US20130095556A1

US20130095556A1 - Novel vesicular stomatitis virus and virus rescue system

Info

Publication number: US20130095556A1
Application number: US13/623,437
Authority: US
Inventors: Christopher L. Parks; Maoli Yuan; Kevin Wright; Christy Jurgens
Original assignee: International AIDS Vaccine Initiative Inc
Current assignee: International AIDS Vaccine Initiative Inc
Priority date: 2011-09-21
Filing date: 2012-09-20
Publication date: 2013-04-18
Also published as: US11667930B2; US20200172932A1; US10544430B2; US20230340535A1; US20170198305A1

Abstract

The present relation relates to recombinant vesicular stomatitis virus for use as prophylactic and therapeutic vaccines as well as the preparation and purification of immunogenic compositions which are formulated into the vaccines of the present invention.

Description

INCORPORATION BY REFERENCE

This application claims priority to U.S. provisional patent application Ser. No. 61/537,497 filed Sep. 21, 2011. Reference is made to U.S. patent application Ser. No. 12/708,940 filed Feb. 19, 2010.
The foregoing applications, and all documents cited therein or during their prosecution (“appln cited documents”) and all documents cited or referenced herein (“herein cited documents”), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention.

FIELD OF THE INVENTION

The present invention relates to a novel vesicular stomatitis virus for use in prophylactic and therapeutic vaccines.

BACKGROUND OF THE INVENTION

Vesicular stomatitis virus (VSV) is a member of the Rhabdoviridae family of enveloped viruses that contain a single-stranded, nonsegmented, negative-sense RNA genome. The VSV genome is composed of 5 genes arranged sequentially 3′-N-P-M-G-L-S′, which each encode a polypeptide found in mature virions (Rose et al. 2001. Rhabdoviridae: the viruses and their replication., p. 1221-1244. In D. M. Knipe and P. M. Howley (ed.), Fields Virology, vol. 1. Lippincott, Williams and Wilkins, Philadelphia). The virus naturally infects livestock, but is known to infect humans producing mild illness or no symptoms of infection (Clarke et al. 2006. Springer seminars in immunopathology 28:239-253 and Letchworth et al. 1999. Vet J 157:239-260).
VSV is an important technology platform. It is a promising human vaccine vector candidate for a variety of reasons, notably, i) as mentioned above, it does not cause serious disease in humans; ii) genetic systems have been developed for producing recombinant viruses (Conzelmann. 2004. Curr Top Microbiol Immunol 283:1-41); iii) it can be modified to express foreign proteins; iv) it expresses foreign proteins abundantly; v) it elicits immune responses in infected humans (Reif et al. 1987. Am J Trop Med Hyg 36:177-182); and vi) it has been safely tested as a vaccine vector in many animal models including nonhuman primates (Clarke et al. 2006. Springer seminars in immunopathology 28:239-253).
There remains a need to express immunogens in recombinant vaccines. To do so, it is advantageous to have a vector that is genetically stable, easily modified, and efficiently propagated.
Citation or identification of any document in this application is not an admission that such document is available as prior art to the present application.

SUMMARY OF THE INVENTION

The invention stems, in part, from Applicants wishing to design a vector with a clearly defined and documented lineage that was specifically modified without altering amino acid coding or the function of cis-acting sequences to facilitate subsequent VSV vector construction. It was also important and practical to start with a VSV isolate adapted for propagation in primate epithelial cell lines (rather than commonly-used BHK fibroblastic cells) to promote greater genetic stability during VSV vector production in Vero cells used for vaccine manufacturing. Because Applicants' vaccine development plans included construction of highly modified VSV vectors that Applicants anticipated to be difficult to rescue, Applicants designed a cloning plasmid that included strategic modifications to increase the productivity of Applicants' recombinant virus rescue system.
The present invention relates to a vesicular stomatitis virus (VSV) genomic clone which may comprise: (a) a VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein, wherein the VSV genome may comprise nucleotide substitutions and amino acid coding changes to improve replicative fitness and genetic stability, (b) a cloning vector, (c) an extended T7 promoter, (d) a hammerhead ribozyme, (e) a hepatitis delta virus ribozyme and T7 terminator, (f) unique restriction endonuclease cleavage sites in a VSV genomic sequence and/or (g) a leader and a trailer that are cis-acting sequences controlling mRNA synthesis and replication.
In one embodiment, the cloning vector may be pSP72 (Genbank X65332.2). In another embodiment, the extended T7 promoter may be PT7-g10 (Lopez et al. 1997. Journal of molecular biology 269:41-51, the disclosure of which is incorporated by reference). RNA polymerase T7 functions first as a DNA binding protein that recognizes a specific DNA sequence and subsequently transitions its activity into an elongating RNA polymerase. The nature of the nucleotide sequence of the region initially transcribed by the polymerase plays a role in the transition from DNA binding protein to an elongating polymerase complex. The transcribed region in the PT7-g10 promoter may include nucleotide sequences that promote more efficient transition from DNA binding protein to elonagating RNA polymerase. (Temiakov D, Mentesana P E, Ma K, Mustaev A, Borukhov S, McAllister W T. The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance. Proc Natl Acad Sci USA. 2000 Dec. 19; 97(26):14109-14, the disclosure of which is incorporated by reference).
In another embodiment, the unique restriction endonuclease cleavage sites may be 1367 NheI, 2194 SpeI, 2194 BstBI, 4687 PacI, 7532 AvaI, 10190 SalI and 11164 AflII. In yet another embodiment, the VSV genomic clones may be depicted in FIG. 1. In another embodiment, SphI and XhoI may be added for cloning into position 1 between the leader and N gene junction of the VSV genomic clones depicted in FIG. 1.
The nucleotide substitutions in the VSV genome may be selected from the group consisting of: 1371 CA>GC (NheI), after 2195 insert TAG (SpeI) (all genome numbers subsequent to this insertion have been adjusted to include +3 bp), 3036 G>T improves match to consensus transcription stop signal, 3853 X>A (an ambiguity in Genbank file EF197793.1), 4691 T>A to generate PacI, 7546 C>A silent change in L coding sequence eliminates a BstBI site. Additionally, amino acids substitutions may be introduced to increase match with a VSV consensus using nucleotide substitutions selected from 1960 TAC>TCC to change Y>S, 3247 GTA>ATA to change V>I, 3729 AAG>GAG to change K>E, 4191 GTA>GAA to change V>E, 4386 GGT>GAT to change G>D, 4491 ACC>ATC to change T>I, 5339 ATT>CTT to change I>L, 5834 ACT>GCT to change T>A and/or 10959 AGA>AAA to change R>K, wherein the nucleotide position is according to GenBank Accession Number EF197793. The nucleotide substitutions in the VSV genome (wherein the nucleotide position is according to GenBank Accession Number EF197793) may be selected from the group consisting of:


Nucleotide position	Nucleotide position	Nucleotide
in EF197793	in rEF197793	Change	Purpose

1	Substitution 1371-2	Substitution 1371-2	CA > GC	Creates a unique NheI cleavage site
				between N and P gens
2	Substitution 1960-2	Substitution 1960-2	TAC > TCC	Y > S substitution in P protein amino
				acid sequence to agree with consensus.
3	Insert after 2195	3 base insert after	Insert TAG	Creates a unique SpeI site
		2195		between P and M genes
4	Substitution 3039	Substitution 3042	G > T	Improves agreement with consensus.
				Also improves agreement with
				consensus transcription stop signal
5	Substitution 3234-6	Substitution 3237-9	GTA > ATA	V > I substitution in P protein amino
				acid sequence to agree with consensus.
6	Substitution 3729-31	Substitution 3732-34	AAG > GAG	K > E substitution in G protein amino
				acid sequence to agree with consensus.
7	Substitution 3856	Substitution 3859	N > A	Replace unknown base in Genbank file
				with consensus
8	Substitution 4191-93	Substitution 4194-6	GTA > GAA	V > E substitution in G protein amino
				acid sequence to agree with consensus.
9	Substitution 4386-88	Substitution 4389-92	GGT > GAT	G > D substitution in G protein amino
				acid sequence to agree with consensus.
10	Substitution 4491-93	Substitution 4494-96	ACC > ATC	T > I substitution in G protein amino
				acid sequence to agree with consensus.
11	Substitution 4694	Substitution 4697	T > A	Creates unique PacI cleavage site
				between G and L genes
12	Substitution 5339-41	Substitution 5342-44	ATT > CTT	I > L substitution in L protein amino
				acid sequence to agree with consensus.
13	Substitution 5834-6	Substitution 5837-40	ACT > GCT	T > A substitution in L protein amino
				acid sequence to agree with consensus.
14	Substitution 10959-61	Substitution 10962-64	AGA > AAA	R > K substitution in L protein amino
				acid sequence to agree with consensus.
15	Substitution 7546	Substitution 7549	C > A	Eliminates a BstBI site in the L gene
				sequence making the BstBI site
				between the M and G genes unique.
				This substitution was silent for amino
				acid coding.

The VSV genomic clone may comprise the nucleotide sequences of the VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein may be selected from the group consisting of FIGS. 2B-2G. The VSV genomic clone may also comprise the nucleotide sequences of the VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein may be selected from the group consisting of FIGS. 3A-3G.
The present invention also relates to method for rescuing VSV, which may comprise combining a T7 RNA polymerase promoter and a hammerhead ribozyme sequence to increase the efficiency of synthesis and processing of full-length VSV genomic RNA in transfected cells.
In one embodiment, the T7 RNA polymerase promoter may be a minimal functional sequence designed to initiate transcription very close to or precisely at the 5′ terminus of the genomic clone. Advantageously, the T7 promoter may be a T7 promoter sequence that enhances formation of stable initiation and elongation complexes and a hammerhead ribozyme sequence at the 5′ terminus that catalyzes removal of extra nucleotides restoring the authentic 5′ terminus of the genomic transcript.
In another embodiment, the plasmids used to support virus rescue encoding VSV nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein may be optimized to improve expression of the trans-acting proteins to initiate virus rescue. Advantageously, the optimization is codon optimization. In one embodiment, the gene optimization may comprise replacing a VSV nucleotide sequence with codons used by highly expressed mammalian genes. In another embodiment, the codon optimization may comprise eliminating potential RNA processing signals in the coding sequence that might direct unwanted RNA splicing or cleavage/polyadenylation reaction, wherein the eliminating may comprise: (a) identifying potential splice site signals and remove by introducing synonymous codons and/or (b) scanning an insert for consensus cleavage/polyadenylation signals (AAUAAA) and introducing synonymous codons to disrupt the consensus cleavage/polyadenylation signals. In yet another embodiment, the gene optimization may comprise (a) adding a preferred translational start sequence (the Kozak sequence) and/or (b) adding a preferred translational stop codon. In still another embodiment, the gene optimization may comprise scanning a sequence for homopolymeric stretches of 5 nucleotides or more and interrupting the sequences by introducing synonymous codons. In another embodiment, the gene optimization may comprise scanning a sequence for restriction endonuclease cleavage sites and eliminate any unwanted recognitions signals. In yet another embodiment, the gene optimization may comprise confirming that a modified sequence translates into the expected amino acid sequence.
Accordingly, it is an object of the invention to not encompass within the invention any previously known product, process of making the product, or method of using the product such that Applicants reserve the right and hereby disclose a disclaimer of any previously known product, process, or method. It is further noted that the invention does not intend to encompass within the scope of the invention any product, process, or making of the product or method of using the product, which does not meet the written description and enablement requirements of the USPTO (35 U.S.C. §112, first paragraph) or the EPO (Article 83 of the EPC), such that Applicants reserve the right and hereby disclose a disclaimer of any previously described product, process of making the product, or method of using the product.
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.
These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following detailed description, given by way of example, but not intended to limit the invention solely to the specific embodiments described, may best be understood in conjunction with the accompanying drawings, in which:

FIG. 1 depicts a schematic structure of a VSV genomic clone of the invention. Features include (a) a cloning vector based on pSP72 (Genbank X65332.2), (b) an extended T7 promoter is PT7-g10 described by Lopez et al. (Lopez et al., 1997. Journal of molecular biology 269:41-51), (c) a hammerhead ribozyme designed following the rules for constructing self-cleaving RNA sequences (Inoue et al. 2003. J Virol Methods 107:229-236 and Ruffner et al. 1990. Biochemistry 29:10695-10702), (d) a hepatitis delta virus ribozyme and T7 terminator as described before for the measles virus rescue system (Radecke et at 1995. The EMBO journal 14:5773-5784, 23 and Sidhu et al, 1995, Virology 208:800-807), (e) unique restriction endonuclease cleavage sites indicated above the VSV genomic sequence (red), (f) leader and trailer as cis-acting sequences in the termini that control mRNA synthesis and replication and (g) N, nucleocapsid; P, phosphoprotein; M, matrix; G, glycoprotein; L, large protein.

FIG. 2A depicts a schematic VSV genome and cloning fragments where fragments A and G are combined to produce fragment VSV-AG. The AG fragment may be cloned first. There are BsmBI sites added to the termini of AG fragment, which may be used to add ribozyme sequences to the termini without addition of nucleotides introduced by the restriction enzyme cleavage site. There may be a polylinker added between the combined A-G fragments (NheI-BstBI-PacI-AvaI-SalI-AflII). After cloning the VSV-AG fragment into the Dual Ribozyme vector, B through F may be inserted in subsequent cloning steps.

FIG. 2B depicts a sequence of genome fragment VSV-A/G (1489 bp).

FIG. 2C depicts a sequence of genome fragment B (1645 bp).

FIG. 2D depicts a sequence of genome fragment C (1689 bp).

FIG. 2E depicts a sequence of genome fragment D (2851 bp).

FIG. 2F depicts a sequence of genome fragment E (2664).

FIG. 2G depicts a sequence of genome fragment F (930).

FIG. 3A depicts a schematic VSV annotated rVSV genomic cDNA and mRNA transcriptional control and processing signals.

FIGS. 3B-3G depict a sequence of the VSV of FIG. 3A.

