














Size (bp, based







RNA Segment
on Human Rota

Molecular

Copies per


(Gene)
C strain)
Protein
weight kDa
Location
particle
Function
















1
3309
VP1
125
At the vertices
<25
RNA-dependent






of the core

RNA polymerase


2
2736
VP2
102
Forms inner shell
120
Stimulates viral






of the core

RNA replicase


3
2283
VP3
88
At the vertices
<25
Guanylyl transferase






of the core

mRNA capping enzyme


4
2166
VP4
87
Surface spike
120
Cell attachment,








virulence


5
1353
NSP1
59
Nonstructural
0
5′RNA binding


6
1350
VP6
45
Inner Capsid
780
Structural and species-








specific antigen


7
1270
NSP3
37
Nonstructural
0
Enhances viral mRNA








activity and shut-offs








cellular protein synthesis


8
1063
NSP2
35
Nonstructural
0
NTPase involved in








RNA packaging


9
1037
VP7, VP7
38, 34
Surface
780
Structural and








neutralization antigen


10
730
NSP4
20
Nonstructural
0
Enterotoxin


11
613
NSP5 NSP6
22
Nonstructural
0
ssRNA and dsRNA binding








modulator of NSP2









An alternate approach would be to produce vaccines comprising immunogenic rotavirus subunit proteins or antigens. At time of filing this disclosure, inventors are aware of no references describing methods of producing rotavirus subunit vaccines (autogenous or otherwise) to immunize porcines against rotavirus, particular the Group C variety. The following patents and applications summarize relevant rotavirus prior art, with emphasis on subunit-based vaccines.
U.S. Pat. No. 7,790,178 (to Intervet) describes trivalent vaccines, which includes inactivated canine rotavirus.
U.S. Pat. No. 7,311,918 & U.S. Pat. No. 6,589,529 (to Children's Hospital Ohio) describe a recombinant rotavirus fusion protein comprising a VP6 protein fragment, intended for vaccinating humans. Mouse data indicated the vaccine generated an immune response directed against the VP6 fusion protein.
U.S. Pat. No. 6,867,353 (to Exploregen) generally describes expression of a cDNA fragment encoding human rotavirus structural protein using transformed tomato.
U.S. Pat. No. 6,716,431 (to Wyeth, now Pfizer) describes alternate forms of NSP4 (i.e. SNPs resulting in amino acid changes), which still retain antigenicity, but exhibit reduced cytotoxicity.
U.S. Pat. No. 6,673,355 & U.S. Pat. No. 6,210,682 (to Baylor College of Medicine) relate to use of NSP4 and fragments thereof (NSP4 114-135, NSP4 120-147, NSP4 112-174, or NSP4 112-150) as a prevention and/or treatment of rotaviral disease. Compositions including an enterotoxin adjuvant are also described. U.S. Pat. No. 5,891,676 & U.S. Pat. No. 5,827,696 (also to Baylor) describe baculoviral expression of rotavirus VP2 and VP7, respectively.
U.S. Pat. No. 6,187,319 (to University of Mass.) generally relates to methods for producing immune responses in animals against a first rotavirus by administering an isolated VP6 polypeptide of a second rotavirus that infects a different species than the animal to be vaccinated.
U.S. Pat. No. 5,298,244 (to University of Saskatchewan) describes assembled viral particles having VP4, VP6, and VP7.
US20110171316 (to US Health and Human Service) describes a recombinant human rotavirus group C virus-like particles.
US20100047763 (to Goes et al.) discloses plasmid DNA encoding rotavirus proteins for use in diagnostic kits.
U.S. Pat. No. 5,186,933 (to Baylor College of Medicine) discloses expression of rotavirus genes, particularly VP3 and VP7) using a baculovirus system.
Until their present disclosure, inventors are aware of no effective porcine rotavirus subunit vaccine prepared by expressing rotavirus type C antigens in E. coli. Further, no methods for producing safe and effective vaccines for porcines have been disclosed, and thus it is an object of the instant disclosure to provide such vaccines.
REFERENCES


    Dennehy P H (2000). “Transmission of rotavirus and other enteric pathogens in the home”. Pediatr. Infect. Dis. J. 19 (10 Suppl): S103-5. doi:10.1097/00006454-200010001-00003. PMID 11052397.
    Bernstein D I (March 2009). “Rotavirus overview”. The Pediatric Infectious Disease Journal 28 (3 Suppl): S50-3.
    Grimwood K, Lambert S B (February 2009). “Rotavirus vaccines: opportunities and challenges”. Human Vaccines 5 (2): 57-69. PMID 18838873.
    Bishop R (October 2009). “Discovery of rotavirus: Implications for child health”. Journal of Gastroenterology and Hepatology 24 Suppl 3: S81-5.
    Rheingans R D, Heylen J, Giaquinto C (2006). “Economics of rotavirus gastroenteritis and vaccination in Europe: what makes sense?”. Pediatr. Infect. Dis. J. 25 (1 Suppl): S48-55.
    Simpson E, Wittet S, Bonilla J, Gamazina K, Cooley L, Winkler J L (2007). “Use of formative research in developing a knowledge translation approach to rotavirus vaccine introduction in developing countries”. BMC Public Health 7: 281.
    Edward J Dubovi; Nigel James MacLachlan (2010). Fenner's Veterinary Virology, Fourth Edition. Boston: Academic Press. p. 288. ISBN 0-12-375158-6.


SUMMARY OF THE INVENTION
An object of this invention is to provide subunit vaccines as well as methods for treatment and prophylaxis of infection by rotavirus.
The present invention further relates to a new vector and to the use thereof for the production of a heterologous protein or of a gene of interest that can be used, for example, in the context of an immunization. In particular embodiments, the heterologous protein is a rotavirus protein. In more particular embodiments, the protein is a porcine rotavirus protein selected from NSP4, VP4, or VP6. In another embodiment, the rotavirus protein is a NSP4-VP4-VP6 triple fusion protein.
Another objective of the present invention is to provide a new vector which can be used on an industrial scale, which has the advantage of producing a high expression yield, this being the case in the absence of any use of antibiotics, and which can therefore be used for small or large scale volumes (for example, 1-10,000 liter cultures).
The present invention therefore provides a self-replicating vector devoid of any antibiotic-resistance gene, comprising: (a) a sequence encoding the ccdA protein functionally linked to a first promoter; and (b) a heterologous sequence functionally linked to a second promoter. According to one particular embodiment, the first promoter is a constitutive promoter. According to another embodiment, the second promoter is an inducible promoter, in particular the second promoter is the T7 promoter. In another embodiment the promoter is the T5 promoter.
According to one particular embodiment, the heterologous sequence encodes a vaccine antigen.
According to another aspect, the present invention relates to a prokaryotic cell expressing the ccdB protein, comprising a vector as defined above.
According to one particular aspect, said prokaryotic cell is an E. coli cell.
According to another aspect, the present invention relates to a method for producing a heterologous protein, comprising the steps of:
(a) inoculating an appropriate culture medium with prokaryotic cells expressing the ccdB protein and containing a vector as defined above;
(b) fermenter culturing the cell thus transformed in the absence of antibiotic; and
(c) recovering the heterologous protein produced during step (b) from the supernatant or from the cell pellet.
According to one particular embodiment, the present invention relates to a method for producing recombinant rotavirus peptides.
According to another aspect, the present invention relates to a method for producing a self-replicating vector as defined above, comprising the steps of:
(a) inoculating an appropriate culture medium with prokaryotic cells expressing the ccdB protein and containing a vector as defined above;
(b) fermenter culturing the cell thus transformed in the absence of antibiotic; and
(c) recovering the vector produced during step (b).
According to another aspect, the present invention relates to a method for constructing a self-replicating vector as defined above, comprising the steps of:
(a) beginning with a self-replicating vector comprising a functional antibiotic-resistance gene and a ccdA gene;
(b) performing inverse PCR to amplify the non-antibiotic resistance gene plasmid sequence;
(c) phosphorylating and ligating the PCR product to produce the antibiotic resistance gene-free version of the vector recited in (a);
(d) transforming a prokaryotic cell expressing the ccdB protein; and
(e) recovering the prokaryotic cells comprising the self-replicating vector.
According to another aspect, biological samples are taken from populations of production animals, including porcines. RNA is harvested therefrom, and reverse transcription is performed, using rotavirus gene-specific primers. The PCR products are then cloned into the self-replicating plasmid defined above, and the new plasmids containing the herd and or region-specific rotavirus genes are transformed into prokaryotic cells expressing ccdB. Rotavirus peptides are harvested from the cells and formulated into the inventive autogenous and/or commercial vaccines.
In a particular embodiment, the autogenous rotavirus subunit vaccines comprise an adjuvant. The adjuvant may be an oil, emulsion, a metal salt (e.g. Al(OH)3), or combinations thereof. In an embodiment, the adjuvant is TRIGEN® or ULTRAGEN® or PrimaVant® (TRIGEN+Quil A), TS6 (described in U.S. Pat. No. 7,371,395 US to Merial), LR4 (described in U.S. Pat. No. 7,691,368, to Merial), or any formulation described in US 2011-0129494 A1 (to Merial).
In an embodiment, the vaccine may comprise a mixture of rotavirus VP4, VP6, and NSP4, and a preserving amount of formaldehyde and/or antimicrobial agents.
The invention further provides methods for inducing an immunological (or immunogenic) or protective response against rotavirus, as well as methods for preventing or treating rotavirus or disease state(s) caused by rotavirus, comprising administering the subunits, or a composition comprising the subunits.
The invention also relates to expression products from the plasmid as well as antibodies generated from the expression products or the expression thereof uses for such products and antibodies, e.g., in diagnostic applications.
Kits comprising at least one rotavirus polypeptide or fragment or variant thereof and instructions for use are also provided.
These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.



