Title of Invention

RECOMBINANT NEWCASTLE DISEASE VIRUS RNA EXPRESSION SYSTEMS AND VACCINES

Abstract The present invention relates to a recombinant RNA molecule comprising a binding site specific for an RNA polymerase of a Newcastle disease virus and signals required for NDV mediated replication and transcription, operatively linked to a heterologous RNA sequence, wherein the binding site specific for an RNA polymerase of a Newcastle disease virus and signals required for NDV mediated replication and transcription is contained in the 3' and 5' - noncoding flanking regions of the NDV viral RNA genome. The present invention also relates to a vaccine forumulation comprising a genetically engineered chimeric Newcastle disease virus containing the recombinant RNA molecule as described above.
Full Text

RECOMBINANT NEWCASTLE DISEASE VIRUS RNA EXPRESSION SYSTEMS AND VACCINES
This application is a continuation-in-part of application no. 09/152,845, filed September 14, 1998, incorporated herein by reference in its entirety.
1. INTRODUCTION
The present invention relates to recombinant Newcastle disease virus RNA templates vhich may be used to express heterologous gene products in appropriate host cell systems md'or to construct recombinant viruses that express, package, and/or present the icterologous gene product. The expression products and chimeric viruses may

advantageously be used in vaccine formulations. The present invention also relates to genetically engineered recombinant Newcastle disease viruses which contain modifications and/or mutations that make the recombinant virus suitable for use in vaccine formulations, such as an attenuated phenotype or enhanced immunogenicity.
The present invention relates to recombinant Newcastle disease viruses which induce interferon and related pathways. The present invention relates to the use of the recombinant Newcastle disease viruses and viral vectors against abroad range of pathogens and/or antigens, including tumor specific antigens. The invention is demonstrated by way of examples in which recombinant Newcastle disease virus RNA templates containing heterologous gene coding sequences in the negative-polarity were constructed. The invention further relates to the construction of recombinant Newcastle disease virus RNA* templates containing heterologous gene coding sequences in the positive-polarity. Such heterologous gene sequences include sequences derived from a human immunodeficiency virus (HIV).
2. BACKGROUND OF THE INVENTION
A number of DNA viruses have been genetically engineered to direct the expression of heterologous proteins in host cell systems'(e.g., vaccinia virus, baculovirus, etc.). Recently, similar advances have been made with positive-strand RNA viruses (e.g., poliovirus). The expression products of these constructs, Le., the heterologous gene product or the chimeric virus which expresses the heterologous gene product, are thought to be



tracts with the viral membrane, is first produced as an inactive precursor, then cleaved st-translationally to produce two disulfide linked polypeptides. The active F protein is /olved in penetration of NDV into host cells by facilitating fusion of the viral envelope th the host cell plasma membrane. The matrix protein (M), is involved with viral sembly, and interacts with both the viral membrane as well as the nucleocapsid proteins.
The main protein subunit of the nucleocapsid is the nucleocapsid protein (NP) which infers helical symmetry on the capsid. In association with the nucleocapsid are the P and L oteins. The phosphoprotein (P), which is subject to phosphorylation, is thought to play a gulatory role in transcription, and may also be involved in mcthylation, phosphorylation id polyadenylation. The L gene, which encodes an RNA-dependent RNA polymerase, is :quired for viral RNA synthesis together with the P protein. The L protein, which takes up early half of the coding capacity of the viral genome is the largest of the viral proteins, and lays an important role in both transcription and replication.
The replication of all negative-strand RNA viruses, including NDV, is complicated y (he absence of cellular machinery required to replicate RNA. Additionally, the negative-trand genome can not be translated directly into protein, but must first be transcribed into a iositive-strand (mRNA) copy. Therefore, upon entry into a host cell, the genomic RNA .lone cannot synthesize the required RNA-dependent RNA polymerase. The L, P and NP >rotcins must enter the cell along with the genome on infection.
It is hypothesized that most or all of the viral proteins that transcribe NDV mRNA ilso carry out their replication. The mechanism that regulates the alternative uses (Le., xanscription or replication) of the same complement of proteins has not been clearly identified but appears to involve the abundance of free forms of one or more of the nucleocapsid proteins, in particular, the NP. Directly following penetration of the virus, transcription is initiated by the L protein using the negative-sense RNA in the nucleocapsid as a template. Viral RNA synthesis is regulated such that it produces monocistronic mRNAs during transcription.
Following transcription, virus genome replication is the second essential event in infection by negative-strand RNA viruses. As with other negative-strand RNA viruses, virus genome replication in Newcastle disease virus (NDV) is mediated by virus-specified

oteins. The first products of replicative RNA synthesis are complementary copies (he., us-polarity) of NDV genome RNA (cRNA). These plus-stranded copies (anti-genomes) ffer from the plus-strand mRNA transcripts in the structure of their termini. Unlike the LRNA transcripts, the anti-genomic cRNAs are not capped and methylated at the 5' termini, id are not truncated and polyadenylated at the 3' termini. The cRNAs are coterminal with leir negative strand templates and contain all the genetic information in each genomic RNA jgment in the complementary form. The cRNAs serve as templates for the synthesis of 7DX negative-strand viral genomes (vRNAs).
Both the NDY negative strand genomes (vRNAs) and antigenomes (cRNAs) are ncapsidated by nucleocapsid proteins; the only unencapsidated RNA species are virus uRXAs. For NDV. the cytoplasm is the site of virus RNA replication, just as it is the site or transcription. Assembly of the viral components appears to take place at the host cell )lasma membrane and mature virus is released by budding.
2.2. ENGINEERING NEGATIVE STRAND RNA VIRUSES
The RNA-directed RNA polymerases of animal viruses have been extensively studied with regard to many aspects of protein structure and reaction conditions. However, the elements of the template RNA which promote optimal expression by the polymerase could only be studied by inference using existing viral RNA sequences. This promoter analysis is of interest since it is unknown how a viral polymerase recognizes specific viral RNAs from among the many host-encoded RNAs found in an infected cell.
Animal viruses containing plus-sense genome RNA can be replicated when plasmic derived RNA is introduced into cells by transfection (for example, Racaniello et al, 1981, Science 214:916-919; Levis, et al., 1986, Cell 44: 137-145). In the case of poliovirus, the purified polymerase will replicate a genome RNA in in vitro reactions and when this plus-sense RNA preparation is transfected into cells it is infectious (Kaplan, et al., 1985, Proc. Natl Acad. Sci. USA 82:8424-8428). However, the template elements which serve as transcription promoter for the poliovirus-encoded polymerase are unknown since even RN homopolymers can be copied (Ward, et ah, 19SS. J. Virol. 62: 558-562). SP6 transcripts have also been used to produce model defective interfering (DI) RNAs for the Sindbis vin


polymerase and packaging of the genome into virus particles were shown to be within 162 nucleotides (nt) of the 5' terminus and 19 nt of the 3' terminus of the genome (Levis, et al., 1986, Cell 44: 137-145). In the case of brome mosaic virus (BMV), a positive strand RNA plant virus, SP6 transcripts have been used to identify the promoter as a 134 nt tRNA-like 3' terminus (Dreher, and Hall, 1988, J. Mol. Biol. 201: 31-40). Polymerase recognition and synthesis were shown to be dependent on both sequence and secondary structural features (Dreher. et a!., 19S4. Nature 311: 171-175).
The negative-sense RNA viruses have been refractory to study of the sequence requirements of the replicase. The purified polymerase of vesicular stomatitis virus is only active in transcription when vims-derived ribonucleoprotein complexes fRNPs) are included as template (De and Banerjee, 1985, Biochem. Biophys. Res. Commun. 126: 40-49; Emerson and Yu, 1975, J. Virol. 15: 134S-1356; Naito and lshihama, 1976. J. Biol. Chem. 251: 4307-4314). With regard to influenza viruses, it was reported that naked RNA purified from virus was used to reconstitute RNPs. The viral nucleocapsid and polymerase proteins were gel-purified and renatured on the viral RNA using thioredoxin (Szewczyk, et al., 19S8, 'Proc. Natl. Acad. Sci. USA, 85: 7907-7911). However, these authors did not show that the activity of the preparation was specific for influenza viral RNA, nor did they analyze the signals which promote transcription.
Only recently has it been possible to recover negative strand RNA viruses using a recombinant reverse genetics approach (U.S. Patent No. 5,166,057 to Palese et al.). Although this method was originally applied to engineer influenza viral genomes (Luytjes et al. 1989, Cell 59: 1107-1113; Enami et al. 1990, Proc. Natl. Acad Sci. USA 92: 11563-11567), it has been successfully applied to a wide variety of segmented and nonsegmentcd negative strand RNA viruses, including rabies (Schnell et al. 1994, EMBO J. 13:4195-4203); respirator}' syncytial virus (Collins et al. 1991, Proc. Natl. Acad. Sci. USA 88:9663-9667); and Sendai virus (Park et al. 1991, Proc. Natl. Acad..Sci. USA 88:5537-5541; Kato et al., 1996, Genes Cells 1:569-579). However, this approach has yet to be applied to Newcastle disease virus RNA genomes.

