# Patent

## Title
Recombinant modified vaccinia ankara (MVA) vaccinia virus containing restructured insertion sites

## Abstract

The present invention relates to recombinant modified vaccinia Ankara (MVA) virus containing restructured sites useful for the integration of heterologous nucleic acid sequences into an intergenic region (IGR) of the virus genome, where the IGR is located between two adjacent, essential open reading frames (ORFs) of the vaccinia virus genome, wherein the adjacent essential ORFs are non-adjacent in a parental MVA virus used to construct the recombinant MVA virus, and to related nucleic acid constructs useful for inserting heterologous DNA into the genome of a vaccinia virus, and further to the use of the disclosed viruses as a medicine or vaccine.

## Background
RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No. 61/252,326 filed Oct. 16, 2009, which is hereby expressly incorporated by reference in its entirety.


FIELD OF THE INVENTION
The present invention relates to insertion sites useful for the stable integration of heterologous DNA sequences into the MVA genome. More specifically, the invention relates to methods of restructuring regions of the modified vaccinia Ankara (MVA) virus genome that contain a combination of essential and non-essential gene, so that heterologous DNA remains stably integrated into the genome.
BACKGROUND
The members of the poxvirus family have large double-stranded DNA genomes encoding several hundred proteins (Moss, B. 2007 “Poxviridae: The Viruses and Their Replication” in Fields Virology, 5th Ed. (D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus, Eds), Lippincott Williams & Wilkins, Philadelphia, Pa.). Poxviruses are divided into the subfamilies Chordopoavirinae and Entomopaxvirinae, based on vertebrate and insect host range. The subfamily Chordopoxvirinae consists of eight genera: Orthopoxvirus, Parapoxvirus, Avipoxvirus, Capripoxvirus, Leporipoxvirus, Suipoxvirus, Molluscipoxvirus, and Yatapoxvirus. The prototypal member of the genus Orthopoxvirus is vaccinia virus. Vaccinia virus (VACV), the first recombinant virus shown to induce a protective immune response against an unrelated pathogen (Moss, B., G. L. Smith, J. L. Geria, and R. H. Purcell. 1984. Live recombinant vaccinia virus protects chimpanzees against hepatitis B. Nature 311:67-69; Paoletti, E., B. R, Lipinskas, C. Samsonolf S. R. Mercer, and D. Panicali. 1984. Construction of live vaccines using genetically engineered poxviruses; biological activity of vaccinia virus recombinants expressing the hepatitis B virus surface antigen and the herpes simplex virus glycoprotein D. Proc. Natl. Acad. Sci. USA 81:193-197), is being employed as a vector for veterinary and wildlife vaccines (Moss, B. 1996. Genetically engineered poxviruses for recombinant gene expression, vaccination, and safety. Proc. Natl. Acad. Sci. USA 93:11341-11348). Development of recombinant VACV for human use, however, has been impeded by safety concerns. For this reason, there is interest in modified VACV Ankara (MVA), a highly attenuated smallpox vaccine with an exemplary safety profile even in immunodeficient animals (Mayr, A., V. Hochstein-Mintzel, and H. Stickl. 1975. Passage history, properties, and applicability of the attenuated vaccinia virus strain MVA. Infection 3:6-14. (In German); Stickl, H., V. Hochstein-Mintzel, A. Mayr, H. C. Huber, H. Schafer, and A. Holzner. 1974. MVA vaccination against smallpox: clinical trial of an attenuated live vaccinia virus strain (MVA). Dtsch. Med. Wschr. 99:2386-2392 (In German); Stittelaar, K. J., T. Kuiken, R. L. de Swart, G. van Amerongen, H. W. Vos, H. G. Niesters, P. van Schalkwijk, T. van der Kwast, L. S. Wyatt, B. Moss, and A. D. Osterhaus. 2001. Safety of modified vaccinia virus Ankara (MVA) in immune-suppressed macaques. Vaccine 19:3700-3709). The genomic sequence of MVA (Mayr, A. et al. 1978 Zentralbl Bakteriol 167:375-390), which cannot grow in most mammalian cells and which is a good candidate for a recombinant vaccine vector, is known (Sutter, G. and Moss, B. 1992 Proc Natl Acad Sci USA 89:10847-10851; and Sutter, G. et al. 1994 Vaccine 12:1032-1040) has been passaged over 570 times in chicken embryo fibroblasts, during which six major deletions relative to the parental wild-type strain Ankara, accompanied by a severe restriction in host range, have occurred (Meyer, H. et al. 1991 J Gen Virol 72:1031-1038). MVA is severely host range restricted and propagates poorly or not at all in most mammalian cells because of a block in virion assembly (Sutter, G., and B. Moss. 1992. Nonreplicating vaccinia vector efficiently expresses recombinant genes. Proc. Natl. Acad. Sci. USA 89:10847-10851). Initial experiments with recombinant MVA (rMVA) demonstrated its ability to robustly express foreign proteins (Sutter, G., and B. Moss. 1992. Nonreplicating vaccinia vector efficiently expresses recombinant genes. Proc. Natl. Acad. Sci. USA 89:10847-10851) and induce protective humoral and cell-mediated immunity (Sutter, G., L. S. Wyatt, P. L. Foley, J. R. Bennink, and B. Moss. 1994. A recombinant vector derived from the host range-restricted and highly attenuated MVA strain of vaccinia virus stimulates protective immunity in mice to influenza virus. Vaccine 12:1032-1040). Currently, rMVA candidate vaccines expressing genes from a wide variety of pathogens are undergoing animal and human testing (Gomez, C. E., J. L. Najera, M. Krupa, and M. Esteban. 2008. The poxvirus vectors MVA and NYVAC a gene delivery systems for vaccination against infection diseases and cancer. Curr. Gene Ther. 8:97-120).
While developing candidate human immunodeficiency virus (HIV) and other vaccines, it was observed that mutant rMVA loses the ability to express foreign proteins after tissue culture passage (Stittelaar, K. J., L. S. Wyatt, R. L. de Swart, H. W. Vos, J. Groen, G. van Amerongen, R. S. van Binnendijk, S. Rozenblatt, B. Moss. and A. Osterhaus. 2000. Protective immunity in macaques vaccinated with a modified vaccinia virus Ankara-based measles virus vaccine in the presence of passively acquired antibodies. J. Virol, 74:4236-4243; Wyatt, L. S., I. M. Belyakov, P. L. Earl, J. A. Berzofsky, and B. Moss. 2008. Enhanced cell surface expression, immunogenicity and genetic stability resulting from a spontaneous truncation of HIV Env expressed by a recombinant MVA. Virology 372:260-272; Wyatt, L. S., S. T. Shors, B. R. Murphy, and B. Moss. 1996. Development of a replication-deficient recombinant vaccinia virus vaccine effective against parainfluenza virus 3 infection in an animal model. Vaccine 14:1451-1458). This instability may initially go undetected, however, unless individual plaques are isolated and analyzed. Nevertheless, once established in the population, the nonexpressors can rapidly overgrow the original rMVA. These considerations are particularly important for production of large vaccine seed stocks of rMVA. The instability of cloned genes in MVA is surprising, since MVA had already undergone genetic changes during its adaptation through hundreds of passages in chicken embryo fibroblasts (CEFs) and is now quite stable. Indeed, identical 167,000-bp genome sequences have been reported for three independent plaque isolates, accession numbers U94848, AY603355, and DQ983236, and by Antoine et al. (Antoine, G., F. Scheiflinger, F. Dorner, and F. G. Falkner. 2006. Corrigendum 10 “The complete genomic sequence of the modified vaccinia Ankara (MVA) strain: comparison with other orthopoxviruses.” Virology 350:501-502. [Correction to 244:365, 1998.]). Although the cause of the instability of the gene inserts had not been previously investigated, harmful effects of the recombinant protein seem to play a role in the selective advantage of nonexpressing mutants. Thus, reducing the expression level of parainfluenza virus and measles virus transmembrane proteins and deleting part of the cytoplasmic tail of HIV Env improves the stability of rMVAs (Stittelaar, K. J., L. S. Wyatt, R. L. de Swart, H. W. Vos, J. Groen, G. van Amerongen, R. S. van Binnandijk, S. Rozenblatt, B. Moss. and A. Osterhaus. 2000. Protective immunity in macaques vaccinated with a modified vaccinia virus Ankara-based measles virus vaccine in the presence of passively acquired antibodies. J. Virol, 74:4236-4243; Wyatt, L. S., I. M. Belyakov, P. L. Earl, J. A. Berzofsky, and B. Moss. 2008. Enhanced cell surface expression, immunogenicity and genetic stability resulting from a spontaneous truncation of HIV Env expressed by a recombinant MVA. Virology 372:260-272; Wyatt, L. S., S. T. Shors, B. R. Murphy, and B. Moss. 1996. Development of a replication-deficient recombinant vaccinia virus vaccine effective against parainfluenza virus 3 infection in an animal model. Vaccine 14:1451-1458). Reducing expression, however, can also decrease immunogenicity and therefore may be undesirable (Wyatt, L. S., P. L. Earl, J. Vogt, L. A. Eller, D. Chandran, J. Liu, H. L. Robinson, and B. Moss. 2008. Correlation of immunogenicities and in vitro expression levels of recombinant modified vaccinia virus Ankara HIV vaccines. Vaccine 26:486-493).
In view of the potential value of rMVA as a vaccine, it is important to understand this pernicious instability problem, and to develop methods for constructing stable, recombinant MVA viruses. Additionally, an understanding of the stability problem might provide insights that have application to other DNA expression vectors. The present invention provides such insights and provides for a solution to the problem of constructing stable, recombinant MVA viruses.
SUMMARY OF THE INVENTION
The present invention relates to the discovery that the genome of a modified vaccinia Ankara (MVA) virus can be made more stable by restructuring regions of the genome. In particular, the inventors have discovered that regions of the genome containing non-essential genes are genetically unstable. Moreover such regions can be made more stable by removing non-essential DNA, and making essential genes in these regions adjacent to one another. Because loss of essential genes results in a virus having a growth disadvantage, such viruses are quickly lost from the population resulting in a population of viruses in which the essential genes, and any intervening DNA, is maintained.
The disclosure provides a recombinant modified vaccinia Ankara (MVA) virus comprising a heterologous nucleic acid sequence located between two adjacent, essential open reading frames of the MVA virus genome. The choice of essential ORFs is such that the ORFs are non-adjacent in the genome of a parental MVA virus used to construct the recombinant viruses of the present invention. That is, the essential ORFs are separated by at least one non-essential ORF. However, in the recombinant modified vaccinia Ankara (MVA) progeny virus, the essential ORFs have been made adjacent. That is, there are no intervening, non-essential ORFs between the essential ORFs. Consequently, the region between the essential ORFs is stable, and is maintained in the virus population. Consequently, this region provides a new and useful site for the insertion of heterologous nucleic acid sequences. Such heterologous nucleic acid sequences can encode therapeutically useful proteins, such as antigens.
The disclosure also provides nucleic acid constructs that can be used to construct recombinant modified vaccinia Ankara (MVA) viruses of the present invention. Such constructs contain essential ORFs from the parental MVA virus, and that are non-adjacent in the parental virus. However, in the disclosed nucleic acid constructs, these essential ORFs have been made adjacent to one another. Moreover, constructs are disclosed that contain intergenic regions between the essential ORFs, which can be used for the insertion of heterologous nucleic acid sequences.
Finally, also disclosed are methods of using viruses of the present invention for the prevention and treatment of disease.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. Phylogenetic relationships of HIV-1 and HIV-2 based on identity of pol gene sequences. SIVcpz and SIVsmm are subhuman primate lentiviruses recovered from a chimpanzee and sooty mangabey monkey, respectively.
FIG. 2. Phylogenetic relationships of HIV-1 groups M, N and O with four different SIVcpz isolates based on full-length pol gene sequences. The bar indicates a genetic distance of 0.1 (10% nucleotide divergence) and the asterisk positions group N HIV-1 isolates based on env sequences.
FIG. 3. Tropic and biologic properties of HIV-1 isolates.
FIG. 4. HIV-encoded proteins. The location of the HIV genes, the sizes of primary translation products (in some cases polyproteins), and the processed mature viral proteins are indicated.
FIG. 5. Schematic representation of a mature HIV-1 virion.
FIG. 6. Linear representation of the HIV-1 Env glycoprotein. The arrow indicates the site of gp160 cleavage to gp120 and gp41. In gp120, cross-hatched areas represent variable domains (V1 to V5) and open boxes depict conserved sequences (C1 to C5). In the gp41 ectodomain, several domains are indicated: the N-terminal fusion peptide, and the two ectodomain helices (N- and C-helix). The membrane-spanning domain is represented by a black box. In the gp41 cytoplasmic domain, the Tyr-X-X-Leu (YXXL) endocytosis motif (SEQ ID NO: 1) and two predicted helical domains (helix-1 and -2) are shown. Amino acid numbers are indicated.
FIG. 7. pLW-73 nucleic acid construct (SEQ ID NO:2 and 3).
FIG. 8. Nucleotide sequence of the pLW-73 transfer vector (top strand, SEQ ID NO: 2; bottom strand, SEQ ID NO: 3).
FIG. 9. Nucleotide sequence encoding Ugandan clade D Env protein (isolate AO7412) (SEQ ID NO: 4).
FIG. 10. Codon altered nucleotide sequence encoding Ugandan clade D gagpol protein (isolate AO3349) (SEQ ID NO: 5).
FIG. 11. Generation of recombinant MVAs and analysis of stability of inserted genes. A) Schematic diagram of insertion of env and gagpol into Del II and Del III sites, respectively. B) Evaluation of stability by immunostaining.
FIG. 12. Types and frequency of envy mutations in MVA/65A/G env.
FIG. 13. Insertion of Env in I8R/G1L IGR and Gag Pol in Del III.
FIG. 14. Modifications to A/G constructs to increase stability.
FIG. 15. Env expression after plaque passages.
FIG. 16. PCR and Western blot analysis of individual clones.
FIG. 17. Expression of A/G env by double recombinant MVA.
FIG. 18. Recombinant viruses expressing env and gagpol from Ugandan HIV-1 isolates.
FIG. 19. MVA/UGD4a—analysis of non-staining env plaques.
FIG. 20. Modification of UGD env gene in recombinant MVA.
FIG. 21. MVA/UGD4b—analysis of non-staining gag plaques. *, location of runs of 4-6 G or C residues.
FIG. 22. Modification of UGD gagpol gene in recombinant MVA.
FIG. 23. Construction of stable recombinant MVA expressing UGD env and gagpol.
FIG. 24. Cellular responses elicited by MVA/UGD4d.
FIG. 25. Antibody responses elicited by MVA/UGD4d.
FIG. 26. Outline of method for restructuring the del III site of MVA virus genome.
FIG. 27 pLW-76 nucleic acid construct (SEQ ID NO:21 and 22).
FIG. 28. Syncytial phenotype in rMVA due to restructuring of the del III site
FIG. 29 Comparison of heterogous nucleic acid stability in different recombinant MVA viruses
FIG. 30 Comparison of UGD Env protein expression level in different recombinant MVA viruses
FIG. 31-1 through FIG. 31-6. Nucleotide sequence of the pLW-76 transfer vector (SEQ ID NO:21 and 22).