BRIEF DESCRIPTION OF DRAWINGS
A full and enabling disclosure of the present invention, including the best mode thereof, to one of ordinary skill in the art, is set forth more particularly in the remainder of the specification, including reference to the accompanying figures, wherein:
FIG. 1 provides a restriction endonuclease map of pStaby1.2 (as provided by the supplier);
FIG. 2 schematizes removal of the ampicillin resistance gene from pStaby1.2;
FIG. 3 schematizes insertion of GST gene into pNPL1 to form pNPL2;
FIG. 4 is a map of flanking regions and the rotavirus gene insertion sites of pNPL2;
FIG. 5 is a schematic diagram of the donor DNA recovery technique;
FIG. 6 schematizes the process of isolating autogenous vaccine candidate rotavirus genes from clinical samples;
FIG. 7 is a schematic of procedure used to insert donor DNA pNPL2 to yield pNPL2-Rota;
FIG. 8 is a PAGE gel confirming expression and size of the rotavirus VP4, VP6 and NSP4 proteins;
FIG. 9A presents nucleotide and peptide sequence alignments (with percent identity table) for NSP4 isolates;
FIG. 9B presents nucleotide and peptide sequence alignments (with percent identity table) for VP4 isolates;
FIG. 9C presents nucleotide and peptide sequence alignments (with percent identity table) for VP6 isolates;
FIG. 10 is a graph showing the overall serology results for the vaccine efficacy study;
FIG. 11 are graphs showing VP4, VP6, and NSP4-specific serology as measured by ELISA;
FIG. 12 is a PAGE gel confirming expression of the Rota C NSP4-VP4-VP6 triple fusion protein. L, ladder; 1, before induction (OD=0.6); 2, un-induced cultures (OD=1.5); 3, induced cultures (OD=1.5);
FIG. 13 is a Western blot (left) and PAGE gel (right) confirming fusion protein expression. L-ladder, 1-BSA 1.5 μg, 2-Fusion protein 1:20 diluted, 3-Fusion protein 1:40 diluted, 4-GST 0.5 μg.



DETAILED DESCRIPTION OF THE INVENTION
The present invention encompasses rotavirus subunits (defined herein, for example, as rotavirus polypeptides, proteins, antigens, epitopes or immunogens) that elicit an immunogenic response in an animal, particularly the rotavirus subunits that elicit, induce or stimulate a response in a porcine.
Particular rotavirus subunits of interest are VP4, VP6, and NSP4, particularly those encoded by nucleic acid sequences from Group C rotavirus-infected porcines. It is recognized that precursors of any of these antigens can be used in the practice of this invention.
In an embodiment, the invention provides for a method for amplifying rotaviral sequences from infected porcines, and using well-known molecular techniques to place said amplified sequences into expression vectors. In a particular embodiment, the amplifying is accomplished by PCR using primers complementary to highly conserved regions of rotavirus genes, such that genes from a wide variety of rotavirus strains may be amplified using the same primers. In an embodiment, the primers are complementary to rotavirus nucleic acid sequence encoding VP4, VP6, and/or NSP4, and have the sequence as set forth in SEQ ID NOs:8-13).
In another aspect, the invention provides for methods for producing expression vectors, which contain and express in a prokaryotic host an antidote gene, which confers viability to bacterial cells expressing proteic toxins. In an embodiment, the antidote is ccdA and the toxin is ccdB.
In another aspect, the novel rotaviral sequences are placed into the expression vectors to produce rotavirus subunits to be used in formulation of subunit vaccines.
In an embodiment, the subunit vaccines further comprise an adjuvant. In a particular embodiment, the adjuvant is an oil-in-water adjuvant. In some embodiments, the adjuvant is TRIGEN, ULTRAGEN, PrimaVant, TS6, LR4, or combinations thereof. In an embodiment, the vaccines further comprise an adjuvanting amount of an aluminum salt. Other adjuvanting compounds may also be added to the subunit vaccines, including, but not limited to saponin and aluminum hydroxide. These additional adjuvanting compounds may improve the vaccine storage stability, the efficacy, or both.
In another aspect, the invention provides methods for providing protective immunity to piglets against rotavirus, comprising administering the inventive subunit vaccines to sows and gilts, prefarrow.







TABLE 1







List of primers used in the construction


of the vectors and cloning the genes











SEQ ID #
#
Description















2
650
GST For. NdeI



3
651
GST Rev. BamHI



4
644
AMPR gene deletion For.



5
645
AMPR gene deletion Rev.



6
660
PCR Verification For.



7
661
PCR Verification Rev.