3. SUMMARY OF THE INVENTION
Recombinant Newcastle disease viral RNA templates are described which may be ised with RNA-directed RNA polymerase to express heterologous gene products in appropriate host cells and/or to rescue the heterologous gene in virus particles. In one embodiment, the invention relates to recombinant Newcastle disease viruses which induce interferon and related pathways. The present invention relates to recombinant Newcastle disease viruses which contain modifications which result in phenotypes which make the recombinant virus more suitable for use in vaccine formulations, e.g., attenuated phenotypes and enhanced immunogenicity. In another embodiment, the present invention relates to engineering recombinant Newcastle disease viruses and viral vectors which contain heterologous genes including genes of other viruses, pathogens, cellular genes, tumor antigens etc.
In another embodiment, the present invention relates to engineering recombinant Newcastle disease viruses and viral vectors for the use as vaccines. The present invention relates to vaccine formulations suitable for administration to humans, as well as veterinary uses. The vaccines of the present invention may be designed for administration to domestic animals, including cats and dogs; wild animals, including foxes and racoons; livestock and fowl, including horses, cattle, sheep, turkeys and chickens.
In yet another embodiment, the invention relates to recombinant Newcastle disease viral vectors and viruses which are engineered to encode mutant Newcastle disease viral genes or to encode combinations of eenes from different strains of Newcastle disease virus. The RNA templates of the present are prepared by transcription of appropriate DNA sequences with a DNA-directed RNA polymerase. The resulting RNA templates are of the negative-polarity and contain appropriate terminal sequences which enable the viral RNA-synthesizing apparatus to recognize the template. Alternatively, positive-polarity RNA templates which contain appropriate terminal sequences which enable the viral RNA-synthesizing apparatus to recognize the template, may also be used. Expression from positive polarity RNA templates may be achieved by transfection of plasmids having promoters which are recognized by the DNA-dependent RNA polymerase. For example,

asmid DNA encloding positive RNA templates under the control of a T7 promoter can be ;ed in combination with the vaccinia virus T7 system. .
Bicistronic mRNAs can be constructed to permit internal initiation of translation of iral sequences and allow for the expression of foreign protein coding sequences from the :gular terminal initiation site, or vice versa. Alternatively, a foreign protein may be ^pressed from internal transcriptional unit in which the transcriptional unit has an initiation ite and polyadenylation site. In another embodiment, the foreign gene is inserted into an IDV gene such that the resulting expressed protein is a fusion protein.
The recombinant mutant Newcastle disease viral RNA templates of the present nvention may be used to transfect transformed cell lines that express the RNA dependent LNA-polymerase and allow for complementation. Alternatively, a plasmid expressing from in appropriate promoter, can be used for virus specific (chimeric) RNA transfection. Complementation may also be achieved with the use of a helper virus which provides the IN A dependent RNA-polymerase. Additionally, a non-virus dependent replication system ~or Newcastle disease virus is also described. The minimum subset of Newcastle disease v'irus proteins needed for specific replication and expression of the virus are the three proteins, L, P and NP, which can be expressed from plasmids by a vaccinia virus T7 system. In yet another embodiment, when plasmids encoding the antigenomic copy of the NDV genome are used to supply the viral genome, the minimum subset of Newcastle disease virus proteins needed for specific replication and expression of the virus are the L and P proteins. When the antigenomic copy of the NDV genome is transcribed, th NP polymerase protein is the first protein transcribed, thus it is not necessary to additionally provide the NP polymerase in trans.
The expression products and/or chimeric virions obtained may advantageously be utilized in vaccine formulations. The expression products and chimeric virions of the present invention may be engineered to create vaccines against a broad range of pathogens, including viral antigens, tumor antigens and auto antigens involved in autoimmune disorders. In particular, the chimeric virions of the present invention may be engineered to create anti-HIV vaccines, wherein an immunogenic polypeptide from gpl60, and/or from internal proteins of HIV is engineered into the glycoprotein HN protein to construct a

vaccine that is able to elicit both vertebrate humoral and cell-mediated immune responses. The use of recombinant Newcastle disease virus for this purpose is especially attractive since Newcastle disease virus is not pathogenic in humans. The use of recombinant Newcastle disease virus for delivering tumor antigens is particularly attractive given the known antineoplastic and immunopotentiating properties of the virus.
3.1. DEFINITIONS
As used herein, the following terms will have the meanings indicated:
cRNA ~ anti-genomic RNA
HIV = human immunodefiency virus
L - large protein
M = matrix protein (lines inside of envelope)
MDCK - Madin Darby canine kidney cells
MDBK = Madin Darby bovine kidney cells
*
moi = multiplicity of infection NA = neuraminidase (envelope glycoprotein) NDV = Newcastle disease Virus
NT = nucleoprotein (associated with RNA and required for polymerase activity) NS = nonstructural protein (function unknown) nt = nucleotide
PA, PB1, PB2 = RNA-directed RNA polymerase components RNP = ribonucleoprotein rRNP = recombinant RNP vRNA = genomic virus RNA WSN = influenza A/WSN/33 via
WSN-HK virus: reassortment virus containing seven genes from WSN virus
and the NA gene from influenza A/HK/8/68 virus

4. DESCRIPTION OF THE FIGURES
FIG. 1- Schematic representation of the NDV minigenome. Top illustration depicts Lhe PNDVCAT plasmid including the T7 promoter; the 5' terminal sequence (5* end of genomic RNA, 191 nt); the inserted nucleotides (CTTAA); 667nt of CAT ORF; the 3' terminal sequence (3' end of genomic RNA, 121 nt) the Bbsl and nuclease sites. Lower illustration depicts the chimeric NDV-CAT RNA resulting from in vitro transcription. As a result of the NDV-based amplification and transcription of the NDV-CAT chimeric minigenome, CAT activity is detected in the transfected cells.
FIG. 2A-C. Schematic representation of the PTMI expression vectors. PTM1-NP encodes the ND\' NP protein. PTM1-P encodes the NDV P protein. PTM1 -L encodes the NDV L protein.
FIG. 3. RNA sequence of NDV 5' and 3' non-coding terminal regions (plus-sense). Sequences 5' to the CAT gene represent 121 nt of the 5' non-coding terminal region of NDV plus sense genome comprising 65nt of the leader sequence (in bold) followed by 56nt of the NT gene UTR. Sequences 3' to the CAT gene represent inserted nucleotides cuuaa (in lower case; and 191m of the non-coding terminal region of NDV plus sense genome comprising 127m of the UTR of the L gene followed by 64nt of the trailer region (in bold).
FIG. 4A-B Schematic representation of a structure of recombinant NDV clones. FIG 4Bf representation of infectious NDV expressing HIV Env and Gag. Top panel, HIV Env and Gag are between the M and L genes. Lower panel HIV Env and Gag are 3' to the NP gene.
FIG. 5 Schematic representation of the 3' and 5' termini of NDV as aligned with sequence of Kurilla et al. 1985 Virology 145:203-212 (3f termini) and Yusoff et al. 1987 Nucleic Acids Research 15:3961-3976 (51 termini)

FIG. 6 Plasmid-based reverse genetics method for NDV-based expression of a foreign gene. Cells are infected with a recombinant vaccinia virus expressing T7 polymerase. In addition, cells are transfected with 1) plasmid DNAs encoding the L, NP and P proteins of NDV under the transcriptional control of a T7 promoter (pTMl-L, pTMl-NP and pTMl-P, respectively) and 2) a plasmid DNA encoding a chimeric NDV-CAT minigenome under the transcriptional control of a T7 promoter (pT7-NDV-CAT-RB). The proper 3* end of the NDV-CAT minigenome is achieved by relying on the cleavage facilitated via a ribozyme sequence (RB). Amplification and transcription of the NDV-CAT chimeric minigenome results in CAT activity detectable in the transfected cells. The noncoding regions at the 3' and 5' ends of the NDV-CAT minigenome are represented as
*
black boxes.
FIG. 7 Rescue of NDV from synthetic DNA. Cells are infected with a recombinant vaccinia virus expressing T7 polymerase. In addition, cells are transfected with 1) plasmid DNAs encoding the L, NP and P proteins of NDV under the transcriptional control of a T7 promoter (pTM 1 -L, pTM 1 -NP and pTM 1 -P, respectively) and 2) a plasmid DNA encoding the NDV antigenome under the transcriptional control of a T7 promoter (pT7-NDV+-RB). The proper 3' end of the NDV antigenome is achieved by relying on the cleavage facilitated via a ribozyme sequence (RB). Amplification and transcription of the NDV antigenome results in the rescue of infectious NDV viruses. The noncodine regions at the 3' and 5' ends of the NDV antigenome are represented as black boxes.
FIG. 8 NDV-based expression of a foreign gene inserted as an internal transcriptional unit into the NDV antigenome. Cells are infected with a recombinant vaccinia virus expressing T7 polymerase. In addition, cells are transfected with 1) plasmid DNAs encoding the L, NP and P proteins of NDV under the transcriptional control of a T7 promoter (pTMl-L, pTMl-NP and pTMl-P, respectively) and 2) a plasmid DNA encoding a chimeric NDV-CAT antigenome under the transcriptional control of a T7 promoter (pT7-NDV-CAT-RB). In the chimeric NDV-CAT antigenome, the CAT open reading frame substitutes the naturally occurring HN open reading frame of the wild-type NDV