DEPOSIT OF MICROORGANISM
The following microorganism has been deposited in accordance with the terms of the Budapest Treaty with the American Type Culture Collection (ATCC), Manassas, Va., on the date indicated:















Microorganism
Accession No.
Date









MVA 1974/NIH Clone 1
PTA-5095
Mar. 27, 2003










MVA 1974/NIH Clone 1 was deposited as ATCC Accession No.: PTA-5095 on Mar. 27, 2003 with the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, Va. 20110-2209, USA. This deposit was made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure and the Regulations thereunder (Budapest Treaty). This assures maintenance of a viable culture of the deposit for 30 years from date of deposit. The deposit will be made available by ATCC under the terms of the Budapest Treaty, and subject to an agreement between Applicant and ATCC which assures permanent and unrestricted availability of the progeny of the culture of the deposit to the public upon issuance of the pertinent U.S. patent or upon laying open to the public of any U.S. or foreign patent application, whichever comes first, and assures availability of the progeny to one determined by the U.S. Commissioner of Patents and Trademarks to be entitled thereto according to 35 USC §122 and the Commissioner's rules pursuant thereto (including 37 CFR §1.14). Availability of the deposited strain is not to be construed as a license to practice the invention in contravention of the rights granted under the authority of any government in accordance with its patent laws.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the claims.
Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. See, e.g., Singleton P and Sainsbury D., Dictionary of Microbiology and Molecular Biology, 3rd ed., J. Wiley & Sons, Chichester, N.Y., 2001 and Fields Virology, 5th Ed. (D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizmnan, and S. E. Straus, eds), Lippincott Williams & Wilkins, Philadelphia, Pa., 2007. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
According to the present invention, an isolated protein, or nucleic acid molecule, is a protein, or nucleic acid molecule, that has been removed from its natural milieu. An isolated protein, or nucleic acid molecule, can, for example, be obtained from its natural source, be produced using recombinant DNA technology, or be synthesized chemically. As such, isolated does not reflect the state or degree to which a protein or nucleic acid molecule is purified.
It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
It should be understood that as used herein, the term “a” entity or “an” entity refers to one or more of that entity. For example, a nucleic acid molecule refers to one or more nucleic acid molecules. As such, the terms “a”, “an”, “one or more” and “at least one” can be used interchangeably. Similarly the terms “comprising”, “including” and “having” can be used interchangeably.
The transitional term “comprising” is synonymous with “including,” “containing” or “characterized by,” is inclusive or open-ended and does not exclude additional, unrecited elements or method steps.
The transitional phrase “consisting of” excludes any element, step, or ingredient not specified in the claim, but does not exclude additional components or steps that are unrelated to the invention such as impurities ordinarily associated therewith.
The transitional phrase “consisting essentially of” limits the scope of a claim to the specified materials or steps and those that do not materially affect the basic and novel characteristic(s) of the claimed invention.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates, which may need to be independently confirmed.
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations are also specifically embraced by the present invention and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.
Complete genome sequences have been reported for at least one member of each chordopoxvirus genus and two entomopoxviruses. Nearly 100 genes are conserved in all chordopoxviruses, and about half of these are also present in entomopoxviruses. Based on the above, several generalizations can be made: Genes are largely nonoverlapping, tend to occur in blocks pointing toward the nearer end of the genome, are usually located in the central region if highly conserved and concerned with essential replication functions, and are usually located in the end regions if variable and concerned with host interactions. The arrangement of the central genes is remarkably similar in all chordopoxviruses. A convention for naming vaccinia virus genes or ORFs (open reading frames), originating prior to sequencing the entire genome and subsequently used for the complete sequence of the Copenhagen strain of vaccinia virus, consists of using the HindIII restriction endonuclease DNA fragment letter, followed by the ORF number (from left to right) within the fragment, and L or R, depending on the direction of the ORF. An exception to this rule was made for the HindIII C fragment; the ORFs were numbered from the right in order to avoid starting at the highly variable left end of the genome. Polypeptide names correspond to gene names, except that L or R is dropped. In most subsequent complete poxvirus genome sequences, ORFs were numbered successively from one end of the genome to the other. Nevertheless, the old letter designations have been retained as common names to provide continuity in the literature. The ORF number of the Western Reserve (WR) strain of vaccinia virus is commonly shown in reference books because this strain has been used for the great majority of biochemical and genetic studies.
The inventors of the present invention have identified new sites, and methods for creating new sites, for the stable insertion of exogenous DNA sequences into the genome of modified vaccinia Ankara (MVA) virus. The present invention resulted from work aimed at identifying methods of constructing stable, recombinant MVA viruses. It had previously been observed that while recombinant MVAs containing heterologous DNA sequences inserted into the MVA genome could be obtained, these insertions were often unstable. Investigations of this instability yielded the conclusion that the insertion of heterologous DNA sequences non-essential for viral propagation into spaces between ORFs could be expected to be deleted by the virus as well. Thus was recognized a need for improved strategies for constructing stable, recombinant MVA viruses.
As used herein, an open reading frame (ORF) means a string of contiguous nucleotides that encode the amino acids of a protein. Such proteins can be peptides, polypeptides, and can be any length greater than a single amino acid. It should be understood that an ORF may also include a stop codon, even though such codon does not encode an amino acid. It will be appreciated by those skilled in the art that, due to recombination events, some ORFs have lost portions of their original coding capacity and thus encode proteins that are non-functional. Such ORFs are sometimes referred to as ORF fragments. ORFs do not include regulatory elements (e.g., promoters, transcriptional control elements, enhancers, etc.) that are located outside of the coding region. In contrast, a gene refers to an ORF (including the stop codon) and regulatory elements capable of regulating transcription of the ORF.
ORFs can be referred to as adjacent or non-adjacent. As used herein, two ORFs are adjacent when they reside in the same nucleic acid molecule, and their two closest ends are not separated by another poxvirus ORF. Non-adjacent ORFs are ORFs whose two closest ends are separated by another poxvirus ORF. Adjacent ORFs can be contiguous, meaning that there is no other nucleotide sequence between a terminal codon belonging to one ORF and a terminal codon belonging to the other ORF. A terminal codon means the first or last codon of an ORF, including the stop codon. One example of a terminal codon is the codon encoding the first 5′ amino acid of the protein encoded by the ORF. Another example of a terminal codon is the codon encoding the last 3′ amino acid of the protein encoded by the ORF. Still another example of a terminal codon is the stop codon for the ORF.
Adjacent ORFs can also be separated by a nucleic acid sequence. Such a sequence is referred to as an intergenic region. As used herein an intergenic region means a nucleic acid sequence between the closest terminal codons of adjacent ORFs that does not contain nucleotide sequences derived from vaccinia virus, other than poxvirus transcriptional control elements. IGR sequences lie outside the stop codons of adjacent ORFs and thus do not encode any portion of the protein encoded by the adjacent ORFs. IGR sequences may contain poxvirus transcriptional control elements. IGRs may also contain sequences derived from organisms other than a poxvirus. Preferably IGRs are free of any poxvirus sequences that are not part of a poxvirus transcriptional control element. In one embodiment, the IGR comprises at least one heterologous nucleic acid sequence. Such sequence can be inserted at a restriction enzyme recognition site, or restriction site, which is naturally present in the IGR or which has been introduced into the IGR for the purpose of inserting other heterologous nucleic acid sequences.
While the nucleotide sequences of ORFs encode proteins, the intergenic regions (IGRs) between two ORFs have no coding capacity. Thus they may serve as sites into which heterologous DNA can be inserted without affecting the production of any viral proteins. IGRs may, however, comprise regulatory elements, binding sites, promoter and/or enhancer sequences essential for or involved in the transcriptional control of the viral gene expression. Thus, the IGR may be involved in the regulatory control of the viral life cycle. Even so, the inventors have found that the IGR's can be used to stably insert heterologous nucleic acid sequences into the MVA genome without influencing or changing the typical characteristics and gene expression of MVA. The new insertion sites are especially useful, since no ORF or coding sequence of MVA is altered.
Before further describing the invention, it is useful to have an understanding of the arrangement of genes in the poxvirus genome. The nucleotide sequence of an ORF regularly starts with a start codon and ends with a stop codon. Depending on the orientation of the two adjacent ORFs the IGR, the region in between these ORFs, is flanked either by the two stop codons of the two adjacent ORFs, or, by the two start codons of the two adjacent ORFs, or, by the stop codon of the first ORF and the start codon of the second ORF, or, by the start codon of the first ORF and the stop codon of the second ORF.
Accordingly, the insertion site for the exogenous DNA sequence into the IGR may be downstream or 3′ of the stop codon of a first ORF. In case the adjacent ORF, also termed second ORF, has the same orientation as the first ORF, this insertion site downstream of the stop codon of the first ORF lies upstream or 5′ of the start codon of the second ORF.
In case the second ORF has an opposite orientation relative to the first ORF, which means the orientation of the two adjacent ORFs points to each other, then the insertion site lies downstream of the stop codons of both ORFs.
As a third alternative, in case the two adjacent ORFs read in opposite directions, but the orientation of the two adjacent ORFs points away from each other, which is synonymous with a positioning that is characterized in that the start codons of the two ORFs are adjacent to each other, then the exogenous DNA is inserted upstream relative to both start codons.
ORFs in the MVA genome occur in two coding directions. Consequently, mRNA synthesis activity occurs from left to right, i.e., forward direction and, correspondingly, from right to left (reverse direction). It is common practice in poxvirology and it became a standard classification for vaccinia viruses to identify ORFs by their orientation and their position on the different HindIII restriction digest fragments of the genome. For the nomenclature, the different HindIII fragments are named by descending capital letters corresponding with their descending size. The ORF are numbered from left to right on each HindIII fragment and the orientation of the ORF is indicated by a capital L (standing for transcription from right to Left) or R (standing for transcription from left to Right). Additionally, there is a more recent publication of the MVA genome structure, which uses a different nomenclature, simply numbering the ORF from the left to the right end of the genome and indicating their orientation with a capital L or R (Antoine, G. et al. 1998 Virology 244:365-396). As an example the I8R ORF, according to the old nomenclature, corresponds to the 069R ORF according to Antoine et al.
In their efforts to make recombinants of modified vaccinia virus Ankara (MVA) expressing HIV genes as candidate vaccines, the inventors determined that one of the causes of instability is due to deletions of the foreign gene and flanking MVA sequences. In an attempt to overcome this problem they set out to insert foreign genes between conserved genes in order to prevent viable deletions from occurring in recombinant MVAs. Viruses with such deletions have a growth advantage and will thus overgrow rMVA virus populations. If one inserts foreign genes between conserved genes in the vaccinia genome (these genes are considered to be required for vaccinia virus replication and are therefore “essential genes”), any deletion of an essential gene would inhibit virus replication, and, therefore, not overgrow the recombinant MVAs. Thus, the stable expression of the rMVA population is maintained. The strain of MVA that the inventors have been using to make their recombinants was provided by them to the Centers for Disease Control and Prevention (CDC) and was subsequently sequenced by Acambis (Genbank Accession number AY603355). The strain of MVA that Bavarian Nordic has based their WO03/097845 publication on is vaccinia virus strain modified vaccinia Ankara (Genbank Accession number U94848) sequenced by Antoine, G. et al. 1998 Virology 244:365-396. (Note that the gene numbers in these two sequences for a given gene are different.)
The inventors initially looked at genes conserved in the Poxviridae family as well as those genes conserved in subfamily Chordopoxvirinae (the vertebrate poxviruses) (Upton, C. et al. 2003 Journal of Virology 77:7590-7600). These genes are listed in the nomenclature of Copenhagen vaccinia virus (Genbank Accession number M35027) given on the Poxvirus Bioinformatics Resource Center found on the world wide web at poxvirus.org. These genes total 49 conserved genes in the Poxvirus family and 41 additional genes conserved in chordopoxviruses, making a total of 90 conserved genes. From these 90 conserved genes, the inventors listed intergenic sites between conserved gene pairs. These gene pairs re listed below in Table 1. (Note that genes are marked that have not been included in the Bavarian Nordic WO03/097845 publication).







TABLE 1







Intergenic Sites between Conserved Genes













Listed in


Genes/
CDC/
Antoine
WO03/097845 publ?


Copenhagen
Acambis Genes
et al. Genes
N = No





F9L-F10L
040-041
038L-039L



F12L-F13L
044-045
042L-043L
N


F17R-E1L
049-050
047R-048L
N


E1L-E2L
050-051
048L-049L
N


E8R-E9L
057-058
055R-056L


E9L-E10R
058-059
056L-057L
N


I1L-I2L
064-065
062L-063L
N


I2L-I3L
065-066
063L-064L
N


I5L-I6L
068-069
066L-067L


I6L-I7L
069-070
067L-068L
N


I7L-I8R
070-071
068L-069R
N


I8R-G1L
071-072
069R-070L
N


G1L-G3L
072-073
070L-071L
N


G3L-G2R
073-074
071L-072R
N


G2R-G4L
074-075
072R-073L
N


G4L-G5R
075-076
073L-074R
N


G5R-G5.5R
076-077
074R-075R
N


G5.5R-G6R
077-078
075R-076R
N


G6R-G7L
078-079
076R-077L
N


G7L-G8R
079-080
077L-078R


G8R-G9R
080-081
078R-079R


G9R-L1R
081-082
079R-080R
N


L1R-L2R
082-083
080R-081R


L2R-L3L
083-084
081R-082L


L3L-L4R
084-085
082L-083R


L4R-L5R
085-086
083R-084R
N


L5R-J1R
086-087
084R-085R
N


J3R-J4R
089-090
087R-088R
N


J4R-J5L
090-091
088R-089L


J5L-J6R
091-092
089L-090R


J6R-H1L
092-093
090R-091L
N


H1L-H2R
093-094
091L-092R
N


H2R-H3L
094-095
092R-093L


H3L-H4L
095-096
093L-094L
N


H4L-H5R
096-097
094L-095R


H5R-H6R
097-098
095R-096R
N


H6R-H7R
098-099
096R-097R


H7R-D1R
099-100
097R-098R


D1R-D2L
100-101
098R-099L
N


D2L-D3R
101-102
099L-100R
N


D3R-D4R
102-103
100R-101R
N


D4R-D5R
103-104
101R-102R


D5R-D6R
104-105
102R-103R
N


D6R-D7R
105-106
103R-104R


D9R-D10R
108-109
106R-107R
N


D10R-D11L
109-110
107R-108L


D11L-D12L
110-111
108L-109L


D12L-D13L
111-112
109L-110L


D13L-A1L
112-113
110L-111L


A1L-A2L
113-114
111L-112L
N


A2L-A2.5L
114-115
112L-113L
N


A2.5L-A3L
115-116
113L-114L


A3L-A4L
116-117
114L-115L


A4L-A5R
117-118
115L-116R


A5R-A6L
118-119
116R-117L
N


A6L-A7L
119-120
117L-118L


A7L-A8R
120-121
118L-119R


A8R-A9L
121-122
119R-120L
N


A9L-A10L
122-123
120L-121L
N


A10L-A11R
123-124
121L-122R
N


A11R-A12L
124-125
122R-123L


A12L-A13L
125-126
123L-124L


A13L-A14L
126-127
124L-125L


A14L-A14.5L
127-128
125L-125.5L
N


A14.5L-A15L
128-129
125.5L-126L
N


A15L-A16L
129-130
126L-127L
N


A16L-A17L
130-131
127L-128L
N


A17L-A18R
131-132
128L-129R
N


A18R-A19L
132-133
129R-130L
N


A19L-A21L
133-134
130L-131L
N


A21L-A20R
134-135
131L-132R
N


A20R-A22R
135-136
132R-133R
N


A22R-A23R
136-137
133R-134R


A23R-A24R
137-138
134R-135R


A28L-A29L
141-142
139L-140L
N


A29L-A30L
142-143
140L-141L
N









The orientations of these genes are variable, with some being transcribed to the right, some to the left. This means that some of the intergenic sites contain promoters that would have to be preserved in the construction of the insertion vector. In addition, for overlapping conserved genes, during vector construction the genes would have to be reconstructed using alternative codons to minimize the repeating sequences
The inventors focused on conserved genes whose orientation is “end to end” such that the 3′ stop codon of the genes are in close proximity to one another. The construction of transfer vectors used in these sites are facilitated by the fact that there would be no promoter in this region between the stop codons. If there are intergenic nucleotides separating the stop codons, then construction of the insertion vector is straightforward. If the stop codon of one gene is within the 3′ end of the other gene, then during construction of the plasmid transfer vector, the gene can be reconstructed using alternative codons to minimize repeating sequences, or, depending on the size of the overlap, simply corrected in the PCR of the flanks so as not to overlap. Table 2 gives the intergenic sites that meet the requirement of the orientation of the conserved genes being “end to end”. The intergenic sites highlighted in bold typeface have no overlapping ends and therefore are simplest to construct.