DETAILED DESCRIPTION

Applicants used VSV to develop several types of HIV vaccine candidate including VSV-SIV and VSV-HIV chimeric viruses in which the natural VSV attachment protein (G) is functionally replaced with SIV/HIV Env and EnvG hybrids, vectors designed with Env epitopes grafted into VSV G and vectors designed to display a variety of Env immunogens as transmembrane proteins on the surface of VSV particles and infected cells.
Applicants used VSV to develop technology platforms for antibody-based screening and selection procedures that will allow Applicants to evolve novel Env immunogens. These methods take advantage of the fact that VSV evolves rapidly when selective pressure is applied (Novella. 2003. Curr Opin Microbiol 6:399-405). Methods in development include a procedure that allows Applicants to select for Env mutants that bind most strongly with monoclonal antibodies, a method for rapidly producing mutants that escape neutralizing antibodies that bind HIV Env, and a method for generating live or inactivated VSV particles displaying Env.
All of the recombinant VSVs are based on a genomic DNA clone Applicants designed. Applicants decided to develop Applicants' own VSV vector for several reasons. First, Applicants wanted to begin Applicants' vaccine development program with a vector that has a clearly defined and documented lineage. Second, Applicants planned to introduce a limited number of strategic nucleotide changes into the genome that would facilitate subsequent VSV vector construction without altering amino acid coding or the function of cis-acting sequences. Third, it was important and practical to start with a VSV isolate adapted for propagation in primate epithelial cell lines (rather than commonly-used BHK fibroblastic cells) to promote greater genetic stability during VSV vector production in Vero cells used for vaccine manufacturing. Finally, because Applicants' vaccine development plans included construction of highly modified VSV vectors that Applicants anticipated to be difficult to rescue, Applicants designed a cloning plasmid that included strategic modifications to increase the productivity of Applicants' rescue system.
Applicants could have used the VSV vector background developed in 1995 at Yale University (Lawson et al. 1995. Proceedings of the National Academy of Sciences of the United States of America 92:4477-4481) as Applicants' starting material. Applicants decided against this option because the Yale vector is a hybrid constructed from sequences originating from multiple VSV isolates propagated under diverse laboratory conditions (it was constructed when molecular cloning was considerably more complex and costly), and for Applicants' purposes, the Yale clone also needed further modification to introduce unique restriction enzyme cleavage sites. Thus, Applicants found it simpler to engineer a vector fitting Applicants' needs by assembling synthetic DNA fragments based on a virus genomic sequence described in a manuscript by Remold and colleagues (Remold et al. 2008. Mol Biol Evol 25:1138-1147). In the end, Applicants' vector nucleotide sequence differs from circulating wild-type viruses (VSV Indiana) and the Yale molecular clone by about 1%.
To construct Applicants' VSV genomic clone (FIG. 1), Applicants started with the sequence (Genbank Accession EF197793) of a VSV isolate (Mudd Summers Strain, Indiana Serotype) adapted to growth in human epithelial cell lines (Remold et al. 2008. Mol Biol Evol 25:1138-1147). Applicants modified EF197793 nucleotide sequence to create unique restriction endonuclease cleavage sites (FIG. 1 and Table 1) that would facilitate subsequent genetic modification, and Applicants also introduced a number of nucleotide substitutions and amino acid coding changes that Applicants anticipated would improve the replicative fitness and genetic stability of Applicants' recombinant vector based on analysis of consensus sequences generated by aligning the genomes of lab-adapted and circulating wild-type viruses. The modified version of the EF197793 sequence (rEF197793 in Table 1) was then used as a template to have 6 DNA fragments synthesized, which Applicants subsequently assembled into the recombinant full-length genomic clone (FIGS. 2A-2G). An annotated modified VSV genomic sequence is included in FIGS. 3A-3G.
Applicants also introduced improvements to the plasmid DNA cloning vector that enhanced Applicants' ability to rescue recombinant VSV vectors from transfected cells. Applicants did this because, as mentioned above, Applicants' vaccine development plans included construction of highly modified VSV vectors that Applicants anticipated would be difficult to rescue because Applicants are adding one or more foreign gene inserts and also introducing changes expected to decrease replicative fitness. Negative-strand RNA virus rescue from cloned DNAs is a multistep process that includes: 1) cotransfection of multiple plasmid DNAs including the plasmid DNA containing the VSV genomic cDNA, a plasmid encoding bacteriophage T7 RNA polymerase, and multiple plasmids expressing viral proteins (i.e. VSV N, P, M, G, and L) needed to initiate virus replication in transfected cells; 2) intracellular synthesis of a full-length genomic RNA by bacteriophage T7 RNA polymerase; 3) precise processing of the primary genomic transcript to produce requisite termini for replication; 4) de novo packaging of the genomic RNA by the viral nucleocapsid protein to generate a functional template for RNA replication; 5) and finally, initiation of RNA synthesis by the viral RNA-dependent RNA polymerase (Conzelmann. 2004. Curr Top Microbiol Immunol 283:1-41 and Neumann et al. 2002. J Gen Virol 83:2635-2662). The rescue process is relatively inefficient and at times it restricts the ability to rescue the desired recombinant, although incremental improvements (Ghanem et al. 2011. European Journal of cell biology, Inoue et al. J Virol Methods 107:229-236, Parks et al. 1999. J Virol 73:3560-3566, Witko et al. 2010. J Virol Methods 164:43-50 and Witko et al. 2006. J Virol Methods 135:91-101) in the rescue procedure have made it more efficient since it was first described (Schnell et al. 1994. Embo J 13:4195-4203). As described herein, to improve Applicants' VSV rescue system, Applicants used a novel combination of a more efficient T7 RNA polymerase promoter and a hammerhead ribozyme sequence to increase the efficiency of synthesis and processing of full-length VSV genomic RNA in transfected cells.
The T7 RNA polymerase promoter used in published virus rescue methods is a minimal functional sequence designed to initiate transcription very close to or precisely at the 5′ terminus of the genomic clone (Lawson et al. 1995. Proceedings of the National Academy of Sciences of the United States of America 92:4477-4481, Radecke et al. 1995. The EMBO Journal 14:5773-5784 and Schnell et al. 1994. Embo J 13:4195-4203). Although this promoter design is effective for forming the 5′ end of the genomic transcript, it is not the most efficient promoter for initiating productive RNA synthesis. Thus, to improve VSV rescue efficiency, Applicants developed a modified plasmid that uses a longer T7 promoter sequence known to enhance formation of stable initiation and elongation complexes (Lopez et al. 1997. Journal of molecular biology 269:41-51). Because the longer T7 promoter includes downstream transcribed bacteriophage sequences, extra nucleotides are added to the primary VSV genomic transcript. To remove these extra nucleotides, Applicants have incorporated a hammerhead ribozyme (Inoue et al. J Virol Methods 107:229-236 and Ruffner et al. 1990. Biochemistry 29:10695-10702) sequence at the 5′ that which catalyzes removal of extra nucleotides restoring the authentic 5′ end of the genomic transcript.
Finally, the VSV rescue system Applicants developed uses protocols similar to those described before with modification (Witko et al. 2006. J Virol Methods 135:91-101). The most significant change is that Applicants have ‘optimized’ (Examples 3 and 4) Applicants' plasmids encoding N, P, M, G, and L and placed the optimized genes under control of the human cytomegalovirus promoter to improve expression of the trans-acting proteins needed to initiate virus rescue. This modification of the rescue system was suggested by results showing that codon optimization significantly enhances expression in transfected cells of plasmid-encoded viral G proteins from respiratory syncytial virus and VSV (Ternette et al. 2007. Virol J 4:51 and Witko et al. 2010. J Virol Methods 164:43-50).
The present invention also encompasses methods of producing or eliciting an immune response that may comprise administering to an animal, advantageously a mammal, any one of the herein disclosed recombinant VSV vectors.
The terms “protein”, “peptide”, “polypeptide”, and “amino acid sequence” are used interchangeably herein to refer to polymers of amino acid residues of any length. The polymer may 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.
As used herein, the terms “antigen” or “immunogen” are used interchangeably to refer to a substance, typically a protein, which is capable of inducing an immune response in a subject. The term also refers to proteins that are immunologically active in the sense that once administered to a subject (either directly or by administering to the subject a nucleotide sequence or vector that encodes the protein) is able to evoke an immune response of the humoral and/or cellular type directed against that protein.
The term “antibody” includes intact molecules as well as fragments thereof, such as Fab, F(ab′)₂, Fv and scFv which are capable of binding the epitope determinant. These antibody fragments retain some ability to selectively bind with its antigen or receptor and include, for example:

- (i) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule may be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;
- (ii) Fab′, the fragment of an antibody molecule may be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule;
- (iii) F(ab′)₂, the fragment of the antibody that may be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)2 is a dimer of two Fab′ fragments held together by two disulfide bonds;
- (iv) scFv, including a genetically engineered fragment containing the variable region of a heavy and a light chain as a fused single chain molecule.