antigenome. The proper 3' end of the chimeric NDV-CAT antigenome is achieved by relying on the cleavage facilitated via a ribozyme sequence (RB). Amplification and transcription of the chimeric NDV-CAT antigenome results in CAT activity detectable in the transfected cells. The noncoding regions at the 3' and 5' ends of the chimeric NDV-CAT antigenome are represented as black boxes.
5. DESCRIPTION OF THE INVENTION
This invention relates to genetically engineered Newcastle disease viruses and viral vectors which express heterologous genes or mutated Newcastle disease viral genes or a combination of viral genes derived from different strains of Newcastle disease virus. The invention relates to the construction and use of recombinant negative strand NDV viral RNA templates which may be used with viral RNA-directed RNA polymerase to express heterologous gene products in appropriate host cells and/or to rescue the heterologous gene in virus particles. In a specific embodiment of the invention, the heterologous gene product is a peptide or protein derived from the genome of a human immunodeficiency virus. The RNA templates of the present invention may be prepared either in vitro or in vivo by transcription of appropriate DNA sequences using a DNA-directed RNA polymerase such as bacteriophage T7, T3, the SP6 polymerase or a eukaryotic polymerase such as polymerase I.
The recombinant RNA templates may be used to transfect continuous/transfected cell lines that express the RNA-directed RNA polymerase proteins allowing for complementation, as demonstrated by way of working examples in which RNA transcripts of cloned DNA containing the coding region.- in negative sense orientation - of the chloramphenicol acetyltransferase (CAT) gene, flanked by the 5' terminal and the 3' terminal nucleotides of the NDV-CL (California strain/11914/1944-like strain) (Meindl et al., 1974 Virology 58: 457-463) RNA were transfected into cells expressing the NDV polymerase proteins. In a preferred embodiment, a non-virus dependent replication system is used to recover chimeric NDV, in which plasmid DNA encoding the NDV genome or antigenome is coexpressed with plasmid DNA encoding the minimum subset of Newcastle disease virus proteins needed for specific replication and expression of the virus, as demonstrated by way of working example as described infra.

The ability to reconstitute NDV in vivo allows the design of novel chimeric NDV viruses which express foreign genes or which express mutant NDV genes. The ability to reconstitute NDV m vivo also allows the design of novel chimeric NDVs which express genes from different strains of NDV. One way to achieve this goal involves modifying existing NDV genes. For example, the HN gene may be modified to contain foreign sequences in its external domains. Where the heterologous sequence are epitopes or antigens of pathogens, these chimeric viruses may be used to induce a protective immune response against the disease agent from which these determinants are derived.
In accordance with the present invention, a chimeric RNA is constructed in which a coding sequence derived from the gpl60 coding region of human immunodeficiency virus is inserted into the HN coding sequence of NDV, and chimeric virus produced from transfection of this chimeric RNA segment into a host cell infected with wild-type NDV. Further, such a chimeric virus should be capable of eliciting both a vertebrate humoral and cell-mediated immune response. The present invention further relates to the induction of interferon and related pathways by recombinant or chimeric NDV viruses.
The present invention relates to the use of viral vectors and chimeric viruses of the invention to formulate vaccines against a broad range of viruses and/or antigens including tumor antigens. The viral vectors and chimeric viruses of the present invention may be used to modulate a subject's immune system by stimulating a humoral immune response, a cellular immune response or by stimulating tolerance to an antigen. As used herein, a
*
subject means: humans, primates, horses, cows, sheep, pigs, goats, dogs, cats, avian species and rodents. When delivering, tumor antigens, the invention may be used to treat subjects having disease amenable to immunity mediated rejection, such as non-solid tumors or solid tumors of small size. It is also contemplated that delivery of tumor antigens by the viral vectors and chimeric viruses described herein will be useful for treatment subsequent to removal of large solid tumors. The invention may also be used to treat subjects who are suspected of having cancer.
The invention may be'divided into the following stages solely for the purpose of description and not by way of limitation: (a) construction of recombinant RNA templates; (b) expression of heterologous gene products using the recombinant RNA templates; and (c)

rescue of the heterologous gene in recombinant virus particles. For clarity of discussion, the invention is described in the working Examples using NDV-CL (California strain/11914/1944-like strain), however any strain of NDV may be utilized.
5.1. CONSTRUCTION OF THE RECOMBINANT RNA TEMPLATES
A specific embodiment of the present invention is the Applicants' identification of the correct nucleotide sequence of the 5' and 3' termini of the negative-sense genomes RNA of NDV. The nucleotide sequence of the 5' and 3' termini of the NDV negative-sense genome RNA of the present invention differs significantly from the NDV 3' termini sequence previously disclosed as shown in Figure 5. The identification of the correct nucleotide sequence of the NDV 5' and 3' termini allows for the first time the engineering of recombinant NDV RNA templates, the expression of the recombinant RNA templates and the rescue of recombinant NDV particles. The present invention encompasses not only 5' and 3' termini having the nucleotide sequence as shown in Figure 5, but also encompasses any modifications or mutations to the termini or any fragments thereof,that still retain the function of the wildtype termini, i.e., the signals required for the viral RNA-synthesizing apparatus to recognize the template.
Heterologous gene coding sequences flanked by the complement of the viral polymerase binding site/promoter, e^g, the complement of 3'-NDV virus terminus of the present invention, or the complements of both the 3'- and 5'-NDV virus termini may be constructed using techniques known in the art. The resulting RNA templates may be of the negative-polarity and contain appropriate terminal sequences which enable the viral RNA-synthesizing apparatus to recognize the template. Alternatively, positive-polarity RNA templates which contain appropriate terminal sequences which enable the viral RNA-synthesizing apparatus to recognize the template, may also be used. Recombinant DNA molecules containing these hybrid sequences can be cloned and transcribed by a DNA-directed RNA polymerase, such as bacteriophage T7, T3, the SPG polymerase or eukaryotic
polymerase such as polymerase I and the like, to produce in vitro or in vivo the recombinant
*
RNA templates which possess the appropriate viral sequences that allow for viral polymerase recognition and activity.

In yet another embodiment, virtually any heterologous sequence may be constructed uo the chimeric viruses of the present invention, including but not limited to antigens, such s 1) antigens that are characteristic of a pathogen; 2) antigens that are characteristic of utoimmune disease; 3) antigens that are characteristic of an allergen; and 4) antigens that re characteristic of a tumor. For example, heterologous gene sequences that can be ngineered into the chimeric viruses of the invention include, but are not limited to, epitopes f human immunodeficiency virus (HIV) such as gpl60; hepatitis B virus surface antigen HBsAg); the glycoproteins of herpes virus (e.g., gD, gE); VPl of poliovirus; and antigenic eterminants of nonviral pathogens such as bacteria and parasites to name but a few.
Antigens that are characteristic of autoimmune disease typically will be derived from ae cell surface, cytoplasm, nucleus, mitochondria and the like of mammalian tissues, ricluding antigens characteristic of diabetes mellitus, multiple sclerosis, systemic lupus rvTiuinjiosus, rheumatoid arthritis, pernicious anemia. Addison's disease, scleroderma. .utoimmune atrophic gastritis, juvenile diabetes, and discoid lupus erythromatosus. Antigens that are allergens are generally proteins or glycoproteins, including mtigens derived from pollens, dust, molds, spores, dander, insects and foods.
Antigens that are characteristic of tumor antigens typically will be derived from the :eii v...r;ace, cytoplasm, nucleus, organelles and the like of cells of tumor tissue. Examples ncliui: antigens characteristic of tumor proteins, including proteins encoded by mutated Micogoses; viral proteins associated with tumors; and glycoproteins. Tumors include, but ire not limited to, those derived from the types of cancer: lip, nasopharynx, pharynx and oral :avit\\ esophagus, stomach, colon, rectum, liver, gall bladder, pancreas, larynx, lung and Dronchus, melanoma of skin, breast, cervix, uterine, ovary, bladder, kidney, uterus, brain and Dther parts of the nervous system, thyroid, prostate, testes, Hodgkin's disease, non-Hodgkin's lymphoma, multiple myeloma and leukemia.
In one specific embodiment of the invention, the heterologous sequences are derived from the genome of human immunodeficiency virus (HIV), preferably human immunodeficiency virus-1 or human immunodeficiency virus-2. In another embodiment of the invention, the heterologous coding sequences may be inserted within an NOV gene coding sequence such that a chimeric gene product is expressed which contains the

heterologous peptide sequence within the NDV viral protein. In such an embodiment of the invention, the heterologous sequences may also be derived from the genome of a human immunodeficiency virus, preferably of human immunodeficiency virus-1 or human immunodeficiency virus-2.
In instances whereby the heterologous sequences are HIV-derived, such sequences may include, but are not limited to sequences derived from the env gene (i.e., sequences encoding all or part of gpl60, gpl20, and/or gp41), the pol gene (i.e., sequences encoding all or part of reverse transcriptase, endonuclease, protease, and/or integrase), the gag gene (i.e.. sequences encoding all or part of p7, p6, p55, pi 7/1S, p24/25) tat, rev, nef, vif, vpu, vpr, and/or vpx.
In vet another embodiment, heterologous eene sequences that can be eneineered into the chimeric viruses include those that encode proteins with immunopotentiating activities. Examples of immunopotentiating proteins include, but are not limited to, cytokines, interferon type 1. gamma interferon, colony stimulating factors, interleukin -1. -2, -4, -5. -6, -12.
One approach for constructing these hybrid molecules is to insert the heterologous coding sequence into a DNA complement of an NDV gene so that the heterologous sequence is flanked by the viral sequences required for viral polymerase activity; Le., the viral polymerase binding site/promoter, hereinafter referred to as the viral polymerase binding site, and a polyadenylation site. In a preferred embodiment, the heterologous coding