8
652
NSP4 For. with BamHI site



9
653
NSP4 Rev. with HindIII site



10
654
VP4 For. with BamHI site



11
655
VP4 Rev. with HindIII site



12
656
VP6 For. with BamHI site



13
657
VP6 Rev. with HindIII site



73
760
KSN760 - rev VP4



74
761
KSN761 - for VP4



75
762
KSN762 - rev VP4



76
763
KSN763 - for VP4



77
772
Primer 1 to insert His Tag in pNPL1



78
773
Primer 2 to insert His Tag in pNPL1



79
774
Rota C NSP4 FOR for pNPL3



80
775
Rota C NSP4 REV for pNPL3 or pNPL1



81
776
Rota C VP4 FOR for pNPL3



82
777
Rota C VP4 REV for pNPL3 or pNPL1



83
778
Rota C VP6 FOR for pNPL3



84
779
Rota C VP6 REV for pNPL3 or pNPL1



85
780
Rota C NSP4 FOR for pNPL1



86
781
Rota C VP4 FOR for pNPL1



87
782
Rota C VP6 FOR for pNPL1



88
783
Rota C VP7 FOR for pNPL3



89
784
Rota C VP7 REV for pNPL3 or pNPL1










The antigenic polypeptides or proteins of the invention are capable of protecting against rotavirus. That is, they are capable of stimulating an immune response in an animal. By “antigen” or “immunogen” means a substance that induces a specific immune response in a host animal. The antigen may comprise a whole organism, killed, attenuated or live; a subunit or portion of an organism; a recombinant vector containing an insert with immunogenic properties; a piece or fragment of DNA capable of inducing an immune response upon presentation to a host animal; a polypeptide, an epitope, a hapten, or any combination thereof. Alternately, the immunogen or antigen may comprise a toxin or antitoxin.
The terms “protein”, “peptide”, “polypeptide” and “polypeptide fragment” are used interchangeably herein to refer to polymers of amino acid residues of any length. The polymer can be linear or branched, it may comprise modified amino acids or amino acid analogs, and it may be interrupted by chemical moieties other than amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling or bioactive component.
The term “immunogenic or antigenic polypeptide” as used herein includes polypeptides that are immunologically active in the sense that once administered to the host, it is able to evoke an immune response of the humoral and/or cellular type directed against the protein. Preferably the protein fragment is such that it has substantially the same immunological activity as the total protein. Thus, a protein fragment according to the invention comprises or consists essentially of or consists of at least one epitope or antigenic determinant. An “immunogenic” protein or polypeptide, as used herein, includes the full-length sequence of the protein, analogs thereof, or immunogenic fragments thereof. By “immunogenic fragment” is meant a fragment of a protein which includes one or more epitopes and thus elicits the immunological response described above. Such fragments can be identified using any number of epitope mapping techniques, well known in the art. See, e.g., Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66 (Glenn E. Morris, Ed., 1996). For example, linear epitopes may be determined by e.g., concurrently synthesizing large numbers of peptides on solid supports, the peptides corresponding to portions of the protein molecule, and reacting the peptides with antibodies while the peptides are still attached to the supports. Such techniques are known in the art and described in, e.g., U.S. Pat. No. 4,708,871; Geysen et al., 1984; Geysen et al., 1986. Similarly, conformational epitopes are readily identified by determining spatial conformation of amino acids such as by, e.g., x-ray crystallography and 2-dimensional nuclear magnetic resonance. See, e.g., Epitope Mapping Protocols, supra. Methods especially applicable to the proteins of T. parva are fully described in PCT/US2004/022605 incorporated herein by reference in its entirety.
As discussed herein, the invention encompasses active fragments and variants of the antigenic polypeptide. Thus, the term “immunogenic or antigenic polypeptide” further contemplates deletions, additions and substitutions to the sequence, so long as the polypeptide functions to produce an immunological response as defined herein. The term “conservative variation” denotes the replacement of an amino acid residue by another biologically similar residue, or the replacement of a nucleotide in a nucleic acid sequence such that the encoded amino acid residue does not change or is another biologically similar residue. In this regard, particularly preferred substitutions will generally be conservative in nature, i.e., those substitutions that take place within a family of amino acids. For example, amino acids are generally divided into four families: (1) acidic—aspartate and glutamate; (2) basic—lysine, arginine, histidine; (3) non-polar—alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar—glycine, asparagine, glutamine, cystine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified as aromatic amino acids. Examples of conservative variations include the substitution of one hydrophobic residue such as isoleucine, valine, leucine or methionine for another hydrophobic residue, or the substitution of one polar residue for another polar residue, such as the substitution of arginine for lysine, glutamic acid for aspartic acid, or glutamine for asparagine, and the like; or a similar conservative replacement of an amino acid with a structurally related amino acid that will not have a major effect on the biological activity. Proteins having substantially the same amino acid sequence as the reference molecule but possessing minor amino acid substitutions that do not substantially affect the immunogenicity of the protein are, therefore, within the definition of the reference polypeptide. All of the polypeptides produced by these modifications are included herein. The term “conservative variation” also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid provided that antibodies raised to the substituted polypeptide also immunoreact with the unsubstituted polypeptide.
The term “epitope” refers to the site on an antigen or hapten to which specific B cells and/or T cells respond. The term is also used interchangeably with “antigenic determinant” or “antigenic determinant site”. Antibodies that recognize the same epitope can be identified in a simple immunoassay showing the ability of one antibody to block the binding of another antibody to a target antigen.
An “immunological response” to a composition or vaccine is the development in the host of a cellular and/or antibody-mediated immune response to a composition or vaccine of interest. Usually, an “immunological response” includes but is not limited to one or more of the following effects: the production of antibodies, B cells, helper T cells, and/or cytotoxic T cells, directed specifically to an antigen or antigens included in the composition or vaccine of interest. Preferably, the host will display either a therapeutic or protective immunological response such that resistance to new infection will be enhanced and/or the clinical severity of the disease reduced. Such protection will be demonstrated by either a reduction or lack of symptoms and/or clinical disease signs normally displayed by an infected host, a quicker recovery time and/or a lowered viral titer in the infected host.
By “animal” is intended mammals, birds, and the like. Animal or host as used herein includes mammals and human. The animal may be selected from the group consisting of equine (e.g., horse), canine (e.g., dogs, wolves, foxes, coyotes, jackals), feline (e.g., lions, tigers, domestic cats, wild cats, other big cats, and other felines including cheetahs and lynx), ovine (e.g., sheep), bovine (e.g., cattle), porcine (e.g., pig), avian (e.g., chicken, duck, goose, turkey, quail, pheasant, parrot, finches, hawk, crow, ostrich, emu and cassowary), primate (e.g., prosimian, tarsier, monkey, gibbon, ape), ferrets, seals, and fish. The term “animal” also includes an individual animal in all stages of development, including newborn, embryonic and fetal stages.
Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. 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.
It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as “comprises”, “comprised”, “comprising” and the like can have the meaning attributed to it in U.S. Patent law; e.g., they can mean “includes”, “included”, “including”, and the like; and that terms such as “consisting essentially of” and “consists essentially of” have the meaning ascribed to them in U.S. Patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art or that affect a basic or novel characteristic of the invention.
Compositions
The present invention relates to a rotavirus vaccine or composition which may comprise a rotavirus polypeptide, antigen, epitope or immunogen and a pharmaceutically or veterinarily acceptable carrier, excipient, or vehicle. The rotavirus polypeptide, protein, antigen, epitope or immunogen may be any rotavirus polypeptide, protein, antigen, epitope or immunogen, such as, but not limited to, a protein, peptide or fragment thereof, that elicits, induces or stimulates a response in an animal.
The present invention relates to a rotavirus vaccine or composition which may comprise a rotavirus VP1, VP2, VP3, VP4, NSP1, VP6, NSP3, NSP2, VP7, NSP4, NSP5, or NSP6 polypeptide and a pharmaceutically or veterinarily acceptable carrier, excipient, or vehicle. In one embodiment, the expression vector may further comprise a polynucleotide encoding the VP4, VP6, or NSP4 polypeptide, or combinations thereof. In a particular embodiment, the polynucleotide comprises the sequence as set forth in SEQ ID NO:16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, or combinations thereof.
In another embodiment, the pharmaceutically or veterinarily acceptable carrier, excipient, or vehicle may be a water-in-oil emulsion. In yet another embodiment, the water-in-oil emulsion may be a water/oil/water (W/O/W) triple emulsion.
In an embodiment, the rotavirus polypeptide, antigen or fragment or variant thereof comprises a rotavirus polypeptide or fragment or variant thereof. In an aspect of this embodiment, the rotavirus polypeptide or fragment or variant thereof is a recombinant polypeptide produced by a rotavirus gene. In another aspect of this embodiment, the rotavirus gene has at least 70% identity to the sequence as set forth in SEQ ID NO: 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, or combinations thereof. In another aspect of this embodiment, the rotavirus polypeptide or fragment or variant thereof has at least 80% identity to the sequence as set forth in SEQ ID NO:17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, or 71, wherein the polypeptide or fragment or variant thereof has the same functional role (i.e. the polypeptide is rotavirus VP4, VP6, or NSP4 polypeptide belonging to a different strain of Group C rotavirus).
Synthetic antigens are also included within the definition, for example, polyepitopes, flanking epitopes, and other recombinant or synthetically derived antigens. See, e.g., Bergmann et al., 1993; Bergmann et al., 1996; Suhrbier, 1997; Gardner et al., 1998. Immunogenic fragments, for purposes of the present invention, will usually include at least about 3 amino acids, at least about 5 amino acids, at least about 10-15 amino acids, or about 15-25 amino acids or more amino acids, of the molecule. There is no critical upper limit to the length of the fragment, which could comprise nearly the full-length of the protein sequence, or even a fusion protein comprising at least one epitope of the protein.
Accordingly, a minimum structure of a polynucleotide expressing an epitope is that it comprises or consists essentially of or consists of nucleotides encoding an epitope or antigenic determinant of a rotavirus polypeptide. A polynucleotide encoding a fragment of a rotavirus polypeptide may comprise or consist essentially of or consist of a minimum of 15 nucleotides, about 30-45 nucleotides, about 45-75, or at least 57, 87 or 150 consecutive or contiguous nucleotides of the sequence encoding the polypeptide. Epitope determination procedures, such as, generating overlapping peptide libraries (Hemmer et al., 1998), Pepscan (Geysen et al., 1984; Geysen et al., 1985; Van der Zee R. et al., 1989; Geysen, 1990; Multipin® Peptide Synthesis Kits de Chiron) and algorithms (De Groot et al., 1999; PCT/US2004/022605) can be used in the practice of the invention.
The term “nucleic acid” and “polynucleotide” refers to RNA or DNA that is linear or branched, single or double stranded, or a hybrid thereof. The term also encompasses RNA/DNA hybrids. The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs, uracyl, other sugars and linking groups such as fluororibose and thiolate, and nucleotide branches. The sequence of nucleotides may be further modified after polymerization, such as by conjugation, with a labeling component. Other types of modifications included in this definition are caps, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for attaching the polynucleotide to proteins, metal ions, labeling components, other polynucleotides or solid support. The polynucleotides can be obtained by chemical synthesis or derived from a microorganism.
The term “gene” is used broadly to refer to any segment of polynucleotide associated with a biological function. Thus, genes include introns and exons as in genomic sequence, or just the coding sequences as in cDNAs and/or the regulatory sequences required for their expression. For example, gene also refers to a nucleic acid fragment that expresses mRNA or functional RNA, or encodes a specific protein, and which includes regulatory sequences.