TABLE 2







Conserved genes with “end to end” orientation











Overlapping
CDC/Acambis
Antoine


Genes end to end
ends
genes
genes





F17R-E1L
Yes
049-050
047R-048L


E8R-E9L
No
057-058
055R-056L


I8R-G1L
No
071-072
069R-070L


G2R-G4L
Yes
074-075
072R-073L


G6R-G7L
Yes
078-079
076R-077L


L2R-L3L
Yes
083-084
081R-082L


J4R-J5L
No
090-091
088R-089L


J6R-H1L
Yes
092-093
090R-091L


H2R-H3L
No
094-095
092R-093L


D1R-D2L
Yes
100-101
098R-099L


D10R-D11L
No
109-110
107R-108L


A5R-A6L
Yes
118-119
116R-117L


A8R-A9L
Yes
121-122
119R-120L


A11R-A12L
No
124-125
122R-123L


A18R-A19L
Yes
132-133
129R-130L





The highlighted (in bold typeface) genes have no overlapping ends and thus are simplest to use as intergenic sites.






From this list, the inventors focused on the six intergenic sites that have no overlapping ends. In a working example, of these six, the intergenic site, 071-072 (I8R-G1L), was chosen as a site into which to insert a heterologous gene. The construction of a recombinant MVA virus using this intergenic site, and the characteristics of the resultant virus, are described in Example 1, and in International Publication Number WO2008/142479 A2, which is herein incorporated by reference in its entirety.
In addition to the conserved genes and corresponding intergenic sites described above, the inventors have discovered other sites useful for the insertion of a heterologous nucleic acid sequence. For example, any gene, for which it has been experimentally demonstrated that the deletion, or inactivation, of which, results in a 0.5 log, 0.75 log or 1 log (10 fold) reduction in titer, could be considered an “essential gene”. Similarly, an essential gene is any gene that results in at least an 50%, at least a 75%, or at least a 90% reduction in titer compared to a virus in which the corresponding gene has not been deleted or inactivated. If this gene lies adjacent to another essential gene, the intergenic site between the two genes would be a useful site for insertion of a heterologous nucleic acid sequence. While deletion of one or more of these ORF, along with the intervening heterologous nucleic acid sequence, would not prevent the virus from growing, it would result in decreased growth compared to a virus containing these ORFs. Thus, over time, virus that has lost one or more essential ORF would slowly become a smaller proportion of the total virus population and, given enough time, would disappear from the virus population entirely.
Thus, one embodiment of the present invention is a recombinant modified vaccinia Ankara (MVA) virus comprising a heterologous nucleic acid sequence located between, or flanked by, two adjacent essential ORFs from MVA virus. In one embodiment, adjacent ORF's are separated by an intergenic region (IGR). As described, the IGR may contain a heterologous nucleic acid sequence. Thus, one embodiment is a recombinant modified vaccinia Ankara (MVA) virus comprising a heterologous nucleic acid sequence in an intergenic region located between, or flanked by, two adjacent essential ORFs from MVA virus.
As used herein, heterologous, or exogenous, nucleic acid sequences are sequences which, in nature, are not normally found associated with the poxvirus as used according to the present invention. According to a further embodiment of the present invention, the exogenous nucleic acid sequence comprises at least one coding sequence. The coding sequence is operatively linked to a transcription control element, preferably to a poxviral transcription control element. Additionally, also combinations between poxviral transcription control element and, e.g., internal ribosomal entry sites can be used.
According to a further embodiment, the heterologous nucleic acid sequence can also comprise two or more coding sequences linked to one or several transcription control elements. Preferably, the coding sequence encodes one or more proteins. In some embodiments, the proteins are antigens, or comprise antigenic epitopes, especially those of therapeutically interesting genes.
Therapeutically interesting genes according to the present invention may be genes derived from or homologous to genes of pathogenous or infectious microorganisms which are disease causing. Accordingly, in the context of the present invention such therapeutically interesting genes are presented to the immune system of an organism in order to affect, preferably induce a specific immune response and, thereby, vaccinate or prophylactically protect the organism against an infection with the microorganism. In further preferred embodiments of the present invention the therapeutically interesting genes are selected from genes of infectious viruses, e.g., —but not limited to—dengue virus, hepatitis virus B or C, or human immunodeficiency viruses such as HIV.
According to a preferred embodiment of the present invention the heterologous nucleic acid sequence is derived from HIV and encodes HIV env, wherein the HIV env gene is preferably inserted into the IGR between the adjacent ORFs. The etiological agent of acquired immune deficiency syndrome (AIDS) is recognized to be a retrovirus exhibiting characteristics typical of the lentivirus genus, referred to as human immunodeficiency virus (HIV). The phylogenetic relationships of the human lentiviruses are shown in FIG. 1. HIV-2 is more closely related to SIVsmm, a virus isolated from sooty mangabey monkeys in the wild, than to HIV-1. It is currently believed that HIV-2 represents a zoonotic transmission of SIVsmm to man. A series of lentiviral isolates from captive chimpanzees, designated SIVcpz, are close genetic relatives of HIV-1.
The earliest phylogenetic analyses of HIV-1 isolates focused on samples from Europe/North America and Africa; discrete clusters of viruses were identified from these two areas of the world. Distinct genetic subtypes or clades of HIV-1 were subsequently defined and classified into three groups: M (major); O (outlier); and N (non-M or O) (FIG. 2). The M group of HIV-1, which includes over 95% of the global virus isolates, consists of at least eight discrete clades (A, B, C, D, F, G, H, and J), based on the sequence of complete viral genomes. Members of HIV-1 group O have been recovered from individuals living in Cameroon, Gabon, and Equatorial Guinea; their genomes share less than 50% identity in nucleotide sequence with group M viruses. The more recently discovered group N HIV-I strains have been identified in infected Cameroonians, fail to react serologically in standard whole-virus enzyme-linked immunosorbent assay (ELISA), yet are readily detectable by conventional Western blot analysis.
Most current knowledge about HIV-1 genetic variation comes from studies of group M viruses of diverse geographic origin. Data collected during the past decade indicate that the HIV-1 population present within an infected individual can vary from 6% to 10% in nucleotide sequence. HIV-1 isolates within a clade may exhibit nucleotide distances of 15% in gag and up to 30% in gp120 coding sequences. Interclade genetic variation may range between 30% and 40% depending on the gene analyzed.
All of the HIV-1 group M subtypes can be found in Africa. Clade A viruses are genetically the most divergent and were the most common HIV-1 subtype in Africa early in the epidemic. With the rapid spread of HIV-1 to southern Africa during the mid to late 1990s, clade C viruses have become the dominant subtype and now account for 48% of HIV-1 infections worldwide. Clade B viruses, the most intensively studied HIV-1 subtype, remain the most prevalent isolates in Europe and North America.
High rates of genetic recombination are a hallmark of retroviruses. It was initially believed that simultaneous infections by genetically diverse virus strains were not likely to be established in individuals at risk for HIV-1. By 1995, however, it became apparent that a significant fraction of the HIV-1 group M global diversity included interclade viral recombinants. It is now appreciated that HIV-1 recombinants will be found in geographic areas such as Africa, South America, and Southeast Asia, where multiple HIV-1 subtypes coexist and may account for more than 10% of circulating HIV-1 strains. Molecularly, the genomes of these recombinant viruses resemble patchwork mosaics, with juxtaposed diverse HIV-1 subtype segments, reflecting the multiple crossover events contributing to their generation. Most HIV-1 recombinants have arisen in Africa and a majority contains segments originally derived from clade A viruses. In Thailand, for example, the composition of the predominant circulating strain consists of a clade A gag plus pol gene segment and a clade B env gene. Because the clade B env gene in Thai HIV-1 strains is closely related to the clade E env present in virus isolates from the Central African Republic, it is believed that the original recombination event occurred in Africa, with the subsequent introduction of a descendent virus into Thailand. Interestingly, no full-length HIV-1 subtype E isolate (i.e., with subtype E gag, pol, and env genes) has been reported to date.
The discovery that α and μ chemokine receptors function as coreceptors for virus fusion and entry into susceptible CD4+ cells has led to a revised classification scheme for HIV-1 (FIG. 3). Isolates can now be grouped on the basis of chemokine receptor utilization in fusion assays in which HIV-1 gp120 and CD4+ coreceptor proteins are expressed in separate cells. As indicated in FIG. 3, HIV-1 isolates using the CXCR4 receptor (now designated X4 viruses) are usually T cell line (TCL)-tropic syncytium inducing (SI) strains, whereas those exclusively utilizing the CCR5 receptor (R5 viruses) are predominantly macrophage (M)-tropic and non-syncytium inducing (NSI). The dual-tropic R5/X4 strains, which may comprise the majority of patient isolates and exhibit a continuum of tropic phenotypes, are frequently SI.
As is the case for all replication-competent retroviruses, the three primary HIV-1 translation products, all encoding structural proteins, are initially synthesized as polyprotein precursors, which are subsequently processed by viral or cellular proteases into mature particle-associated proteins (FIG. 4). The 55-kd Gag precursor Pr55Gag is cleaved into the matrix (MA), capsid (CA), nucleocapsid (NC), and p6 proteins. Autocatalysis of the 160-kd Gag-Pol polyprotein, Pr160Gag-Pol, gives rise to the protease (PR), the heterodimeric reverse transcriptase (RT), and the integrase (IN) proteins, whereas proteolytic digestion by a cellular enzyme(s) converts the glycosylated 160-kd Env precursor gp160 to the gp120 surface (SU) and gp41 transmembrane (TM) cleavage products. The reining six HIV-1-encoded proteins (Vif, Vpr, Tat, Rev, Vpu, and Nef) are the primary translation products of spliced mRNAs.
Gag
The Gag proteins of HIV, like those of other retroviruses, are necessary and sufficient for the formation of noninfectious, virus-like particles. Retroviral Gag proteins are generally synthesized as polyprotein precursors; the HIV-1 Gag precursor has been named, based on its apparent molecular mass, Pr55Gag. As noted previously, the mRNA for Pr55Gag is the unspliced 9.2-kb transcript (FIG. 4) that requires Rev for its expression in the cytoplasm. When the pol ORF is present, the viral protease (PR) cleaves Pr55Gag during or shortly after budding from the call to generate the mature Gag proteins p17 (MA), p24 (CA), p7 (NC), and p6 (see FIG. 4). In the viral, MA is localized immediately inside the lipid bilayer of the viral envelope, CA forms the outer portion of the cone-shaped core structure in the center of the particle, and NC is present in the core in a ribonucleoprotein complex with the viral RNA genome (FIG. 5).
The HIV Pr55Gag precursors oligomerizes following its translation and is targeted to the plasma membrane, where particles of sufficient size and density to be visible by EM are assembled. Formation of virus-like particles by Pr55Gag is a self-assembly process, with critical Gag-Gag interactions taking place between multiple domains along the Gag precursor. The assembly of virus-like particles does not require the participation of genomic RNA (although the presence of nucleic acid appears to be essential), pol-encoded enzymes, or Env glycoproteins, but the production of infectious virions requires the encapsidation of the viral RNA genome and the incorporation of the Env glycoproteins and the Gag-Pol polyprotein precursor Pr160Gag-Pol.
Pol
Downstream of gag lies the most highly conserved region of the HIV genome, the pol gene, which encodes three enzymes: PR, RT, and IN (see FIG. 4). RT and IN are required, respectively, for reverse transcription of the viral RNA genome to a double-stranded DNA copy, and for the integration of the viral DNA into the host cell chromosome. PR plays a critical role late in the life cycle by mediating the production of mature, infectious virions. The pol gene products are derived by enzymatic cleavage of a 160-kd Gag-Pol fusion protein, referred to as Pr160Gag-Pol. This fusion protein is produced by ribosomal frameshifting during translation of Pr55Gag (see FIG. 4). The frame-shifting mechanism for Gag-Pol expression, also utilized by many other retroviruses, ensures that the pol-derived proteins are expressed at a low level, approximately 5% to 10% that of Gag. Like Pr55Gag, the N-terminus of Pr160Gag-Pol is myristylated and targeted to the plasma membrane.
Protease
Early pulse-chase studies performed with avian retroviruses clearly indicated that retroviral Gag proteins are initially synthesized as polyprotein precursors that are cleaved to generate smaller products. Subsequent studies demonstrated that the processing function is provided by a viral rather than a cellular enzyme, and that proteolytic digestion of the Gag and Gag-Pol precursors is essential for virus infectivity. Sequence analysis of retroviral PRs indicated that they are related to cellular “aspartic” proteases such as pepsin and resin. Like these cellular enzymes, retroviral PRs use two apposed Asp residues at the active site to coordinate a water molecule that catalyzes the hydrolysis of a peptide bond in the target protein. Unlike the cellular aspartic proteases, which function as pseudodimers (using two folds within the same molecule to generate the active site), retroviral PRs function as true dimers. X-ray crystallographic data from HIV-1 PR indicate that the two monomers are held together in part by a four-stranded antiparallel β-sheet derived from both N- and C-terminal ends of each monomer. The substrate-binding site is located within a cleft formed between the two monomers. Like their cellular homologs, the HIV PR dimer contains flexible “flaps” that overhang the binding site and may stabilize the substrate within the cleft; the active-site Asp residues lie in the center of the dimer. Interestingly, although some limited amino acid homology is observed surrounding active-site residues, the primary sequences of retroviral PRs are highly divergent, yet their structures are remarkably similar.
Reverse Transcriptase
By definition, retroviruses possess the ability to convert their single-stranded RNA genomes into double-stranded DNA during the early stages of the infection process. The enzyme that catalyzes this reaction is RT, in conjunction with its associated RNaseH activity. Retroviral RTs have three enzymatic activities: (a) RNA-directed DNA polymerization (for minus-strand DNA synthesis), (b) RNaseH activity (for the degradation of the tRNA primer and genomic RNA present in DNA-RNA hybrid intermediates), and (c) DNA-directed DNA polymerization (for second- or plus-strand DNA synthesis).
The mature HIV-1 RT holoenzyme is a heterodimer of 66 and 51 kd subunits. The 51-kd subunit (p51) is derived from the 66-kd (p66) subunit by proteolytic removal of the C-terminal 15-kd RNaseH domain of p66 by PR (see FIG. 4). The crystal structure of HIV-1 RT reveals a highly asymmetric folding in which the orientations of the p66 and p51 subunits differ substantially. The p66 subunit can be visualized as a right hand, with the polymerase active site within the palm, and a deep template-binding cleft formed by the palm, fingers, and thumb subdomains. The polymerase domain is linked to RNaseH by the connection subdomain. The active site, located in the palm, contains three critical Asp residues (110, 185, and 186) in close proximity, and two coordinated Mg2+ ions. Mutation of these Asp residues abolishes RT polymerizing activity. The orientation of the three active-site Asp residues is similar to that observed in other DNA polymerases (e.g., the Klenow fragment of E. coli DNA polI). The p51 submit appears to be rigid and does not form a polymerizing cleft; Asp 110, 185, and 186 of this subunit are buried within the molecule. Approximately 18 base pairs of the primer-template duplex lie in the nucleic acid binding cleft, stretching from the polymerase active site to the RNaseH domain.
In the RT-primer-template-dNTP structure, the presence of a dideoxynucleotide at the 3′ end of the primer allows visualization of the catalytic complex trapped just prior to attack on the incoming dNTP. Comparison with previously obtained structures suggests a model whereby the fingers close in to trap the template and dNTP prior to nucleophilic attack of the 3′-OH of the primer on the incoming dNTP. After the addition of the incoming dNTP to the growing chain, it has been proposed that the fingers adopt a more open configuration, thereby releasing the pyrophosphate and enabling RT to bind the next dNTP. The structure of the HIV-1 RNaseH has also been determined by x-ray crystallography; this domain displays a global folding similar to that of E. coli RNaseH.
Integrase
A distinguishing feature of retrovirus replication is the insertion of a DNA copy of the viral genome into the host cell chromosome following reverse transcription. The integrated viral DNA (the provirus) serves as the template for the synthesis of viral RNAs and is maintained as part of the host cell genome for the lifetime of the infected cell. Retroviral mutants deficient in the ability to integrate generally fail to establish a productive infection.
The integration of viral DNA is catalyzed by integrase, a 32-kd protein generated by PR-mediated cleavage of the C-terminal portion of the HIV-1 Gag-Pol polyprotein (see FIG. 4).