General methods of making these fragments are known in the art. (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1988), which is incorporated herein by reference).
It should be understood that the proteins, including the antibodies and/or antigens of the invention may differ from the exact sequences illustrated and described herein. Thus, the invention contemplates deletions, additions and substitutions to the sequences shown, so long as the sequences function in accordance with the methods of the invention. 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, cysteine, serine threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified as aromatic amino acids. It is reasonably predictable that an isolated replacement of leucine with isoleucine or valine, or vice versa; an aspartate with a glutamate or vice versa; a threonine with a serine or vice versa; or a similar conservative replacement of an amino acid with a structurally related amino acid, will not have a major effect on the biological activity. Proteins having substantially the same amino acid sequence as the sequences illustrated and described but possessing minor amino acid substitutions that do not substantially affect the immunogenicity of the protein are, therefore, within the scope of the invention.
As used herein the terms “nucleotide sequences” and “nucleic acid sequences” refer to deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequences, including, without limitation, messenger RNA (mRNA), DNA/RNA hybrids, or synthetic nucleic acids. The nucleic acid may be single-stranded, or partially or completely double-stranded (duplex). Duplex nucleic acids may be homoduplex or heteroduplex.
As used herein the term “transgene” may used to refer to “recombinant” nucleotide sequences that may be derived from any of the nucleotide sequences encoding the proteins of the present invention. The term “recombinant” means a nucleotide sequence that has been manipulated “by man” and which does not occur in nature, or is linked to another nucleotide sequence or found in a different arrangement in nature. It is understood that manipulated “by man” means manipulated by some artificial means, including by use of machines, codon optimization, restriction enzymes, etc.
For example, in one embodiment the nucleotide sequences may be mutated such that the activity of the encoded proteins in vivo is abrogated. In another embodiment the nucleotide sequences may be codon optimized, for example the codons may be optimized for human use. In preferred embodiments the nucleotide sequences of the invention are both mutated to abrogate the normal in vivo function of the encoded proteins, and codon optimized for human use. For example, each of the Gag, Pol, Env, Nef, RT, and IN sequences of the invention may be altered in these ways.
As regards codon optimization, the nucleic acid molecules of the invention have a nucleotide sequence that encodes the antigens of the invention and may be designed to employ codons that are used in the genes of the subject in which the antigen is to be produced. Many viruses, including HIV and other lentiviruses, use a large number of rare codons and, by altering these codons to correspond to codons commonly used in the desired subject, enhanced expression of the antigens may be achieved. In a preferred embodiment, the codons used are “humanized” codons, i.e., the codons are those that appear frequently in highly expressed human genes (Andre et al., J. Virol. 72:1497-1503, 1998) instead of those codons that are frequently used by HIV. Such codon usage provides for efficient expression of the transgenic HIV proteins in human cells. Any suitable method of codon optimization may be used. Such methods, and the selection of such methods, are well known to those of skill in the art. In addition, there are several companies that will optimize codons of sequences, such as Geneart (geneart.com). Thus, the nucleotide sequences of the invention may readily be codon optimized.
The invention further encompasses nucleotide sequences encoding functionally and/or antigenically equivalent variants and derivatives of the antigens of the invention and functionally equivalent fragments thereof. These functionally equivalent variants, derivatives, and fragments display the ability to retain antigenic activity. For instance, changes in a DNA sequence that do not change the encoded amino acid sequence, as well as those that result in conservative substitutions of amino acid residues, one or a few amino acid deletions or additions, and substitution of amino acid residues by amino acid analogs are those which will not significantly affect properties of the encoded polypeptide. Conservative amino acid substitutions are glycine/alanine; valine/isoleucine/leucine; asparagine/glutamine; aspartic acid/glutamic acid; serine/threonine/methionine; lysine/arginine; and phenylalanine/tyrosine/tryptophan. In one embodiment, the variants have at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% homology or identity to the antigen, epitope, immunogen, peptide or polypeptide of interest.
For the purposes of the present invention, sequence identity or homology is determined by comparing the sequences when aligned so as to maximize overlap and identity while minimizing sequence gaps. In particular, sequence identity may be determined using any of a number of mathematical algorithms. A nonlimiting example of a mathematical algorithm used for comparison of two sequences is the algorithm of Karlin & Altschul, Proc. Natl. Acad. Sci. USA 1990; 87: 2264-2268, modified as in Karlin & Altschul, Proc. Natl. Acad. Sci. USA 1993; 90: 5873-5877.
Another example of a mathematical algorithm used for comparison of sequences is the algorithm of Myers & Miller, CABIOS 1988; 4: 11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 may be used. Yet another useful algorithm for identifying regions of local sequence similarity and alignment is the FASTA algorithm as described in Pearson & Lipman, Proc. Natl. Acad. Sci. USA 1988; 85: 2444-2448.
Advantageous for use according to the present invention is the WU-BLAST (Washington University BLAST) version 2.0 software. WU-BLAST version 2.0 executable programs for several UNIX platforms may be downloaded from ftp://blast.wust1.edu/blast/executables. This program is based on WU-BLAST version 1.4, which in turn is based on the public domain NCBI-BLAST version 1.4 (Altschul & Gish, 1996, Local alignment statistics, Doolittle ed., Methods in Enzymology 266: 460-480; Altschul et al., Journal of Molecular Biology 1990; 215: 403-410; Gish & States, 1993; Nature Genetics 3: 266-272; Karlin & Altschul, 1993; Proc. Natl. Acad. Sci. USA 90: 5873-5877; all of which are incorporated by reference herein).
The various recombinant nucleotide sequences and antibodies and/or antigens of the invention are made using standard recombinant DNA and cloning techniques. Such techniques are well known to those of skill in the art. See for example, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook et al. 1989).
The nucleotide sequences of the present invention may be inserted into “vectors.” The term “vector” is widely used and understood by those of skill in the art, and as used herein the term “vector” is used consistent with its meaning to those of skill in the art. For example, the term “vector” is commonly used by those skilled in the art to refer to a vehicle that allows or facilitates the transfer of nucleic acid molecules from one environment to another or that allows or facilitates the manipulation of a nucleic acid molecule.
Any vector that allows expression of the antibodies and/or antigens of the present invention may be used in accordance with the present invention. In certain embodiments, the antigens and/or antibodies of the present invention may be used in vitro (such as using cell-free expression systems) and/or in cultured cells grown in vitro in order to produce the encoded HIV-antigens and/or antibodies which may then be used for various applications such as in the production of proteinaceous vaccines. For such applications, any vector that allows expression of the antigens and/or antibodies in vitro and/or in cultured cells may be used.
For applications where it is desired that the antibodies and/or antigens be expressed in vivo, for example when the transgenes of the invention are used in DNA or DNA-containing vaccines, any vector that allows for the expression of the antibodies and/or antigens of the present invention and is safe for use in vivo may be used. In preferred embodiments the vectors used are safe for use in humans, mammals and/or laboratory animals.
For the antibodies and/or antigens of the present invention to be expressed, the protein coding sequence should be “operably linked” to regulatory or nucleic acid control sequences that direct transcription and translation of the protein. As used herein, a coding sequence and a nucleic acid control sequence or promoter are said to be “operably linked” when they are covalently linked in such a way as to place the expression or transcription and/or translation of the coding sequence under the influence or control of the nucleic acid control sequence. The “nucleic acid control sequence” may be any nucleic acid element, such as, but not limited to promoters, enhancers, IRES, introns, and other elements described herein that direct the expression of a nucleic acid sequence or coding sequence that is operably linked thereto. The term “promoter” will be used herein to refer to a group of transcriptional control modules that are clustered around the initiation site for RNA polymerase II and that when operationally linked to the protein coding sequences of the invention lead to the expression of the encoded protein. The expression of the transgenes of the present invention may be under the control of a constitutive promoter or of an inducible promoter, which initiates transcription only when exposed to some particular external stimulus, such as, without limitation, antibiotics such as tetracycline, hormones such as ecdysone, or heavy metals. The promoter may also be specific to a particular cell-type, tissue or organ. Many suitable promoters and enhancers are known in the art, and any such suitable promoter or enhancer may be used for expression of the transgenes of the invention. For example, suitable promoters and/or enhancers may be selected from the Eukaryotic Promoter Database (EPDB).
The present invention relates to a recombinant vesicular stomatitis virus (VSV) vector expressing a foreign epitope. Advantageously, the epitope is an HIV epitope. Any HIV epitope may be expressed in a VSV vector. Advantageously, the HIV epitope is an HIV antigen, HIV epitope or an HIV immunogen, such as, but not limited to, the HIV antigens, HIV epitopes or HIV immunogens of U.S. Pat. Nos. 7,341,731; 7,335,364; 7,329,807; 7,323,553; 7,320,859; 7,311,920; 7,306,798; 7,285,646; 7,285,289; 7,285,271; 7,282,364; 7,273,695; 7,270,997; 7,262,270; 7,244,819; 7,244,575; 7,232,567; 7,232,566; 7,223,844; 7,223,739; 7,223,534; 7,223,368; 7,220,554; 7,214,530; 7,211,659; 7,211,432; 7,205,159; 7,198,934; 7,195,768; 7,192,555; 7,189,826; 7,189,522; 7,186,507; 7,179,645; 7,175,843; 7,172,761; 7,169,550; 7,157,083; 7,153,509; 7,147,862; 7,141,550; 7,129,219; 7,122,188; 7,118,859; 7,118,855; 7,118,751; 7,118,742; 7,105,655; 7,101,552; 7,097,971 7,097,842; 7,094,405; 7,091,049; 7,090,648; 7,087,377; 7,083,787; 7,070,787; 7,070,781; 7,060,273; 7,056,521; 7,056,519; 7,049,136; 7,048,929; 7,033,593; 7,030,094; 7,022,326; 7,009,037; 7,008,622; 7,001,759; 6,997,863; 6,995,008; 6,979,535; 6,974,574; 6,972,126; 6,969,609; 6,964,769; 6,964,762; 6,958,158; 6,956,059; 6,953,689; 6,951,648; 6,946,075; 6,927,031; 6,919,319; 6,919,318; 6,919,077; 6,913,752; 6,911,315; 6,908,617; 6,908,612; 6,902,743; 6,900,010; 6,893,869; 6,884,785; 6,884,435; 6,875,435; 6,867,005; 6,861,234; 6,855,539; 6,841,381 6,841,345; 6,838,477; 6,821,955; 6,818,392; 6,818,222; 6,815,217; 6,815,201; 6,812,026; 6,812,025; 6,812,024; 6,808,923; 6,806,055; 6,803,231; 6,800,613; 6,800,288; 6,797,811; 6,780,967; 6,780,598; 6,773,920; 6,764,682; 6,761,893; 6,753,015; 6,750,005; 6,737,239; 6,737,067; 6,730,304; 6,720,310; 6,716,823; 6,713,301; 6,713,070; 6,706,859; 6,699,722; 6,699,656; 6,696,291; 6,692,745; 6,670,181; 6,670,115; 6,664,406; 6,657,055; 6,657,050; 6,656,471; 6,653,066; 6,649,409; 6,649,372; 6,645,732; 6,641,816; 6,635,469; 6,613,530; 6,605,427; 6,602,709 6,602,705; 6,600,023; 6,596,477; 6,596,172; 6,593,103; 6,593,079; 6,579,673; 6,576,758; 6,573,245; 6,573,040; 6,569,418; 6,569,340; 6,562,800; 6,558,961; 6,551,828; 6,551,824; 6,548,275; 6,544,780; 6,544,752; 6,544,728; 6,534,482; 6,534,312; 6,534,064; 6,531,572; 6,531,313; 6,525,179; 6,525,028; 6,524,582; 6,521,449; 6,518,030; 6,518,015; 6,514,691; 6,514,503; 6,511,845; 6,511,812; 6,511,801; 6,509,313; 6,506,384; 6,503,882; 6,495,676; 6,495,526; 6,495,347; 6,492,123; 6,489,131; 6,489,129; 6,482,614; 6,479,286; 6,479,284; 6,465,634; 6,461,615 6,458,560; 6,458,527; 6,458,370; 6,451,601; 6,451,592; 6,451,323; 6,436,407; 6,432,633; 6,428,970; 6,428,952; 6,428,790; 6,420,139; 6,416,997; 6,410,318; 6,410,028; 6,410,014; 6,407,221; 6,406,710; 6,403,092; 6,399,295; 6,392,013; 6,391,657; 6,384,198; 6,380,170; 6,376,170; 6,372,426; 6,365,187; 6,358,739; 6,355,248; 6,355,247; 6,348,450; 6,342,372; 6,342,228; 6,338,952; 6,337,179; 6,335,183; 6,335,017; 6,331,404; 6,329,202; 6,329,173; 6,328,976; 6,322,964; 6,319,666; 6,319,665; 6,319,500; 6,319,494; 6,316,205; 6,316,003; 6,309,633; 6,306,625 6,296,807; 6,294,322; 6,291,239; 6,291,157; 6,287,568; 6,284,456; 6,284,194; 6,274,337; 6,270,956; 6,270,769; 6,268,484; 6,265,562; 6,265,149; 6,262,029; 6,261,762; 6,261,571; 6,261,569; 6,258,599; 6,258,358; 6,248,332; 6,245,331; 6,242,461; 6,241,986; 6,235,526; 6,235,466; 6,232,120; 6,228,361; 6,221,579; 6,214,862; 6,214,804; 6,210,963; 6,210,873; 6,207,185; 6,203,974; 6,197,755; 6,197,531; 6,197,496; 6,194,142; 6,190,871; 6,190,666; 6,168,923; 6,156,302; 6,153,408; 6,153,393; 6,153,392; 6,153,378; 6,153,377; 6,146,635; 6,146,614; 6,143,876 6,140,059; 6,140,043; 6,139,746; 6,132,992; 6,124,306; 6,124,132; 6,121,006; 6,120,990; 6,114,507; 6,114,143; 6,110,466; 6,107,020; 6,103,521; 6,100,234; 6,099,848; 6,099,847; 6,096,291; 6,093,405; 6,090,392; 6,087,476; 6,083,903; 6,080,846; 6,080,725; 6,074,650; 6,074,646; 6,070,126; 6,063,905; 6,063,564; 6,060,256; 6,060,064; 6,048,530; 6,045,788; 6,043,347; 6,043,248; 6,042,831; 6,037,165; 6,033,672; 6,030,772; 6,030,770; 6,030,618; 6,025,141; 6,025,125; 6,020,468; 6,019,979; 6,017,543; 6,017,537; 6,015,694; 6,015,661; 6,013,484; 6,013,432 6,007,838; 6,004,811; 6,004,807; 6,004,763; 5,998,132; 5,993,819; 5,989,806; 5,985,926; 5,985,641; 5,985,545; 5,981,537; 5,981,505; 5,981,170; 5,976,551; 5,972,339; 5,965,371; 5,962,428; 5,962,318; 5,961,979; 5,961,970; 5,958,765; 5,958,422; 5,955,647; 5,955,342; 5,951,986; 5,951,975; 5,942,237; 5,939,277; 5,939,074; 5,935,580; 5,928,930; 5,928,913; 5,928,644; 5,928,642; 5,925,513; 5,922,550; 5,922,325; 5,919,458; 5,916,806; 5,916,563; 5,914,395; 5,914,109; 5,912,338; 5,912,176; 5,912,170; 5,906,936; 5,895,650; 5,891,623; 5,888,726; 5,885,580 5,885,578; 5,879,685; 5,876,731; 5,876,716; 5,874,226; 5,872,012; 5,871,747; 5,869,058; 5,866,694; 5,866,341; 5,866,320; 5,866,319; 5,866,137; 5,861,290; 5,858,740; 5,858,647; 5,858,646; 5,858,369; 5,858,368; 5,858,366; 5,856,185; 5,854,400; 5,853,736; 5,853,725; 5,853,724; 5,852,186; 5,851,829; 5,851,529; 5,849,475; 5,849,288; 5,843,728; 5,843,723; 5,843,640; 5,843,635; 5,840,480; 5,837,510; 5,837,250; 5,837,242; 5,834,599; 5,834,441; 5,834,429; 5,834,256; 5,830,876; 5,830,641; 5,830,475; 5,830,458; 5,830,457; 5,827,749; 5,827,723; 5,824,497 5,824,304; 5,821,047; 5,817,767; 5,817,754; 5,817,637; 5,817,470; 5,817,318; 5,814,482; 5,807,707; 5,804,604; 5,804,371; 5,800,822; 5,795,955; 5,795,743; 5,795,572; 5,789,388; 5,780,279; 5,780,038; 5,776,703; 5,773,260; 5,770,572; 5,766,844; 5,766,842; 5,766,625; 5,763,574; 5,763,190; 5,762,965; 5,759,769; 5,756,666; 5,753,258; 5,750,373; 5,747,641; 5,747,526; 5,747,028; 5,736,320; 5,736,146; 5,733,760; 5,731,189; 5,728,385; 5,721,095; 5,716,826; 5,716,637; 5,716,613; 5,714,374; 5,709,879; 5,709,860; 5,709,843; 5,705,331; 5,703,057; 5,702,707 5,698,178; 5,688,914; 5,686,078; 5,681,831; 5,679,784; 5,674,984; 5,672,472; 5,667,964; 5,667,783; 5,665,536; 5,665,355; 5,660,990; 5,658,745; 5,658,569; 5,643,756; 5,641,624; 5,639,854; 5,639,598; 5,637,677; 5,637,455; 5,633,234; 5,629,153; 5,627,025; 5,622,705; 5,614,413; 5,610,035; 5,607,831; 5,606,026; 5,601,819; 5,597,688; 5,593,972; 5,591,829; 5,591,823; 5,589,466; 5,587,285; 5,585,254; 5,585,250; 5,580,773; 5,580,739; 5,580,563; 5,573,916; 5,571,667; 5,569,468; 5,558,865; 5,556,745; 5,550,052; 5,543,328; 5,541,100; 5,541,057; 5,534,406 5,529,765; 5,523,232; 5,516,895; 5,514,541; 5,510,264; 5,500,161; 5,480,967; 5,480,966; 5,470,701; 5,468,606; 5,462,852; 5,459,127; 5,449,601; 5,447,838; 5,447,837; 5,439,809; 5,439,792; 5,418,136; 5,399,501; 5,397,695; 5,391,479; 5,384,240; 5,374,519; 5,374,518; 5,374,516; 5,364,933; 5,359,046; 5,356,772; 5,354,654; 5,344,755; 5,335,673; 5,332,567; 5,320,940; 5,317,009; 5,312,902; 5,304,466; 5,296,347; 5,286,852; 5,268,265; 5,264,356; 5,264,342; 5,260,308; 5,256,767; 5,256,561; 5,252,556; 5,230,998; 5,230,887; 5,227,159; 5,225,347; 5,221,610; 5,217,861; 5,208,321; 5,206,136; 5,198,346; 5,185,147; 5,178,865; 5,173,400; 5,173,399; 5,166,050; 5,156,951; 5,135,864; 5,122,446; 5,120,662; 5,103,836; 5,100,777; 5,100,662; 5,093,230; 5,077,284; 5,070,010; 5,068,174; 5,066,782; 5,055,391; 5,043,262; 5,039,604; 5,039,522; 5,030,718; 5,030,555; 5,030,449; 5,019,387; 5,013,556; 5,008,183; 5,004,697; 4,997,772; 4,983,529; 4,983,387; 4,965,069; 4,945,082; 4,921,787; 4,918,166; 4,900,548; 4,888,290; 4,886,742; 4,885,235; 4,870,003; 4,869,903; 4,861,707; 4,853,326; 4,839,288; 4,833,072 and 4,795,739.
Advantageously, the HIV epitope may be an Env precursor or gp160 epitope. The Env precursor or gp160 epitope may be recognized by antibodies PG9, PG16, 2G12, b12, 2F5, 4E10, Z13, or other broad potent neutralizing antibodies.
In another embodiment, HN, or immunogenic fragments thereof, may be utilized as the HIV epitope. For example, the HN nucleotides of U.S. Pat. Nos. 7,393,949, 7,374,877, 7,306,901, 7,303,754, 7,173,014, 7,122,180, 7,078,516, 7,022,814, 6,974,866, 6,958,211, 6,949,337, 6,946,254, 6,896,900, 6,887,977, 6,870,045, 6,803,187, 6,794,129, 6,773,915, 6,768,004, 6,706,268, 6,696,291, 6,692,955, 6,656,706, 6,649,409, 6,627,442, 6,610,476, 6,602,705, 6,582,920, 6,557,296, 6,531,587, 6,531,137, 6,500,623, 6,448,078, 6,429,306, 6,420,545, 6,410,013, 6,407,077, 6,395,891, 6,355,789, 6,335,158, 6,323,185, 6,316,183, 6,303,293, 6,300,056, 6,277,561, 6,270,975, 6,261,564, 6,225,045, 6,222,024, 6,194,391, 6,194,142, 6,162,631, 6,114,167, 6,114,109, 6,090,392, 6,060,587, 6,057,102, 6,054,565, 6,043,081, 6,037,165, 6,034,233, 6,033,902, 6,030,769, 6,020,123, 6,015,661, 6,010,895, 6,001,555, 5,985,661, 5,980,900, 5,972,596, 5,939,538, 5,912,338, 5,869,339, 5,866,701, 5,866,694, 5,866,320, 5,866,137, 5,864,027, 5,861,242, 5,858,785, 5,858,651, 5,849,475, 5,843,638, 5,840,480, 5,821,046, 5,801,056, 5,786,177, 5,786,145, 5,773,247, 5,770,703, 5,756,674, 5,741,706, 5,705,612, 5,693,752, 5,688,637, 5,688,511, 5,684,147, 5,665,577, 5,585,263, 5,578,715, 5,571,712, 5,567,603, 5,554,528, 5,545,726, 5,527,895, 5,527,894, 5,223,423, 5,204,259, 5,144,019, 5,051,496 and 4,942,122 are useful for the present invention.
Any epitope recognized by an HIV antibody may be used in the present invention. For example, the anti-HIV antibodies of U.S. Pat. Nos. 6,949,337, 6,900,010, 6,821,744, 6,768,004, 6,613,743, 6,534,312, 6,511,830, 6,489,131, 6,242,197, 6,114,143, 6,074,646, 6,063,564, 6,060,254, 5,919,457, 5,916,806, 5,871,732, 5,824,304, 5,773,247, 5,736,320, 5,637,455, 5,587,285, 5,514,541, 5,317,009, 4,983,529, 4,886,742, 4,870,003 and 4,795,739 are useful for the present invention. Furthermore, monoclonal anti-HIV antibodies of U.S. Pat. Nos. 7,074,556, 7,074,554, 7,070,787, 7,060,273, 7,045,130, 7,033,593, RE39,057, 7,008,622, 6,984,721, 6,972,126, 6,949,337, 6,946,465, 6,919,077, 6,916,475, 6,911,315, 6,905,680, 6,900,010, 6,825,217, 6,824,975, 6,818,392, 6,815,201, 6,812,026, 6,812,024, 6,797,811, 6,768,004, 6,703,019, 6,689,118, 6,657,050, 6,608,179, 6,600,023, 6,596,497, 6,589,748, 6,569,143, 6,548,275, 6,525,179, 6,524,582, 6,506,384, 6,498,006, 6,489,131, 6,465,173, 6,461,612, 6,458,933, 6,432,633, 6,410,318, 6,406,701, 6,395,275, 6,391,657, 6,391,635, 6,384,198, 6,376,170, 6,372,217, 6,344,545, 6,337,181, 6,329,202, 6,319,665, 6,319,500, 6,316,003, 6,312,931, 6,309,880, 6,296,807, 6,291,239, 6,261,558, 6,248,514, 6,245,331, 6,242,197, 6,241,986, 6,228,361, 6,221,580, 6,190,871, 6,177,253, 6,146,635, 6,146,627, 6,146,614, 6,143,876, 6,132,992, 6,124,132, RE36,866, 6,114,143, 6,103,238, 6,060,254, 6,039,684, 6,030,772, 6,020,468, 6,013,484, 6,008,044, 5,998,132, 5,994,515, 5,993,812, 5,985,545, 5,981,278, 5,958,765, 5,939,277, 5,928,930, 5,922,325, 5,919,457, 5,916,806, 5,914,109, 5,911,989, 5,906,936, 5,889,158, 5,876,716, 5,874,226, 5,872,012, 5,871,732, 5,866,694, 5,854,400, 5,849,583, 5,849,288, 5,840,480, 5,840,305, 5,834,599, 5,831,034, 5,827,723, 5,821,047, 5,817,767, 5,817,458, 5,804,440, 5,795,572, 5,783,670, 5,776,703, 5,773,225, 5,766,944, 5,753,503, 5,750,373, 5,747,641, 5,736,341, 5,731,189, 5,707,814, 5,702,707, 5,698,178, 5,695,927, 5,665,536, 5,658,745, 5,652,138, 5,645,836, 5,635,345, 5,618,922, 5,610,035, 5,607,847, 5,604,092, 5,601,819, 5,597,896, 5,597,688, 5,591,829, 5,558,865, 5,514,541, 5,510,264, 5,478,753, 5,374,518, 5,374,516, 5,344,755, 5,332,567, 5,300,433, 5,296,347, 5,286,852, 5,264,221, 5,260,308, 5,256,561, 5,254,457, 5,230,998, 5,227,159, 5,223,408, 5,217,895, 5,180,660, 5,173,399, 5,169,752, 5,166,050, 5,156,951, 5,140,105, 5,135,864, 5,120,640, 5,108,904, 5,104,790, 5,049,389, 5,030,718, 5,030,555, 5,004,697, 4,983,529, 4,888,290, 4,886,742 and 4,853,326, are also useful for the present invention.
The vectors used in accordance with the present invention should typically be chosen such that they contain a suitable gene regulatory region, such as a promoter or enhancer, such that the antigens and/or antibodies of the invention may be expressed.
For example, when the aim is to express the antibodies and/or antigens of the invention in vitro, or in cultured cells, or in any prokaryotic or eukaryotic system for the purpose of producing the protein(s) encoded by that antibody and/or antigen, then any suitable vector may be used depending on the application. For example, plasmids, viral vectors, bacterial vectors, protozoan vectors, insect vectors, baculovirus expression vectors, yeast vectors, mammalian cell vectors, and the like, may be used. Suitable vectors may be selected by the skilled artisan taking into consideration the characteristics of the vector and the requirements for expressing the antibodies and/or antigens under the identified circumstances.