The invention further comprises a complementary strand to a polynucleotide encoding a rotavirus antigen, epitope or immunogen. The complementary strand can be polymeric and of any length, and can contain deoxyribonucleotides, ribonucleotides, and analogs in any combination.
An “isolated” biological component (such as a nucleic acid or protein or organelle) refers to a component that has been substantially separated or purified away from other biological components in the cell of the organism in which the component naturally occurs, for instance, other chromosomal and extra-chromosomal DNA and RNA, proteins, and organelles. Nucleic acids and proteins that have been “isolated” include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant technology as well as chemical synthesis.
The term “purified” as used herein does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a partially purified polypeptide preparation is one in which the polypeptide is more enriched than the polypeptide is in its natural environment. That is the polypeptide is separated from cellular components. By “substantially purified” is intended that such that at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98%, or more of the cellular components or materials have been removed. Likewise, a polypeptide may be partially purified. By “partially purified” is intended that less than 60% of the cellular components or material is removed. The same applies to polynucleotides. The polypeptides disclosed herein can be purified by any of the means known in the art.
Moreover, homologs of rotavirus polypeptides are intended to be within the scope of the present invention. As used herein, the term “homologs” includes orthologs, analogs and paralogs. The tem “analogs” refers to two polynucleotides or polypeptides that have the same or similar function, but that have evolved separately in unrelated organisms. The term “orthologs” refers to two polynucleotides or polypeptides from different species, but that have evolved from a common ancestral gene by speciation. Normally, orthologs encode polypeptides having the same or similar functions. The term “paralogs” refers to two polynucleotides or polypeptides that are related by duplication within a genome. Paralogs usually have different functions, but these functions may be related. For example, analogs, orthologs, and paralogs of a wild-type rotavirus polypeptide can differ from the wild-type rotavirus polypeptide by post-translational modifications, by amino acid sequence differences, or by both. In particular, homologs of the invention will generally exhibit at least 80-85%, 85-90%, 90-95%, or 95%, 96%, 97%, 98%, 99% sequence identity, with all or part of the wild-type rotavirus polypeptide or polynucleotide sequences, and will exhibit a similar function.
In another aspect, the present invention provides a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, 96%, 97%, 98% or 99% sequence identity to a polypeptide having a sequence as set forth in SEQ ID NO: 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, or 71. In yet another aspect, the present invention provides fragments and variants of the rotavirus polypeptides identified above (SEQ ID NO:17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, or 71) which may readily be prepared by one of skill in the art using well-known molecular biology techniques.
Variants are homologous polypeptides having an amino acid sequence at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence as set forth in SEQ ID NO:17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, or 71.
Variants include allelic variants. The term “allelic variant” refers to a polynucleotide or a polypeptide containing polymorphisms that lead to changes in the amino acid sequences of a protein and that exist within a natural population (e.g., a virus species or variety). Such natural allelic variations can typically result in 1-5% variance in a polynucleotide or a polypeptide. Allelic variants can be identified by sequencing the nucleic acid sequence of interest in a number of different species, which can be readily carried out by using hybridization probes to identify the same gene genetic locus in those species. Any and all such nucleic acid variations and resulting amino acid polymorphisms or variations that are the result of natural allelic variation and that do not alter the functional activity of gene of interest, are intended to be within the scope of the invention.
As used herein, the term “derivative” or “variant” refers to a polypeptide, or a nucleic acid encoding a polypeptide, that has one or more conservative amino acid variations or other minor modifications such that (1) the corresponding polypeptide has substantially equivalent function when compared to the wild type polypeptide or (2) an antibody raised against the polypeptide is immunoreactive with the wild-type polypeptide. These variants or derivatives include polypeptides having minor modifications of the rotavirus polypeptide primary amino acid sequences that may result in peptides which have substantially equivalent activity as compared to the unmodified counterpart polypeptide. Such modifications may be deliberate, as by site-directed mutagenesis, or may be spontaneous. The term “variant” further contemplates deletions, additions and substitutions to the sequence, so long as the polypeptide functions to produce an immunological response as defined herein.
The term “conservative variation” denotes the replacement of an amino acid residue by another biologically similar residue, or the replacement of a nucleotide in a nucleic acid sequence such that the encoded amino acid residue does not change or is another biologically similar residue. In this regard, particularly preferred substitutions will generally be conservative in nature, as described above.
An immunogenic fragment of a rotavirus polypeptide includes at least 8, 10, 13, 14, 15, or consecutive amino acids, at least 21 amino acids, at least 23 amino acids, at least 25 amino acids, or at least 30 amino acids of a rotavirus polypeptide having a sequence as set forth in SEQ ID NO:16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, or variants or functional fragments thereof.
In another aspect, the present invention provides a polynucleotide encoding a rotavirus polypeptide, such as a polynucleotide encoding a polypeptide having a sequence as set forth in SEQ ID NO:16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, or variants or functional fragments thereof. In yet another aspect, the present invention provides a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, 96%, 97%, 98% or 99% sequence identity to a polypeptide having a sequence as set forth in SEQ ID NO: 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, or a conservative variant, an allelic variant, a homolog or an immunogenic fragment comprising at least eight or at least ten consecutive amino acids of one of these polypeptides, or a combination of these polypeptides.
In another aspect, the present invention provides a polynucleotide having a nucleotide sequence as set forth in SEQ ID NO:17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, or 71, or a variant or functional fragment thereof. In yet another aspect, the present invention provides a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 95%, 96%, 97%, 98% or 99% sequence identity to one of a polynucleotide having a sequence as set forth in SEQ ID NO: 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, or 71, or a variant thereof.
The polynucleotides of the disclosure include sequences that are degenerate as a result of the genetic code, e.g., optimized codon usage for a specific host. As used herein, “optimized” refers to a polynucleotide that is genetically engineered to increase its expression in a given species. To provide optimized polynucleotides coding for rotavirus polypeptides, the DNA sequence of the rotavirus gene can be modified to 1) comprise codons preferred by highly expressed genes in a particular host cell expression system (e.g. bacterial host cell); 2) comprise an A+T or G+C content in nucleotide base composition to that substantially found in said host cell; 3) form an initiation sequence of said host cell; or 4) eliminate sequences that cause destabilization, degradation and termination of RNA, or that form secondary structure hairpins. Increased expression of rotavirus protein in said host cell expression system can be achieved by utilizing the distribution frequency of codon usage in prokaryotes.
The sequence identity between two amino acid sequences may be established by the NCBI (National Center for Biotechnology Information) pairwise blast and the blosum62 matrix, using the standard parameters (see, e.g., the BLAST or BLASTX algorithm available on the “National Center for Biotechnology Information” (NCBI, Bethesda, Md., USA) server, as well as in Altschul et al.; and thus, this document speaks of using the algorithm or the BLAST or BLASTX and BLOSUM62 matrix by the term “blasts”).
The “identity” with respect to sequences can refer to the number of positions with identical nucleotides or amino acids divided by the number of nucleotides or amino acids in the shorter of the two sequences wherein alignment of the two sequences can be determined in accordance with the Wilbur and Lipman algorithm (Wilbur and Lipman), for instance, using a window size of 20 nucleotides, a word length of 4 nucleotides, and a gap penalty of 4, and computer-assisted analysis and interpretation of the sequence data including alignment can be conveniently performed using commercially available programs (e.g., IntelligeneticsTM Suite, Intelligenetics Inc. CA). When RNA sequences are said to be similar, or have a degree of sequence identity or homology with DNA sequences, thymidine (T) in the DNA sequence is considered equal to uracil (U) in the RNA sequence. Thus, RNA sequences are within the scope of the invention and can be derived from DNA sequences, by thymidine (T) in the DNA sequence being considered equal to uracil (U) in RNA sequences.
The sequence identity or sequence similarity of two amino acid sequences, or the sequence identity between two nucleotide sequences can be determined using Vector NTI software package (Invitrogen, 1600 Faraday Ave., Carlsbad, Calif.).
The following documents provide algorithms for comparing the relative identity or homology of sequences, and additionally or alternatively with respect to the foregoing, the teachings in these references can be used for determining percent homology or identity: Needleman S B and Wunsch C D; Smith T F and Waterman M S; Smith T F, Waterman M S and Sadler J R; Feng D F and Dolittle R F; Higgins D G and Sharp P M; Thompson J D, Higgins D G and Gibson T J; and, Devereux J, Haeberlie P and Smithies O. And, without undue experimentation, the skilled artisan can consult with many other programs or references for determining percent homology.
Hybridization reactions can be performed under conditions of different “stringency.” Conditions that increase stringency of a hybridization reaction are well known. See for example, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook et al., 1989).
The invention further encompasses the rotavirus polynucleotide contained in a vector molecule or an expression vector and operably linked to a promoter element and optionally to an enhancer.
A “vector” refers to a recombinant DNA or RNA plasmid or virus that comprises a heterologous polynucleotide to be delivered to a target cell, either in vitro or in vivo. The heterologous polynucleotide may comprise a sequence of interest for purposes of prevention or therapy, and may optionally be in the form of an expression cassette. As used herein, a vector needs not be capable of replication in the ultimate target cell or subject. The term includes cloning vectors and viral vectors.
The term “recombinant” means a polynucleotide with semisynthetic, or synthetic origin which either does not occur in nature or is linked to another polynucleotide in an arrangement not found in nature.
“Heterologous” means derived from a genetically distinct entity from the rest of the entity to which it is being compared. For example, a polynucleotide may be placed by genetic engineering techniques into a plasmid or vector derived from a different source, and is a heterologous polynucleotide. A promoter removed from its native coding sequence and operatively linked to a coding sequence other than the native sequence is a heterologous promoter.
The polynucleotides of the invention may comprise additional sequences, such as additional encoding sequences within the same transcription unit, controlling elements such as promoters, ribosome binding sites, 5′UTR, 3′UTR, transcription terminators, polyadenylation sites, additional transcription units under control of the same or a different promoter, sequences that permit cloning, expression, homologous recombination, and transformation of a host cell, and any such construct as may be desirable to provide embodiments of this invention.
Elements for the expression of a rotavirus polypeptide, antigen, epitope or immunogen are advantageously present in an inventive vector. In minimum manner, this comprises an initiation codon (ATG), a stop codon and a promoter, and optionally also a polyadenylation sequence for certain vectors such as plasmid and certain viral vectors, e.g., viral vectors other than poxviruses. When the polynucleotide encodes a polypeptide fragment, e.g. a rotavirus polypeptide, advantageously, in the vector, an ATG is placed at 5′ of the reading frame and a stop codon is placed at 3′. Other elements for controlling expression may be present, such as enhancer sequences, stabilizing sequences, such as intron and signal sequences permitting the secretion of the protein.