sequence is flanked by the viral sequences that comprise the replication promoters of the 5' and 3' termini, the gene start and gene end sequences, and the packaging signals that are found in the 5' and/or the 3' termini. In an alternative approach, oligonucleotides encoding the viral polymerase binding site, e^g., the complement of the S'-terminus or both termini of the virus genomic segments can be ligated to the heterologous coding sequence to construct the hybrid molecule. The placement of a foreign gene or segment of a foreign gene within a target sequence was formerly dictated by the presence of appropriate restriction enzyme sites within the target sequence. However, recent advances in molecular biology have lessened this problem greatly. Restriction enzyme sites can readily be placed anywhere within a target sequence through the use of site-directed mutagenesis (e^g., see, for example, the

techniques described by Kunkel, 19S5, Proc. Natl..Acad. Sci. U.S.A. 82;488). Variations in polymerase chain reaction (PCR) technology, described infra, also allow for the specific insertion of sequences (he., restriction enzyme sites) and allow for the facile construction of hybrid molecules. Alternatively, PCR reactions could be used to prepare recombinant templates without the need of cloning. For example, PCR reactions could be used to prepare double-stranded DNA molecules containing a DNA-directed RNA polymerase promoter (e.g., bacteriophase T3, T7 or SP6) and the hybrid sequence containing the heterologous gene and the NDV polymerase binding site. RNA templates could then be transcribed directlv from this recombinant DNA. In vet another embodiment, the recombinant RNA templates may be prepared by Iigating RNAs specifying the negative polarity of the heterologous gene and the viral polymerase binding site using an RNA ligase. Sequence requirements for viral polymerase activity and constructs which may be used in accordance with the invention are described in the subsections below.
5.1.1. INSERTION OF THE HETEROLOGOUS GENE
SEQUENCE INTO THE HN, P. NP, M, F, L GENES
The gene segments coding for the HN, P, NP, M, F, or L proteins may be used for
the insertion of heterologous gene products. Insertion of a foreign gene sequence into any of
these segments could be accomplished by either a complete replacement of the viral coding
region with the foreign gene or by a partial replacement. Complete replacement would
probably best be accomplished through the use of PCR-directed mutagenesis. Briefly, PCR-
primer A would contain, from the 5' to 3!end: a unique restriction enzyme site, such as a
class IIS restriction enzyme site (Le., a "shifter" enzyme; that recognizes a specific sequence
but cleaves the DNA either upstream or downstream of that sequence); a stretch of
nucleotides complementary to a region of the NDV gene; and a stretch of nucleotides
complementary to the carboxy-terminus coding portion of the foreign gene product. PCR-
primer B would contain from the 5' to 3' end: a unique restriction enzyme site; a stretch of
nucleotides complementary to a NDV gene; and a stretch of nucleotides corresponding to the
5' coding portion of the foreign gene. After a PCR reaction using these primers with a
cloned copy of the foreign gene, the product may be excised and cloned using the unique
restriction sites. Digestion with the class IIS enzyme and transcription with the purified

phage polymerase would generate an RNA molecule containing the exact untranslated ends of the NDV'gene with a foreign gene insertion. In an alternate embodiment, PCR-primed reactions could be used to prepare double-stranded DNA containing the bacteriophage promoter sequence, and the hybrid gene sequence so that RNA templates can be transcribed directly without cloning.
5.1.2. INSERTION OF THE HETEROLOGOUS GENE SEQUENCE INTO THE HN GENE
The hemagglutinin and neuraminidase activities of NDV are coded for by a single gene, I IN. The HN protein is a major surface glycoprotein of the virus. For a variety of viruses, such as influenza, the hemagglutinin and neuraminidase proteins have been demonstrated to contain a number of antigenic sites. Consequently, this protein is a potential target for the humoral immune response after infection. Therefore, substitution of antigenic sites within PFN with a portion of a foreign protein may provide for a vigorous humorai response against this foreign peptide. If a sequence is inserted within the HN molecule and it is expressed on the outside surface of the HN it will be immunogenic. For example, a peptide derived from gpl60 of HIV could replace an antigenic site of the HN protein, resulting in the elicitation of both a humoral immune response. In a different approach, the foreign peptide sequence may be inserted within the antigenic site without deleting any viral sequences. Expression products of such constructs may be useful in vaccines against the foreign antigen, and may indeed circumvent a problem discussed earlier, that of propagation of the recombinant virus in the vaccinated host. An intact HN molecule with a substitution only in antigenic sites may allow for HN function and thus allow for the construction of a viable virus. Therefore, this virus can be grown without the need for additional helper functions. The virus may also be attenuated in other ways to avoi-d any danger of accidental'escape.
Other hybrid constructions may be made to express proteins on the cell surface or enable them to be released from the cell. As a surface glycoprotein, the HN has an amino-terminal cleavable signal sequence necessary for transport to the cell surface, and a carboxy-terminal sequence necessary for membrane anchoring. In order to express an intact foreign protein on the cell surface it may be necessary to use these HN signals to create a hybrid

protein. In this case, the fusion protein may be expressed as a separate fusion protein from an additional internal promoter. Alternatively, if only the transport signals are present and the membrane anchoring domain is absent, the protein may be secreted out of the cell.
5.1.3. CONSTRUCTION OF BICISTRONIC RNA AND HETEROLOGOUS
PROTEIN EXPRESSION __
Bicistronic mRNA could be constructed to permit internal initiation of translation of viral sequences and allow for the expression of foreign protein coding sequences from the regular terminal initiation site. Alternatively, a bicistronic mRNA sequence may be constructed wherein the viral sequence is translated from the regular terminal open reading frame, while the foreign sequence is initiated from an internal site. Certain internal ribosome entry site (IRES) sequences may be utilized. The IRES sequences which are :hosen should be short enough to not interfere with Newcastle disease virus packaging [imitations. Thus, it is preferable that the IRES chosen for such a bicistronic approach be no :nore than 500 nucleotides in length, with less than 250 nucleotides being preferred. Further, it is preferable that the IRES utilized not share sequence or structural homology ■vith picornaviral elements. Preferred IRES elements include, but are not limited to the mammalian BiP IRES and the hepatitis C virus IRES.
Alternatively, a foreign protein may be expressed from a new internal transcriptional mit in which the transcriptional unit has an initiation site and polyadenylation site. In mother embodiment, the foreism eene is inserted into an NDV sene such that the resulting expressed protein is a fusion protein.
5.2. EXPRESSION OF HETEROLOGOUS GENE
PRODUCTS USING RECOMBINANT RNA TEMPLATE
The recombinant templates prepared as described above can be used in a variety of
»
vays to express the heterologous gene products in appropriate host cells or to create :himeric viruses that express the heterologous gene products. In one embodiment, the ecombinant template can be used to transfect appropriate host cells, may direct the expression of the heterologous gene product at high levels. Host cell systems which provide

for high levels of expression include continuous cell lines that supply viral functions such as cell lines superinfected with NDV, cell lines engineered to complement NDV functions, etc.
In an alternate embodiment of the invention, the recombinant templates may be used to transfect cell lines that express a viral polymerase protein in order to achieve expression of the heterologous gene product. To this end, transformed cell lines that express a polymerase protein such as the L protein may be utilized as appropriate host cells. Host cells may be similarly engineered to provide other viral functions or additional functions such as NP or HN.
In another embodiment, a helper virus may provide the RNA polymerase protein utilized by the cells in order to achieve expression of the heterologous gene product.
In yet another embodiment, cells may be transfected with vectors encoding viral proteins such as the NP, P and L proteins. Examples of such vectors are illustrated in FIG 2A-2C.
5.3. PREPARATION OF CHIMERIC NEGATIVE
STRAND RNA VIRUS
In order to prepare chimeric virus, modified NDV virus RNAs, cDNAs or RNA coding for the NDV genome and/or foreign proteins in the plus or minus sense may be used to transfect cells which provide viral proteins and functions required for replication and rescue or are also infected with a "parent" NDV virus. In an alternative approach, plasmids encoding the genomic or antigenomic NDV RNA, either wild type or modified, may be co-transfected into host cells with plasmids encoding viral polymerase proteins, e^g., NP, P or L. In another embodiment, plasmids encoding the antigenomic NDV RNA may be co-transfected with plasmids encoding viral polymerase proteins P and L, as the NP polymerase protein is the first protein transcribed by the antigenomic copy of the NDV genome, it is not necessary to additionally provide the NP polymerase in trans.
In an embodiment of the present invention, the reverse genetics technique may be utilized to engineer the chimeric negative strand RNA virus, this technique involves the preparation of synthetic recombinant viral RNAs that contain the non-coding regions of the negative strand virus RNA which are essential for the recognition by viral polymerases and for packaging signals necessary to generate a mature virion. The synthetic recombinant