When the aim is to express the antibodies and/or antigens of the invention in vivo in a subject, for example in order to generate an immune response against an HIV-1 antigen and/or protective immunity against HIV-1, expression vectors that are suitable for expression on that subject, and that are safe for use in vivo, should be chosen. For example, in some embodiments it may be desired to express the antibodies and/or antigens of the invention in a laboratory animal, such as for pre-clinical testing of the HIV-1 immunogenic compositions and vaccines of the invention. In other embodiments, it will be desirable to express the antibodies and/or antigens of the invention in human subjects, such as in clinical trials and for actual clinical use of the immunogenic compositions and vaccine of the invention. Any vectors that are suitable for such uses may be employed, and it is well within the capabilities of the skilled artisan to select a suitable vector. In some embodiments it may be preferred that the vectors used for these in vivo applications are attenuated to vector from amplifying in the subject. For example, if plasmid vectors are used, preferably they will lack an origin of replication that functions in the subject so as to enhance safety for in vivo use in the subject. If viral vectors are used, preferably they are attenuated or replication-defective in the subject, again, so as to enhance safety for in vivo use in the subject.
In preferred embodiments of the present invention viral vectors are used. Viral expression vectors are well known to those skilled in the art and include, for example, viruses such as adenoviruses, adeno-associated viruses (AAV), alphaviruses, herpesviruses, retroviruses and poxviruses, including avipox viruses, attenuated poxviruses, vaccinia viruses, and the modified vaccinia Ankara virus (MVA; ATCC Accession No. VR-1566). Such viruses, when used as expression vectors are innately non-pathogenic in the selected subjects such as humans or have been modified to render them non-pathogenic in the selected subjects. For example, replication-defective adenoviruses and alphaviruses are well known and may be used as gene delivery vectors.
The present invention relates to recombinant vesicular stomatitis (VSV) vectors, however, other vectors may be contemplated in other embodiments of the invention such as, but not limited to, prime boost administration which may comprise administration of a recombinant VSV vector in combination with another recombinant vector expressing one or more HIV epitopes.
VSV is a very practical, safe, and immunogenic vector for conducting animal studies, and an attractive candidate for developing vaccines for use in humans. VSV is a member of the Rhabdoviridae family of enveloped viruses containing a nonsegmented, negative-sense RNA genome. The genome is composed of 5 genes arranged sequentially 3′-N-P-M-G-L-5′, each encoding a polypeptide found in mature virions. Notably, the surface glycoprotein G is a transmembrane polypeptide that is present in the viral envelope as a homotrimer, and like Env, it mediates cell attachment and infection.
The VSVs of U.S. Pat. Nos. 7,468,274; 7,419,829; 7,419,674; 7,344,838; 7,332,316; 7,329,807; 7,323,337; 7,259,015; 7,244,818; 7,226,786; 7,211,247; 7,202,079; 7,198,793; 7,198,784; 7,153,510; 7,070,994; 6,969,598; 6,958,226; RE38,824; PPI5,957; 6,890,735; 6,887,377; 6,867,326; 6,867,036; 6,858,205; 6,835,568; 6,830,892; 6,818,209; 5 6,790,641; 6,787,520; 6,743,620; 6,740,764; 6,740,635; 6,740,320; 6,682,907; 6,673,784; 6,673,572; 6,669,936; 6,653,103; 6,607,912; 6,558,923; 6,555,107; 6,533,855; 6,531,123; 6,506,604; 6,500,623; 6,497,873; 6,489,142; 6,410,316; 6,410,313; 6,365,713; 6,348,312; 6,326,487; 6,312,682; 6,303,331; 6,277,633; 6,207,455; 6,200,811; 6,190,650; 6,171,862; 6,143,290; 6,133,027; 6,121,434; 6,103,462; 6,069,134; 6,054,127; 6,034,073; 5,969,211; 10 5,935,822; 5,888,727; 5,883,081; 5,876,727; 5,858,740; 5,843,723; 5,834,256; 5,817,491; 5,792,604; 5,789,229; 5,773,003; 5,763,406; 5,760,184; 5,750,396; 5,739,018; 5,698,446; 5,686,279; 5,670,354; 5,540,923; 5,512,421; 5,090,194; 4,939,176; 4,738,846; 4,622,292; 4,556,556 and 4,396,628 may be contemplated by the present invention.
The nucleotide sequences and vectors of the invention may be delivered to cells, for example if the aim is to express HIV-1 antigens in cells in order to produce and isolate the expressed proteins, such as from cells grown in culture. For expressing the antibodies and/or antigens in cells any suitable transfection, transformation, or gene delivery methods may be used. Such methods are well known by those skilled in the art, and one of skill in the art would readily be able to select a suitable method depending on the nature of the nucleotide sequences, vectors, and cell types used. For example, transfection, transformation, microinjection, infection, electroporation, lipofection, or liposome-mediated delivery could be used. Expression of the antibodies and/or antigens may be carried out in any suitable type of host cells, such as bacterial cells, yeast, insect cells, and mammalian cells. The antibodies and/or antigens of the invention may also be expressed including using in vitro transcription/translation systems. All of such methods are well known by those skilled in the art, and one of skill in the art would readily be able to select a suitable method depending on the nature of the nucleotide sequences, vectors, and cell types used.
In preferred embodiments, the nucleotide sequences, antibodies and/or antigens of the invention are administered in vivo, for example where the aim is to produce an immunogenic response in a subject. A “subject” in the context of the present invention may be any animal. For example, in some embodiments it may be desired to express the transgenes of the invention in a laboratory animal, such as for pre-clinical testing of the HIV-1 immunogenic compositions and vaccines of the invention. In other embodiments, it will be desirable to express the antibodies and/or antigens of the invention in human subjects, such as in clinical trials and for actual clinical use of the immunogenic compositions and vaccine of the invention. In preferred embodiments the subject is a human, for example a human that is infected with, or is at risk of infection with, HIV-1.
For such in vivo applications the nucleotide sequences, antibodies and/or antigens of the invention are preferably administered as a component of an immunogenic composition which may comprise the nucleotide sequences and/or antigens of the invention in admixture with a pharmaceutically acceptable carrier. The immunogenic compositions of the invention are useful to stimulate an immune response against HIV-1 and may be used as one or more components of a prophylactic or therapeutic vaccine against HIV-1 for the prevention, amelioration or treatment of AIDS. The nucleic acids and vectors of the invention are particularly useful for providing genetic vaccines, i.e. vaccines for delivering the nucleic acids encoding the antibodies and/or antigens of the invention to a subject, such as a human, such that the antibodies and/or antigens are then expressed in the subject to elicit an immune response.
The compositions of the invention may be injectable suspensions, solutions, sprays, lyophilized powders, syrups, elixirs and the like. Any suitable form of composition may be used. To prepare such a composition, a nucleic acid or vector of the invention, having the desired degree of purity, is mixed with one or more pharmaceutically acceptable carriers and/or excipients. The carriers and excipients must be “acceptable” in the sense of being compatible with the other ingredients of the composition. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include, but are not limited to, water, saline, phosphate buffered saline, dextrose, glycerol, ethanol, or combinations thereof, buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).
An immunogenic or immunological composition may also be formulated in the form of an oil-in-water emulsion. The oil-in-water emulsion may be based, for example, on light liquid paraffin oil (European Pharmacopea type); isoprenoid oil such as squalane, squalene, EICOSANE™ or tetratetracontane; oil resulting from the oligomerization of alkene(s), e.g., isobutene or decene; esters of acids or of alcohols containing a linear alkyl group, such as plant oils, ethyl oleate, propylene glycol di(caprylate/caprate), glyceryl tri(caprylate/caprate) or propylene glycol dioleate; esters of branched fatty acids or alcohols, e.g., isostearic acid esters. The oil advantageously is used in combination with emulsifiers to form the emulsion. The emulsifiers may be nonionic surfactants, such as esters of sorbitan, mannide (e.g., anhydromannitol oleate), glycerol, polyglycerol, propylene glycol, and oleic, isostearic, ricinoleic, or hydroxystearic acid, which are optionally ethoxylated, and polyoxypropylene-polyoxyethylene copolymer blocks, such as the Pluronic® products, e.g., L121. The adjuvant may be a mixture of emulsifier(s), micelle-forming agent, and oil such as that which is commercially available under the name Provax® (IDEC Pharmaceuticals, San Diego, Calif.).
The immunogenic compositions of the invention may contain additional substances, such as wetting or emulsifying agents, buffering agents, or adjuvants to enhance the effectiveness of the vaccines (Remington's Pharmaceutical Sciences, 18th edition, Mack Publishing Company, (ed.) 1980).
Adjuvants may also be included. Adjuvants include, but are not limited to, mineral salts (e.g., AlK(SO₄)₂, AlNa(SO₄)₂, AlNH(SO₄)₂, silica, alum, Al(OH)₃, Ca3(PO₄)₂, kaolin, or carbon), polynucleotides with or without immune stimulating complexes (ISCOMs) (e.g., CpG oligonucleotides, such as those described in Chuang, T. H. et al, (2002) J. Leuk. Biol. 71(3): 538-44; Ahmad-Nejad, P. et al (2002) Eur. J. Immunol. 32(7): 1958-68; poly IC or poly AU acids, polyarginine with or without CpG (also known in the art as IC31; see Schellack, C. et al (2003) Proceedings of the 34th Annual Meeting of the German Society of Immunology; Lingnau, K. et al (2002) Vaccine 20(29-30): 3498-508), JuvaVax™ (U.S. Pat. No. 6,693,086), certain natural substances (e.g., wax D from Mycobacterium tuberculosis, substances found in Cornyebacterium parvum, Bordetella pertussis, or members of the genus Brucella), flagellin (Toll-like receptor 5 ligand; see McSorley, S. J. et al (2002) J. Immunol. 169(7): 3914-9), saponins such as QS21, QS17, and QS7 (U.S. Pat. Nos. 5,057,540; 5,650,398; 6,524,584; 6,645,495), monophosphoryl lipid A, in particular, 3-de-O-acylated monophosphoryl lipid A (3D-MPL), imiquimod (also known in the art as IQM and commercially available as Aldara®; U.S. Pat. Nos. 4,689,338; 5,238,944; Zuber, A. K. et al (2004) 22(13-14): 1791-8), and the CCR5 inhibitor CMPD167 (see Veazey, R. S. et al (2003) J. Exp. Med. 198: 1551-1562).
Aluminum hydroxide or phosphate (alum) are commonly used at 0.05 to 0.1% solution in phosphate buffered saline. Other adjuvants that may be used, especially with DNA vaccines, are cholera toxin, especially CTA1-DD/ISCOMs (see Mowat, A. M. et al (2001) J. Immunol. 167(6): 3398-405), polyphosphazenes (Allcock, H. R. (1998) App. Organometallic Chem. 12(10-11): 659-666; Payne, L. G. et al (1995) Pharm. Biotechnol. 6: 473-93), cytokines such as, but not limited to, IL-2, IL-4, GM-CSF, IL-12, IL-15 IGF-1, IFN-α, IFN-β, and IFN-γ (Boyer et al., (2002) J. Liposome Res. 121:137-142; WO01/095919), immunoregulatory proteins such as CD4OL (ADX40; see, for example, WO03/063899), and the CD1a ligand of natural killer cells (also known as CRONY or α-galactosyl ceramide; see Green, T. D. et al, (2003) J. Virol. 77(3): 2046-2055), immunostimulatory fusion proteins such as IL-2 fused to the Fc fragment of immunoglobulins (Barouch et al., Science 290:486-492, 2000) and co-stimulatory molecules B7.1 and B7.2 (Boyer), all of which may be administered either as proteins or in the form of DNA, on the same expression vectors as those encoding the antigens of the invention or on separate expression vectors.
In an advantageous embodiment, the adjuvants may be lecithin is combined with an acrylic polymer (Adjuplex-LAP), lecithin coated oil droplets in an oil-in-water emulsion (Adjuplex-LE) or lecithin and acrylic polymer in an oil-in-water emulsion (Adjuplex-LAO) (Advanced BioAdjuvants (ABA)).
The immunogenic compositions may be designed to introduce the nucleic acids or expression vectors to a desired site of action and release it at an appropriate and controllable rate. Methods of preparing controlled-release formulations are known in the art. For example, controlled release preparations may be produced by the use of polymers to complex or absorb the immunogen and/or immunogenic composition. A controlled-release formulation may be prepared using appropriate macromolecules (for example, polyesters, polyamino acids, polyvinyl, pyrrolidone, ethylenevinylacetate, methylcellulose, carboxymethylcellulose, or protamine sulfate) known to provide the desired controlled release characteristics or release profile. Another possible method to control the duration of action by a controlled-release preparation is to incorporate the active ingredients into particles of a polymeric material such as, for example, polyesters, polyamino acids, hydrogels, polylactic acid, polyglycolic acid, copolymers of these acids, or ethylene vinylacetate copolymers. Alternatively, instead of incorporating these active ingredients into polymeric particles, it is possible to entrap these materials into microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacrylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in New Trends and Developments in Vaccines, Voller et al. (eds.), University Park Press, Baltimore, Md., 1978 and Remington's Pharmaceutical Sciences, 16th edition.
Suitable dosages of the nucleic acids and expression vectors of the invention (collectively, the immunogens) in the immunogenic composition of the invention may be readily determined by those of skill in the art. For example, the dosage of the immunogens may vary depending on the route of administration and the size of the subject. Suitable doses may be determined by those of skill in the art, for example by measuring the immune response of a subject, such as a laboratory animal, using conventional immunological techniques, and adjusting the dosages as appropriate. Such techniques for measuring the immune response of the subject include but are not limited to, chromium release assays, tetramer binding assays, IFN-γ ELISPOT assays, IL-2 ELISPOT assays, intracellular cytokine assays, and other immunological detection assays, e.g., as detailed in the text “Antibodies: A Laboratory Manual” by Ed Harlow and David Lane.
When provided prophylactically, the immunogenic compositions of the invention are ideally administered to a subject in advance of HIV infection, or evidence of HIV infection, or in advance of any symptom due to AIDS, especially in high-risk subjects. The prophylactic administration of the immunogenic compositions may serve to provide protective immunity of a subject against HIV-1 infection or to prevent or attenuate the progression of AIDS in a subject already infected with HIV-1. When provided therapeutically, the immunogenic compositions may serve to ameliorate and treat AIDS symptoms and are advantageously used as soon after infection as possible, preferably before appearance of any symptoms of AIDS but may also be used at (or after) the onset of the disease symptoms.
The immunogenic compositions may be administered using any suitable delivery method including, but not limited to, intramuscular, intravenous, intradermal, mucosal, and topical delivery. Such techniques are well known to those of skill in the art. More specific examples of delivery methods are intramuscular injection, intradermal injection, and subcutaneous injection. However, delivery need not be limited to injection methods. Further, delivery of DNA to animal tissue has been achieved by cationic liposomes (Watanabe et al., (1994) Mol. Reprod. Dev. 38:268-274; and WO 96/20013), direct injection of naked DNA into animal muscle tissue (Robinson et al., (1993) Vaccine 11:957-960; Hoffman et al., (1994) Vaccine 12: 1529-1533; Xiang et al., (1994) Virology 199: 132-140; Webster et al., (1994) Vaccine 12: 1495-1498; Davis et al., (1994) Vaccine 12: 1503-1509; and Davis et al., (1993) Hum. Mol. Gen. 2: 1847-1851), or intradermal injection of DNA using “gene gun” technology (Johnston et al., (1994) Meth. Cell Biol. 43:353-365). Alternatively, delivery routes may be oral, intranasal or by any other suitable route. Delivery may also be accomplished via a mucosal surface such as the anal, vaginal or oral mucosa. Immunization schedules (or regimens) are well known for animals (including humans) and may be readily determined for the particular subject and immunogenic composition. Hence, the immunogens may be administered one or more times to the subject. Preferably, there is a set time interval between separate administrations of the immunogenic composition. While this interval varies for every subject, typically it ranges from 10 days to several weeks, and is often 2, 4, 6 or 8 weeks. For humans, the interval is typically from 2 to 6 weeks. The immunization regimes typically have from 1 to 6 administrations of the immunogenic composition, but may have as few as one or two or four. The methods of inducing an immune response may also include administration of an adjuvant with the immunogens. In some instances, annual, biannual or other long interval (5-10 years) booster immunization may supplement the initial immunization protocol.
The present methods also include a variety of prime-boost regimens, for example DNA prime-VSV boost regimens. In these methods, one or more priming immunizations are followed by one or more boosting immunizations. The actual immunogenic composition may be the same or different for each immunization and the type of immunogenic composition (e.g., containing protein or expression vector), the route, and formulation of the immunogens may also be varied. For example, if an expression vector is used for the priming and boosting steps, it may either be of the same or different type (e.g., DNA or bacterial or viral expression vector). One useful prime-boost regimen provides for two priming immunizations, four weeks apart, followed by two boosting immunizations at 4 and 8 weeks after the last priming immunization. It should also be readily apparent to one of skill in the art that there are several permutations and combinations that are encompassed using the DNA, bacterial and viral expression vectors of the invention to provide priming and boosting regimens.
The prime-boost regimen may also include VSV vectors that derive their G protein or G/Stem protein from different serotype vesicular stomatitis viruses (Rose N F, Roberts A, Buonocore L, Rose J K. Glycoprotein exchange vectors based on vesicular stomatitis virus allow effective boosting and generation of neutralizing antibodies to a primary isolate of human immunodeficiency virus type 1. J. Virol. 2000 December; 74(23):10903-10). The VSV vectors used in these examples contain a G or G/Stem protein derived from the Indiana serotype of VSV. Vectors may also be constructed to express G or G/Stem molecules derived from other VSV serotypes (i.e. vesicular stomatitis New Jersey virus or vesicular stomatitis Alagoas virus) or other vesiculoviruses (i.e. Chandipura virus, Cocal virus, Isfahan virus). Thus a prime may be delivered in the context of a G or G/Stem moelcule that is from the Indiana serotype and the immune system may be boosted with a vector that expresses epitopes in the context of second serotype like New Jersey. This circumvents anti-G immunity elicited by the prime, and helps focus the boost response against the foreign epitope.
A specific embodiment of the invention provides methods of inducing an immune response against HIV in a subject by administering an immunogenic composition of the invention, preferably which may comprise an VSV vector containing RNA encoding one or more of the epitopes of the invention, one or more times to a subject wherein the epitopes are expressed at a level sufficient to induce a specific immune response in the subject. Such immunizations may be repeated multiple times at time intervals of at least 2, 4 or 6 weeks (or more) in accordance with a desired immunization regime.
The immunogenic compositions of the invention may be administered alone, or may be co-administered, or sequentially administered, with other HIV immunogens and/or HIV immunogenic compositions, e.g., with “other” immunological, antigenic or vaccine or therapeutic compositions thereby providing multivalent or “cocktail” or combination compositions of the invention and methods of employing them. Again, the ingredients and manner (sequential or co-administration) of administration, as well as dosages may be determined taking into consideration such factors as the age, sex, weight, species and condition of the particular subject, and the route of administration.
When used in combination, the other HIV immunogens may be administered at the same time or at different times as part of an overall immunization regime, e.g., as part of a prime-boost regimen or other immunization protocol. In an advantageous embodiment, the other HIV immunogen is env, preferably the HIV env trimer.
Many other HIV immunogens are known in the art, one such preferred immunogen is HIVA (described in WO 01/47955), which may be administered as a protein, on a plasmid (e.g., pTHr.HIVA) or in a viral vector (e.g., MVA.HIVA). Another such HIV immunogen is RENTA (described in PCT/US2004/037699), which may also be administered as a protein, on a plasmid (e.g., pTHr.RENTA) or in a viral vector (e.g., MVA.RENTA).
For example, one method of inducing an immune response against HIV in a human subject may comprise administering at least one priming dose of an HIV immunogen and at least one boosting dose of an HIV immunogen, wherein the immunogen in each dose may be the same or different, provided that at least one of the immunogens is an epitope of the present invention, a nucleic acid encoding an epitope of the invention or an expression vector, preferably a VSV vector, encoding an epitope of the invention, and wherein the immunogens are administered in an amount or expressed at a level sufficient to induce an HIV-specific immune response in the subject. The HIV-specific immune response may include an HIV-specific T-cell immune response or an HIV-specific B-cell immune response. Such immunizations may be done at intervals, preferably of at least 2-6 or more weeks.
It is to be understood and expected that variations in the principles of invention as described above may be made by one skilled in the art and it is intended that such modifications, changes, and substitutions are to be included within the scope of the present invention.
The invention will now be further described by way of the following non-limiting examples.