The present invention also relates to preparations comprising vectors, such as expression vectors, e.g., therapeutic compositions. The preparations can comprise one or more vectors, e.g., expression vectors, such as in vivo expression vectors, comprising and expressing one or more rotavirus polypeptides, antigens, epitopes or immunogens. In one embodiment, the vector contains and expresses a polynucleotide that comprises a polynucleotide coding for and/or expressing a rotavirus antigen, epitope or immunogen, in a pharmaceutically or veterinarily acceptable carrier, excipient or vehicle. Thus, according to an embodiment of the invention, the other vector or vectors in the preparation comprises, consists essentially of or consists of a polynucleotide that encodes, and under appropriate circumstances the vector expresses one or more other proteins of a rotavirus polypeptide, antigen, epitope or immunogen (e.g., hemagglutinin, capsid, neuraminidase, nucleoprotein, non-structural protein, enterotoxin) or a fragment thereof.
According to another embodiment, the vector or vectors in the preparation comprise, or consist essentially of, or consist of polynucleotide(s) encoding one or more proteins or fragment(s) of a rotavirus polypeptide, antigen, epitope or immunogen. In another embodiment, the preparation comprises one, two, or more vectors comprising polynucleotides encoding and expressing, advantageously in vivo, a rotavirus polypeptide, antigen, fusion protein or an epitope thereof. The invention is also directed at mixtures of vectors that comprise polynucleotides encoding and expressing different a rotavirus polypeptides, antigens, epitopes, fusion protein, or immunogens, e.g., a rotavirus polypeptide, antigen, epitope or immunogen from different species such as, but not limited to, humans, pigs, cows or cattle, dogs, cats, and avian.
According to a yet further embodiment of the invention, the expression vector is a plasmid vector, in particular an in vivo expression vector. In a specific, non-limiting example, the pVR1020 or 1012 plasmid (VICAL Inc.; Luke et al., 1997; Hartikka et al., 1996, see, e.g., U.S. Pat. Nos. 5,846,946 and 6,451,769) can be utilized as a vector for the insertion of a polynucleotide sequence. The pVR1020 plasmid is derived from pVR1012 and contains the human tPA signal sequence. In one embodiment the human tPA signal comprises from amino acid M(1) to amino acid S(23) in Genbank under the accession number HUMTPA14. In another specific, non-limiting example, the plasmid utilized as a vector for the insertion of a polynucleotide sequence can contain the signal peptide sequence of equine IGF1 from amino acid M(24) to amino acid A(48) in Genbank under the accession number U28070. Additional information on DNA plasmids which may be consulted or employed in the practice are found, for example, in U.S. Pat. Nos. 6,852,705; 6,818,628; 6,586,412; 6,576,243; 6,558,674; 6,464,984; 6,451,770; 6,376,473 and 6,221,362.
The term plasmid covers any DNA transcription unit comprising a polynucleotide according to the invention and the elements necessary for its in vivo expression in a cell or cells of the desired host or target; and, in this regard, it is noted that a supercoiled or non-supercoiled, circular plasmid, as well as a linear form, are intended to be within the scope of the invention.
Each plasmid comprises or contains or consists essentially of, in addition to the polynucleotide encoding a rotavirus polypeptide, antigen, epitope or immunogen, optionally fused with a heterologous peptide sequence, variant, analog or fragment, operably linked to a promoter or under the control of a promoter or dependent upon a promoter. In general, it is advantageous to employ a strong promoter functional in eukaryotic cells. The strong promoter may be, but not limited to, the immediate early cytomegalovirus promoter (CMV-IE) of human or murine origin, or optionally having another origin such as the rat or guinea pig.
In more general terms, the promoter has either a viral, or a cellular origin. A strong viral promoter other than CMV-IE that may be usefully employed in the practice of the invention is the early/late promoter of the SV40 virus or the LTR promoter of the Rous sarcoma virus. A strong cellular promoter that may be usefully employed in the practice of the invention is the promoter of a gene of the cytoskeleton, such as e.g. the desmin promoter (Kwissa et al., 2000), or the actin promoter (Miyazaki et al., 1989).
As to the polyadenylation signal (polyA) for the plasmids and viral vectors other than poxviruses, use can be made of the poly(A) signal of the bovine growth hormone (bGH) gene (see U.S. Pat. No. 5,122,458), or the poly(A) signal of the rabbit β-globin gene or the poly(A) signal of the SV40 virus.
A “host cell” denotes a prokaryotic or eukaryotic cell that has been genetically altered, or is capable of being genetically altered by administration of an exogenous polynucleotide, such as a recombinant plasmid or vector. When referring to genetically altered cells, the term refers both to the originally altered cell and to the progeny thereof.
Methods of Use and Article of Manufacture
The present invention includes the following method embodiments. In an embodiment, a method of vaccinating an animal comprising administering a composition comprising a vector comprising a rotavirus polypeptide or fragment or variant thereof and a pharmaceutical or veterinarily acceptable carrier, excipient, or vehicle to an animal is disclosed. In one aspect of this embodiment, the animal is a porcine.
In one embodiment of the invention, a prime-boost regimen can be employed, which is comprised of at least one primary administration and at least one booster administration using at least one common polypeptide, antigen, epitope or immunogen. Typically the immunological composition or vaccine used in primary administration is different in nature from those used as a booster. However, it is noted that the same composition can be used as the primary administration and the booster administration. This administration protocol is called “prime-boost”.
A prime-boost regimen comprises at least one prime-administration and at least one boost administration using at least one common polypeptide and/or variants or fragments thereof. The vaccine used in prime-administration may be different in nature from those used as a later booster vaccine. The prime-administration may comprise one or more administrations. Similarly, the boost administration may comprise one or more administrations.
The dose volume of compositions for target species that are mammals, e.g., the dose volume of pig or swine compositions, based on viral vectors, e.g., non-poxvirus-viral-vector-based compositions, is generally between about 0.1 to about 2.0 ml, between about 0.1 to about 1.0 ml, and between about 0.5 ml to about 1.0 ml.
The efficacy of the vaccines may be tested about 2 to 4 weeks after the last immunization by challenging animals, such as porcine, with a virulent strain of rotavirus. Both homologous and heterologous strains are used for challenge to test the efficacy of the vaccine. The animal may be challenged by IM or SC injection, spray, intra-nasally, intra-ocularly, intra-tracheally, and/or orally. The challenge virus may be about 105-8 EID50, TCID50 or 103-8 genome equivalents as determined by qPCR in a volume depending upon the route of administration. For example, if the administration is by spray, a virus suspension is aerosolized to generate about 1 to 100 μm droplets, if the administration is intra-nasal, intra-tracheal or oral, the volume of the challenge virus is about 0.5 ml, 1-2 ml, and 5-10 ml, respectively. Animals may be observed daily for 14 days following challenge for clinical signs, for example, dehydration, diarrhea, pasty to watery feces, death, and/or loss of weight, failure to thrive, virus shedding. In addition, the groups of animals may be euthanized and evaluated for pathological findings intestinal disease, villous atrophy. Rectal or fecal swabs may be collected from all animals post challenge for virus isolation or quantification, or detection. The presence or absence of viral antigens in intestinal tissues or feces may be evaluated by quantitative real time reverse transcriptase polymerase chain reaction (qRT-PCR). Blood samples may be collected before and post-challenge and may be analyzed for the presence of rotavirus-specific antibody.
The compositions comprising the recombinant antigenic polypeptides of the invention used in the prime-boost protocols are contained in a pharmaceutically or veterinary acceptable vehicle, diluent or excipient. The protocols of the invention protect the animal from rotavirus and/or prevent disease progression in an infected animal.
The various administrations are preferably carried out 1 to 6 weeks apart. Preferred time interval is 3 to 5 weeks, and optimally 4 weeks According to one embodiment, an annual booster is also envisioned. The animals, for example pigs, may be at least 8 weeks of age at the time of the first administration.
It should be understood by one of skill in the art that the disclosure herein is provided by way of example and the present invention is not limited thereto. From the disclosure herein and the knowledge in the art, the skilled artisan can determine the number of administrations, the administration route, and the doses to be used for each injection protocol, without any undue experimentation.
The present invention contemplates at least one administration to an animal of a sufficient amount of the therapeutic composition made according to the invention. For example, the sufficient amount may be from about 10 μg to about 300 μg of protein. In an embodiment, about 100 μg of each of three different group C rotavirus proteins be present in a sufficient amount of the therapeutic composition. The animal may be male, female, pregnant female and newborn. This administration may be via various routes including, but not limited to, intramuscular (IM), intradermal (ID), intraperitoneal (IP) or subcutaneous (SC) injection or via intranasal or oral administration. The therapeutic composition according to the invention can also be administered by a needleless apparatus (as, for example with a Pulse Needle Free, Pulse Needlefree, Lenexa, Kans., USA, Pigjet, Dermojet, Biojector, Avijet (Merial, Ga., USA), Vetjet or Vitajet apparatus (Bioject, Oregon, USA)). Another approach to administering plasmid compositions is to use electroporation (see, e.g. Tollefsen et al., 2002; Tollefsen et al., 2003; Babiuk et al., 2002; PCT Application No. WO99/01158). In another embodiment, the therapeutic composition is delivered to the animal by gene gun or gold particle bombardment. In an advantageous embodiment, the animal is a pig, dog, ferret or seal.
Another embodiment of the invention is a kit for performing a method of eliciting or inducing an immunological or protective response against rotavirus in an animal comprising a rotavirus subunit immunological composition or vaccine and instructions for performing the method of delivery in an effective amount for eliciting an immune response in the animal.
Another embodiment of the invention is a kit for performing a method of inducing an immunological or protective response against rotavirus in an animal comprising a composition or vaccine comprising a rotavirus polypeptide or antigen of the invention, and instructions for performing the method of delivery in an effective amount for eliciting an immune response in the animal.
Yet another aspect of the present invention relates to a kit for prime-boost vaccination according to the present invention as described above. The kit may comprise at least two vials: a first vial containing a vaccine or composition for the prime-vaccination according to the present invention, and a second vial containing a vaccine or composition for the boost-vaccination according to the present invention. The kit may advantageously contain additional first or second vials for additional prime-vaccinations or additional boost-vaccinations.
The pharmaceutically or veterinarily acceptable carriers or vehicles or excipients are well known to the one skilled in the art. For example, a pharmaceutically or veterinarily acceptable carrier or vehicle or excipient can be a 0.9% NaCl (e.g., saline) solution or a phosphate buffer. Other pharmaceutically or veterinarily acceptable carrier or vehicle or excipients that can be used for methods of this invention include, but are not limited to, poly-(L-glutamate) or polyvinylpyrrolidone. The pharmaceutically or veterinarily acceptable carrier or vehicle or excipients may be any compound or combination of compounds facilitating the administration of the vector (or protein expressed from an inventive vector in vitro); advantageously, the carrier, vehicle or excipient may facilitate transfection and/or improve preservation of the vector (or protein). Doses and dose volumes are herein discussed in the general description and can also be determined by the skilled artisan from this disclosure read in conjunction with the knowledge in the art, without any undue experimentation.
The cationic lipids containing a quaternary ammonium salt which are advantageously but not exclusively suitable for plasmids, are advantageously those having the following formula:




in which R1 is a saturated or unsaturated straight-chain aliphatic radical having 12 to 18 carbon atoms, R2 is another aliphatic radical containing 2 or 3 carbon atoms and X is an amine or hydroxyl group, e.g. the DMRIE. In another embodiment the cationic lipid can be associated with a neutral lipid, e.g. the DOPE.
Among these cationic lipids, preference is given to DMRIE (N-(2-hydroxyethyl)-N,N-dimethyl-2,3-bis(tetradecyloxy)-1-propane ammonium; WO96/34109), advantageously associated with a neutral lipid, advantageously DOPE (dioleoyl-phosphatidyl-ethanol amine; Behr, 1994), to form DMRIE-DOPE.
When DOPE is present, the DMRIE:DOPE molar ratio is advantageously about 95:about 5 to about 5:about 95, more advantageously about 1:about 1, e.g., 1:1.
In another embodiment, pharmaceutically or veterinarily acceptable carrier, excipient, or vehicle may be a water-in-oil emulsion. Examples of suitable water-in-oil emulsions include oil-based water-in-oil vaccinal emulsions which are stable and fluid at 4° C. containing from 6 to 50 v/v % of an antigen-containing aqueous phase, preferably from 12 to 25 v/v %, from 50 to 94 v/v % of an oil phase containing in total or in part a non-metabolizable oil (e.g., mineral oil such as paraffin oil) and/or metabolizable oil (e.g., vegetable oil, or fatty acid, polyol or alcohol esters), from 0.2 to 20 p/v % of surfactants, preferably from 3 to 8 p/v %, the latter being in total or in part, or in a mixture either polyglycerol esters, said polyglycerol esters being preferably polyglycerol (poly)ricinoleates, or polyoxyethylene ricin oils or else hydrogenated polyoxyethylene ricin oils. Examples of surfactants that may be used in a water-in-oil emulsion include ethoxylated sorbitan esters (e.g., polyoxyethylene (20) sorbitan monooleate (TWEEN 80®), available from AppliChem, Inc., Cheshire, Conn.) and sorbitan esters (e.g., sorbitan monooleate (SPAN 80®), available from Sigma Aldrich, St. Louis, Mo.). In addition, with respect to a water-in-oil emulsion, see also U.S. Pat. No. 6,919,084. In some embodiments, the antigen-containing aqueous phase comprises a saline solution comprising one or more buffering agents. An example of a suitable buffering solution is phosphate buffered saline. In an advantageous embodiment, the water-in-oil emulsion may be a water/oil/water (W/O/W) triple emulsion (U.S. Pat. No. 6,358,500). Examples of other suitable emulsions are described in U.S. Pat. No. 7,371,395.
The immunological compositions and vaccines according to the invention may comprise or consist essentially of one or more adjuvants. Suitable adjuvants for use in the practice of the present invention are (1) polymers of acrylic or methacrylic acid, maleic anhydride and alkenyl derivative polymers, (2) immunostimulating sequences (ISS), such as oligodeoxyribonucleotide sequences having one or more non-methylated CpG units (Klinman et al., 1996; WO98/16247), (3) an oil in water emulsion, such as the SPT emulsion described on page 147 of “Vaccine Design, The Subunit and Adjuvant Approach” published by M. Powell, M. Newman, Plenum Press 1995, and the emulsion MF59 described on page 183 of the same work, (4) cation lipids containing a quaternary ammonium salt, e.g., DDA (5) cytokines, (6) aluminum hydroxide or aluminum phosphate, (7) saponin or (8) other adjuvants discussed in any document cited and incorporated by reference into the instant application, or (9) any combinations or mixtures thereof.
The oil in water emulsion (3), which is especially appropriate for viral vectors, can be based on: light liquid paraffin oil (European pharmacopoeia type), isoprenoid oil such as squalane, squalene, oil resulting from the oligomerization of alkenes, e.g. isobutene or decene, esters of acids or alcohols having a straight-chain alkyl group, such as vegetable oils, ethyl oleate, propylene glycol, di(caprylate/caprate), glycerol tri(caprylate/caprate) and propylene glycol dioleate, or esters of branched, fatty alcohols or acids, especially isostearic acid esters.
The oil is used in combination with emulsifiers to form an emulsion. The emulsifiers may be nonionic surfactants, such as: esters of on the one hand sorbitan, mannide (e.g. anhydromannitol oleate), glycerol, polyglycerol or propylene glycol and on the other hand oleic, isostearic, ricinoleic or hydroxystearic acids, said esters being optionally ethoxylated, or polyoxypropylene-polyoxyethylene copolymer blocks, such as Pluronic, e.g., L121.
Among the type (1) adjuvant polymers, preference is given to polymers of crosslinked acrylic or methacrylic acid, especially crosslinked by polyalkenyl ethers of sugars or polyalcohols. These compounds are known under the name carbomer (Pharmeuropa, vol. 8, no. 2, June 1996). One skilled in the art can also refer to U.S. Pat. No. 2,909,462, which provides such acrylic polymers crosslinked by a polyhydroxyl compound having at least three hydroxyl groups, preferably no more than eight such groups, the hydrogen atoms of at least three hydroxyl groups being replaced by unsaturated, aliphatic radicals having at least two carbon atoms. The preferred radicals are those containing 2 to 4 carbon atoms, e.g. vinyls, allyls and other ethylenically unsaturated groups. The unsaturated radicals can also contain other substituents, such as methyl. Products sold under the name Carbopol (BF Goodrich, Ohio, USA) are especially suitable. They are crosslinked by allyl saccharose or by allyl pentaerythritol. Among them, reference is made to Carbopol 974P, 934P and 971P.
As to the maleic anhydride-alkenyl derivative copolymers, preference is given to EMA (Monsanto), which are straight-chain or crosslinked ethylene-maleic anhydride copolymers and they are, for example, crosslinked by divinyl ether. Reference is also made to J. Fields et al., 1960.
With regard to structure, the acrylic or methacrylic acid polymers and EMA are preferably formed by basic units having the following formula:




in which:

    
    
        R1 and R2, which can be the same or different, represent H or CH3
        x=0 or 1, preferably x=1
        y=1 or 2, with x+y=2.
    
    


For EMA, x=0 and y=2 and for carbomers x=y=1.
These polymers are soluble in water or physiological salt solution (20 g/l NaCl) and the pH can be adjusted to 7.3 to 7.4, e.g., by soda (NaOH), to provide the adjuvant solution in which the expression vector(s) can be incorporated. The polymer concentration in the final immunological or vaccine composition can range between about 0.01 to about 1.5% w/v, about 0.05 to about 1% w/v, and about 0.1 to about 0.4% w/v.
The cytokine or cytokines (5) can be in protein form in the immunological or vaccine composition, or can be co-expressed in the host with the immunogen or immunogens or epitope(s) thereof. Preference is given to the co-expression of the cytokine or cytokines, either by the same vector as that expressing the immunogen or immunogens or epitope(s) thereof, or by a separate vector thereof.
The invention comprehends preparing such combination compositions; for instance by admixing the active components, advantageously together and with an adjuvant, carrier, cytokine, and/or diluent.
Cytokines that may be used in the present invention include, but are not limited to, granulocyte colony stimulating factor (G-CSF), granulocyte/macrophage colony stimulating factor (GM-CSF), interferon Δ (IFNγ), interferon β (IFNβ), interferon γ, (IFNγ), interleukin-1α(IL-1α), interleukin-1β (IL-1β), interleukin-2 (IL-2), interleukin-3 (IL-3), interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-6 (IL-6), interleukin-7 (IL-7), interleukin-8 (IL-8), interleukin-9 (IL-9), interleukin-10 (IL-10), interleukin-11 (IL-11), interleukin-12 (IL-12), tumor necrosis factor α (TNFα), tumor necrosis factor β (TNFβ), and transforming growth factor β (TGFβ). It is understood that cytokines can be co-administered and/or sequentially administered with the immunological or vaccine composition of the present invention. Thus, for instance, the vaccine of the instant invention can also contain an exogenous nucleic acid molecule that expresses in vivo a suitable cytokine, e.g., a cytokine matched to this host to be vaccinated or in which an immunological response is to be elicited (for instance, a canine cytokine for preparations to be administered to canine).
The invention will now be further described by way of the following non-limiting examples.
EXAMPLES
Summary
Viral vaccines are typically made using whole virus isolated from clinical samples from infected animals, by virus adaptation and propagation in egg embryo or in vitro cell culture. Group C Porcine Rotaviruses are notoriously difficult to recover by these conventional virological techniques, and rotaviruses generally are thought to be prone to antigenic distortion during adaptation to egg embryo or cell culture growth, resulting in suboptimal vaccine production from the isolated whole virus. Thus, an expression vector (pNPL2, SEQ ID NO:15) was constructed to enable production of vaccine comprising Porcine Rotavirus Group C VP4, VP6 and/or NSP4 Recombinant Proteins. Rotavirus genetic material was rescued by PCR from clinical material submitted by a herd veterinarian. To pNPL2 was added (via the process described herein and depicted in FIG. 7) a gene encoding VP4 (18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, or 40), VP6 (42, 44, 46, 48, or 50), or NSP4 (52, 54, 56, 58, 60, 62, 64, 66, 68, 70, or 72) polypeptides/subunits, to yield pNPL2-RotaC vectors, each of which encoding and capable of expressing in a bacterial host cell a portion of either NSP4, VP4, or VP6. These vectors were then grown in SE1 E. coli cells, which constitutively express the ccdB proteic toxin, which kills the bacteria in absence of the vector. Cells were grown, inactivated, and then the recombinantly-expressed rotaviral proteins were harvested and formulated with adjuvant for use as a non-viable subunit protein autogenous vaccine. The inventive vaccine compositions elicited in the porcines protective immunity against rotavirus.
Example 1
Construction of Vector for Autogenous or Commercial Production of Rotavirus Subunit Vaccines
pNPL1 & 2 expression vector construction. The expression vector pNPL2 (SEQ ID NO:15) was constructed from the pStaby1.2 vector (SEQ ID NO:1) of Delphi Genetics (pStaby1.2 user's manual, as published in 2011), by deletion of the ampicillin resistance gene and insertion of a GST (glutathione S-transferase) gene, to facilitate down-stream protein processing during production. The vector contains nor expresses no known mammalian virulence features, and furthermore, all antibiotic resistance genes were removed from same during its construction. pNPL2 were grown in SE1 E. coli, and together they are a B Strain E. coli host/vector production system (pStaby User Manual).
The restriction map of pStaby1.2 is presented in FIG. 1, and as indicated, contains a T7 promoter to drive the expression of the gene encoding the recombinant protein. The plasmid also contains the ccdA gene, which codes for an unstable antidote protein, which inhibits expression of a stable antigyrase protein (ccdB) which is toxic to Enterobacteriaceae cells. The ccdB protein is coded for by the ccdB gene which is present in the chromosome of the host SE1 E. coli host cells (the ccdB gene is not present in the pStaby1.2 plasmid). After transformation, the presence of the ccdA gene in the plasmid ensures successfully transformed cells are viable while non-plasmid-bearing SE1 cells produce toxin without antidote and are thus non-viable.
The ampicillin resistance gene of pStaby1.2 vector was considered undesirable for use in subunit rotavirus vaccine production, and was therefore removed using inverse PCR technique (FIG. 2). A list of primers used for all disclosed procedures is shown in Table 1. The final PCR product was phosphorylated and self-ligated to yield pNPL1 (SEQ ID NO:14). GST was then added to pNPL1 to increase the size of any expressed protein, and to improve downstream processing/inline analysis. GST was PCR amplified from pGEX4T.1 (GE Life Sciences) using primers #650 (SEQ ID NO:2) and #651 (SEQ ID NO:3), and then the amplicon (SEQ ID NO:16) was digested and cloned into NdeI-BamHI-linearized pNPL1 to yield pNPL2 (FIGS. 2-4). pNPL2 digested with BamHI and HindIII yield two bands visible on an agarose gel (5682 bp and 25 bp).
Construction of pNPL3.
PCR was performed using primers KSN772 (SEQ ID NO:77) and KSN773 (SEQ ID NO:78), and pNPL1 as the template. The PCR product is phosphorylated and self-ligated to from pNPL3, which now contained a hexa-HIS Tag. NSP4, VP4, VP6 or VP7 genes can be cloned into the BamHI and HindIII digested pNPL3 vector by infusion reaction using the PCR products generated by using primers at set forth in SEQ ID NOs:79-89. pNPL3 is similar to pNPL2, except that pNPL3 lacks sequence coding for GST gene. Instead, pNPL3 has a sequence coding for a His Tag, allowing for N-terminal His Tagged fusion peptides.
Example 2
Production of Autogenous Rotavirus Subunit Vaccine
Rotaviral RNAs were isolated, purified directly from clinical samples collected from infected pigs, and subjected to reverse transcription-PCR (RTPCR) using primers specific for genes encoding VP4 (primers given by SEQ ID NOs:10, 11), VP6 (primers given by SEQ ID NO:12, 13), and NSP4 (primers given by SEQ ID NO:8, 9). Each primer pair was designed to bind to a highly conserved region on each end of the target gene (FIG. 5), enabling amplification of group C rotaviral genes from many different viral isolates. If the genes cannot be amplified using the Rotavirus C gene-specific primers as set forth in SEQ ID NOs:8, 9, 10, 11, 12, and 13, alternate primers may be designed and used by skilled persons using techniques well-known in the art. For example, degenerate primers may be employed, such that critical primer positions (e.g. the 3′ terminal nucleotide) can be varied to accommodate template deviation from the conserved sequences. Primers having the sequence as set forth in SEQ ID NOs:73, 74, 75, and 76 may be used to amplify and clone VP4 sequences into pNPL1 and/or pNPL2. SEQ ID NOs:73 and 74 can be used to amplify the VP4 sequence and clone it into the TOPO vector. Thereafter, SEQ ID NOs:75 and 76 can be used to insert the VP4 sequence into the pNPL2 vector, for subsequent subunit vaccine production.
The 5′ end of each primer included a 15-nucleotide sequence to allow for insertion into pNPL2 during a subsequent infusion reaction. Isolation and amplification of the field-origin rotaviral genes for production of Donor DNA to be used in the expression system are shown in FIGS. 4, 5 and 6. The presence of both the ccdA (vector encoded) and ccdB (cell genome encoded) genes within transformed SE1 cells results in viable stable cultures expressing the rotavirus gene. Any non-transformed or plasmid-cured cells are nonviable. Gene insertion was characterized and verified by sequencing, and protein expression was verified by SDS PAGE (FIG. 8), which indicated approximate molecular weights of 36 kDa (NSP4), 52 kDa (VP4), and 68 kDa (VP6). This approach is envisioned to be applicable to any rotavirus field strain having sufficient homology to the cloning primers in the conserved regions.
For large scale production, single colonies or multiple uniform colonies were transferred to 10 mL-200,000 mL LB media. When the optical density, measured at 600 nm, reached 0.4-1.0, IPTG ([Isopropyl β-D-thiogalactopyranoside] Sigma Aldrich Catalog No. I5502 or equivalent) was added at a final concentration of 1 mM. The cultures were incubated for an additional 2-6 hours. Cultures may be grown in a fermenter, as follows:
a. Temperature of the culture is maintained at 36°±3° C.
b. Filtered compressed air flow is maintained at 0.1-300 L/minute.
c. pH of the culture is maintained at 7.4±0.3.
d. When the optical density, measured at 600 nm, reaches 0.4-1.0, IPTG is added at a final concentration of 1 mM. The cultures are incubated for an additional 2-6 hours.
Harvest Technique.
The spent culture medium was separated from the E. coli cells by filtration or centrifugation, and the cells were concentrated by filtration using a 0.1-0.45 micron filter. Concentrated cells were then lysed using B-PER reagent (Thermo Scientific, Catalog No. 78248 or equivalent) then stirring or agitating the solution for 0.5-2 hours. The lysed cells were concentrated by centrifugation at 5000-10000 g for 15-30 minutes or by filtration using 0.1-0.45 micron filter and the supernatant/permeate was discarded. The pellet/concentrate was resuspended in wash buffer A (20 mM Tris-HCL, 2 mM EDTA and 0.1% TritonX-100, adjust pH to 7.5-8.5) by stirring or agitating for 0.1-0.5 hours, and the resulting suspension was concentrated by centrifugation at 5000-10000 g for 15-30 minutes or by filtration using a 0.1-0.45 micron filter. The pellet/concentrate was resuspended in wash buffer B (20 mM Tris-HCL and 2 mM EDTA, adjust pH to 7.5-8.5) by stirring or agitating for 0.1-0.5 hours, then the suspension was concentrated by centrifugation at 5000-10000 g for 15-30 minutes or by filtration using a 0.1-0.4 micron filter. After suspending in 8M Urea (Sigma-Aldrich, Catalog No. U6504 or equivalent) and stirring or agitating for 0.5-2 hours, the final suspension was diluted with sterile PBS.
Vaccine Formulations.
After harvest, rotavirus subunits were formulated with TRIGEN (oil-in-water) and preservatives (gentamicin at a concentration of <30.0 μg/mL and amphotericin B at a concentration of <2.50 μg/mL or polymyxin B at a concentration of <30 μg/mL). To the mixture was added a) aluminum hydroxide gel (ALHYDROGEL® “85”, manufactured by Brenntag Biosector, Cat. No. EMS 2485-2 or REHYDRAGEL HPA, Reheis Cat. No. 203130070600, REHYDRAGEL LV, Reheis Cat. No. 203120070602 or equivalent) providing from about 0.1 to about 0.5% Al2O3 in the final product. Alternatively, Quil A adjuvant was present in the formulations at a rate of 0.5 to 2.5% of inactivated fluids with oil in water adjuvant. Adjuvants comprise from about 10 to about 50% of the final product.
Example 3
Immunization of Sows Using Autogenous Rotavirus Subunit Vaccines
Summary.
48 research sows, chronically infected with Rotavirus C and of similar parity were enrolled into the vaccine efficacy study. Twenty-six (26) animals were placebo vaccinated controls, while 22 animals received rotavirus subunit vaccine comprising a mixture of VP4, VP6, NSP4, and emulsion/additional adjuvants. The vaccine is formulated such that there is about 100 microgram of each protein (total of 300 microgram of protein) and 10% Trigen per each dose of vaccine. Vaccines were administered intramuscularly at 6 and 3 weeks prefarrowing. Sow blood serum was collected prior to vaccination and farrowing, and piglets blood serum was subsequently collected at 7 days post farrowing.
Results.
Piglets born from non-vaccinated sows had a 21% mortality rate, as compared to piglets born from vaccinated sows, which had a 14% mortality rate (i.e. 33% decrease). Morbidity was also significantly decreased in pigs born to vaccinated sows. Piglets from vaccinated sows also had significantly (p<0.05) higher antibody titers than did control piglets (FIG. 9).
Example 4
Efficacy of a Novel Rotavirus C Vaccine in Reducing Suckling Pig Scour Incidence and Improving Performance
Summary.
A 3600 sow breed to wean herd was selected to evaluate the efficacy of a novel Rotavirus C vaccine. The herd consisted of PIC L03 females crossed with Line 02 boars. All diets fed on the farm are formulated to meet or exceed nutrient requirements (NRC, 1998). Sows and gilts were randomly assigned to one of two treatments (control (CON) or Rota C RS vaccine (VACC) based on the day of breeding and within parity. Animals in the assigned VACC group received 2 ml of vaccine intramuscularly at 3 weeks; 3 and 5 weeks; or 3, 5, and 8 weeks pre-farrow. All litters from these animals were cross fostered within 24 hours of birth by treatment. Scour scores were conducted daily from day of birth to day 5. A score was given as 0 (no scour), 1 (small number scouring), 2 (50% of the litter scouring), or 3 (more than 50% of the litter scouring). Pigs removed from the original litters due to mortality associated with scours were recorded. There were no differences scour scores or mortality associated with scours when either the 3 week or the 3, 5, and 8 week vaccination programs were used. However, scour scores were reduced between the CON and VACC (3 and 5 week) treatments (0.56 vs. 0.41, P<0.05). In addition, the percent of scouring litters was reduced from day 1 through day 5 with the VACC treatment (week 3 and 5) versus the CON. In conclusion, the novel Rotavirus C vaccine did not alter the incidence of suckling pig scour rate or mortality when sows were vaccinated once or three times. However, the use of the novel vaccine did appear to reduce scour incidence when given at 3 and 5 weeks pre-farrow.
Treatments.
Sows and gilts were randomly assigned to one of four treatments (control (CON) or Newport vaccine treatments 1-3 (VACC) based on the day of breeding and within parity. The formulation was 100 micrograms of each polypeptide: VP4 (SEQ ID NO:42), VP6 (SEQ ID NO:52) and NSP4 (SEQ ID NO:18), which originated from rotavirus isolate 1. These protein subunits were combined with 10% TRIGEN (composed approximately of 1.6% polyoxyethylene sorbitan monooleate, 10% aluminum hydroxide gel, 38% aqueous/saline, 45% purified mineral oil, and 5% sorbitan monooleate) formulated for a 2 cc dose. Animals in the assigned VACC treatment group 1 received 2 ml of vaccine intramuscularly at 3 weeks pre farrow, animals in the assigned VACC treatment group 2 received 2 ml of vaccine intramuscularly at 5 weeks pre farrow and then again 3 weeks pre farrow, animals in the assigned VACC treatment group 3 received 2 ml of vaccine intramuscularly at 7 weeks pre farrow, 5 weeks pre farrow, and then again 3 weeks pre-farrow. All litters from these animals were cross fostered within 24 hours of birth by treatment.
Data Collection.
Scour scores were conducted daily from day of birth to day 5. The individual collecting all data was blinded from the original treatment assignments. Pigs removed from the original litters due to mortality associated with scours were noted on the day of removal and were compiled as mortality/morbidity in the data set.
Data Analysis.
Mortality/morbidity and scour scores were analyzed using GLM procedures. Room and parity were also included in the model.
Results.
Piglet mortality and morbidity was reduced in the group that received two doses of vaccine prior to farrowing compared to their respective control counterparts although not significant. However, in the groups that received either one or three doses of vaccine, there were no differences. Scour scores were only significantly different on Day 1 post-farrow for the two dose vaccination treatment. No other differences were noted in the scour scores at any other time-point or with either the one or three dose program. Interestingly in this study, the vaccine showed reduction using the two dose vaccination program and not the single or triple dose program.