plasmid DNAs and RNAs can be replicated and rescued into infectious virus particles by any number of techniques known in the art, as described in U.S. Patent No. 5,166,057 issued November 24, 1992; in U.S. Patent No. 5,854,037 issued December 29, 1998; in European Patent Publication EP 0702085A1, published February 20, 1996; in U.S. Patent Application Serial No. 09/152,845; in International Patent Publications PCT WO97/12032 published April 3, 1997; W096/34625 published November 7, 1996; in European Patent Publication EP-A780475; WO 99/02657 published January 21, 1999; WO 98/53078 published November 26, 1998; WO 98/02530 published January 22, 1998; WO 99/15672 published April 1, 1999; WO 9S/13501 published April 2, 1998; WO 97/06270 published February 20, 1997; and EPO 7S0 47SA1 published June 25, 1997, each of which is incorporated by reference herein in its entirety.
There are a number of different approaches which may be used to apply the reverse genetics approach to rescue negative strand RNA viruses. First, the recombinant RNAs are synthesized from a recombinant DNA template and reconstituted in vitro with purified viral polymerase complex to form recombinant ribonucleoprotcins (RNPs) which can be used to transfect cells. In another approach, a more efficient transfection is achieved if the viral polymerase proteins are present during transcription of the synthetic RNAs either in vitro or in vivo. With this approach the synthetic RNAs may be transcribed from cDNA plasmids which are either co-transcribed in vitro with cDNA plasmids encoding the polymerase proteins, or transcribed in vivo in the presence of polymerase proteins, Le., in cells which transiently or constitutively express the polymerase proteins.
In an alternate embodiment, a combination of reverse genetics techniques and reassortant techniques can be used to engineer attenuated viruses having the desired epitopes in segmented RNA viruses. For example, an attenuated virus (generated by natural selection, mutagenesis or by reverse genetics techniques) and a strain carrying the desired vaccine epitope (generated by natural selection, mutagenesis or by reverse genetics techniques) can be co-infected in hosts that permit reassortment of the segmented genomes. Reassortants that display both the attenuated phenotype and the desired epitope can then be selected.

Following reassortment, the novel viruses may be isolated and their genomes identified through hybridization analysis. In additional approaches described herein, the production of infectious chimeric virus may be replicated in host cell systems that express an NDV viral polymerase protein (e.g., in virus/host cell expression systems; transformed cell lines engineered to express a polymerase protein, etc.), so that infectious chimeric virus are rescued. In this instance, helper virus need not be utilized since this function is provided by the viral polymerase proteins expressed.
In accordance with the present invention, any technique known to those of skill in the art may be used to achieve replication and rescue of chimeric viruses. One approach involves supplying viral proteins and functions required for replication in vitro prior to transfectjng host cells. In such an embodiment, viral proteins may be supplied in the form of wildtype virus, helper virus, purified viral proteins or recombinantly expressed viral proteins. The viral proteins may be supplied prior to, during or post transcription of the svnthetic cDNAs or RNAs encoding the chimeric virus. The entire mixture may be used to transfect host celjs. In another approach, viral proteins and functions required for replication may be supplied prior to or during transcription of the synthetic cDNAs or RNAs encoding the chimeric virus. In such an embodiment, viral proteins and functions required for replication are supplied in the form of wildtype virus, helper virus, viral extracts, synthetic cDNAs or RNAs which express the viral proteins are introduced into the host cell via infection or transfection. This infection/transfection takes place prior to or simultaneous to the introduction of the synthetic cDNAs or RNAs encoding the chimeric virus.
In a particularly desirable approach, cells engineered to express all NDV viral genes may result in the production of infectious chimeric virus which contain the desired genotype; thus eliminating the need for a selection system. Theoretically, one can replace any one of the six genes or part of any one of the six genes of NDV with a foreign sequence. However, a necessary part of this equation is the ability to propagate the defective virus (defective because a normal viral gene product is missing or altered). A number of possible approaches exist to circumvent this problem. In one approach a virus having a mutant protein can be grown in cell lines which are constructed to constitutively express the wild type version of the same protein. By this way, the cell line complements the mutation in the

virus. Similar techniques may be used to construct transformed cell lines that constitutively express any of the NDV genes. These cell lines which are made to express the viral protein may be used to complement the defect in the recombinant virus and thereby propagate it. Alternatively, certain natural host range systems may be available to propagate recombinant virus.
In yet another embodiment, viral proteins and functions required for replication may be supplied as genetic material in the form of synthetic cDNAs or RNAs so that they are co-transcribed with the synthetic cDNAs or RNAs encoding the chimeric virus. In a particularly desirable approach, plasmids which express the chimeric virus and the viral polymerase and/or other viral functions are co-transfected into host cells, as described in the Examples, see Section 11 supra.
Another approach to propagating the recombinant virus may involve co-cultivation with wild-type virus. This could be done by simply taking recombinant virus and co-infecting cells with this and another wild-type virus (preferably a vaccine strain). The wild-type virus should complement for the defective virus gene product and allow growth of both the wild-type and recombinant virus. Alternatively, a helper virus may be used to support propagation of the recombinant virus.
In another approach, synthetic templates may be replicated in cells co-infected with recombinant viruses that express the NDV virus polymerase protein. In fact, this method may be used to rescue recombinant infectious virus in accordance with the invention. To
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this end, the NDV polymerase protein may be expressed in any expression vector/host cell system, including but not limited to viral expression vectors (e.g., vaccinia virus, adenovirus, baculovirus, etc.) or cell lines that express a polymerase protein (e.g., see Krystal et ah, 1986, Proc. Natl. Acad. Sci. USA S3: 2709-2713). Moreover, infection of host cells expressing all six NDV proteins may result in the production of infectious chimeric virus particles. This system would eliminate the need for a selection system, as all recombinant virus produced would be of the desired genotype. It should be noted that it
may be possible to construct a recombinant virus without altering virus viability. These
*
altered viruses would then be growth competent and would not need helper functions to replicate.

5.4. VACCINE FORMULATIONS USING
THE CHIMERIC VIRUSES
The invention encompasses vaccine formulations comprising the engineered negative strand RNA virus of the present invention. The invention encompasses the use of recombinant NDV viruses which have been modified in vaccine formulations to confer L protection against NDV infection. In yet another embodiment, the recombinant NDV viruses of the present invention may be used as a vehicle to express foreign epitopes that . induce a protective response to any of a variety of pathogens.
The invention encompasses vaccine formulations to be administered to humans and animals. In particular, the invention encompasses vaccine formulations to be administered to domestic animals, including dogs and cats; wild animals, including foxes and racoons; and livestock, including cattle, horses, and pigs, sheep and goats; and fowl, including chicken and turkey.
The invention encompasses vaccine formulations which are useful against avian disease causing agents including NDV, Marek's Disease Virus (MDV), Infectious Bursal Disease Virus (IBDV), Infectious Bronchitis Virus (IBV), Infectious Bursitis Virus, Chicken Anemia Virus (CAV), Infectious Laryngotracheitis Virus (ILV), Avian Leukosis Virus (ALV). Rcticuloendotheliosis Virus (RV) and Avian Influenza Virus.
In another embodiment, the invention encompasses vaccine formulations which are useful against domestic disease causing agents including rabies virus, feline leukemia virus (FLV) and canine distemper virus. In yet another embodiment, the invention encompasses vaccine formulations which are useful to protect livestock against vesicular stomatitis virus, rabies virus, rinderpest virus, swinepox virus, and further, to protect wild animals against rabies virus.
Attenuated viruses generated by the reverse genetics approach can be used in the vaccine and pharmaceutical formulations described herein. Reverse genetics techniques can also be used to engineer additional mutations to other viral genes important for vaccine production — iLe.., the epitopes of useful vaccine strain variants can be engineered into the attenuated virus. Alternatively, completely foreign epitopes, including antigens derived from other viral or non-viral pathogens can be engineered into the attenuated strain. For