EXAMPLES

Example 1

Recombinant VSV Vector Construction

Structure of the IAVI VSV genomic clone as depicted in FIG. 1.
Features include:

- 1. The cloning vector is based on pSP72 (Genbank X65332.2).
- 2. The extended T7 promoter is PT7-g10 described by Lopez et al. (Lopez et al., 1997. Journal of molecular biology 269:41-51)
- 3. The hammerhead ribozyme was designed following the rules for constructing self-cleaving RNA sequences (Inoue et al. 2003. J Virol Methods 107:229-236 and Ruffner et al. 1990. Biochemistry 29:10695-10702).
- 4. The hepatitis delta virus ribozyme and T7 RNA polymerase terminator were used as described before for the measles virus rescue system (Radecke et al. 1995. The EMBO journal 14:5773-5784, 23 and Sidhu et al, 1995. Virology 208:800-807)
- 5. Unique restriction endonuclease cleavage sites in the recombinant VSV genomne (red) are indicated above the genome map.
- 6. The Leader and Trailer are cis-acting sequences in the termini that control mRNA synthesis and replication.
- 7. The viral proteins N, nucleocapsid; P, phosphoprotein; M, matrix; G, glycoprotein; L, large protein.

Recombinant VSV Vector Construction

- Indiana Serotype
- Based on Genbank EF197793—modified as described below:
- Nucleotide substitutions introduced to generate unique restriction sites or bring sequence closer to consensus
  - 1371 CA>GC (NheI)
  - After 2195 insert TAG (SpeI) (all genome numbers below adjusted to include +3 by introduced by this insertion)
  - 3036 G>T improves match to consensus transcription stop signal
  - 3853 X>A (X was an ambiguity in Genbank file)
  - 4691 T>A to generate PacI
  - 7546 C>A silent change in L coding sequence eliminates a BstBI site
  - 1960 TAC>TCC to change Y>S
  - 3247 GTA>ATA to change V>I
  - 3729 AAG>GAG to change K>E
  - 4191 GTA>GAA to change V>E
  - 4386 GGT>GAT to change G>D
  - 4491 ACC>ATC to change T>I
  - 5339 ATT>CTT to change I>L
  - 5834 ACT>GCT to change T>A
  - 10959 AGA>AAA to change R>K

A VSV genome and cloning fragments are depicted in FIGS. 2A-G.

TABLE 1

Modifications introduced into the VSV genomic sequence (Genbank accession EF197793)
are listed. Note that Line 3 includes a 3 base insertion, which shifts numbering in
the recombinant genomic clone (rEF197793). If nucleotide substitutions were introduced
to change amino acid coding, the base change in the codon is indicated in red.

Genbank X65332.2: Cloning vector pSP72

LOCUS		X65332 2462 bp DNA circular SYN 25 JAN. 2000
DEFINITION		Cloning vector pSP72.
ACCESSION		X65332
VERSION		X65332.2 GI:6759494
KEYWORDS		beta-lactamase; bla gene; cloning vector; multiple cloning site;
		promoter.
SOURCE		Cloning vector pSP72
ORGANISM		Cloning vector pSP72
		other sequences; artificial sequences; vectors.
REFERENCE		1
AUTHORS		Technical, Services.
TITLE		Direct Submission
JOURNAL		Submitted (23 MAR. 1992) Technical Services, Promega Corporation,
		2800 Woods Hollow Road, Madison, Wi 53711-5399, USA
REMARK		revised by [2]
REFERENCE		2
AUTHORS		Technical, Services.
TITLE		Direct Submission
JOURNAL		Submitted (28 MAY 1993) Technical Services, Promega Corporation,
		2800 Woods Hollow Road, Madison, Wi 53711-5399, USA
REMARK		revised by [3]
REFERENCE		3 (bases 1 to 2462)
AUTHORS		Technical, Services.
TITLE		Direct Submission
JOURNAL		Submitted (12 JAN. 2000) Technical Services, Promega Corporation,
		2800 Woods Hollow Road, Madison, Wi 53711-5399, USA
COMMENT		On Jan. 26, 2000 this sequence version replaced gi:58239.
		See X65300-X65335 for related vector sequences
		This vector can be obtained from Promega Corporation, Madison, WI
		Call one of the following numbers for order or technical
		information:
		Order or Technical 800-356-9526
		In Wisconsin 800-356-9526
		Outside U.S. 608-274-4330.

FEATURES		Location/Qualifiers
	source	1 . . . 2462
		/organism=“Cloning vector pSP72”
		/mol_type=“other DNA”
		/db_xref=“taxon:90137”
	promoter	join(2446 . . . 2462,1 . . . 3)
		/note=“SP6 promoter”
	misc_feature	1
		/note=“SP6 transcription initiation site”
	misc_feature	4 . . . 90
		/note=“multiple cloning sites”
	promoter	99 . . . 118
		/note=“T7 promoter”
	misc_feature	101
		/note=“T7 transcription initiation site”
	gene	complement(1135 . . . 1995)
		/gene=“bla”
	CDS	complement(1135 . . . 1995)
		/gene=“bla”
		/codon_start=1
		/transl_table=11
		/product=“Beta-lactamase”
		/protein_id=“CAA46432.1”
		/db_xref=“GI:58240”

/translation=“MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGY
IELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVE
YSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRL
DRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPL
LRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIA
EIGASLIKHW”

ORIGIN
	1	gaactcgagc agctgaagct tgcatgcctg caggtcgact ctagaggatc cccgggtacc
	61	gagctcgaat tcatcgatga tatcagatct gccggtctcc ctatagtgag tcgtattaat
	121	ttcgataagc caggttaacc tgcattaatg aatcggccaa cgcgcgggga gaggcggttt
	181	gcgtattggg cgctcttccg cttcctcgct cactgactcg ctgcgctcgg tcgttcggct
	241	gcggcgagcg gtatcagctc actcaaaggc ggtaatacgg ttatccacag aatcagggga
	301	taacgcagga aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc
	361	cgcgttgctg gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg
	421	ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg
	481	aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt
	541	tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcagttcggt
	601	gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg
	661	cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgact tatcgccact
	721	ggcagcagcc actggtaaca ggattagcag agcgaggtat gtaggcggtg ctacagagtt
	781	cttgaagtgg tggcctaact acggctacac tagaagaaca gtatttggta tctgcgctct
	841	gctgaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca aacaaaccac
	901	cgctggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc
	961	tcaagaagat cctttgatct tttctacggg gtctgacgct cagtggaacg aaaactcacg
	1021	ttaagggatt ttggtcatga gattatcaaa aaggatcttc acctagatcc ttttaaatta
	1081	aaaatgaagt tttaaatcaa tctaaagtat atatgagtaa acttggtctg acagttacca
	1141	atgcttaatc agtgaggcac ctatctcagc gatctgtcta tttcgttcat ccatagttgc
	1201	ctgactcccc gtcgtgtaga taactacgat acgggagggc ttaccatctg gccccagtgc
	1261	tgcaatgata ccgcgagacc cacgctcacc ggctccagat ttatcagcaa taaaccagcc
	1321	agccggaagg gccgagcgca gaagtggtcc tgcaacttta tccgcctcca tccagtctat
	1381	taattgttgc cgggaagcta gagtaagtag ttcgccagtt aatagtttgc gcaacgttgt
	1441	tgccattgct acaggcatcg tggtgtcacg ctcgtcgttt ggtatggctt cattcagctc
	1501	cggttcccaa cgatcaaggc gagttacatg atcccccatg ttgtgcaaaa aagcggttag
	1561	ctccttcggt cctccgatcg ttgtcagaag taagttggcc gcagtgttat cactcatggt
	1621	tatggcagca ctgcataatt ctcttactgt catgccatcc gtaagatgct tttctgtgac
	1681	tggtgagtac tcaaccaagt cattctgaga atagtgtatg cggcgaccga gttgctcttg
	1741	cccggcgtca atacgggata ataccgcgcc acatagcaga actttaaaag tgctcatcat
	1801	tggaaaacgt tcttcggggc gaaaactctc aaggatctta ccgctgttga gatccagttc
	1861	gatgtaaccc actcgtgcac ccaactgatc ttcagcatct tttactttca ccagcgtttc
	1921	tgggtgagca aaaacaggaa ggcaaaatgc cgcaaaaaag ggaataaggg cgacacggaa
	1981	atgttgaata ctcatactct tcctttttca atattattga agcatttatc agggttattg
	2041	tctcatgagc ggatacatat ttgaatgtat ttagaaaaat aaacaaatag gggttccgcg
	2101	cacatttccc cgaaaagtgc cacctgacgt ctaagaaacc attattatca tgacattaac
	2161	ctataaaaat aggcgtatca cgaggccctt tcgtctcgcg cgtttcggtg atgacggtga
	2221	aaacctctga cacatgcagc tcccggagac ggtcacagct tgtctgtaag cggatgccgg
	2281	gagcagacaa gcccgtcagg gcgcgtcagc gggtgttggc gggtgtcggg gctggcttaa
	2341	ctatgcggca tcagagcaga ttgtactgag agtgcaccat atggacatat tgtcgttaga
	2401	acgcggctac aattaataca taaccttatg tatcatacac atacgattta ggtgacacta
	2461	ta//