Retroviral IN proteins are composed of three structurally and functionally distinct domains: an N-terminal, zinc-finger-containing domain, a core domain, and a relatively nonconserved C-terminal domain. Because of its low solubility, it has not yet been possible to crystallize the entire 288-amino-acid HIV-1 IN protein. However, the structure of all three domains has been solved independently by x-ray crystallography or NMR methods. The crystal structure of the core domain of the avian sarcoma virus IN has also been determined. The N-terminal domain (residues 1 to 55), whose structure was solved by NMR spectroscopy, is composed of four helices with a zinc coordinated by amino acids His-12, His-16, Cys-40, and Cys-43. The structure of the N-terminal domain is reminiscent of helical DNA binding proteins that contain a so-called helix-turn-helix motif however, in the HIV-1 structure this motif contributes to dimer formation. Initially, poor solubility hampered efforts to solve the structure of the core domain. However, attempts at crystallography were successful when it was observed that a Phe-to-Lys change at IN residue 185 greatly increased solubility without disrupting in vitro catalytic activity. Each monomer of the HIV-1 IN core domain (IN residues 50 to 212) is composed of a five-stranded n-sheet flanked by helices; this structure bears striking resemblance to other polynucleotidyl transferases including RNaseH and the bacteriophage MuA transposase. Three highly conserved residues are found in analogous positions in other polynucleotidyl transferases; in HIV-1 IN these are Asp-64, Asp-116 and Glu-152, the so-called D,D-35-E motif. Mutations at these positions block HIV IN function both in vive and in vitro. The close proximity of these three amino acids in the crystal structure of both avian sarcoma virus and HIV-1 core domains supports the hypothesis that these residues play a central role in catalysis of the polynucleotidyl transfer reaction that is at the heart of the integration process. The C-terminal domain, whose structure has been solved by NMR methods, adopts a five-stranded β-barrel folding topology reminiscent of a Src homology 3 (SH3) domain. Recently, the x-ray structures of SIV and Rous sarcoma virus IN protein fragments encompassing both the core and C-terminal domains have been solved.
Env
The HIV Env glycoproteins play a major role in the virus life cycle. They contain the determinants that interact with the CD4 receptor and coreceptor, and they catalyze the fusion reaction between the lipid bilayer of the viral envelope and the host cell plasma membrane. In addition, the HIV Env glycoproteins contain epitopes that elicit immune responses that are important from both diagnostic and vaccine development perspectives.
The HIV Env glycoprotein is synthesized from the singly spliced 43-kb Vpu/Env bicistronic mRNA (see FIG. 4); translation occurs an ribosomes associated with the rough endoplasmic reticulum (ER). The 160-kd polyprotein precursor (gp160) is an integral membrane protein that is anchored to cell membranes by a hydrophobic stop-transfer signal in the domain destined to be the mature TM Env glycoprotein, gp41 (FIG. 6). The gp160 is cotranslationally glycosylated, forms disulfide bonds, and undergoes oligomerization in the ER. The predominant oligomeric form appears to be a trimer, although dimers and tetramers are also observed. The gp160 is transported to the Golgi, where, like other retroviral envelope precursor proteins, it is proteolytically cleaved by cellular enzymes to the mature SU glycoprotein gp120 and TM glycoprotein gp41 (see FIG. 6). The cellular enzyme responsible for cleavage of retroviral Env precursors following a highly conserved Lys/Arg-X-Lys/Arg-Arg motif is furin or a furin-like protease, although other enzymes may also catalyze gp160 processing. Cleavage of gp160 is required for Env-induced fusion activity and virus infectivity. Subsequent to gp160 cleavage, gp120 and gp41 form a noncovalent association that is critical for transport of the Env complex from the Golgi to the cell surface. The gp120-gp41 interaction is fairly weak, and a substantial amount of gp120 is shed from the surface of Env-expressing cells.
The HIV Env glycoprotein complex, in particular the SU (gp120) domain, is very heavily glycosylated; approximately half the molecular mass of gp160 is composed of oligosaccharide side chains. During transport of Env from its site of synthesis in the ER to the plasma membrane, many of the side chains are modified by the addition of complex sugars. The numerous oligosaccharide side chains form what could be imagined as a sugar cloud obscuring much of gp120 from host immune recognition. As shown in FIG. 6, gp120 contains interspersed conserved (C1 to C5) and variable (V1 to V5) domains. The Cys residues present in the gp120s of different isolates are highly conserved and form disulfide bonds that link the first four variable regions in large loops.
A primary function of viral Env glycoproteins is to promote a membrane fusion reaction between the lipid bilayers of the viral envelope and host cell membranes. This membrane fusion event enables the viral core to gain entry into the host cell cytoplasm. A number of regions in both gp120 and gp41 have been implicated, directly or indirectly, in Env-mediated membrane fusion. Studies of the HA2 hemagglutinin protein of the orthomyxovixuses and the F protein of the paramyxoviruses indicated that a highly hydrophobic domain at the N-terminus of these proteins, referred to as the fusion peptide, plays a critical role in membrane fusion. Mutational analyses demonstrated that an analogous domain was located at the N-terminus of the HIV-1, HIV-2, and SIV TM glycoproteins (see FIG. 6). Nonhydrophobic substitutions within this region of gp41 greatly reduced or blocked syncytium formation and resulted in the production of noninfectious progeny virions.
C-terminal to the gp41 fusion peptide are two amphipathic helical domains (see FIG. 6) which play a central role in membrane fusion. Mutations in the N-terminal helix (referred to as the N-helix), which contains a Leu zipper-like heptad repeat motif impair infectivity and membrane fusion activity, and peptides derived from these sequences exhibit potent antiviral activity in culture. The structure of the ectodomain of HIV-1 and SIV gp41, the two helical motifs in particular, has been the focus of structural analyses in recent years. Structures were determined by x-ray crystallography or NMR spectroscopy either for fusion proteins containing the helical domains, a mixture of peptides derived from the N- and C-helices, or in the case of the SIV structure, the intact gp41 ectodomain sequence from residue 27 to 149. These studies obtained fundamentally similar trimeric structures, in which the two helical domains pack in an antiparallel fashion to generate a six-helix bundle. The N-helices form a coiled-coil in the center of the bundle, with the C-helices packing into hydrophobic grooves on the outside.
In the steps leading to membrane fusion CD4 binding induces conformation changes in Env that facilitate coreceptor binding. Following the formation of a ternary gp120/CD4/coreceptor complex, gp41 adopts a hypothetical conformation that allows the fusion peptide to insert into the target lipid bilayer. The formation of the gp41 six-helix bundle (which involves antiparallel interactions between the gp41 N- and C-helices) brings the viral and cellular membranes together and membrane fusion takes place.
Furthermore, therapeutically interesting genes according to the present invention also comprise disease related genes, which have a therapeutic effect an proliferative disorder, cancer or metabolic diseases. For example, a therapeutically interesting gene regarding cancer could be a cancer antigen that has the capacity to induce a specific anti-cancer immune reaction.
According to a further embodiment of the present invention, the heterologous nucleic acids sequence comprises at least one marker or selection gene.
Selection genes transduce a particular resistance to a cell, whereby a certain selection method becomes possible. The skilled practitioner is familiar with a variety of selection genes, which can be used in a poxviral system. Among these are, e.g., neomycin resistance gene (NPT) or phosphoribosyl transferase gene (gpt).
Marker genes induce a color reaction in transduced cells, which can be used to identify transduced cells. The skilled practitioner is familiar with a variety of marker genes, which can be used in a poxviral system. Among these are the gene encoding, e.g., β-galactosidase (β-gal), β-glucosidase (β-glu), green fluorescence protein (EGFP) or blue fluorescence protein.
According to still a further embodiment of the present invention the heterologous nucleic acid sequence comprises a spacing sequence, which separates poxviral transcription control element and/or coding sequence in the heterologous nucleic acid sequence from the stop codon and/or the start codon of the adjacent ORFs. This spacer sequence between the stop/start codon of the adjacent ORF and the inserted coding sequence in the heterologous nucleic acid sequence has the advantage to stabilize the inserted heterologous nucleic acid sequence and, thus, any resulting recombinant virus. The size of the spacer sequence is variable as long as the sequence is without its own coding or regulatory function.
According to a further embodiment, the spacer sequence separating the poxviral transcription control element and/or the coding sequence in the heterologous nucleic acid sequence from the stop codon of the adjacent ORF is at least one nucleotide long.
According to another embodiment of the present invention, the spacing sequence separating the poxviral transcription control element and/or the coding sequence in the heterologous nucleic acid sequence from the start codon of the adjacent ORF is at least 30 nucleotides. Particularly, in cases where a typical vaccinia virus promoter element is identified upstream of a start codon the insertion of heterologous nucleic acid sequence may not separate the promoter element from the start codon of the adjacent ORF. A typical vaccinia promoter element can be identified by scanning for e.g., the sequence “TAAAT” for late promoters (Davison & Moss 1989 J. Mol. Biol.; 210:771-784) and an A/T rich domain for early promoters. A spacing sequence of about 30 nucleotides is the preferred distance to secure that a poxviral promoter located upstream of the start codon of the ORF is not influenced. Additionally, according to a further preferred embodiment, the distance between the inserted heterologous nucleic acid sequence and the start codon of the adjacent ORF is around 50 nucleotides and more preferably around 100 nucleotides.
According to a further preferred embodiment of the present invention, the spacing sequence comprises an additional poxviral transcription control element which is capable of controlling the transcription of the adjacent ORF.
Thus far, the disclosure has focused on recombinant MVA viruses using ORFs that are adjacent in parental MVA virus. However, the present invention also includes recombinant viruses, and methods of making such viruses, in which heterologous nucleic acid sequences are inserted between adjacent, essential ORFs techniques, wherein the ORfs used for insertion are not adjacent in the parental MVA virus. That is, viruses can be constructed so that ORFs that are adjacent in the recombinant MVA virus are separated by one or more poxvirus ORFs (intervening ORFs) in the parental MVA virus. As used herein, a parental MVA virus is one from which a progeny, recombinant virus is constructed. An example of a parental MVA virus is MVA 1974/NIH Clone 1. Parental viruses can be used to construct recombinant viruses using techniques disclosed herein, such that the intervening ORFs can be removed during the construction process. It is appreciated by those skilled in the poxvirus arts that by using nucleic acid molecules comprising carefully selected poxvirus ORF's, sections of the viral genome between those two ORFs can be deleted through the process of homologous recombination. For example, it can be supposed that two essential ORFs are separated by a one kilobase region of the genome containing a non-essential ORF. A nucleic acid construct can be made in which the two essential ORFs are cloned, for example, into a plasmid such that the two ORFs are adjacent in the nucleic acid construct. Upon introduction of the nucleic acid construct into a poxvirus infected cell (e.g., a parental MVA virus infected cell), the essential ORFs will recombine with the corresponding ORFs in the viral genome of the parental virus. Through further recombination events understood by those skilled in the art, the one kilobase region will be excised from the viral genome, resulting in the two essential ORF becoming adjacent. Thus, one embodiment of the present invention is a recombinant modified vaccinia Ankara (MVA) virus comprising a heterologous nucleic acid sequence located between two adjacent essential ORFs from the MVA virus genome, wherein the recombinant MVA virus lacks non-essential ORFs that are present between the corresponding essential ORFs in the parental MVA virus. Thus the heterologous nucleic acid sequence is flanked by essential ORFs that are non-adjacent in the parental MVA virus. The essential ORF are chosen from pairs of essential ORFs present in the MVA genome that are separated by non-essential ORFs. In one embodiment, the essential ORFs are selected from the group consisting of A50R (MVA163), B1R (MVA167), F10 (MVA-039), F12 (MVA042), F13L (MVA043), F15L (MVA045), F17L (MVA047), E4L (MVA051), E6L (MVA053), E8L (MVA055), E10L (MVA057), I1L (MVA062), I3L (MVA064), I5L (MVA066), J1R (MVA085), J3R (MVA087), D7L (MVA104), D9L (MVA106), A24R (MVA135), and A28R (MVA139). In one embodiment, the two essential ORFs are selected from pairs of essential ORFs in the group of consisting of A50R-B1R (MVA163-MVA167), F10-F12 (MVA039-MVA042), F13L-F15L (MVA043-MVA045), F15L-F17L (MVA045-MVA047), E4L-B6L (MVA051-MVA053), E6L-E8L (MVA053-MVA055), E10L-I1L (MVA057-MVA062), I3L-I5L (MVA064-MVA066), J1R-J3R (MVA085-MVA087), D7L-D9L (MVA104-MVA106), and A24R-A28R (MVA135-MVA139). In one embodiment, the essential ORFs are selected from A50R (MVA163) and B1R (MVA167). In one embodiment, one essential ORF is A50R (MVA163) and the other essential ORF is B1R (MVA167).
As previously discussed, as a result of extensive passage in cell culture, the MVA virus genome contains six major deletions, referred to as Del I, II, II, IV, V and VI. Historically, the region around Del III, which is a deletion of approximately 31,000 nucleotides, has been used for insertion of heterologous nucleic acid sequences. Thus, in one embodiment of the present invention, the non-essential ORFs deleted during construction of the recombinant MVA virus flank the Del III region in the wild-type MVA virus.
As has been described, recombinant MVA viruses can contain additional sequences, such as IGRs and/or heterologous nucleic acid sequences, between the two adjacent, essential ORFs. Such sequences have been described herein. Thus, one embodiment of the present invention is a recombinant modified vaccinia Ankara (MVA) virus comprising a heterologous nucleic acid sequence located between two adjacent essential ORFs from the MVA virus genome, wherein the recombinant MVA virus lacks non-essential ORFs that are present between the corresponding essential ORFs in the parental MVA virus, and wherein the heterologous nucleic acid sequence is inserted into an IGR. The heterologous can contain coding sequences under the control of a transcriptional control element, as has been described elsewhere in the disclosure.
While the inventors have disclosed specific essential ORFs, and sequences thereof; the present invention also comprises recombinant MVA virus, and methods of making such, using portions or variants of the disclosed ORF. For example, while the present invention discloses ORF A50R, and portions thereof; (SEQ ID NO: 1 and SEQ ID NO:14), and ORF B1R, and portions thereof (SEQ ID NO:16 and SEQ ID NO:19), the present invention comprises recombinant MVA viruses comprising variants of these sequences, so long as the variant ORF encodes a protein having essentially the same function as the protein encoded by the corresponding wild-type ORF. Two proteins are considered as having essentially the same function if MVA viruses comprising the respective proteins produce titers that are within about 10%, about 20%, about 30% or about 40% of each other when grown using the same cell line. Thus, one embodiment of the present invention is a recombinant modified vaccinia Ankara (MVA) virus comprising a heterologous nucleic acid sequence located between two adjacent ORFs, wherein the adjacent ORFs comprise a nucleotide sequence at least 90%, at least 95%, at least 97% or at least 99% sequence identity with an essential ORF from MVA. In one embodiment, the adjacent ORFs comprise a nucleotide sequence at least 90%, at least 95%, at least 97% or at least 99% identical to essential ORFs selected from the group consisting of A50R (MVA163), B1R (MVA167), F10 (MVA-039), F12 (MVA042), F13L (MVA043), F15L (MVA045), F17L (MVA047), E4L (MVA051), E6L (MVA053), E8L (MVA055), E10L (MVA057), I1L (MVA062), I3L (MVA064), I5L (MVA066), J1R (MVA085), J3R (MVA087), D7L (MVA104), D9L (MVA106), A24R (MVA135), and A28R (MVA139). In a preferred embodiment, the two adjacent ORf's are not derived from the same essential ORF. In one embodiment, the two adjacent ORFs comprise nucleotide sequences at least 90%, at least 95%, at least 97% or at least 99% identical to pairs of essential ORFs in the group of consisting of A50R-B1R (MVA163-MVA167), F10-F12 (MVA039-MVA042), F13L-F15L (MVA043-MVA045), F15L-F17L (MVA045-MVA047), E4L-E6L (MVA051-MVA053), E6L-E8L (MVA053-MVA055), E10L-I1L (MVA057-MVA062), I3L-I5L (MVA064-MVA066), J1R-J3R (MVA085-MVA087), D7L-D9L (MVA104-MVA106), and A24R-A28R (MVA135-MVA139). In one embodiment one adjacent ORF comprises a nucleotide sequence at least 90%, at least 95%, at least 97% or at least 99% sequence identical with SEQ ID NO:A50R (MVA163) and the second adjacent ORF comprises a nucleotide sequence at least 90%, at least 95%, at least 97% or at least 99% sequence identical to a second essential ORF. In one embodiment one adjacent ORF comprises a nucleotide sequence at least 90%, at least 95%, at least 97% or at least 99% sequence identical with SEQ ID NO:B1R.