example, antigens of non-related viruses such as HIV (gpl60, gpl20, gp41) parasite antigens (e.g.., malaria), bacterial or fungal antigens or tumor.antigens can be engineered into the attenuated strain. Alternatively, epitopes which alter the tropism of the virus in vivo can be engineered into the chimeric attenuated viruses of the invention.
Virtually any heterologous gene sequence may be constructed into the chimeric viruses of the invention for use in vaccines. Preferably, epitopes that induce a protective immune response to any of a variety of pathogens, or antigens that bind neutralizing antibodies may be expressed by or as part of the chimeric viruses. For example, heterologous gene sequences that can be constructed into the chimeric viruses of the invention include, but are not limited to influenza glycoproteins, in particular, hemagglutinin H5, H.7, Marek's Disease Viral epitopes; epitopes of Infectious Bursal Disease Virus (IBDV), Infectious Bronchitis Virus (IBV), Chicken Anemia Virus (CAV), Infectious Laryngotracheitis Virus (ILV), Avian Leukosis Virus (ALV), Reticuloendothcliosis Virus (RV). Avian Influenza Virus (AIV), rabies virus, feline leukemia virus, canine distemper virus, vesicular stomatitis virus, rinderpest virus, and swinepox virus (see Fields et al. (ed.), 1991, Fundamental Virology, Second Edition, Raven Press, New York, incorporated by reference herein in its entirety).
In yet another embodiment, heterologous gene sequences that can be engineered into the chimeric viruses include those that encode proteins with immunopotentiating activities. Examples of immunopotentiating proteins include, but are not limited to, cytokines,
#
interferon type 1, gamma interferon, colony stimulating factors, interleukin -1,-2, -4, -5, -6, -12.
In addition, heterologous gene sequences that can be constructed into the chimeric viruses of the invention for use in vaccines include but are not limited to sequences derived from a human immunodeficiency virus (HIV), preferably type 1 or type 2. In a preferred embodiment, an immunogenic HIV-derived peptide which may be the source of an antigen may be constructed into a chimeric NDV that may then be used to elicit a vertebrate immune
response. Such HIV-derived peptides may include, but are not limited to sequences derived
*
from the env gene (i.e., sequences encoding all or part of gpl60, gpl20, and/or gp41), the pol gene (i.e., sequences encoding all or part of reverse transcriptase, endonuclease,

protease, and/or integrase), the gag gene (i.e., sequences encoding all or part of p7, p6, p55, pi7/18, p24/25), tat, rev, nef, vif, vpu, vpr, and/or vpx.
Other heterologous sequences may be derived from hepatitis B virus surface antigen (HBsAg); hepatitis A or C virus surface antigens, the glycoproteins of Epstein Barr virus; the glycoproteins of human papillomavirus; the glycoproteins of respiratory syncytial virus, parainfluenza virus, Sendai virus, simianvims 5 or mumps virus; the glycoproteins of influenza virus; the glycoproteins of herpes virus (e.g. gD, gE); VP1 of poliovirus; antigenic determinants of non-viral pathogens such as bacteria and parasites, to name but a few. In another embodiment, all or portions of immunoglobulin genes may be expressed. For example, variable regions of anti-idiotypic immunoglobulins that mimic such epitopes may be constructed into the chimeric vjruses of the invention.
Other heterologous sequences may be derived from tumor antigens, and the resulting chimeric viruses be used to generate an immune response against the tumor cells leading to tumor regression in vivo. These vaccines may be used in combination with other therapeutic regimens, including but not limited to chemotherapy, radiation therapy, surgery, bone marrow transplantation, etc. for the treatment of tumors. In accordance with the present invention, recombinant viruses may be engineered to express tumor-associated antigens (TAAs), including but not limited to, human tumor antigens recognized by T cells (Robbins and Kawakami, 1996, Curr. Opin. Immunol. S:62S-636, incorporated herein by reference in its entirety), melanocyte lineage proteins, including gplOO, MART-1/MelanA, TRP-1 (gp75), tyrosinase; Tumor-specific widely shared antigens, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-1, N-acetylglucosaminyltransferase-V, pi5; Tumor-specific mutated antigens, P-catenin, MUM-1, CDK4; Nonmelanoma antigens for breast, ovarian, cervical and pancreatic carcinoma, HER-2/neu, human papillomavirus -E6, -E7, MUC-1.
Either a live recombinant viral vaccine or an inactivated recombinant viral vaccine

can be formulated. A live vaccine may be preferred because multiplication in the host leads to a prolonged stimulus of similar kind and magnitude to that occurring in natural infections, and therefore, confers substantial, long-lasting immunity. Production of such live recombinant virus vaccine formulations may be accomplished using conventional methods involving propagation of the virus in cell culture or in the allantois of the chick embryo

followed by purification. Additionally, as NDV has been demonstrated to be nonpathogenic in humans, this virus is highly suited for use as a live vaccine.
In this regard, the use of genetically engineered NDV (vectors) for vaccine purposes may desire the presence of attenuation characteristics in these strains. The introduction of appropriate mutations (e.g., deletions) into the templates used for transfection may provide the novel viruses with attenuation characteristics. For example, specific missense mutations which are associated with temperature sensitivity or cold adaption can be made into deletion mutations. These mutations should be more stable than the point mutations associated with' cold or temperature sensitive mutants and reversion frequencies should be extremely low.
Alternatively, chimeric viruses with "suicide" characteristics may be constructed. Such viruses would go through only one or a few rounds of replication within the host. When used as a vaccine, the recombinant virus would go through limited replication cycle(s) and induce a sufficient level of immune response but it would not go further in the human host and cause disease. Recombinant viruses lacking one or more of the NDV genes or possessing mutated NDV genes would not be able to undergo successive rounds of replication. Defective viruses can be produced in cell lines which permanently express such a gc-nc(s). Viruses lacking an essential gene(s) will be replicated in these cell lines but when administered to the human host will not be able to complete a round of replication. Such preparations may transcribe and translate —in this abortive cycle — a sufficient number of genes to induce an immune response. Alternatively, larger quantities of the strains could be administered, so that these preparations serve as inactivated (killed) virus vaccines. For inactivated vaccines, it is preferred that the heterologous gene product be expressed as a viral component, so that the gene product is associated with the virion. The advantage of such preparations is that they contain native proteins and do not undergo inactivation by treatment with formalin or other agents used in the manufacturing of killed virus vaccines. Alternatively, mutated NDV made from cDNA may be highly attenuated so that it replicates for only a few rounds.
In another embodiment of this aspect of the invention, inactivated vaccine formulations may be prepared using conventional techniques to "kill" the chimeric viruses. Inactivated vaccines are "dead" in the sense that their infectivity has been destroyed.

Ideally, the infectivity of the virus is destroyed without affecting its immunogenicity. In order to prepare inactivated vaccines, the chimeric virus may be grown in cell culture or in the allantois of the chick embryo, purified by zonal ultracentrifugation, inactivated by formaldehyde or P-propiolactone, and pooled. The resulting vaccine is usually inoculated intramuscularly.
Inactivated viruses may be formulated with a suitable adjuvant in order to enhance the immunological response. Such adjuvants may include but are not limited to mineral gels, ej;., aluminum hydroxide; surface active substances such as lysolecithin, pluronic polyols, polyanions; peptides; oil emulsions; and potentially useful human adjuvants such as BCG and Coniiebacterium parvum.
Many methods may be used to introduce the vaccine formulations described above, these include but are not limited to oral, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, and intranasal routes. It may be preferable to introduce the chimeric virus vaccine formulation via the natural route of infection of the pathogen for which the vaccine is designed.
6. EXAMPLE: EXPRESSION AND PACKAGING OF A
FOREIGN GENE BY RECOMBINANT NDV
The expression of the chloramphenicol transferase gene (CAT) using the NDV "nini genome is described. The NDV mini genome was prepared using pNDVCAT, a ■ecombinant plasmid containing the CAT gene. The pNDVCAT plasmid is a pUC19 Dlasmid containing in sequence: the T7-promoter; the 5'-end of the NDV genomic RNA :omprising 191 nucleotides of noncoding NDV RNA sequence; 5 inserted nucleotides 3'CTTAA); the complete coding sequence of the chloramphenicol transferase (CAT) gene n the reversed and complemented order; the 3'- end of the NDV genomic RNA sequence :omprising 121 nucleotides of noncoding NDV RNA sequence; a Bbsl cloning site and several restriction sites allowing run-off transcription of the template. The pNDVCAT can )e transcribed using T7 polymerase to create an RNA with Newcastle disease viral-sense banking sequences around a CAT gene in reversed orientation.
The length of a paramyxovirus RNA can be a major factor that determines the level tf RNA replication, with uenome replication boing most efficient when the total number of

nucleotides is a multiple of six. For NDV, the question of whether this rule of six is critical for replication was examined by generating CAT mini-replicons of varying lengths, differing by one to five nucleotides. Only one construct whose genome was divisible by six was able
to induce high CAT activity.
6.1. CONSTRUCTION OF THE NEWCASTLE
DISEASE VIRUS MINIGENOME
In order to construct an NDV minigenome, as described supra, the following strategy
was used. The 5' terminal sequence of genomic NDV RNA was obtained by RACE (Gibco,
BRL) using standard techniques in the art. The template for the RACE reaction was
genomic RNA which was purified from NDV virions (NDV-CL : California/l 1914/1944-
like). As illustrated in Figure 3, this terminal sequence comprised 64 nucleotides of a trailer
sequence plus 127 nucleotides of the untranslated region of the L gene. Located adjacent to
the 191 viral nucleotide sequence, a 5 nucleotide sequence (3'CCTTAA) was inserted. A
CAT gene comprised 667 nucleotides of the CAT open reading frame which was placed
between the viral 5'and 3'terminal non-coding regions. In order to obtain the 3' terminal
region of the NDV sequence, RT-PCR was used. The template for the RT-PCR reaction
was in vitro polyadenylated genomic RNA of NDV. As illustrated in Figure 3, the 3'
terminal region of 121 nucleotides was comprised of 56 nucleotides of the untranslated
region of the NP gene plus 65 nucleotides of a leader sequence. The resulting construct of
the NDV minigenome is shown in FIG. 1. Nucleotide sequences of 3' and 5' non-coding
terminal region shown in FIG. 3
6.2. CONSTRUCTION OF THE NDV NP,
P & L EXPRESSION PLASMIDS
As described in Section 5, the transcription or replication of a negative strand RNA
genome requires several protein components to be brought in with the virus, including the L
protein, P protein and NP protein. In order to facilitate the expression from the NDV
minigenome, the genes encoding each of the L, P and NP proteins were cloned into pTMl
expression vectors as illustrated in FIG. 2A-C. The pTMl expression vectors comprises a T7
promoter, several cloning sites for insertion of the gene of interest (L, P or NP), a T7