Genbank EF197793: Vesicular stomatitis Indiana virus, complete genome

LOCUS		EF197793 11161 bp cRNA linear VRL 15 APR. 2007
DEFINITION		Vesicular stomatitis Indiana virus, complete genome.
ACCESSION		EF197793
VERSION		EF197793.1 GI:144678900
SOURCE		Vesicular stomatitis Indiana virus
ORGANISM		Vesicular stomatitis Indiana virus
		Viruses; ssRNA negative-strand viruses; Mononegavirales;
		Rhabdoviridae; Dimarhabdovirus supergroup; Vesiculovirus.
REFERENCE		1 (bases 1 to 11161)
AUTHORS		Remold, S. K., Rambaut, A. and Turner, P. T.
TITLE		Evolutionary genomics of host adaptation in Vesicular stomatitis
		virus
JOURNAL		Unpublished
REFERENCE		2 (bases 1 to 11161)
AUTHORS		Remold, S.K.
TITLE		Direct Submission
JOURNAL		Submitted (22 DEC. 2006) Biology, University of Louisville, 139

Life Sciences Building, Louisville, KY 40292, USA

FEATURES			Location/Qualifiers
	source
		1 . . . 11161
			/organism=“Vesicular stomatitis Indiana virus”
			/mol_type=“viral cRNA”
			/isolate=“MARMC from S.F. Elena Lab, 2001”
			/db_xref=“taxon:11277”
			/country=“USA”
	gene		51 . . . 1376
			/gene=“N”
	CDS		64 . . . 1332
			/gene=“N”
			/codon_start=1
			/product=“nucleoprotein”
			/protein_id=“ABP01780.1”
			/db_xref=“GI:144678901”

/translation=“MSVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINT
TKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDIRGKLDKDWSSFGINIGKAGDTI
GIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKRLMDGL
TNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTI
VSRFKDCAALATFGHLCKITGMSTEDVTTWILNREVADEMVQMMLPGQEIDKADSYMP
YLIDFGLSSKSPYSSVKNPAFHFWGQLTALLLRSTRARNARQPDDIEYTSLTTAGLLY
AYAVGSSADLAQQFCVGDSKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPD
MMQYAKRAVMSLQGLREKTIGKYAKSEFDK”

	gene		1386 . . . 2199
			/gene=“P”
	CDS		1396 . . . 2193
			/gene=“P”
			/codon_start=1
			/product=“phosphoprotein”
			/protein_id=“ABP01781.1”
			/db_xref=“GI:144678902”

/translation=“MDNLTKVREYLKSYSRLDQAVGEIDEIEAQRAEKSNYELFQEDG
VEEHTRPSYFQAADDSDTESEPEIEDNQGLYVPDPEAEQVEGFIQGPLDDYADEDVDV
VFTSDWKQPELESDEHGKTLRLTLPEGLSGEQKSQWLLTIKAVVQSAKHWNLAECTFE
ASGEGVIIKKRQITPDVYKVTPVMNTHPYQSEAVSDVWSLSKTSMTFQPKKASLQPLT
ISLDELFSSRGEFISVGGNGRMSHKEAILLGLRYKKLYNQARVKYSL”

	gene		2209 . . . 3039
			/gene=“M”
	CDS		2250 . . . 2939
			/gene=“M”
			/codon_start=1
			/product=“matrix”
			/protein_id=“ABP01782.1”
			/db_xref=“GI:144678903”

/translation=“MSSLKKILGLKGKGKKSKKLGIAPPPYEEDTNMEYAPSAPIDKS
YFGVDEMDTHDPNQLRYEKFFFTVKMTVRSNRPFRTYSDVAAAVSHWDHMYIGMAGKR
PFYKILAFLGSSNLKATPAVLADQGQPEYHAHCEGRAYLPHRMGKTPPMLNVPEHFRR
PFNIGLYKGTIELTMTIYDDESLEAAPMIWDHFNSSKFSDFREKALMFGLIVEKKASG
AWVLDSVSHFK”

	gene		3049 . . . 4713
			/gene=“G”
	CDS		3078 . . . 4613
			/gene=“G”
			/codon_start=1
			/product=“glycoprotein”
			/protein_id=“ABP01783.1”
			/db_xref=“GI:144678904”

/translation=“MKCLLYLAFLFIGVNCKFTIVFPHNQKGNWKNVPSNYHYCPSSS
DLNWHNDLVGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGPKYITHSIRSFT
PSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAAIVQVTPHHVLVDEYTGEWV
DSQFINGKCSNDICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKKG
TGFRSNYFAYETGDKACKMQYCKHWGVRLPSGVWFEMADKXLFAAARFPECPEGSSIS
APSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPVDLSYLAPKNPGTGPVFTI
INGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERVLWDDWAPYEDVEIGPNGVLRT
SSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDGETLFFGDTGLSKNP
IEFVEGWFSSWKSSIASFFFTIGLIIGLFLVLRVGIYLCIKLKHTKKRQIYTDIEMNR
LGK”

	gene		4723 . . . 11095
			/gene=“L”
	CDS		4733 . . . 11062
			/gene=“L”
			/codon start=1
			/product=“large protein”
			/protein_id=“ABP01784.1”
			/db_xref=“GI:144678905”

/translation=“MEVHDFETDEFNDFNEDDYATREFLNPDERMTYLNHADYNLNSP
LISDDIDNLIRKFNSLPIPSMWDSKNWDGVLEMLTSCQANPISTSQMHKWMGSWLMSD
NHDASQGYSFLHEVDKEAEITFDVVETFIRGWGNKPIEYIKKERWTDSFKILAYLCQK
FLDLHKLTLILNAVSEVELLNLARTFKGKVRRSSHGTNICRIRVPSLGPTFISEGWAY
FKKLDILMDRNFLLMVKDVIIGRMQTVLSMVCRIDNLFSEQDIFSLLNIYRIGDKIVE
RQGNFSYDLIKMVEPICNLKLMKLARESRPLVPQFPHFENHIKTSVDEGAKIDRGIRF
LHDQIMSVKTVDLTLVIYGSFRHWGHPFIDYYTGLEKLHSQVTMKKDIDVSYAKALAS
DLARIVLFQQFNDHKKWFVNGDLLPHDHPFKSHVKENTWPTAAQVQDFGDKWHELPLI
KCFEIPDLLDPSIIYSDKSHSMNRSEVLKHVRMNPNTPIPSKKVLQTMLDTKATNWKE
FLKEIDEKGLDDDDLIIGLKGKERELKLAGRFFSLMSWKLREYFVITEYLIKTHFVPM
FKGLTMADDLTAVIKKMLDSSSGQGLKSYEAICIANHIDYEKWNNHQRKLSNGPVFRV
MGQFLGYPSLIERTHEFFEKSLIYYNGRPDLMRVHNNTLINSTSQRVCWQGQEGGLEG
LRQKGWSILNLLVIQREAKIRNTAVKVLAQGDNQVICTQYKTKKSRNVVELQGALNQM
VSNNEKIMTAIKIGTGKLGLLINDDETMQSADYLNYGKIPIFRGVIRGLETKRWSRVT
CVTNDQIPTCANIMSSVSTNALTVAHFAENPINAMIQYNYFGTFARLLLMMHDPALRQ
SLYEVQDKIPGLHSSTFKYAMLYLDPSIGGVSGMSLSRFLIRAFPDPVTESLSFWRFI
HVHARSEHLKEMSAVFGNPEIAKFRITHIDKLVEDPTSLNIAMGMSPANLLKTEVKKC
LIESRQTIRNQVIKDATIYLYHEEDRLRSFLWSINPLFPRFLSEFKSGTFLGVADGLI
SLFQNSRTIRNSFKKKYHRELDDLIVRSEVSSLTHLGKLHLRRGSCKMWTCSATHADT
LRYKSWGRTVIGTTVPHPLEMLGPQHRKETPCAPCNTSGFNYVSVHCPDGIHDVFSSR
GPLPAYLGSKTSESTSILQPWERESKVPLIKRATRLRDAISWFVEPDSKLAMTILSNI
HSLTGEEWTKRQHGFKRTGSALHRFSTSRMSHGGFASQSTAALTRLMATTDTMRDLGD
QNFDFLFQATLLYAQITTTVARDGWITSCTDHYHIACKSCLRPIEEITLDSSMDYTPP
DVSHVLKTWRNGEGSWGQEIKQIYPLEGNWKNLAPAEQSYQVGRCIGFLYGDLAYRKS
THAEDSSLFPLSIQGRIRGRGFLKGLLDGLMRASCCQVIHRRSLAHLKRPANAVYGGL
IYLIDKLSVSPPFLSLTRSGPIRDELETIPHKIPTSYPTSNRDMGVIVRNYFKYQCRL
IEKGKYRSHYSQLWLFSDVLSIDFIGPFSISTTLLQILYKPFLSGKDKNELRELANLS
SLLRSGEGWEDIHVKFFTKDILLCPEEIRHACKFGIAKDNNKDMSYPPWGRESRGTIT
TIPVYYTTTPYPKMLEMPPRIQNPLLSGIRLGQLPTGAHYKIRSILHGMGIHYRDFLS
CGDGSGGMTAALLRENVHSRGIFNSLLELSGSVMRGASPEPPSALETLGGDKSRCVNG
ETCWEYPSDLCDPRTWDYFLRLKAGLGLQIDLIVMDMEVRDSSTSLKIETNVRNYVHR
ILDEQGVLIYKTYGTYICESEKNAVTILGPMFKTVDLVQTEFSSSQTSEVYMVCKGLK
KLIDEPNPDWSSINESWKNLYAFQSSEQEFARAKKVSTYFTLTGIPSQFIPDPFVNIE
TMLQIFGVPTGVSHAAALKSSDRPADLLTISLFYMAIISYYNINHIRVGPIPPNPPSD
GIAQNVGIAITGISFWLSLMEKDIPLYQQCLAVIQQSFPIRWEAVSVKGGYKQKWSTR
GDGLPKDTRISDSLAPIGNWIRSLELVRNQVRLNPFNEILFNQLCRTVDNHLKWSNLR
RNTGMIEWINRRISKEDRSILMLKSDLHEENSWRD”