The present invention also discloses nucleic add constructs useful for producing recombinant viruses of the present invention. As used herein a nucleic acid construct is a recombinant nucleic acid molecule comprising at least a portion of at least one essential ORF from MVA virus. The nucleic acid construct enables transport of useful nucleic acid sequences to a cell within an environment, such as, but not limited to, an organism, tissue, or cell culture. A nucleic acid construct of the present disclosure is produced by human intervention. The nucleic acid construct can be DNA, RNA or variants thereof. The nucleic acid molecule can be linear DNA, a DNA plasmid, a viral vector, or other vector. In one embodiment, a nucleic acid molecule can be a DNA plasmid. In one embodiment, a nucleic acid molecule can be a DNA plasmid comprising viral components, plasmid components, transcriptional control elements, and any other useful elements know to those skilled in the art that enable nucleic acid molecule delivery and expression. Methods for the general construction of recombinant nucleic acid molecules are well known. See, for example, Molecular Cloning: a Laboratory Manual, 3rd edition, Sambrook et al. 2001 Cold Spring Harbor Laboratory Press, and Current Protocols in Molecular Biology, Ausubel et al. eds., John Wiley & Sons, 1994.
One embodiment of the present invention is an isolated nucleic acid construct comprising: (a) a first nucleic acid sequence derived from, or homologous to, a first essential ORF from a modified vaccinia Ankara (MVA) virus genome; and (b) a second nucleic acid sequence derived from, or homologous to, a second essential ORF from a MVA virus genome; wherein the first and second essential MVA virus ORFs are separated by at least one non-essential ORF in the MVA virus genome, and wherein the first and second nucleic acid sequences are adjacent to each other in the isolated nucleic acid construct, and wherein the first and second nucleic acid sequences comprise at least 25 contiguous nucleotides from the first and second essential MVA ORFs, respectively. Such a nucleic acid construct is useful for constructing recombinant MVA viruses through the process of homologous recombination. Using this process, isolated nucleic acid constructs of the present invention can be used to construct recombinant MVA viruses in which ORFs that are not adjacent in a parental MVA virus (i.e, they are separated by other, non-essential MVA ORFs), are made adjacent in the progeny, recombinant MVA virus. This can be done, for example, by cloning non-adjacent ORFs from a parental MVA virus into a nucleic acid molecule, such as a plasmid, without also cloning the intervening non-essential ORFs. Thus, the no-adjacent ORFs are made adjacent in the nucleic acid construct. As has been described, recombination of such a nucleic acid construct into the MVA viral genome will result in deletion of the intervening non-essential ORFs from the parental MVA virus resulting in a progeny, recombinant MVA virus in which the originally non-adjacent ORFs are adjacent. Thus, in a preferred embodiment, the first and second nucleic acid sequences are derived from, or homologous to, first and second essential MVA ORFs, respectively, that are not adjacent in the parental MVA virus. That is, the first and second essential ORFs are separated by at least one non-essential ORF in the parental MVA virus genome.
As used herein, the phrase derived from refers to the source nucleic acid (i.e., ORF) from which the nucleic acid sequence was obtained. Thus, in this regard the nucleic acid sequence may be identical to all or part of the originating ORF. However, the nucleic acid sequence may also vary in sequence from the originating ORF. Thus, a nucleic acid sequence that is derived from an MVA ORF may or may not be identical in sequence to all, or a portion, of an MVA ORF, so long as the function of the original ORF is maintained in the derived nucleic acid sequence. For example, it is understood in the art that nucleic acid molecules from related species of poxviruses can recombine, even though the sequences of such molecules are not identical. Thus, in one embodiment of the present invention, the first and second nucleic acid sequences have sufficient sequence identity with the essential MVA ORFs from which they area derived to allow homologous recombination between a nucleic acid molecule comprising the first or second nucleic acid sequence, and a nucleic acid molecule comprising the essential MVA ORF from which such sequence was derived. In one embodiment, the first and second nucleic acid sequences are at least 75%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to at least a portion of the essential MVA ORF from which they are derived. In one embodiment, the nucleic acid sequence is identical to at least a portion of the essential MVA ORF from which it was derived.
It is also appreciated in the art that small polynucleotide molecules are capable of engaging in the process of homologous recombination. Consequently, nucleic acid sequences present in nucleic acid constructs of the present invention need not comprise the entire sequence of an essential MVA ORF in order for the nucleic acid construct to be able to recombine into the MVA virus genome. In fact, it has been shown that fragments of the poxvirus genome as small as 20 bases in length are capable of engaging in homologous recombination with their respective sequence in the viral genome. Thus, in one embodiment of the present invention, the first and second nucleic acid sequences can comprise 25, 30, 35, 40, 45, 50, 100, 150, 200, 250, or 300 nucleotides from an essential MVA ORF. One embodiment of the present invention is an isolated nucleic acid construct comprising: (a) a first nucleic acid sequence comprising at least 25 contiguous nucleotides from a first essential MVA ORF; and (b) a second nucleic acid sequence comprising at least 25 contiguous nucleotides from a second essential MVA ORF; wherein the first and second essential MVA virus ORFs are separated by at least one non-essential ORF in the MVA virus genome, and wherein the first and second nucleic acid sequences are adjacent to each other in the isolated nucleic acid construct. In one embodiment, the first nucleic acid sequences comprise 25 contiguous nucleotides from an essential ORF selected from the group consisting of A50R (MVA163), B1R (MVA167), F10 (MVA-039), F12 (MVA042), F13L (MVA043), F15L (MVA045), F17L (MVA047), E4L (MVA051), E6L (MVA053), E8L (MVA055), E10L (MVA057), I1L (MVA062), I3L (MVA064), I5L (MVA066), J1R (MVA085), J3R (MVA087), D7L (MVA104), D9L (MVA106), A24R (MVA135), and A28R (MVA139). In one embodiment, the second nucleic acid sequences comprise 25 contiguous nucleotides from an essential ORF selected from the group consisting of A50R (MVA163), B1R (MVA167), F10 (MVA-039), F12 (MVA042), F13L (MVA043), F15L (MVA045), F17L (MVA047), E4L (MVA051), E6L (MVA053), E8L (MVA055), E10L (MVA057), I1L (MVA062), I3L (MVA064), I5L (MVA066), J1R (MVA085), J3R (MVA087), D7L (MVA104), D9L (MVA106), A24R (MVA135), and A28R (MVA139). In one embodiment, the first nucleic acid sequence comprises at least 25 contiguous nucleotides from SEQ ID NO: 11 or SEQ ID NO:14, and the second nucleic add sequence comprises at least 25 contiguous nucleotides from SEQ ID NO:16 or SEQ ID NO:19.
Nucleic acid constructs of the present invention are used to deliver heterologous nucleic acid sequences into the genome of MVA virus. Thus, one embodiment, a nucleic acid construct of the present invention comprises a heterologous nucleic acid molecule between the first and second nucleic acid sequences. Exemplary heterologous nucleic acid sequences have been described elsewhere in the disclosure. Any heterologous nucleic add sequence disclosed herein is suitable for inclusion in a nucleic acid construct of the present invention.
Because nucleic acid constructs of the present invention can recombine with the genome of a parental MVA virus, they can be used to insert heterologous nucleic acid sequences into the viral genome. Thus, in one embodiment of the present invention a nucleic acid contrast of the present invention contains an intergenic region between the first and second nucleic acid sequences. The intergenic region can comprise such things as transcriptional control elements, restriction sites and non-vaccinia open reading frames. Thus, the intergenic region can be used to insert heterologous nucleic acid sequences comprising genes under the control of a transcriptional control element. Upon recombination of the nucleic acid construct with the MVA virus genome, the heterologous nucleic acid sequence will be inserted into the MVA viral genome between the essential ORFs corresponding to the two adjacent, essential ORFs flanking the nucleic acid sequence in the nucleic acid construct. The resulting MVA virus will be a recombinant MVA virus containing the heterologous nucleic acid sequence stably integrated into the MVA virus genome.
In one embodiment, a nucleic acid construct of the present invention comprises complete or partial fragment of an IGR sequence located between the two adjacent ORFs of the viral genome. Preferably, the nucleic acid construct comprises inserted into said IGR-derived sequence at least one cloning site for the insertion of an heterologous DNA sequence of interest and, preferably, for the insertion of a poxviral transcription control element operatively linked to said heterologous DNA sequence. Optionally, the nucleic acid construct comprises a reporter- and/or selection gene cassette. The nucleic acid construct preferably also comprises sequences of the two adjacent ORFs flanking said complete or partial fragment of the IGR sequence.
Some IGRs have been identified which do not include nucleotide sequences. In these cases, the plasmid vector comprises DNA sequences of the IGR flanking sequences, i.e., DNA sequences of the two adjacent ORFs. Preferably, the cloning site for the insertion of the heterologous DNA sequence is inserted into the IGR. The DNA of the IGR flanking sequences is used to direct the insertion of exogenous DNA sequences into the corresponding IGR in the MVA genome. Such a plasmid vector may additionally include a complete or partial fragment of an IGR sequence which comprises the cloning site for the insertion of the heterologous DNA sequence and, optionally, of the, reporter- and/or selection gone cassette.
One embodiment of the present invention is a method to produce a stable, recombinant modified vaccinia Ankara virus. Such a method makes use of the nucleic acid constructs disclosed herein. Thus, the method comprises first obtaining a nucleic acid construct comprising a heterologous nucleic acid sequence located between, or flanked by, two adjacent essential open reading frames (ORFs) of the MVA virus genome, wherein the MVA virus is lacking non-essential ORFS, or ORF fragments, that are present between the corresponding two essential ORFS in the parental MVA virus. For example, to obtain an appropriate nucleic acid construct, nucleic acid sequences from essential MVA ORFs can be isolated and cloned into a standard cloning vector, such as pBluescript (Stratagene), so that they flank the heterologous DNA to be inserted into the MVA genome. This construct can then be introduced into a cell using methods know to those in the art (e.g., transfection). The call containing the nucleic acid construct is then infected with a MVA virus and cultured under conditions suitable to allow homologous recombination between the nucleic acid construct and the MVA virus genome. At the appropriate time the cells are then harvested and the recombinant MVA virus isolated. The resultant virus will be a stable, recombinant MVA virus. Such a virus may also be called a derivative virus. It will be appreciated that the order of the steps of introducing the nucleic acid construct into the cell, and infecting the cell can be reversed, or that these two steps may happen simultaneously.
General methods to introduce heterologous nucleic acid sequences in a nucleic acid construct into an MVA genome and methods to obtain recombinant MVA are well known to the person skilled in the art and, additionally, can be deduced can be deduced from Molecular Cloning, A Laboratory Manual, Second Edition, J. Sambrook, E. F. Fritsch and T. Maniatis, Cold Spring Harbor Laboratory Press, 1989 and Current Protocols in Molecular Biology, John Wiley and Son Inc. 1998, Chapter 16, section IV, “Expression of proteins in mammalian cells using vaccinia viral vectors”.
The DNA sequences according to the invention can be used to identify or isolate the MVA or its derivatives according to the invention and cells or individuals infected with an MVA according to the present invention. The DNA sequences are, e.g., used to generate PCR-primers, hybridization probes or are used in array technologies.
The term derivative virus, and the like, according to the present invention refers to progeny viruses showing the same characteristic features as the parent virus but showing differences in one or more parts of its genome. The term “derivative of MVA” describes a virus, which has the sane functional characteristics compared to MVA. For example, a derivative of MVA 1974/NIH Clone 1 has the characteristic features of MVA 1974/NIH Clone 1. One of these characteristics of MVA 1974/NIH Clone 1 or derivatives thereof is its attenuation and severe restriction in host range.
The recombinant MVA according to the present invention is useful as a medicament or vaccine. Thus, one embodiment of the present invention is a method to protect an individual from a disease using a recombinant MVA virus of the present invention.
A recombinant MVA virus of the present invention can also be used for the introduction of the exogenous coding sequence into a target cell, said sequence being either homologous or heterologous to the genome of the target cell. The introduction of an exogenous coding sequence into a target cell may be done in vitro to produce proteins, polypeptides, peptides, antigens or antigenic epitopes. This method comprises the infection of a host cell with the recombinant MVA according to the invention, cultivation of the infected host cell under suitable conditions, and isolation and/or enrichment of the polypeptide, peptide, protein, antigen, epitope and/or virus produced by said host cell.
Furthermore, the method for introduction of one or more homologous or one or more heterologous sequence into cells may be applied for in vitro and in vivo therapy. For in vitro therapy, isolated cells that have been previously (ax vivo) infected with the recombinant MVA according to the invention are administered to the living animal body for affecting, preferably inducing an immune response. For in vivo therapy, the recombinant poxvirus according to the invention is directly administered to the living animal body for affecting, preferably inducing an immune response. In this case, the cells surrounding the site of inoculation, but also cells where the virus is transported to via, e.g., the blood stream, are directly infected in vivo by the recombinant MVA according to the invention. After infection, these cells synthesize the proteins, peptides or antigenic epitopes of the therapeutic genes, which are encoded by the exogenous coding sequences and, subsequently, present them or parts thereof on the cellular surface. Specialized cells of the immune system recognize the presentation of such heterologous proteins, peptides or epitopes and launch a specific immune response.
Since the MVA is highly growth restricted and, thus, highly attenuated, it is useful for the treatment of a wide range of mammals including humans, including immune-compromised animals or humans. The present invention also provides pharmaceutical compositions and vaccines for inducing an immune response in a living animal body, including a human.
The pharmaceutical composition may generally include one or more pharmaceutical acceptable and/or approved carriers, additives, antibiotics, preservatives, adjuvants, diluents and/or stabilizers. Such auxiliary substances can be water, saline, glyceol, ethanol, wetting or emulsifying agents, pH buffering substances, or the like. Suitable carriers are typically large, slowly metabolized molecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates, or the like.
For the preparation of vaccines, the recombinant poxvirus according to the invention is converted into a physiologically acceptable form. This can be done based on the experience in the preparation of poxvirus vaccines used for vaccination against smallpox (as described by Stickl, H. et al. 1974 Dtsch Med Wochenschr. 99:2386-2392). For example, the purified virus is stored at −80° C. with a titer of 5×10E8 TCID50/ml formulated in about 10 mM Tris, 140 mM NaCl pH 7.4. For the preparation of vaccine shots, e.g., 10E2-10E8 particles of the virus are lyophilized in 100 ml of phosphate buffered saline (PBS) in the presence of 2% peptone and 1% human albumin in an ampoule, preferably a glass ampoule. Alternatively, the vaccine shots can be produced by stepwise freeze-drying of the virus in a formulation. This formulation can contain additional additives such as mannitol, dextran, sugar, glycine, lactose or polyvinylpyrrolidone or other aids such as antioxidants or inert gas, stabilizers or recombinant proteins (e.g., human serum albumin) suitable for in viva administration. The glass ampoule is then sealed and can be stored between 4° C. and room temperature for several months. However, as long as no need exists the ampoule is stored preferably at temperatures below −20° C.
For vaccination or therapy the lyophilisate can be dissolved in 0.1 to 0.5 ml of an aqueous solution, preferably physiological saline or Tris buffer, and administered either systemically or locally, i.e., parenterally, subcutaneous, intramuscularly, by scarification or any other path of administration know to the skilled practitioner. The mode of administration, the dose and the number of administrations can be optimized by those skilled in the art in a known manner. However, most commonly a patient is vaccinated with a second shot about one month to six weeks after the first vaccination shot.