TABLE 2







Performance data measured with 2 dose vaccination.











CON
VACC
P value
















Mortality due to scours, n
37
23




Mortality due to scours, %
1.72
1.02
.19



Fallouts, %
.69
.92
.53

















TABLE 3







Average scour score by day post-farrow with 2 dose vaccination.












CON
VACC
SEM
P value

















Day 1
.56
.41
.06
.05



Day 2
.87
.84
.07
.77



Day 3
1.01
1.00
.08
.98



Day 4
.51
.40
.10
.41



Day 5
.29
.24
.04
.37

















TABLE 4







Average scour score by day post-farrow with 3 dose vaccination.












CON
VACC
SEM
P value

















Day 1
.30
.32
.10
.84



Day 2
.61
.40
.12
.15



Day 3
.80
.76
.13
.79



Day 4
.25
.15
.09
.32



Day 5
.02
.00
.02
.31










Example 5
Production of Triple Fusion Rotavirus C Vaccine
Summary.
As described above, Rota C subunit vaccine production was accomplished by cloning the three different genes (NSP4, VP4 and VP6) into three different vectors and growing three different E. coli cultures. To simply this process, all three genes were placed into a single plasmid vector, tandem and in frame, thus enabling vaccine production using a single batch of E. coli culture. This construct was built by cloning the Rota C (isolate 12-1260-5) genes into pNPL2 (GST tag in-frame at the N-terminus). The three gene fusion (not including the GST tag) has the sequence as set forth in SEQ ID NO:94. The encoded polyprotein has the sequence as set forth in SEQ ID NO:95.
Materials and Methods.
RNA is extracted from a clinical sample using Qiagen Viral RNA extraction kit as per manufacturer's protocol. The concentration and purity of the RNA was verified by measuring absorbance at 260 and 280 using Nanodrop. The RNA was qualified if the 260/280 ratio was at least 1.7 and concentration of RNA was at least 50 ng/μl. The rotaviral genes were amplified (primers set forth in Table 5) and PCR products were purified using Qiagen PCR purification kit. the size of the products are confirmed by running on a DNA gel (NSP4-300 bp, VP4-750 bp, VP6-1200 bp) and concentration estimated using nanodrop.







TABLE 5







Rota C triple fusion primers










SEQ ID
Name
Orientation
Sequence





 8
KSN652
NSP4 Forward
GGTTCCGCGTGGATCCATCACCTCAAAAACTG


 


13
KSN657
VP6 Reverse
GTGCGGCCGCAAGCTTCTACATCACCATTCTCTTC


 


96
KSN859
NSP4 Reverse
AAGTGAGGACGCCCTTAGACAAACTTCCGTCTCC


 


97
KSN860
VP4 Forward
AGGGCGTCCTCACTTTATC


 


98
KSN861
VP4 Reverse
TGAAAACAGCACGTCTAACACCATCATTCTC


 


99
KSN862
VP6 Forward
GACGTGCTGTTTTCAATTGC









Cloning of PCR Products into pNPL2.
All three products were simultaneously cloned into the expression vector. The reaction was set up as below and incubated at 50° C. for 15 min following by 4° C. hold. About 5 ul of the reaction products are used to transform CYS21 E. coli competent cells (Cat # GE-STCB-22) as per manufacturer's recommendations (Delphi Genetics). The recombinant E. coli containing the plasmid is grown in LB media and plasmid DNA is sequenced using primers listed the Table 5 along with T7 promoter and T7 terminator primers (standard free primers). Sequences were aligned to generate a large open reading frame and verified for its accuracy; the ORF contained all three genes in frame with GST tag (GST-NSP4-VP4-VP6; about 2.9 kb).







TABLE 6







Triple fusion ligation reaction mixture










Label
Volume







BamH I and Hind III cut pNPL2 (~50 ng/ul)
3 μl



NSP4 PCR product (~50 ng/ul)
0.5 μl 



VP4 PCR product (~50 ng/ul)
1 μl



VP6 PCR product (~50 ng/ul)
1.5 μl 



5X Infusion HD cloning mix (Cat # 639646, Clontech)
2 μl



Nuclease free water
2 μl










NSP4-VP4-VP6 Polyprotein Expression Analysis.
Protein expression was induced in the SE1 strain of E. coli by adding IPTG according to standard protocols. The culture fluids were resolved on a PAGE gel to verify expression of the fusion protein (FIG. 12). The fusion protein was present in the urea soluble fraction of the fluids, but not in the B-per solution fraction (PAGE, data not shown). The urea-soluble fusion protein was diluted with water 1:20 and 1:40, and run on a PAGE for subsequent Western blot. The blot was probed using monoclonal antibody against GST (Genscript Cat A00866) at 0.1 μg/mL final concentration using standard protocol (FIG. 13).
Having thus described in detail preferred embodiments of the present invention, it is to be understood that the invention defined by the above paragraphs is not to be limited to particular details set forth in the above description as many apparent variations thereof are possible without departing from the spirit or scope of the present invention.

## Claims

1. A safe and effective immunological composition comprising:
a) a recombinant, non-naturally-occurring fusion polypeptide, comprising an NSP4, a VP4 and a VP6 porcine rotavirus C polypeptide; and
b) a pharmaceutically or veterinary acceptable vehicle, diluent or excipient;

wherein the composition is effective in eliciting in a porcine animal a protective immune response against a subsequent virulent rotavirus challenge;
wherein the polypeptide has at least 95% sequence identity to the sequence set forth in Seq. Id. No.: 95; and
wherein the NSP4 polypeptide has at least 90% identity to the sequence set forth in Seq. Id. No.: 18, the VP4 polypeptide has at least 90% identity to the sequence set forth in Seq. Id. No.: 42, and the VP4 polypeptide has at least 90% identity to the sequence set forth in Seq. Id. No.: 52.

2. The composition of claim 1 further comprising an adjuvant.

3. The composition of claim 2 wherein the adjuvant is an oil-in-water adjuvant.

4. A safe and effective immunological composition comprising:
a) a recombinant, non-naturally-occurring triple polypeptide, consisting essentially of a rotavirus C NSP4-VP4-VP6 triple fusion protein having the sequence set forth in SEQ ID NO:95; and
b) a pharmaceutically or veterinary acceptable vehicle, diluent or excipient;
c) an adjuvant comprising mineral oil and surfactants; and

wherein the composition is effective in eliciting in a porcine animal in need thereof a protective immune response that is protective against a subsequent virulent rotavirus challenge.

5. The composition of claim 4, further comprising at least one additional antigen associated with a pathogen other than rotavirus.

6. The composition of claim 5, wherein the at least one additional antigen elicits in a porcine an immune response against Mycoplasma hyopneumoniae (M. hyo), Porcine Circovirus Type 2 (PCV2), Porcine reproductive and respiratory syndrome virus (PRRSV), Swine influenza virus (SIV) or other pathogen capable of infecting and causing illness or susceptibility to illness in a porcine.

7. A method of vaccinating a procine animal, comprising administering to the animal at least one dose of the composition of claim 4.

8. The method of claim 7, wherein the porcine is a sow from about 3 weeks to about 6 weeks prefarrowing.

9. The method of 8, wherein the resulting piglets have a reduced morbidity and/or mortality as compared to piglets coming from unvaccinated sows.