terminator, a pUC19 origin of replication and an ampicillin resistance gene. In order to construct the expression plasrnids, fiill length DNA of NDV nucleoprotein (NP), phosphoprotein (P) and polymerase (L) were obtained by RT-PCR amplification. These DNAs were cloned into T7 polymerase expression vector pTMl, respectively (FIG. 2A-C).
6.3. RNA TRANSCRIPTION OF THE NDV MINIGENOME
RNA transcription from the NDV minigene plasmid was performed with the Ribomax kit (Promega) as specified by the manuscripts. In order to allow run-off transcription, 1 ug of NDV minigenome plasmid (pNDVCAT) was digested with Bhs I. The linearized plasmid was then used as a template of transcription reaction (for 2 hours at 37 ~C). In order to remove template DNA, the resulting reaction mixture was treated with RNase-free DNase (for 15 min. at 37°C) and purified by phenol-chloroform extraction, followed by ethanol precipitation.
6.4. CELL TRANSFECTIONS
Cos-1 cells, or 293T cells were grown on 35mm dishes and infected with the helper rirus rVV T7 at a multiplicity of infection (moi) of approximately 1 for 1 hour before iransfection. The cells were then transfected with the expression vectors encoding the NP. P and L proteins of NDV. Specifically, transfections were performed with DOTAP [Bochrmger Mannheim). Following helper virus infection, cells were transfected with the pTMl-NP (1 ug), pTMl-P (1 \ig) and pTMl-L (0.1 \ig) for 4 hours. Control transfections, lacking the L protein, were performed on a parallel set of cells with pTMl-NP (1 |ig), pTMl-P (1 (ig) and mock pTMl-L (0 (ig). After the 4 hour incubation period, cells were subjected to RNA transfection with 0.5 \ig of the NDV-CAT chimeric (-) RNA (see FIG. 1). Following RNA transfection, cells were allowed to incubate for 18 hours. The cell lysates were subsequently harvested for the CAT assay.
6.5. CAT ASSAYS
CAT assays were done according to standard procedures, adapted from Gorman et al., 1982, Mol. Cell. Biol. 2: 1044-1051. The assays contained 10 ul of 14C chloramphenicol

(0.5 (iCi; 8.3 nM; NEN), 20 jxl of 40 mM acetyl CoA (Boehringer) and 50 jil of cell extracts in 0.25 M Tris.buffer (pH 7.5). Incubation times were 16-18 hours.
6.6. RESULTS
In each cell line transfected with the NP, P, L expression vectors, and the chimeric NDV-CAT RNA, high levels of expression of CAT was obtained 18 hours post-infection. In addition, control transfected cells lacking the L protein did not express CAT.
7. RESCUE OF INFECTIOUS NDV VIRUSES USING
RNA DERIVED FROM SPECIFIC RECOMBINANT DNA
The experiments described in the subsections below demonstrate the rescue of
infectious NDV using RNA which is derived from specific recombinant DNAs. RNAs
corresponding to the chimeric NDV-CAT RNA may be used to show that the 191
nucleotides of the 5' terminal and the 121 nucleotides of the 3* terminal nucleotides of the
viral RNAs contain all the signals necessary for transcription, replication and packaging of#
model NDV RNAs. RNAs containing all the transcriptional units of the NDV genomes can
be expressed from transfected plasmids. Thus, this technology allows the engineering of
infectious NDV viruses using cDNA clones and site-specific mutagenesis of their genomes.
Furthermore, this technology may allow for the construction of infectious chimeric NDV
viruses which can be used as efficient vectors for gene expression in tissue culture, animals
or man.
8. EXAMPLE: RECOMBINANT NEWCASTLE DISEASE VIRUS CONTAINING AN HIV ANTIGEN gpl60 EPITOPE INSERTED INTO THE NDV GENOME
In the Example presented herein, a chimeric NDV is constructed to express a
heterologous antigen derived from gpl60 of HIV. The experiments described in the
subsections below demonstrate the use of a recombinant RNA template to generate a
chimeric NDV that expresses a HIV gpl60-derived peptide within the NDV genome and,
further, this chimeric NDV is used to elicit a vertebrate humoral and cell-mediated immune
response.

8.1. CONSTRUCTION OF PLASMID
Recombinant NDV cDNA clones expressing HIV gpl60 proteins may be constructed ■n a number of ways known in the art. For example, as illustrated in Figure 4, the HIV Env md Gag proteins may be inserted into the NDV in a number of locations. In one example, the Env and Gag proteins are inserted between the M and L genes. In a different example, the Env and Gag proteins are inserted 3' to the NP gene (between the leader sequence and NP). Alternatively, these HIV proteins will be incorporated between the NDV envelope proteins (HN and F) at the 3' end. These proteins may also be inserted into or between any of the NDV genes.
8.2. GENERATION OF INFECTIOUS CHIMERIC VIRUS
Transfection of RNA derived from plasmid comprising a recombinant NDV genome may be transfected into cells such as, for example, COS, 293 MDBK and selection of infectious chimeric virus may be done as previously described. See U.S. Patent No. 5,166,057, incorporated herein by reference in its entirety. The resulting RNA may be transfected into cells infected with wild type virus by using standard transfection protocol procedures, Posttransfection, the supernatant may be collected and used at different dilutions to infect fresh cells in the presence of NDV antiserum. The supernatant may also be used for plaque assays in the presence of the same antiserum. The rescued virus can then
be purified and characterized, and used, for example, in antibody production.
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8.3. HEMAGGLUTINATION INHIBITION AND VIRUS NEUTRALIZATION ASSAYS
Hemagglutination inhibition (HI) assays are performed as previously described (Palmer, D.F. et ah, 1975, Immunol. Ser. 6:51-52). Monoclonal antibodies (2G9, 4B2, 2F10, 25-5) are prepared by standard procedures with a human anti-gpl20 monoclonal antibody. Ascites fluid containing monoclonal antibodies is treated with receptor-destroying enzyme as previously described (Palmer, D.F. et al., 1975, Immunol. Ser. 6:51-52).
For virus neutralization assay, cells in 30-mm-diameter dishes are infected virus. After a 1 h adsorption, agar overlay containing antibody at different dilutions is added. The cell monolayer is then stained with 0.1% crystal vidlet at 72 h postinfection.

8.4. IMMUNIZATION
6 weeks old BALB/c mice are infected either via the aerosol route with the virus, or ire immunized intraperitoneally (i.p.) with 10 /ig of purified virus. For all booster immunizations, 10 /ug of purified virus is administered i.p. Sera is collected 7 days after each immunization.
8.5. RADIOIMMUNOASSAY
The radioimmunoassay is performed as previously described (Zaghouani, H. et al., 1991, Proc. Natl. Acad. Sci. USA 88:5645-6549). Briefly, microtiter plates are coated with 5 j.ig;ml peptide-BSA conjugate, saturated with 2% BSA in phosphate-buffered saline(PBS) md incubated with various dilution of serum. Bound antibodies are revealed bv usinq 1251 .abellcd antimouse kappa monoclonal antibody.
8.6. RADIOIMMUNOPRECIPITATION
The H9 human T cell line is acutely infected with HIV. Four days postinfection, 5x10 infected cells are labelled with 35S-cysteine, 35S-methionine, and 3H-isoleucine at 2x10° ml in media containing 100 i^Ci of each isotope per ml. After 20 h of metabolic labelling, the radioactive virions are pelleted by centrifugation for 1 h at 45,000 rpm. The relict is then resuspended in 1.0 ml of lysis buffer containing 1% Triton X-100 and 2mM Dhenylmethylsulfonyl fluoride (PMSF). Approximately 20 fA of sera or 0.5 /ug of monoclonal antibody (in 20 /A PBS) and 175 fx\ of virion lysate are incubated overnight at 4°C in 0.5 ml immunoprecipitation buffer containing 0.5% sodium dodecyl sulfate (SDS), 1 mg/ml BSA, 2% Triton X-100, and 50 mM sodium phosphate (pH 7.4). The antigen-antibody complexes are bound to protein A-Sepharose beads, and are analyzed by electrophoresis on a 10% SDS-polyacrylamide gel.
8.7. HIV-1 NEUTRALIZATION ASSAYS
The in vitro neutralization assay are performed as described previously (Nara, P.L. et al., 1987, AIDS Res. Hum. Retroviruses 3:283-302). Briefly, serial twofold dilutions of heat-inactivated serum are incubated for 1 h at room temperature with 150-200 syncytium