One embodiment of the present invention is a method to generate an immune response against antigen. Such a response can be a CD8+ T cell immune response or an antibody response. More particularly, the present invention relates to “prime and boost” immunization regimes in which the immune response induced by administration of a priming composition is boosted by administration of a boosting composition. The present invention is based on prior experimental demonstration that effective boosting can be achieved using modified vaccinia Ankara (MVA) vectors, following priming with any of a variety of different types of priming compositions including recombinant MVA itself.
A major protective component of the immune response against a number of pathogens is mediated by T lymphocytes of the CD8+ type, also known as cytotoxic T lymphocytes (CTL). An important function of CD8+ cells is secretion of gamma interferon (IFNγ), and this provides a measure of CD8+ T cell immune response. A second component of the immune response is antibody directed to the proteins of the pathogen.
The present invention employs MVA which, as prior experiments show, has been found to be an effective means for providing a boost to a CD8+ T cell immune response primed to antigen using any of a variety of different priming compositions and also eliciting an antibody response.
Notably, prior experimental work demonstrates that use of predecessors of the present invention allows for recombinant MVA virus expressing an HIV antigen to boost a CD8+ T cell immune response primed by a DNA vaccine and also eliciting an antibody response. The MVA may be found to induce a CD8+ T cell response after immunization. Recombinant MVA may also be shown to prime an immune response that is boosted by one or more inoculations of recombinant MVA.
Non-human primates immunized with plasmid DNA and boosted with the MVA were effectively protected against intramucosal challenge with live virus (Amara et al 2001 Science 292:69-74). Advantageously, the inventors contemplate that a vaccination regime using intradermal, intramuscular or mucosal immunization for both prime and boost can be employed, constituting a general immunization regime suitable for inducing CD8+ T cells and also eliciting an antibody response, e.g., in humans.
The present invention in various aspects and embodiments employs an MVA vector encoding an HIV antigen for boosting a CD8+ T cell immune response to the antigen primed by previous administration of nucleic acid encoding the antigen and also eliciting an antibody response.
A general aspect of the present invention provides for the use of an MVA vector for boosting a CD8+ T cell immune response to an HIV antigen and also eliciting an antibody response.
One aspect of the present invention provides a method of boosting a CD8+ T cell immune response to an HIV antigen in an individual, and also eliciting an antibody response, the method including provision in the individual of an MVA vector including nucleic acid encoding the antigen operably linked to regulatory sequences for production of antigen in the individual by expression from the nucleic acid, whereby a CD8+ T cell immune response to the antigen previously primed in the individual is boosted.
An immune response to an HIV antigen may be primed by immunization with plasmid DNA or by infection with an infectious agent.
A further aspect of the invention provides a method of inducing a CD8+ T cell immune response to an HIV antigen in an individual, and also eliciting an antibody response, the method comprising administering to the individual a priming composition comprising nucleic acid encoding the antigen and then administering a boosting composition which comprises an MVA vector including nucleic acid encoding the antigen operably linked to regulatory sequences for production of antigen in the individual by expression from the nucleic acid.
A further aspect provides for use of an MVA vector, as disclosed, in the manufacture of a medicament for administration to a mammal to boost a CD8+ T cell immune response to an HIV antigen, and also eliciting an antibody response. Such a medicament is generally for administration following prior administration of a priming composition comprising nucleic acid encoding the antigen.
The priming composition may comprise DNA encoding the antigen, such DNA preferably being in the form of a circular plasmid that is not capable of replicating in mammalian cells. Any selectable marker should not be resistance to an antibiotic used clinically, so for example Kanamycin resistance is preferred to Ampicillin resistance. Antigen expression should be driven by a promoter which is active in mammalian cells, for instance the cytomegalovirus immediate early (CMV IE) promoter.
In particular embodiments of the various aspects of the present invention, administration of a priming composition is followed by boosting with a boosting composition, or first and second boosting compositions, the first and second boosting compositions being the same or different from one another. Still further boosting compositions may be employed without departing from the present invention. In one embodiment, a triple immunization regime employs DNA, then adenovirus as a first boosting composition, then MVA as a second boosting composition, optionally followed by a further (third) boosting composition or subsequent boosting administration of one or other or both of the same or different vectors. Another option is DNA then MVA then adenovirus, optionally followed by subsequent boosting administration of one or other or both of the same or different vectors.
The antigen to be encoded in respective priming and boosting compositions (however many boosting compositions are employed) need not be identical, but should share at least one CD8+ T cell epitope. The antigen may correspond to a complete antigen, or a fragment thereof. Peptide epitopes or artificial strings of epitopes may be employed, more efficiently cutting out unnecessary protein sequence in the antigen and encoding sequence in the vector or vectors. One or more additional epitopes may be included, for instance epitopes which are recognized by T helper cells, especially epitopes recognized in individuals of different HLA types.
An HIV antigen of the invention to be encoded by a recombinant MVA virus includes polypeptides having immunogenic activity elicited by an amino acid sequence of an HIV Env, Gag. Pol, Vif Vpr, Tat, Rev, Vpu, or Nef amino acid sequence as at least one CD8+ T cell epitope. This amino acid sequence substantially corresponds to at least one 10-900 amino acid fragment and/or consensus sequence of a known HIV Env or Pol; or at least one 10-450 amino acid fragment and/or consensus sequence of a known HIV Gag; or at least one 10-100 amino acid fragment and/or consensus sequence of a known HIV Vif, Vpr, Tat, Rev, Vpu, or Nef.
Although a full length Env precursor sequence is presented for use in the present invention, Env is optionally deleted of subsequences. For example, regions of the gp120 surface and gp41 transmembrane cleavage products can be deleted.
Although a full length Gag precursor sequence is presented for use in the present invention, Gag is optionally deleted of subsequences. For example, regions of the matrix protein (p17), regions of the capsid protein (p24), regions of the nucleocapsid protein (p7), and regions of p6 (the C-terminal peptide of the Gag polyprotein) can be deleted.
Although a full length Pol precursor sequence is presented for use in the present invention, Pol is optionally deleted of subsequences. For example, regions of the protease protein (p10), regions of the reverse transcriptase protein (p66/p51), and regions of the integrase protein (p32) can be deleted.
Such an HIV Env, Gag, or Pol can have overall identity of at least 50% to a known Env, Gag, or Pol protein amino acid sequence, such as 50-99% identity, or any range or value therein, while eliciting an immunogenic response against at least one strain of an HIV.
Percent identity can be determined, for example, by comparing sequence information using the GAP computer program, version 6.0, available from the University of Wisconsin Genetics Computer Group (UWGCG). The GAP program utilizes the alignment method of Needleman and Wunsch (J Mol Biol 1970 48:443), as revised by Smith and Waterman (Adv Appl Math 1981 2:482). Briefly, the GAP program defines identity as the number of aligned symbols (i.e., nucleotides or amino acids) which are identical, divided by the total number of symbols in the shorter of the two sequences. The preferred default parameters for the GAP program include: (1) a unitary comparison matrix (containing a value of 1 for identities and 0 for non-identities) and the weighted comparison matrix of Gribskov and Burgess (Nucl Acids Res 1986 14:6745), as described by Schwartz and Dayhoff (eds., Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, D.C. 1979, pp. 353-358); (2) a penalty of 3.0 for each gap and an additional 0.10 penalty for each symbol in each gap; and (3) no penalty for end gaps.
In a preferred embodiment, an Env of the present invention is a variant form of at least one HIV envelope protein. Preferably, the Env is composed of gp120 and the membrane-spanning and ectodomain of gp41 but lacks part or all of the cytoplasmic domain of gp41.
Known HIV sequences are readily available from commercial and institutional HIV sequence databases, such as GENBANK, or as published compilations, such as Myers et al. eds., Human Retroviruses and AIDS, A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences, Vol. I and II, Theoretical Biology and Biophysics, Los Alamos, N. Mex. (1993), or on the world wide web at hiv-web.lanl.gov/.
Substitutions or insertions of an HIV Env, Gag, or Pol to obtain an additional HIV Env, Gag, or Pol, encoded by a nucleic acid for use in a recombinant MVA virus of the present invention, can include substitutions or insertions of at least one amino acid residue (e.g., 1-25 amino acids). Alternatively, at least one amino acid (e.g., 1-25 amino acids) can be deleted from an HIV Env, Gag, or Pol sequence. Preferably, such substitutions, insertions or deletions are identified based on safety features, expression levels, immunogenicity and compatibility with high replication rates of MVA.
Amino acid sequence variations in an HIV Env, Gag, or Pol of the present invention can be prepared e.g., by mutations in the DNA. Such HIV Env, Gag, or Pol include, for example, deletions, insertions or substitutions of nucleotides coding for different amino acid residues within the amino acid sequence. Obviously, mutations that will be made in nucleic acid encoding an HIV Env, Gag, or Pol must not place the sequence out of reading frame and preferably will not create complementary domains that could produce secondary mRNA structures.
HIV Env, Gag, or Pol-encoding nucleic acid of the present invention can also be prepared by amplification or site-directed mutagenesis of nucleotides in DNA or RNA encoding an HIV Env, Gag, or Pol and thereafter synthesizing or reverse transcribing the encoding DNA to produce DNA or RNA encoding an HIV Env, Gag, or Pol, based on the teaching and guidance presented herein.
Recombinant MVA viruses expressing HIV Env, Gag, or Pol of the present invention, include a finite set of HIV Env, Gag, or Pol-encoding sequences as substitution nucleotides that can be routinely obtained by one of ordinary skill in the art, without undue experimentation, based on the teachings and guidance presented herein. For a detailed description of protein chemistry and structure, see Schulz, G. E. et al., 1978 Principles of Protein Structure, Springer-Verlag, New York, N.Y., and Creighton, T. E., 1983 Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco, Calif. For a presentation of nucleotide sequence substitutions, such as codon preferences, see Ausubel et al. eds. Current Protocols in Molecular Biology, Greene Publishing Assoc., New York, N.Y. 1994 at §§A.1.1-A.1.24, and Sambrook, J. et al. 1989 Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. at Appendices C and D.
Thus, one of ordinary skill in the art, given the teachings and guidance presented herein, will know how to substitute other amino acid residues in other positions of an HIV env, gag, or pol DNA or RNA to obtain alternative HIV Env, Gag, or Pol, including substitutional, deletional or insertional variants.
Within the MVA vector, regulatory sequences for expression of the encoded antigen will include a promoter. By “promoter” is meant a sequence of nucleotides from which transcription may be initiated of DNA operably linked downstream (i.e., in the 3′ direction on the sense strand of double-stranded DNA). “Operably linked” means joined as part of the same nucleic acid molecule, suitably positioned and oriented for transcription to be initiated from the promoter. DNA operably linked to a promoter is “under transcriptional initiation regulation” of the promoter. Other regulatory sequences including terminator fragments, polyadenylation sequences, marker genes and other sequences may be included as appropriate, in accordance with the knowledge and practice of the ordinary person skilled in the art: see, for example, Moss, B. (2001). Poxviridae: the viruses and their replication. In Fields Virology, D. M. Knipe, and P. M. Howley, eds. (Philadelphia, Lippincott Williams & Wilkins), pp. 2849-2883. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Current Protocols in Molecular Biology, 1998 Ausubel et al. eds., John Wiley & Sons.
Promoters for use in aspects and embodiments of the present invention may be compatible with poxvirus expression systems and include natural, modified and synthetic sequences.
Either or both of the priming and boosting compositions may include an adjuvant, such as granulocyte macrophage-colony stimulating factor (GM-CSF) or encoding nucleic acid therefor.
Administration of the boosting composition is generally about 1 to 6 months after administration of the priming composition, preferably about 1 to 3 months.
Preferably, administration of priming composition, boosting composition, or both priming and boosting compositions, is intradermal, intramuscular or mucosal immunization.
Administration of MVA vaccines may be achieved by using a needle to inject a suspension of the virus. An alternative is the use of a needleless injection device to administer a virus suspension (using. e.g., BiojectorTM needleless injector) or a resuspended freeze-dried powder containing the vaccine, providing for manufacturing individually prepared doses that do not need cold storage. This would be a great advantage for a vaccine that is needed in rural areas of Africa.
MVA is a virus with an excellent safety record in human immunizations. The generation of recombinant viruses can be accomplished simply, and they can be manufactured reproducibly in large quantities. Intradermal, intramuscular or mucosal administration of recombinant MVA virus is therefore highly suitable for prophylactic or therapeutic vaccination of humans against AIDS which can be controlled by a CD8+ T cell response.
The individual may have AIDS such that delivery of the antigen and generation of a CD8+ T cell immune response to the antigen is of benefit or has a therapeutically beneficial effect.
Most likely, administration will have prophylactic aim to generate an immune response against HIV or AIDS before infection or development of symptoms.
Components to be administered in accordance with the present invention may be formulated in pharmaceutical compositions. These compositions may comprise a pharmaceutically acceptable excipient, carrier, buffer, stabilizer or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material may depend on the route of administration, e.g., intravenous, cutaneous or subcutaneous, nasal, intramuscular, intraperitoneal routes.
As noted, administration is preferably intradermal, intramuscular or mucosal.
Physiological saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may be included.
For intravenous, cutaneous, subcutaneous, intramuscular or mucosal injection, or injection at the site of affliction, the active ingredient will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilizers, buffers, antioxidants and/or other additives may be included as required.
A slow-release formulation may be employed.
Following production of MVA particles and optional formulation of such particles into compositions, the particles may be administered to an individual, particularly human or other primate. Administration may be to another mammal, e.g., rodent such as mouse, rat or hamster, guinea pig, rabbit, sheep, goat, pig, horse, cow, donkey, dog or cat.
Administration is preferably in a “prophylactically effective amount” or a “therapeutically effective amount” (as the case may be, although prophylaxis may be considered therapy), this being sufficient to show benefit to the individual. The actual amount administered, and rate and time-course of administration, will depend on the nature and severity of what is being treated. Prescription of treatment, e.g., decisions on dosage etc, is within the responsibility of general practitioners and other medical doctors, or in a veterinary context a veterinarian, and typically takes account of the disorder to be treated, the condition of the individual patient, the site of delivery, the method of administration and other factors known to practitioners. Examples of the techniques and protocols mentioned above can be found in Remington's Pharmaceutical Sciences, 16th edition, 1980, Osol, A. (ed.).
In one preferred regimen, DNA is administered at a dose of 300 μg to 3 mg/injection, followed by MVA at a dose of 106 to 109 infectious virus particles/injection.
A composition may be administered alone or in combination with other treatments, either simultaneously or sequentially dependent upon the condition to be treated.
Delivery to a non-human mammal need not be for a therapeutic purpose, but may be for use in an experimental context, for instance in investigation of mechanisms of immune responses to an antigen of interest, e.g., protection against HIV or AIDS.
EXAMPLES
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the embodiments, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, and temperature is in degrees Celsius. Standard abbreviations are used.
Example 1
The following Example demonstrates a shuttle plasmid, recombinant MVA/HIV1 clinical vaccine construct and mechanism for retention of intact foreign gene inserts in recombinant MVA by codon alteration of the foreign gone and insertion of the foreign gene between two vaccinia virus essential genes. The disclosure provides mechanisms for.