ORIGIN
	1	acgaagacaa acaaaccatt attatcatta aaaggctcag gagaaacttt aacagtaatc
	61	aaaatgtctg ttacagtcaa gagaatcatt gacaacacag tcatagttcc aaaacttcct
	121	gcaaatgagg atccagtgga atacccggca gattacttca gaaaatcaaa ggagattcct
	181	ctttacatca atactacaaa aagtttgtca gatctaagag gatatgtcta ccaaggcctc
	241	aaatccggaa atgtatcaat catacatgtc aacagctact tgtatggagc attgaaggac
	301	atccggggta agttggataa agattggtca agtttcggaa taaacatcgg gaaggcaggg
	361	gatacaatcg gaatatttga ccttgtatcc ttgaaagccc tggacggtgt acttccagat
	421	ggagtatcgg atgcttccag aaccagcgca gatgacaaat ggttgccttt gtatctactt
	481	ggcttataca gagtgggcag aacacaaatg cctgaataca gaaaaaggct catggatggg
	541	ctgacaaatc aatgcaaaat gatcaatgaa cagtttgaac ctcttgtgcc agaaggtcgt
	601	gacatttttg atgtgtgggg aaatgacagt aattacacaa aaattgtcgc tgcagtggac
	661	atgttcttcc acatgttcaa aaaacatgaa tgtgcctcgt tcagatacgg aactattgtt
	721	tccagattca aagattgtgc tgcattggca acatttggac acctctgcaa aataaccgga
	781	atgtctacag aagatgtgac gacctggatc ttgaaccgag aagttgcaga tgagatggtc
	841	caaatgatgc ttccaggcca agaaattgac aaggctgatt catacatgcc ttatttgatc
	901	gactttggat tgtcttctaa gtctccatat tcttccgtca aaaaccctgc cttccacttc
	961	tgggggcaat tgacagctct tctgctcaga tccaccagag caaggaatgc ccgacagcct
	1021	gatgacattg agtatacatc tcttactaca gcaggtttgt tgtacgctta tgcagtagga
	1081	tcctctgctg acttggcaca acagttttgt gttggagata gcaaatacac tccagatgat
	1141	agtaccggag gattgacgac taatgcaccg ccacaaggca gagatgtggt cgaatggctc
	1201	ggatggtttg aagatcaaaa cagaaaaccg actcctgata tgatgcagta tgcgaaacga
	1261	gcagtcatgt cactgcaagg cctaagagag aagacaattg gcaagtatgc taagtcagag
	1321	tttgacaaat gaccctataa ttctcagatc acctattata tattatgcta catatgaaaa
	1381	aaactaacag atatcatgga taatctcaca aaagttcgtg agtatctcaa gtcctattct
	1441	cgtctagatc aggcggtagg agagatagat gagatcgaag cacaacgagc tgaaaagtcc
	1501	aattatgagt tgttccaaga ggacggagtg gaagagcata ctaggccctc ttattttcag
	1561	gcagcagatg attctgacac agaatctgaa ccagaaattg aagacaatca aggcttgtat
	1621	gtaccagatc cggaagctga gcaagttgaa ggctttatac aggggccttt agatgactat
	1681	gcagatgagg acgtggatgt tgtattcact tcggactgga aacagcctga gcttgaatcc
	1741	gacgagcatg gaaagacctt acggttgaca ttgccagagg gtttaagtgg agagcagaaa
	1801	tcccagtggc ttttgacgat taaagcagtc gttcaaagtg ccaaacactg gaatctggca
	1861	gagtgcacat ttgaagcatc gggagaaggg gtcatcataa aaaagcgcca gataactccg
	1921	gatgtatata aggtcactcc agtgatgaac acacatccgt accaatcaga agccgtatca
	1981	gatgtttggt ctctctcaaa gacatccatg actttccaac ccaagaaagc aagtcttcag
	2041	cctctcacca tatccttgga tgaattgttc tcatctagag gagaattcat ctctgtcgga
	2101	ggtaacggac gaatgtctca taaagaggcc atcctgctcg gtctgaggta caaaaagttg
	2161	tacaatcagg cgagagtcaa atattctctg tagactatga aaaaaagtaa cagatatcac
	2221	aatctaagtg ttatcccaat ccattcatca tgagttcctt aaagaagatt ctcggtctga
	2281	aggggaaagg taagaaatct aagaaattag ggatcgcacc acccccttat gaagaggaca
	2341	ctaacatgga gtatgctccg agcgctccaa ttgacaaatc ctattttgga gttgacgaga
	2401	tggacactca tgatccgaat caattaagat atgagaaatt cttctttaca gtgaaaatga
	2461	cggttagatc taatcgtccg ttcagaacat actcagatgt ggcagccgct gtatcccatt
	2521	gggatcacat gtacatcgga atggcaggga aacgtccctt ctacaagatc ttggcttttt
	2581	tgggttcttc taatctaaag gccactccag cggtattggc agatcaaggt caaccagagt
	2641	atcatgctca ctgtgaaggc agggcttatt tgccacacag aatggggaag acccctccca
	2701	tgctcaatgt accagagcac ttcagaagac cattcaatat aggtctttac aagggaacga
	2761	ttgagctcac aatgaccatc tacgatgatg agtcactgga agcagctcct atgatctggg
	2821	atcatttcaa ttcttccaaa ttttctgatt tcagagagaa ggccttaatg tttggcctga
	2881	ttgtcgagaa aaaggcatct ggagcttggg tcctggattc tgtcagccac ttcaaatgag
	2941	ctagtctagc ttccagcttc tgaacaatcc ccggtttact cagtctctcc taattccagc
	3001	ctttcgaaca actaatatcc tgtcttctct atcccgatga aaaaaactaa cagagatcga
	3061	tctgtttcct tgacaccatg aagtgccttt tgtacttagc ttttttattc atcggggtga
	3121	attgcaagtt caccatagtt tttccacaca accaaaaagg aaactggaaa aatgttcctt
	3181	ccaattacca ttattgcccg tcaagctcag atttaaattg gcataatgac ttagtaggca
	3241	cagccttaca agtcaaaatg cccaagagtc acaaggctat tcaagcagac ggttggatgt
	3301	gtcatgcttc caaatgggtc actacttgtg atttccgctg gtacggaccg aagtatataa
	3361	cacattccat ccgatccttc actccatctg tagaacaatg caaggaaagc attgaacaaa
	3421	cgaaacaagg aacttggctg aatccaggct tccctcctca aagttgtgga tatgcaactg
	3481	tgacggatgc tgaagcagcg attgtccagg tgactcctca ccatgtgctt gttgatgaat
	3541	acacaggaga atgggttgat tcacagttca tcaacggaaa atgcagcaat gacatatgcc
	3601	ccactgtcca taactccaca acctggcatt ccgactataa ggtcaaaggg ctatgtgatt
	3661	ctaacctcat ttccatggac atcaccttct tctcagagga cggagagcta tcatccctag
	3721	gaaagaaggg cacagggttc agaagtaact actttgctta tgaaactgga gacaaggcct
	3781	gcaaaatgca gtactgcaag cattggggag tcagactccc atcaggtgtc tggttcgaga
	3841	tggctgataa ggmtctcttt gctgcagcca gattccctga atgcccagaa gggtcaagta
	3901	tctctgctcc atctcagacc tcagtggatg taagtctcat tcaggacgtt gagaggatct
	3961	tggattattc cctctgccaa gaaacctgga gcaaaatcag agcgggtctt cccatctctc
	4021	cagtggatct cagctatctt gctcctaaaa acccaggaac cggtcctgtc tttaccataa
	4081	tcaatggtac cctaaaatac tttgagacca gatacatcag agtcgatatt gctgctccaa
	4141	tcctctcaag aatggtcgga atgatcagtg gaactaccac agaaagggta ctgtgggatg
	4201	actgggctcc atatgaagac gtggaaattg gacccaatgg agttctgagg accagttcag
	4261	gatataagtt tcctttatat atgattggac atggtatgtt ggactccgat cttcatctta
	4321	gctcaaaggc tcaggtgttt gaacatcctc acattcaaga cgctgcttcg cagcttcctg
	4381	atggtgagac tttatttttt ggtgatactg ggctatccaa aaatccaatc gagtttgtag
	4441	aaggttggtt cagtagttgg aagagctcta ttgcctcttt tttctttacc atagggttaa
	4501	tcattggact attcttggtt ctccgagttg gtatttatct ttgcattaaa ttaaagcaca
	4561	ccaagaaaag acagatttat acagacatag agatgaaccg acttggaaag taactcaaat
	4621	cctgcacaac agattcttca tgtttgaacc aaatcaactt gtgatatcat gctcaaagag
	4681	gccttaatta tattttaatt tttaattttt atgaaaaaaa ctaacagcaa tcatggaagt
	4741	ccacgatttt gagaccgacg agttcaatga tttcaatgaa gatgactatg ccacaagaga
	4801	attcctgaat cccgatgagc gcatgacgta cttgaatcat gctgattaca atttgaattc
	4861	tcctctaatt agtgatgata ttgacaattt gatcaggaaa ttcaattctc ttccgattcc
	4921	ctcgatgtgg gatagtaaga actgggatgg agttcttgag atgttaacat catgtcaagc
	4981	caatcccatc tcaacatctc agatgcataa atggatggga agttggttaa tgtctgataa
	5041	tcatgatgcc agtcaagggt atagtttttt acatgaagtg gacaaagagg cagaaataac
	5101	atttgacgtg gtggagacct tcatccgcgg ctggggcaac aaaccaattg aatacatcaa
	5161	aaaggaaaga tggactgact cattcaaaat tctcgcttat ttgtgtcaaa agtttttgga
	5221	cttacacaag ttgacattaa tcttaaatgc tgtctctgag gtggaattgc tcaacttggc
	5281	gaggactttc aaaggcaaag tcagaagaag ttctcatgga acgaacatat gcaggattag
	5341	ggttcccagc ttgggtccta cttttatttc agaaggatgg gcttacttca agaaacttga
	5401	tattctaatg gaccgaaact ttctgttaat ggtcaaagat gtgattatag ggaggatgca
	5461	aacggtgcta tccatggtat gtagaataga caacctgttc tcagagcaag acatcttctc
	5521	ccttctaaat atctacagaa ttggagataa aattgtggag aggcagggaa atttttctta
	5581	tgacttgatt aaaatggtgg aaccgatatg caacttgaag ctgatgaaat tagcaagaga
	5641	atcaaggcct ttagtcccac aattccctca ttttgaaaat catatcaaga cttctgttga
	5701	tgaaggggca aaaattgacc gaggtataag attcctccat gatcagataa tgagtgtgaa
	5761	aacagtggat ctcacactgg tgatttatgg atcgttcaga cattggggtc atccttttat
	5821	agattattac actggactag aaaaattaca ttcccaagta accatgaaga aagatattga
	5881	tgtgtcatat gcaaaagcac ttgcaagtga tttagctcgg attgttctat ttcaacagtt
	5941	caatgatcat aaaaagtggt tcgtgaatgg agacttgctc cctcatgatc atccctttaa
	6001	aagtcatgtt aaagaaaata catggcctac agctgctcaa gttcaagatt ttggagataa
	6061	atggcatgaa cttccgctga ttaaatgttt tgaaataccc gacttactag acccatcgat
	6121	aatatactct gacaaaagtc attcaatgaa taggtcagag gtgttgaaac atgtccgaat
	6181	gaatccgaac actcctatcc ctagtaaaaa ggtgttgcag actatgttgg acacaaaggc
	6241	taccaattgg aaagaatttc ttaaagagat tgatgagaag ggcttagatg atgatgatct
	6301	aattattggt cttaaaggaa aggagaggga actgaagttg gcaggtagat ttttctccct
	6361	aatgtcttgg aaattgcgag aatactttgt aattaccgaa tatttgataa agactcattt
	6421	cgtccctatg tttaaaggcc tgacaatggc ggacgatcta actgcagtca ttaaaaagat
	6481	gttagattcc tcatccggcc aaggattgaa gtcatatgag gcaatttgca tagccaatca
	6541	cattgattac gaaaaatgga ataaccacca aaggaagtta tcaaacggcc cagtgttccg
	6601	agttatgggc cagttcttag gttatccatc cttaatcgag agaactcatg aattttttga
	6661	gaaaagtctt atatactaca atggaagacc agacttgatg cgtgttcaca acaacacact
	6721	gatcaattca acctcccaac gagtttgttg gcaaggacaa gagggtggac tggaaggtct
	6781	acggcaaaaa ggatggagta tcctcaatct actggttatt caaagagagg ctaaaatcag
	6841	aaacactgct gtcaaagtct tggcacaagg tgataatcaa gttatttgca cacagtataa
	6901	aacgaagaaa tcgagaaacg ttgtagaatt acagggtgct ctcaatcaaa tggtttctaa
	6961	taatgagaaa attatgactg caatcaaaat agggacaggg aagttaggac ttttgataaa
	7021	tgacgatgag actatgcaat ctgcagatta cttgaattat ggaaaaatac cgattttccg
	7081	tggagtgatt agagggttag agaccaagag atggtcacga gtgacttgtg tcaccaatga
	7141	ccaaataccc acttgtgcta atataatgag ctcagtttcc acaaatgctc tcaccgtagc
	7201	tcattttgct gagaacccaa tcaatgccat gatacagtac aattattttg ggacatttgc
	7261	tagactcttg ttgatgatgc atgatcctgc tcttcgtcaa tcattgtatg aagttcaaga
	7321	taagataccg ggcttgcaca gttctacttt caaatacgcc atgttgtatt tggacccttc
	7381	cattggagga gtgtcgggca tgtctttgtc caggtttttg attagagcct tcccagatcc
	7441	cgtaacagaa agtctctcat tctggagatt catccatgta catgctcgaa gtgagcatct
	7501	gaaggagatg agtgcagtat ttggaaaccc cgagatagcc aagtttcgaa taactcacat
	7561	agacaagcta gtagaagatc caacctctct gaacatcgct atgggaatga gtccagcgaa
	7621	cttgttaaag actgaggtta aaaaatgctt aatcgaatca agacaaacca tcaggaacca
	7681	ggtgattaag gatgcaacca tatatttgta tcatgaagag gatcggctca gaagtttctt
	7741	atggtcaata aatcctctgt tccctagatt tttaagtgaa ttcaaatcag gcactttttt
	7801	gggagtcgca gacgggctca tcagtctatt tcaaaattct cgtactattc ggaactcctt
	7861	taagaaaaag tatcataggg aattggatga tttgattgtg aggagtgagg tatcctcttt
	7921	gacacattta gggaaacttc atttgagaag gggatcatgt aaaatgtgga catgttcagc
	7981	tactcatgct gacacattaa gatacaaatc ctggggccgt acagttattg ggacaactgt
	8041	accccatcca ttagaaatgt tgggtccaca acatcgaaaa gagactcctt gtgcaccatg
	8101	taacacatca gggttcaatt atgtttctgt gcattgtcca gacgggatcc atgacgtctt
	8161	tagttcacgg ggaccattgc ctgcttatct agggtctaaa acatctgaat ctacatctat
	8221	tttgcagcct tgggaaaggg aaagcaaagt cccactgatt aaaagagcta cacgtcttag
	8281	agatgctatc tcttggtttg ttgaacccga ctctaaacta gcaatgacta tactttctaa
	8341	catccactct ttaacaggcg aagaatggac caaaaggcag catgggttca aaagaacagg
	8401	gtctgccctt cataggtttt cgacatctcg gatgagccat ggtgggttcg catctcagag
	8461	cactgcagca ttgaccaggt tgatggcaac tacagacacc atgagggatc tgggagatca
	8521	gaatttcgac tttttattcc aagcaacgtt gctctatgct caaattacca ccactgttgc
	8581	aagagacgga tggatcacca gttgtacaga tcattatcat attgcctgta agtcctgttt
	8641	gagacccata gaagagatca ccctggactc aagtatggac tacacgcccc cagatgtatc
	8701	ccatgtgctg aagacatgga ggaatgggga aggttcgtgg ggacaagaga taaaacagat
	8761	ctatccttta gaagggaatt ggaagaattt agcacctgct gagcaatcct atcaagtcgg
	8821	cagatgtata ggttttctat atggagactt ggcgtataga aaatctactc atgccgagga
	8881	cagttctcta tttcctctat ctatacaagg tcgtattaga ggtcgaggtt tcttaaaagg
	8941	gttgctagac ggattaatga gagcaagttg ctgccaagta atacaccgga gaagtctggc
	9001	tcatttgaag aggccggcca acgcagtgta cggaggtttg atttacttga ttgataaatt
	9061	gagtgtatca cctccattcc tttctcttac tagatcagga cctattagag acgaattaga
	9121	aacgattccc cacaagatcc caacctccta tccgacaagc aaccgtgata tgggggtgat
	9181	tgtcagaaat tacttcaaat accaatgccg tctaattgaa aagggaaaat acagatcaca
	9241	ttattcacaa ttatggttat tctcagatgt cttatccata gacttcattg gaccattctc
	9301	tatttccacc accctcttgc aaatcctata caagccattt ttatctggga aagataagaa
	9361	tgagttgaga gagctggcaa atctttcttc attgctaaga tcaggagagg ggtgggaaga
	9421	catacatgtg aaattcttca ccaaggacat attattgtgt ccagaggaaa tcagacatgc
	9481	ttgcaagttc gggattgcta aggataataa taaagacatg agctatcccc cttggggaag
	9541	ggaatccaga gggacaatta caacaatccc tgtttattat acgaccaccc cttacccaaa
	9601	gatgctagag atgcctccaa gaatccaaaa tcccctgctg tccggaatca ggttgggcca
	9661	attaccaact ggcgctcatt ataaaattcg gagtatatta catggaatgg gaatccatta
	9721	cagggacttc ttgagttgtg gagacggctc cggagggatg actgctgcat tactacgaga
	9781	aaatgtgcat agcagaggaa tattcaatag tctgttagaa ttatcagggt cagtcatgcg
	9841	aggcgcctct cctgagcccc ccagtgccct agaaacttta ggaggagata aatcgagatg
	9901	tgtaaatggt gaaacatgtt gggaatatcc atctgactta tgtgacccaa ggacttggga
	9961	ctatttcctc cgactcaaag caggcttggg gcttcaaatt gatttaattg taatggatat
	10021	ggaagttcgg gattcttcta ctagcctgaa aattgagacg aatgttagaa attatgtgca
	10081	ccggattttg gatgagcaag gagttttaat ctacaagact tatggaacat atatttgtga
	10141	gagcgaaaag aatgcagtaa caatccttgg tcccatgttc aagacggtcg acttagttca
	10201	aacagaattt agtagttctc aaacgtctga agtatatatg gtatgtaaag gtttgaagaa
	10261	attaatcgat gaacccaatc ccgattggtc ttccatcaat gaatcctgga aaaacctgta
	10321	cgcattccag tcatcagaac aggaatttgc cagagcaaag aaggttagta catactttac
	10381	cttgacaggt attccctccc aattcattcc tgatcctttt gtaaacattg agactatgct
	10441	acaaatattc ggagtaccca cgggtgtgtc tcatgcggct gccttaaaat catctgatag
	10501	acctgcagat ttattgacca ttagcctttt ttatatggcg attatatcgt attataacat
	10561	caatcatatc agagtaggac cgatacctcc gaacccccca tcagatggaa ttgcacaaaa
	10621	tgtggggatc gctataactg gtataagctt ttggctgagt ttgatggaga aagacattcc
	10681	actatatcaa cagtgtttag cagttatcca gcaatcattc ccgattaggt gggaggctgt
	10741	ttcagtaaaa ggaggataca agcagaagtg gagtactaga ggtgatgggc tcccaaaaga
	10801	tacccgaatt tcagactcct tggccccaat cgggaactgg atcagatctc tggaattggt
	10861	ccgaaaccaa gttcgtctaa atccattcaa tgagatcttg ttcaatcagc tatgtcgtac
	10921	agtggataat catttgaaat ggtcaaattt gcgaagaaac acaggaatga ttgaatggat
	10981	caatagacga atttcaaaag aagaccggtc tatactgatg ttgaagagtg acctacacga
	11041	ggaaaactct tggagagatt aaaaaatcat gaggagactc caaactttaa gtatgaaaaa
	11101	aactttgatc cttaagaccc tcttgtggtt tttatttttt atctggtttt gtggtcttcg

11161

t//

Example 2

Vsv Genome and Cloning Fragments

FIG. 2A depicts a schematic of a VSV genome and cloning fragments.
In the sequences provided in FIGS. 2B-2G, terminal fragments A and G are combined to produce fragment VS V-AG.