Drming units of HIV virus produced in H9 cells. The virus/serum mixture is incubated for h at 37°C with 50,000 DEAE-dextran treated CEMss cells (adhered to micropiate dishes ,sing poly-L-lysine), or 50,000 H9 suspension cells. After virus adsorption, the unbound 'irus is removed and 200 ju\ of media is added to each well. Four days postinfection, 50 y\ >f supernatant media is removed for viral p24gag protein quantitation (Coulter Source, Inc.). lie total number of syncytia in CEMss cells is counted five days postinfection. The leutralization titers are calculated by comparison with control wells of virus only, and are xpressed as the reciprocal of the highest serum dilution which reduced syncytia numbers by nore than 50% or inhibited the p24 synthesis by more than 50%.
8.8. INDUCTION OF CTL RESPONSE
BALB/c mice is immunized with 0.2 ml viral suspension containing 10 PFU of ■himeric NDV virus. 7 days later, spleen cells are obtained and restimulated in vitro for 5 lays with irradiated spleen cells, alone or coated with immunogenic peptides, in the iresence of 10% concanavalin A in the supernatant as previously described (Zaghouani, H. * aL 1992, J. Immunol. 148:3604-3609).
8.9, CYTOLYSIS ASSAY
The target cells coated with peptides are labeled with Na5ICr4 (100 /^Ci/106 cells) for h at 37 °C. After being washed twice, the cells are transferred to V-bottom 96-well plates, he effector cells are added, and incubated at 37°C in 7% C02. Four hours later, the supernatant is harvested and counted. The maximum chromium release is determined by ncubating the cells with 1% Nonidet P40 detergent. The percentage of specific lysis is :alculated according to the following formula: [(cpm samples - cpm spontaneous
'elease)/(cpm maximum release - cpm spontaneous release)] x 100.
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9. INTRACELLULAR EXPRESSION OF CHIMERIC NDV-CAT RNA
In order to increase the efficiency of expression of NDV'minigenomes, a plasmid
(pT7-NDV-CAT-RB) was constructed for intracellular expression of NDV-CAT RNA. This
was achieved by inserting a ribozyme derived from hepatitis delta virus directly after the end

of the 3* noncoding region of the NDV-CAT RNA. Cotransfection of pTMl-NP, pTMl-P, pTMl-L and pT7-NDV-CAT-RT) into 293, 293T, COS1, CV1, or chicken embryo fibroblast (CEF) cells which were previously infected with rVV-T7 or with modified Ankara vaccinia virus expressing T7 polymerase (MVA-T7) resulted in high levels of CAT activity (Fig. 6). CAT activity was approximately 100 to 1,000 times higher than that achieved by direct RNA transfeciion of the NDV-CAT RNA.
10. RESCUE OF INFECTIOUS NDV VIRUS USING RNA
DERIVED SPECIFIC RECOMBINANT DNA
In order to achieve rescue recombinant virus from a non-virus dependent, plasmid derived system, a plasmid allowing intracellular expression of the full-length antigenome of NDV was assembled. The NDV cDNA was RT-PCRed in several pieces from purified RNA of a California-like strain of NDV (NDV-CL)(Meindl et al., 1974 Virology 58:457-463). The cDNA pieces were ligated and assembled into a plasmid with T7 promoter and ribozymc flanking sequences, resulting in plasmid pT7-NDV+RB. A silent mutation creating a new Xmal restriction site was introduced into the L open reading frame of pT7-NDV-f-RB. CEF cell monolayers in 10 cm dishes were infected with MVA-T7 at a multiplicity of infection of approximately 0.1. One hour later, cells were transfected Oipofectcd) with 2.4 ng of pTMl-NP, 1.2 \xg of pTMl-P, 1.2 \xg of pTM-lL and 1.5 ug of pT7-NDV+-RB. After S h of incubation at 37 °C. fresh medium was added. 20h .postransfection, the vaccinia virus inhibitor araC was added at a final concentration of 60 Hg/ml. Two days postransfection, fresh'medium containing 100 ng/ml of araC was added. Supernatant from transfected cells at a day 4 postransfection was used to inoculate the allantoic chamber of 10-days-old embryonatcd chicken eggs. After two days of incubation at 37 °C, the allantoic fluid was harvested and found to be positive for the presence of NDV-CAT virus by hemagglutination. Analysis df the RNA isolated from the rescued virus confirmed the presence of the newly inserted Xmal site, confirming that the virus was derived from the cloned plasmid cDNA. A schematic representation of the rescue procedure is protocol is shown in Fig. 7.





WHAT IS CLAIMED IS:
1. A recombinant RNA molecule comprising a binding site specific for an RNA polymerase of a Newcastle disease virus and signals required for NDV mediated replication and transcription, operatively linked to a heterologous RNA sequence.
2. A recombinant RNA molecule comprising a binding site for an RNA polymerase of a Newcastle disease virus and signals required for NDV mediated replication and transcription, operatively linked to a Newcastle disease viral gene; wherein the RNA molecule contains a mutation, insertion or deletion.
3. The recombinant RNA molecule of claim 1 or 2 in which the polymerase binding site comprises the polymerase binding site contained in the 3' and 5'-noncoding flanking region of a Newcastle disease viral RNA genome.
4. The recombinant RNA molecule of claim 3 in which the 3' and 5'-noncodins flanking region has a viral sense sequence as shown in Figure 1.
5. The recombinant RNA molecule of claim 1 in which the heterologous RNA encodes a viral antigen.
6. The recombinant RNA molecule of claim 5 in which the viral antigen is derived human immunodeficiency virus, Newcastle disease virus, influenza, respiratory syncytial virus, Marek's disease virus, infectious bursal disease virus, infectious bronchitis virus, infectious bursitis virus, chicken anemia virus, infectious laryngotracheitis virus, avian luekosis virus, reticuloendotheliosis virus, avian influenza virus, rabies virus, feline distemper virus, vesicular stomatitis virus, rinderpest virus, or swinepox virus.
7. A recombinant cell comprising nucleotide sequences encoding a recombinant NDV molecule of Claim 1 and NDV RNA polymerase proteins P and L.

8. A chimeric vims comprising a negative strand RNA virus containing a the recombinant RNA molecule of Claim 1 or 2.
9. The chimeric virus of claim 8 in which the heterologous RNA is derived from a viral antigen.
10. The chimeric virus of claim 9 in which the viral antigen is derived human immunodeficiency virus, Newcastle disease virus, influenza, respiratory syncytial virus, Marek's disease virus, infectious bursal disease virus, infectious bronchitis virus, infectious bursitis vims, chicken anemia virus, infectious laryngotracheitis vims, avian luekosis vims, reticuloendotheliosis virus, avian influenza virus, rabies virus, feline distemper vims, vesicular stomatitis virus, rinderpest vims, or swinepox virus.

11. The chimeric vims of claim 8 in which the heterologous RNA is contained within the HN gene of Newcastle disease vims.
12. A method for producing a chimeric negative-strand RNA vims, comprising transfecting a host cell with nucleotide sequences encoding the recombinant RNA of Claim 1 or 2 and the viral functions required for replication and transcription, and recovering the chimeric virus from the culture.
13. A vaccine formulation comprising a genetically engineered Newcastle disease vims containing modifications which result in an attenuated phenotype, and a physiologically acceptable excipient.
14. The vaccine formulation of Claim 13 in which the modification is derived from a naturally occurring mutant.

15. A vaccine formulation comprising a genetically engineered chimeric
Newcastle disease virus the genome of which encodes a heterologous epitope, and a
pharmaceutical!}' acceptable excipient.
16. The vaccine formulation of Claim 15 in which the heterologous epitope is a
viral antigen.


20. A recombinant RNA molecule substantially as herein described with
reference to the accompanying drawings.
21. A method for producing a chimeric negative-strand RNA virus
substantially as herein described with reference to the accompanying
drawings.
22. A vaccine formulation substantially as herein described with reference
to the accompanying drawings.


Documents:

486-chenp-2004 abstract.jpg

in-pct-2001-515-che description (complete) granted.pdf

in-pct-2001-515-che abstract.jpg

in-pct-2001-515-che-claims .pdf

in-pct-2001-515-che-correspondance others.pdf

in-pct-2001-515-che-correspondance po.pdf

in-pct-2001-515-che-description complete.pdf

in-pct-2001-515-che-drawings.pdf

in-pct-2001-515-che-form 1.pdf

in-pct-2001-515-che-form 19.pdf

in-pct-2001-515-che-form 26.pdf

in-pct-2001-515-che-form 3.pdf

in-pct-2001-515-che-form 5.pdf

in-pct-2001-515-che-pct.pdf


Patent Number 234619
Indian Patent Application Number IN/PCT/2001/515/CHE
PG Journal Number 29/2009
Publication Date 17-Jul-2009
Grant Date 10-Jun-2009
Date of Filing 11-Apr-2001
Name of Patentee MOUNT SINAI SCHOOL OF MEDICINE OF NEW YORK UNIVERSITY
Applicant Address One Gustave Levy Place New York, NY 10029-6574
Inventors:
# Inventor's Name Inventor's Address
1 PALESE PETER 414, Highwood Avenue, Leonia, NJ 07605
2 GARCIA-SASTRE ADOLFO 1249 Park Avenue, 8D, New York, NY 10029
PCT International Classification Number C12Q1/70
PCT International Application Number PCT/US99/21081
PCT International Filing date 1999-09-14
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 09/152,845 1998-09-14 U.S.A.