    
    
        retention of intact foreign genes by inserting than between two vaccinia virus genes that are essential for MVA replication. Deletion of the foreign gone can provide a significant growth advantage for the recombinant MVA allowing it to compete with MVA containing the intact foreign gene upon repeated passage. However, most deletions of a foreign gene include loss of some part of the flanking vaccinia virus DNA. If that vaccinia virus DNA is essential, then those viruses with deletions will not replicate and compete with the MVA containing the intact foreign gene. This methodology will be useful in production of recombinant vaccinia viruses that must be amplified to large scale such as for use in clinical trials, and
        stabilizing foreign gene inserts by alteration of specific “hot spots” that otherwise readily undergo mutation after repeated passage of the recombinant virus. This methodology is useful in production of recombinant viruses that must be amplified to large scale such as for use in clinical trials.
    
    


And describes:

    
    
        the shuttle plasmid, pLW-73, used for insertion of a foreign gene between 2 essential vaccinia virus genes; and
        the recombinant MVA/HIV-1 clinical vaccine construct MVA/UGD4d, a material that embodies use of these two mechanisms.

Generation of Stable Recombinant MVA Viruses

    
    


Modified vaccinia virus Ankara (MVA) recombinants expressing env and gagpol genes from HIV-1 isolates from different geographical locations were constructed. The foreign genes were inserted into 2 sites, Deletion II and Deletion III of MVA. The stability of these genes after repeated passage of recombinant MVA in tissue culture has proven to be variable. The inventors demonstrated that the instability was due to either deletion of the entire foreign gene and some flanking DNA or specific point mutations resulting in propagation of progeny virions that have a growth advantage because they do not express the foreign gene. Here the inventors describe two novel methods of retaining the intact foreign gene recombinant MVA. First, the inventors constructed a transfer vector that directs insertion of a foreign gene between two essential vaccinia virus genes in the conserved central region of the genome. Use of this site for insertion of genes prevents the outgrowth of variants containing large deletions that include the essential vaccinia virus DNA. In addition, this plasmid can be used for insertion of additional genes into recombinant viruses. Second, analysis of isolates with point mutations revealed certain “hot spots” with a propensity for insertion or deletion of a single base that causes premature termination during translation. The inventors showed that generation of silent mutations in these sites resulted in stabilization of the inserted gene.
I. Novel Transfer Vector Construction and Application
Construction of Novel Transfer Vector, pLW-73
1. The central region of the MVA genome, K7R-A24R, was examined for 1) pairs of genes conserved in the poxvirus family or chordopoxvirus subfamily and 2) genes that are in opposite orientation such that their 3′ ends are in close proximity, thereby providing an insertion site that would not disrupt a vaccinia promoter. The site chosen as the new insertion site was between two essential genes, I8R and G1L.
2. The left flank of the new vector was constructed in the following way Plasmid LAS-1 was cut with restriction enzymes EcoRI and XhoI to remove the del III MVA flank, GFP, and direct repeat of MVA flank. This insert was cut with AscI and SacI and the GFP fragment was isolated. Five hundred thirty one base pairs at the end of the I8R gene (including the TAA stop codon) was PCR amplified with EcoRI and AscI restriction sites on the ends of the PCR product. PCR amplification of 229 base pairs of the direct repeat (from the end of the I8R gene including the TAA stop codon) was performed with oligonucleotides containing SacI and XhoI restriction sites. All four pieces of DNA, 1) the vector backbone with EcoRI and Xho I ends, 2) new left flank containing end of I8R with EcoRI and AscI ends, 3) GFP with AcsI and SacI ends and the 4) direct repeat of the I8R flank with SacI and XhoI ends were ligated together to make plasmid pLW-72.
3. The right flank was made as follows: pLW-72 was cut with restriction enzymes PstI and HindIII to release del III flank of the MVA in the plasmid. Seven hundred and two base pairs at the end of the G1L gene was PCR amplified with PstI and HindIII restriction enzyme sites on the ends and ligated into the pLW-72 vector to make pLW-73 (FIG. 7). The sequence of pLW-73 is given in FIG. 8.
4. The salient features of pLW-73 are: 1) the vector was designed for insertion of foreign genes between essential genes in MVA genome. The left flank consists of end of I8R gene and right flank consists of end of G1L gene. 2) the GFP gene is included for easy initial selection of recombinant virus 3) the GFP is flanked by direct repeats of the I8R gene which allows for transient expression of GFP as the GFP will be lost upon repeated passage of the recombinant virus. Referring to WO 2004/087201, features 2 and 3 were also contained in earlier plasmids used for making MVA/HIV recombinants, pLAS-1 and pLAS-2.
Application of pLW-73
1. The any gene from the clade B ADA isolate of HIV-1 was cloned into pLW-73 and a recombinant MVA virus was made. DNA sequencing confirmed the location and integrity of the envy gene.
2. A recombinant MVA virus expressing the Ugandan clade D (isolate AO7412) env gene (FIG. 9) in the Deletion II site of MVA proved to be unstable, i.e., after repeated serial passage in culture, the gene was deleted from a significant portion of the virus progeny. The same gene was then cloned into pLW-73 and a recombinant MVA virus was made and characterized. The env gene insert was stable after repeated serial passage (8×) in culture i.e., no deletions of the inserted gene or the MVA flanking region were found. In addition, no other mutations arose when the gene was inserted into this site.
II. Point Mutation of “Hot Spots”
Analysis of Point Mutations
A recombinant MVA virus expressing the Ugandan Clade D (isolate AO3349) gagpol gene in the Deletion III site of MVA proved to be unstable. The major genetic alteration was the generation of single point mutations in runs of 4-6 G or C residues (Table 3). In addition, similar point mutations were found in non-staining plaques from similar recombinant viruses expressing the gagpol genes from a Kenyan clade A isolate and a Tanzanian clade C isolate of HIV-1.
Mutagenesis of Hot Spots and Analysis of Stability in Recombinant Virus
Using site-directed mutagenesis, silent mutations were made in 6 such regions of the gag gene from the Ugandan HIV-1 isolate. This altered gene, UGD 4d gagpol orf (FIG. 10), was cloned into pLAS-1 and recombined into the same Deletion III site of MVA as was done in construction of the unstable virus. After repeated serial passage (8×) in culture, no non-expressing plaques were found. DNA sequencing of the passage 8 virus stock verified that the integrity of the gagpol gene was maintained.
III. Double Recombinant Construction
MVA/UGD4d Virus
MVA/UGD4d virus, a recombinant virus that expresses the Ugandan subtype D AO7412 envelope and the AO3349 gagpol, was constructed in the following way: The envelope and gagpol genes were inserted into MVA 1974/NIH Clone 1 by homologous recombination utilizing shuttle plasmids pLW-73 and pLAS-1, respectively. MVA/UGD4d was isolated by 6 rounds of plaque purification in chicken embryo fibroblast cells and subsequently amplified and characterized.
Summary
1. A plasmid transfer vector was constructed that directs recombination of a foreign gene between two essential genes, I8R and G1L, in the conserved central region of the MVA genome. The use of this site was shown to inhibit selection of mutant viruses with deletions of inserted gene/MVA flanks.
2. Highly mutable runs of G and C residues were altered by site-directed mutagenesis and silent mutations in the coding sequence were generated. This change was shown to stabilize the gene when inserted into Deletion III of MVA.
3. Utilizing these two methods above, UGD4d double MVA recombinant that stably expresses both the env and gagpol of Ugandan Clade D was constructed.
Example 2
Recombinant MVAs expressing HIV-1 my and gagpol genes from many different isolates have been made. The stability of inserted genes after repeated passage in tissue culture has proven to be variable. Here the inventors (1) demonstrate that the instability represents a combination of spontaneous mutation or deletion of the inserted gene and selection for non-expressing mutants and (2) describe novel methods for reducing instability.
Overview
Recombinant MVAs expressing env and gagpol from many different isolates were constructed. Each virus was subjected to repeated passages in chicken embryo fibroblast cells to mimic the large-scale amplification required for production of virus for clinical trials. Insert stability was monitored by env and gag immunostaining of individual plaques. For some recombinant viruses, any and/or gag expression was found to be rapidly lost in a significant fraction of the virus population. To identify the mechanism(s) of loss of expression, individual plaques were isolated and the nature of the mutations was characterized. In some cases, specific DNA sequences with propensity to mutate by addition or deletion of a single nucleotide were identified. Generation of such mutations could be avoided by altering codons without changing the predicted translation product. In other cases, loss of expression was caused by large deletions that frequently extended into flanking non-essential MVA genes. To prevent this from occurring, a new shuttle plasmid was constructed that was designed to direct insertion of foreign genes between two essential MVA genes. Recombination into this site reduced deletions of the foreign DNA. In one case, however, the toxicity associated with high-level HIV env expression was so severe that the selection of rare mutants still resulted in an unstable population. In this case, only truncation of the transmembrane domain of env allowed the construction of a stable recombinant MVA.
Generation of Recombinant MVAs and Analysis of Stability of Inserted Genes
Env and gagpol genes were cloned into MVA shuttle vectors. Expression and function were analyzed by transient expression assays. Gagpol was recombined into MVA 1974/NIH Clone 1. Recombinant MVA were plaque purified with 6-8 rounds followed by amplification of virus. Env was recombined into the MVA/gagpol isolate and double-recombinant MVA (FIG. 11A) were plaque purified with 6-8 rounds and were amplified. To assess the stability of inserts, virus was serially passaged in CEF cells using a multiplicity of infection (m.o.i.) of  ̃1 pfu/cell to mimic large-scale production. Stability was evaluated by determining the percentage of cells expressing env or gag, as determined by immunostaining with monoclonal antibodies (FIG. 11B).
Stability of Recombinant MVAs
Recombinant MVAs expressing genes from HIV-1 isolates from different geographical locations were constructed. The any and gagpol genes were inserted into deletions II and III of MVA, respectively; both under control of the modified H5 promoter. The stability of env and gagpol genes from seven recombinant MVAs is shown in Table 4. Varying degrees of instability were observed in the seven viruses. In MVA/65A/G, expression of env was rapidly lost with only 25% of virions expressing any by passage 6. In MVA/UGD4a, both env and gagpol expression were increasingly lost with successive virus passages. Since at least 6-7 passages are required for production of a lot of virus for a Phase I trial, these two viruses were deemed unsuitable.
Analysis of Expression of MVA/65A/G
Referring to FIG. 12, thirteen plaques were randomly picked from P3 and P5 of MVA/65A/G and analyzed by immunostaining with T-24 mAb (binding site shown on a), Western blotting, PCR, and sequencing. Five types of plaques were found and the number of these plaques obtained for each type are given at right of FIG. 12. Plaques a, b, and c stained, but b and c were truncated versions due to base substitution (causing stop codon) (b) and deletion of the end of the any gene and part of MVA flank (c). Nonstaining plaques d and a resulted from addition of G to a 5G run causing a frameshift (d) and large deletion of entire env gene and parts of MVA flanks (e). Thus, base pair addition, substitution, and deletions all contributed to unstable expression of the env gene in MVA/65A/G. This A/G any, the most unstable example worked with, was picked to study modifications that might enhance stability.
Modifications to A/G Constructs to Increase Stability
1. Synthetic envelope was made by removing 4 and 5 G and C runs by silent mutations to prevent point mutations.
2. Vector I8/G1, i.e., pLW-73, was constructed with an insertion site between essential genes I8R and G1L to prevent deletions of genes and MVA flanks from being viable. The ends of the I8R (500 bp) and G1L (750 bp) genes of MVA were amplified by PCR and inserted into a vector containing vaccinia virus early/late mH5 promoter controlling foreign gene expression. This I8/G1 vector was used to insert foreign genes into MVA by homologous recombination (FIG. 13). Deletions of inserted genes and MVA flanking the inserted gene would not be viable because parts of essential genes would be deleted. Therefore, viruses with these mutations would not be able to overgrow the population with their normal growth advantage.
3. A/G gp140 envelope was mutated by deleting the transmembrane domain and the cytoplasmic tail of gp41, resulting in a secreted protein.
Testing Modifications to Increase Stability
Seven single recombinant viruses were made with env modifications and/or use of new vector as shown in FIG. 14. Five plaques of each virus were isolated and passaged independently in CEF to determine if modifications enhanced envelope stable expression. Passaged plaques were analyzed by immunostaining with mAb T-43 (binding site mapped to 101-125aa of env), Western blotting, PCR, and sequencing.
Env Expression after Plaque Passages
Referring to FIG. 15, five independently passaged plaque isolates of each of the 7 recombinants listed above, were characterized at passages 1, 3, 5, and 7 by immunostaining with mAb T-43 (binds between 101-125a.a. in gp120). Four of 7 viruses (FIG. 15, a, b, c, e) had unstable protein expression in each of the 5 passaged plaques; two plaque passages of (FIG. 15f) also had unstable env expression. These included viruses with the synthetic env in both del II (FIG. 15c) and in the essential gene site (FIG. 15f) of MVA genome. Only recombinant viruses containing the envelope as truncated, secreted gp140 remained stably expressing envelope (FIGS. 15, d and g).
Western Blotting PCR and Sequence Analyses
From selected plaque passages, clones were picked to analyze protein expression by Western blotting, PCR, and sequence analysis (FIG. 16). For Western blot analysis, T-24 and T-32 binding at the beginning and end of the clade A envelope, respectively, were used in order to determine if only partial or full length envelope was being made. Control viruses, marked c, are at the right of each blot. For the three viruses made in deletion II of MVA (FIGS. 16a, b, and c), only in FIG. 16e (i.e., gp140 clones), were all the clones expressing detectable protein in Western. This protein (as measured by T-32) was not truncated. When envelope was inserted into the essential gene site by vector I8/G1 (FIGS. 16d, e and f), again, only the gp140 envelope was being expressed in all clones and was not truncated. Although use of I8/G1 vector did not prevent mutations to the env sequence, it did prevent deletions which had been seen in envelope inserted into del II. (Note positive PCR products from all clones tested from I8/G1 vector, but negative PCR products from clones tested using del II vector.)
Expression of Env in Clade A/G Double Recombinant
Based on previous results with single my analysis, double recombinants expressing gagpol with either gp140 or the synthetic gp160 gene were made and tested for stability of my expression (FIG. 17). Five plaques were isolated from each as previously described, and passaged 7 times to analyze stability of env expression. At passage 7, the passaged plaques were immunostained with both T-43 and T-32 mAbs (which bind to gp120 and gp41, respectively). With T-43 mAb, one of five clones of recombinant expressing synthetic envelope consisted of only non-staining plaques. Subsequent T-32 staining of these plaques showed another plaque had truncated envelope expression. All passaged plaques from double recombinant containing gp140 envelope appeared stable by both T-43 and T-32 immunostaining. Titers were also 2 logs higher than with the other double recombinant. Thus a clade A/G double recombinant stably expressing envelope could only be made with gp140 envelope.
Recombinant Viruses Expressing Env and Gagpol from Ugandan HIV-1 Isolates
Recombinant MVA viruses expressing HIV-1 env and gagpol genes from Ugandan isolates AO7412 and AO3349 were constructed as shown in FIG. 18. Four to six independent isolates of each were serially passaged and both genes were found to be unstable whether expressed alone or in combination (Table 5). In contrast, expression of gp140 instead of membrane bound gp160 resulted in stability of the env gene after serial passage (FIG. 18 and Table 5).
MVA/UGD4a—Analysis of Non-Staining Env Plaques
To determine the mechanism of instability, 24 individual non-staining plaques (using Mab T-43) were isolated from passage 6 of MVA/UGD4a, amplified, and characterized. Two small deletions (1.2 and 0.3 kb) were identified by PCR amplification and DNA sequencing (FIG. 19). All other isolates contained very large deletions that extended into the flanking MVA. The approximate break-points for these deletions were identified using primer pairs from within the env ene or flanking MVA regions.
Modification of UGD Env Gene in Recombinant MVA
To ameliorate the problem of instability of the UGD env gene, the AO7412 env gene was inserted into MVA using the new vector, I8/G1, which directs recombination of a foreign gone between 2 essential vaccinia virus genes, I8 and G1 and uses the modified H5 promoter (FIG. 20). Four independent plaques were serially passaged and analyzed for env expression by immunostaining with Mabs T-43 and T-32 at passage 5. In all isolates, the gene was stable (Table 6).
MVA/UGD4b—Analysis of Non-Staining Gag Plaques
To determine the mechanism of instability of the gag gene, 8 individual non-staining plaques (using Mab 183-H12-5C-NIAID AIDS Repository) were picked from passage 6 of MVA/UGD4b, amplified, and the gagpol insert was sequenced (Table 7). In 7 isolates, an insertion or deletion of a single G residue at position 564-569 was found. In one isolate, a C residue was deleted from the sequence CCCC at position 530-534. Furthermore, non-staining plaques from high-passage stocks of MVA/KEA and MVA/TZC revealed a similar hot-spot for mutation, i.e., position 564-569. Examination of the full sequence of the UGD AO7412 gagpol gene demonstrated 22 runs of 4 or more G or C residues (FIG. 21).
Modification of UGD Gagpol Gene in Recombinant MVA
Since the mechanism of instability of the gagpol gene was primarily insertion or deletion of a single nucleotide within a run of 4-6 G or C residues, the strategy to improve the stability of this gene was to generate silent mutations at such sites. Thus, site-directed mutagenesis at 6 sites in p17 and p24 gag (Table 3) was employed. The resulting codon altered (c.a.) gene inserted into MVA at the same location, i.e., Deletion III, proved to be stable upon serial passage (FIG. 22 and Table 8).
Construction of Stable, Recombinant MVA Expressing UGD Env and Gagpol
A recombinant virus expressing the UGD env gene in the I8/G1 locus and the codon altered gagpol gene in Deletion III of MVA was constructed (FIG. 23). Serial passage demonstrated no instability of either gene. Furthermore, the level of protein expression and DNA sequence were unaltered during passage (Table 9).
Conclusions
Instability of env and gagpol inserts is attributed to the generation of point mutations and deletions and the growth advantage of non-expressing MVA mutants. Instability can generally be reduced by codon alteration and/or insertion into an essential region of the MVA genome (MVA/UGD4d) but my had to be altered in one case (MVA/65A/G).
Example 3
Immunogenicity of MVA/UGD4d in BALB/c Mice
Groups of 10 mice each were immunized by the intraperitoneal route with either 106 or 107 infectious units of MVA/UGD4d. Groups of 5 mice each were similarly immunized with parental MVA-1974. Mice were immunized at weeks 0 and 3 and bled at weeks 0, 3, and 5. Spleens were harvested at week 5.
Cellular responses were measured in fresh splenocytes by intracellular cytokine staining. Splenocytes were separately stimulated with the following: 1) immunodominant gag peptide (AMQMLKETI (SEQ ID NO: 6)), 2) env peptides (DTEVHNVWATHACVP (SEQ ID NO: 7) and QQQSNLLRAIEAQQH (SEQ ID NO: 8)), 3) pol peptides (8 peptides with single amino acid variants of ELRQHLLRWGLTT (SEQ ID NO: 9) and HGVYYDPSKDLIAE (SEQ ID NO: 10)), and 4) MVA.
Cells were stained for surface expression of CD4 and CD8 and then for Intracellular expression of IFN-γ and either IL2 or TNF. As shown in FIG. 24, MVA/UGD4d elicited CD8/IFN-γ responses to the gag peptide, pol peptides, and MVA. The gag peptide responses were multifunctional, expressing both IFN-γ and either IL2 or TNF. Also, CD4/IFN-γ responses were elicited to the pool of env peptides.
Humoral responses were measured by ELISA (FIG. 25). Strong responses to UGD env were demonstrated at 3 weeks after one immunization and were boosted by the second immunization. In addition, strong vaccinia virus responses were elicited after one and two immunizations.