- The DNA fragments are designed for cloning into pSP72 or other similar cloning vectors. Before adding VSV cDNA sequences, the cloning plasmid is modified by insertion of the hammerhead and hepatitis delta virus ribozyme sequences. A BsmBI restriction enzyme cleavage site is placed between the ribozyme sequences (5′-hammerhead ribozyme-BsmBI-hepatitis delta virus ribozyme-3′) for the purpose of inserting the VSV-AG fragment.
- The AG fragment was designed with BsmBI sites at the 5′ and 3′ termini (lower case nucleotides) for insertion between the ribozyme sequences introduced in the step above. Because BsmBI cleaves distal to its recognition sequence (see bullet below), this enzyme may be used to join the AG fragment directly to the ribozymes while also eliminating the non-VSV nucleotides added to create the enzyme cleavage signal. (Ball L A, Pringle C R, Flanagan B, Perepelitsa V P, Wertz G W. Phenotypic consequences of rearranging the P, M, and G genes of vesicular stomatitis virus. J. Virol. 1999 June; 73(6):4705-12, the disclosure of which is incorporated by reference).
- Like other restriction endonucleases of this type (BspMI, Earl, Plel, SfaNI and others), BsmBI cleaves distal to its recognition sequence:

	5′-CGTCTC/N-3′

	3′-GCAGAGNNNNN/N-5′

- - N is any nucleotide and/indicates cleavage site.
- The VSV-AG fragment also is designed to facilitate subsequent cloning. Between the fused A and G fragments there is a polylinker sequence (noted in red nucleotides) that contains restriction endonuclease cleavage sites needed for sequential cloning of Fragments B-F to assemble a full-length clone. The polylinker contains 5′-NheI-BstBI-PacI-AvaI-SalI-AflII-3′ restriction endonuclease cleavage sites. Polylinker nucleotides are replaced by VSV genomic sequence as the full-length clone is assembled.

Example 3

Virus Rescue Support Plasmid Insert Optimization

Strategy for optimizing gene inserts encoding VSV N, P, M, G, and L for construction of plasmid DNAs encoding trans-acting proteins needed to initiate virus rescue. Gene inserts were optimized using steps in Example 4 then synthesized by a contract lab and subsequently cloned into a plasmid under the control of the hCMV promoter and enhancer.

Example 4

Coding Sequence Optimization and Gene Design

Step 1. Replace VSV sequence with codons used by highly expressed mammalian genes. Use the CodonJuggle program found in the GeneDesign Webtool (Richardson et al. 2010. Nucleic Acids Res 38:2603-2606 and Richardson et al. 2006. Genome Res 16:550-556).
Step 2. Eliminate potential RNA processing signals in the coding sequence that might direct unwanted RNA splicing or cleavage/polyadenylation reaction.

- a) Identify potential splice site signals and remove by introducing synonymous codons. Splice site predictions were made with the webtool at the Berkeley Drosophila Genome Project website (Reese et al. 1997. J Comput Biol 4:311-323).
- b) Scan the insert for consensus cleavage/polyadenylation signals (AAUAAA) (Zhao et al. 1999. MMBR 63:405-445). Disrupt by introducing synonymous codons.

Step 3

- a) Add a preferred translational start sequence (the Kozak sequence) (Kochetov et al. 1998. FEBS letters 440:351-355, Kozak. 1999. Gene 234:187-208, Kozak. 1991. J Biol Chem 266:19867-19870 and Zhang. 1998. Human molecular genetics 7:919-932).
- b) Add a preferred translational stop codon at the 3′ end (Kochetov et al. 1998. FEBS letters 440:351-355, Sun et al. 2005. J Mol Evol 61:437-444 and Zhang. 1998. Human molecular genetics 7:919-932).

Step 4. Scan the sequence for homopolymeric stretches of 5 nucleotides or more. Interrupt these sequences by introducing synonymous codons.
Step 5. Scan the sequence for restriction endonuclease cleavage sites and eliminate any unwanted recognitions signals.
Step 6. Confirm that the modified sequence translates into the expected amino acid sequence.
The invention is further described by the following numbered paragraphs:
1. A vesicular stomatitis virus (VSV) genomic clone comprising:
(a) a VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein, wherein the VSV genome comprises nucleotide substitutions and amino acid coding changes to improve replicative fitness and genetic stability,
(b) a cloning vector,
(c) an extended T7 promoter,
(d) a hammerhead ribozyme,
(e) a hepatitis delta virus ribozyme and T7 terminator
(f) unique restriction endonuclease cleavage sites in a VSV genomic sequence
(g) a leader and a trailer that are cis-acting sequences controlling mRNA synthesis and replication
2. The VSV genomic clone of paragraph 1, wherein the cloning vector is pSP72 (Genbank X65332.2)
3. The VSV genomic clone of paragraph 1 or 2, wherein the extended T7 promoter is PT7-g10.
4. The VSV genomic clone of any one of paragraphs 1 to 3, wherein the unique restriction endonuclease cleavage sites are 1367 NheI, 2194 SpeI, 2194 BstBI, 4687 PacI, 7532 AvaI, 10190 SalI and 11164 AflII.
5. The VSV genomic clone of any one of paragraphs 1 to 4, wherein the VSV genomic clone is depicted in FIG. 1.
6. The VSV genomic clone of any one of paragraphs 1 to 5, wherein the nucleotide position is according to GenBank Accession Number EF197793 and wherein the nucleotide substitutions are selected from the group consisting of

- 1371 CA>GC (NheI)
- After 2195 insert TAG (SpeI) (all genome numbers below adjusted to include +3 bp)
- 3036 G>T improves match to consensus transcription stop signal
- 3853 X>A (was an ambiguity in Genbank file)
- 4691 T>A to generate PacI
- 7546 C>A silent change in L coding sequence eliminates a BstBI site
- 1960 TAC>TCC to change Y>S
- 3247 GTA>ATA to change V>I
- 3729 AAG>GAG to change K>E
- 4191 GTA>GAA to change V>E
- 4386 GGT>GAT to change G>D
- 4491 ACC>ATC to change T>I
- 5339 ATT>CTT to change I>L
- 5834 ACT>GCT to change T>A and
- 10959 AGA>AAA to change R>K.

7. The VSV genomic clone of any one of paragraphs 1 to 6, wherein the nucleotide position is according to GenBank Accession Number EF197793 and wherein the nucleotide substitutions are selected from the group consisting of:

8. The VSV genomic clone of any one of paragraphs 1 to 7, wherein the nucleotide sequences of the VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein are selected from the group consisting of FIGS. 2B-2G.
9. The VSV genomic clone of any one of paragraphs 1 to 7, wherein the nucleotide sequences of the VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein are selected from the group consisting of FIGS. 3A-3G, 10. A method for rescuing VSV comprising combining a T7 RNA polymerase promoter and a hammerhead ribozyme sequence to increase the efficiency of synthesis and processing of full-length VSV genomic RNA in transfected cells.
11. The method of paragraph 10, wherein the T7 RNA polymerase promoter is a minimal functional sequence designed to initiate transcription very close to or precisely at the 5′ terminus of the genomic clone.
12. The method of paragraph 11, wherein the T7 promoter is a T7 promoter sequence that enhances formation of stable initiation and elongation complexes and a hammerhead ribozyme sequence at the 5′ terminus that catalyzes removal of extra nucleotides restoring the authentic 5′ terminus of the genomic transcript.
13. The method of any one of paragraphs 10 to 12, wherein the plasmids encoding VSV nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein are optimized to improve expression of the trans-acting proteins to initiate virus rescue.
14. The method of paragraph 13, where the optimization is codon optimization.
15. The method of paragraph 14, wherein the codon optimization comprises replacing a VSV nucleotide sequence with codons used by highly expressed mammalian genes.
16. The method of paragraph 14 or 15, wherein the codon optimization comprises eliminating potential RNA processing signals in the coding sequence that might direct unwanted RNA splicing or cleavage/polyadenylation reaction, wherein the eliminating comprises:

- (a) identifying potential splice site signals and remove by introducing synonymous codons and/or
- (b) scanning an insert for consensus cleavage/polyadenylation signals (AAUAAA) and introducing synonymous codons to disrupt the consensus cleavage/polyadenylation signals.

17. The method of any one of paragraphs 14 to 16, wherein the codon optimization comprises

- (a) adding a preferred translational start sequence (the Kozak sequence) and/or
- (b) adding a preferred translational stop codon.

18. The method of any one of paragraphs 14 to 17, wherein the codon optimization comprises scanning a sequence for homopolymeric stretches of 5 nucleotides or more and interrupting the sequences by introducing synonymous codons.
19. The method of any one of paragraphs 14 to 18, wherein the codon optimization comprises scanning a sequence for restriction endonuclease cleavage sites and eliminate any unwanted recognitions signals.
20. The method of any one of paragraphs 14 to 19, wherein the codon optimization comprises confirming that a modified sequence translates into an expected amino acid sequence.
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

What is claimed is:

1. A vesicular stomatitis virus (VSV) genomic clone comprising:

(a) a VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein, wherein the VSV genome comprises nucleotide substitutions and amino acid coding changes to improve replicative fitness and genetic stability,

(b) a cloning vector,

(c) an extended T7 promoter,

(d) a hammerhead ribozyme,

(e) a hepatitis delta virus ribozyme and T7 terminator

(f) unique restriction endonuclease cleavage sites in a VSV genomic sequence

(g) a leader and a trailer that are cis-acting sequences controlling mRNA synthesis and replication

2. The VSV genomic clone of claim 1, wherein the cloning vector is pSP72 (Genbank X65332.2)

3. The VSV genomic clone of claim 1, wherein the extended T7 promoter is PT7-g10.

4. The VSV genomic clone of claim 1, wherein the unique restriction endonuclease cleavage sites are 1367 NheI, 2194 SpeI, 2194 BstBI, 4687 PacI, 7532 AvaI, 10190 SalI and 11164 AflII.

5. The VSV genomic clone of claim 1, wherein the VSV genomic clone is depicted in FIG. 1.

6. The VSV genomic clone of claim 1, wherein the nucleotide position is according to GenBank Accession Number EF197793 and wherein the nucleotide substitutions are selected from the group consisting of

1371 CA>GC (NheI)

After 2195 insert TAG (SpeI) (all genome numbers below adjusted to include +3 bp)

3036 G>T improves match to consensus transcription stop signal

3853 X>A (was an ambiguity in Genbank file)

4691 T>A to generate PacI

7546 C>A silent change in L coding sequence eliminates a BstBI site

1960 TAC>TCC to change Y>S

3247 GTA>ATA to change V>I

3729 AAG>GAG to change K>E

4191 GTA>GAA to change V>E

4386 GGT>GAT to change G>D

4491 ACC>ATC to change T>I

5339 ATT>CTT to change I>L

5834 ACT>GCT to change T>A and

10959 AGA>AAA to change R>K.

7. The VSV genomic clone of claim 1, wherein the nucleotide position is according to GenBank Accession Number EF197793 and wherein the nucleotide substitutions are selected from the group consisting of:

Nucleotide position in Nucleotide position Nucleotide EF197793 in rEF197793 Change Purpose 1 Substitution 1371-2 Substitution 1371-2 CA > GC Creates a unique NheI cleavage site between N and P gens 2 Substitution 1960-2 Substitution 1960-2 TAC > TCC Y > S substitution in P protein amino acid sequence to agree with consensus. 3 Insert after 2195 3 base insert after Insert TAG Creates a unique SpeI site 2195 between P and M genes 4 Substitution 3039 Substitution 3042 G > T Improves agreement with consensus. Also improves agreement with consensus transcription stop signal 5 Substitution 3234-6 Substitution 3237-9 GTA > ATA V > I substitution in P protein amino acid sequence to agree with consensus. 6 Substitution 3729-31 Substitution 3732-34 AAG > GAG K > E substitution in G protein amino acid sequence to agree with consensus. 7 Substitution 3856 Substitution 3859 N > A Replace unknown base in Genbank file with consensus 8 Substitution 4191-93 Substitution 4194-6 GTA > GAA V > E substitution in G protein amino acid sequence to agree with consensus. 9 Substitution 4386-88 Substitution 4389-92 GGT > GAT G > D substitution in G protein amino acid sequence to agree with consensus. 10 Substitution 4491-93 Substitution 4494-96 ACC > ATC T > I substitution in G protein amino acid sequence to agree with consensus. 11 Substitution 4694 Substitution 4697 T > A Creates unique PacI cleavage site between G and L genes 12 Substitution 5339-41 Substitution 5342-44 ATT > CTT I > L substitution in L protein amino acid sequence to agree with consensus. 13 Substitution 5834-6 Substitution 5837-40 ACT > GCT T > A substitution in L protein amino acid sequence to agree with consensus. 14 Substitution 10959-61 Substitution 10962-64 AGA > AAA R > K substitution in L protein amino acid sequence to agree with consensus. 15 Substitution 7546 Substitution 7549 C > A Eliminates a BstBI site in the L gene sequence making the BstBI site between the M and G genes unique. This substitution was silent for amino acid coding.

8. The VSV genomic clone of claim 1, wherein the nucleotide sequences of the VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein are selected from the group consisting of FIGS. 2B-2G.

9. The VSV genomic clone of claim 1, wherein the nucleotide sequences of the VSV genome encoding and expressing a nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein are selected from the group consisting of FIGS. 3A-3G.

10. A method for rescuing VSV comprising combining a T7 RNA polymerase promoter and a hammerhead ribozyme sequence to increase the efficiency of synthesis and processing of full-length VSV genomic RNA in transfected cells.

11. The method of claim 10, wherein the T7 RNA polymerase promoter is a minimal functional sequence designed to initiate transcription very close to or precisely at the 5′ terminus of the genomic clone.

12. The method of claim 11, wherein the T7 promoter is a T7 promoter sequence that enhances formation of stable initiation and elongation complexes and a hammerhead ribozyme sequence at the 5′ terminus that catalyzes removal of extra nucleotides restoring the authentic 5′ terminus of the genomic transcript.

13. The method of claim 10, wherein the plasmids encoding VSV nucleocapsid, phosphoprotein, matrix, glycoprotein and large protein are optimized to improve expression of the trans-acting proteins to initiate virus rescue.

14. The method of claim 13, where the optimization is codon optimization.

15. The method of claim 14, wherein the codon optimization comprises replacing a VSV nucleotide sequence with codons used by highly expressed mammalian genes.

16. The method of claim 14, wherein the codon optimization comprises eliminating potential RNA processing signals in the coding sequence that might direct unwanted RNA splicing or cleavage/polyadenylation reaction, wherein the eliminating comprises:

(a) identifying potential splice site signals and remove by introducing synonymous codons and/or

(b) scanning an insert for consensus cleavage/polyadenylation signals (AAUAAA) and introducing synonymous codons to disrupt the consensus cleavage/polyadenylation signals.

17. The method of claim 14, wherein the codon optimization comprises

(a) adding a preferred translational start sequence (the Kozak sequence) and/or

(b) adding a preferred translational stop codon.

18. The method of claim 14, wherein the codon optimization comprises scanning a sequence for homopolymeric stretches of 5 nucleotides or more and interrupting the sequences by introducing synonymous codons.

19. The method of claim 14, wherein the codon optimization comprises scanning a sequence for restriction endonuclease cleavage sites and eliminate any unwanted recognitions signals.

20. The method of claim 14, wherein the codon optimization comprises confirming that a modified sequence translates into an expected amino acid sequence.