TABLE 3 







MVA/UGD Nucleotide Changes Made to Eliminate 


Runs of G and C (HIV-1 isolate AO3349)









Nucleotide #
Original



starting with ATG
Sequence
Modified Sequence





28-32
GGGGG
GGAGG


 


70-74
GGGGG
GGAGG


 


408-411
GGGG
GGGA


 


530-533
CCCC
CACC


 


564-569
GGGGGG
AGGAGG


 


686-689
GGGG
GAGG
















TABLE 4







Stability of Recombinant MVAs









Percent non-staining plaques
















LVD
passage
passage
passage
passage
vaccine



Geographic
seed
3/4
6/7
9/9
10-13
lot





















Virus
Clade
origin
env
gag
env
gag
env
gag
env
gag
env
gag
env
gag
























KEA5b
A
Kenya
<1
<1
0.13
0.33
0.34
0.36


0.54
2.4
0.64
0.77


65A/G
A/G
Ivory Coast
<2
<1
28
1
75


62B
B
US
<1
<1
<1
<1


6
<1
10
1


TZCa
C
Tanzania
<1
<1
<1
<1
1.7
2.8
3.6
3.7


71C
C
India
<1
<1
<1
1
<1
2
12
14


UGD4a
D
Uganda
<1
<1
3
0.28
6.7
6
12.2
17.4


CMDR
E/A
Thailand
<1
<1
<1
<1
<1
<1




<1
<1
















TABLE 5







Recombinant Viruses Expressing env and gagpol from Ugandan HIV-1


isolates










% non-staining












passage
env
gag
















UGD4a
9
12.2
17.4




5
5.8
2.6




5
2.7
17.6




5
8.4
7.2




5
11.4
8.0



UGD4b
6
1.5
17.0




5
3.3
9.3




5
3.7
8.3




5
7.9
4.4




5
15.2
5.0



UGD1a
4
nd
18.8




4
nd
46.7




4
nd
64.9




4
nd
38.1




5
7.9
44.8



UGD gag3349
8

36.6




8

25.4




6

22.9




6

33.1



UGD env
8
9.0




8
2.9




8
13.3




8
12.5




8
14.3



UGDgag/gp140
5
1.2
18.9




5
2.3
17.6

















TABLE 6







Modification of UGD env Gene in Recombinant MVA










% non-staining












passage
env
gag
















UGD9
5
0.5





5
0.4




5
0.0




5
0.5

















TABLE 7 







MVA/UGD4b-Analysis of Non-Staining gag Plaques









# individual plaques



with mutation












gene
base #
sequence
MVA/UGD
MVA/KEA
MVA/TZC















p17
28
GGGGG






70
GGGGG

n = 1



 


p24
408
GGGG






530
CCCC
n = 1





564
GGGGGG
n = 7
n = 16
n = 21



686
GGGG






1050
GGGGGG





 


p7
1133
GGGG





 


p1
1320
GGGG





 


p6
1361
CCCC






1387
GGGG






1419
GGGG






1473
CCCC





 


Protease
1494
GGGGG





RT
1590
GGGGG






1599
GGGGG






2362
GGGG






2380
GGGG






2528
GGGGGG






2596
GGGG






2893
GGGG






3001
CCCC
















TABLE 8







Modification of UGD gagpol Gene in Recombinant MVA










% non-staining












Passage
env
gag
















UGD gag (c.a.)
6

0.9




6

0.0




6

0.5

















TABLE 9







Construction of Stable Recombinant MVA Expressing UGD env and


gagpol










% non-staining












Passage
env
gag
















UGD4d
11
0.0
0.7










Example 4
This Example demonstrates the use of additional insertion sites for generating stable, recombinant MVA viruses. The Del III region of the MVA virus genome contains several non-essential genes, and fragments of genes, and thus has historically been used to insert heterologous nucleic acid sequences. Thus, the flanking region around the del III insertion site of MVA was analyzed for the presence of fragmented or non-essential genes. Genes known to be important for VACV replication in some cells, i.e. A50R DNA ligase and B1R kinase were located about 1 kbp and 1.8 kbp, respectively, from the del III insertion site. We reasoned we could make this a more stable insertion site if we removed the non-essential genes flanking the Del III insertion site. To this end, a nucleic acid construct (e.g., shuttle vector) with flanking sequences comprising the 3′ end part of A50R DNA ligase ORF (left), and the 5′ end of the B1R ORF, and promoter (right), was constructed as follows. This would effectively remove the area of non-essential genes between these two important genes when homologous recombination occurred.
A. Preparation of the A50R/B1R Shuttle Vector
Analysis of the flanking regions around the del III insertion site in the MVA genome, (bp number 143552, Acambis 3000 Genbank AY603355) revealed that at least two genes known to be important for VACV replication in some cells. Specifically, A50R DNA ligase (ORF 163; ACAM3000_MVA_163; SEQ ID NO:11) and B1R kinase (ORF167; ACAM3000_MVA_167; SEQ ID NO:16) were located about 1 kbp and 1.8 kbp, respectively, from the del III insertion site. Thus, non-essential or fragmented genes located between ORF 163 and ORF 167 were targeted for removal. In particular, ORF 164, fragments of A51R-A55, ORF 165 (missing the part of the A56R promoter), ORF 166, and fragmented A57R were targeted for removal. In order to effect removal these non-essential and fragmented genes, a nucleic acid construct (i.e., a shuttle vector) was designed that would be capable of homologously recombining into the MVA genome between ORF 163 and ORF 167, thereby removing the intervening sequences. To achieve such recombination, the nucleic acid construct would comprise one nucleic acid sequence from ACAM3000_MVA_163 (the left flanking sequence), and one nucleic acid sequence from ACAM3000_MVA_167 (the right flanking sequence). These sequences would be adjacent in the nucleic acid construct, meaning that they would not be separated by any poxvirus ORF's. More specifically, the left flank would contain the C terminal end of the A50R ligase ORF and the right flank would contain the promoter region and the N terminal and of the B1R ORF. The design of the vector is shown in FIG. 26.
To construct the shuttle vector, each flank was created separately. The left flank of the restructured Del III vector was constructed first, as follows.
Plasmid LW-73 (FIG. 7) was digested with EcoRI and XhoI to excise the entire left flank (Flank 1 containing a portion of the I8R gene) along with the gene encoding green fluorescent protein (GFP) and direct repeat. The GFP containing fragment was then digested with restriction enzymes AcsI and SacI to liberate the GFP gene.
To create the left flank containing C-terminal portion of ORF 163, a DNA fragment was amplified from the MVA genome by the polymerase chain reaction (PCR) method using the primers LW470 (SEQ ID NO:23) and LW471 (SEQ ID NO:24). PCR amplification was performed using standard conditions. Next, the direct terminal repeat portion of ORF 163 was amplified from the MVA genome using the primers LW-472 (SEQ ID NO:25) and LW-473 (SEQ ID NO:26). Finally, the vector backbone, with EcoRI and XhoI sites, the GFP gene, with AcsI and SacI sites, the ORF 163 fragment (left flank) containing EcoRI and AscI sites, and the direct repeat from the ORF 163 C-terminus region, containing the SacI and XhoI sites, were ligated together to form the interim plasmid #2743.
To create the right flank containing the N-terminal portion of ORF 167, including its promoter region, interim plasmid #2743 was digested with the restriction enzymes Pst I and HindIII to release the right flank. Next, a DNA fragment was PCR amplified from the MVA genome using the primers LW-474 (SEQ ID NO:27) and LW-475 (SEQ ID NO 28). This fragment was digested with the restriction enzymes Pst I and Hind III, and the digested fragment ligated into similarly-digested, shuttle vector backbone to produce the LW-676 nucleic acid construct. (FIG. 27)
The salient features of pLW-76 are:
1) the vector is designed for insertion of foreign genes between the end of the A50R DNA ligase gene (ORF 163) and the promoter and N terminal portion of the B1R kinase gene (ORF 167) in MVA genome. The left flank consists of and of A50R ligase gene and right flank consists of promoter and beginning of the B1R kinase.
2) the GFP gene is included for easy initial selection of recombinant virus.
3) the GFP is flanked by direct repeat of the A50R ligase gene which allows for transient expression of GFP as the GFP will be lost upon repeated passage of the recombinant virus. Features 2 and 3 were also contained in earlier plasmids used for making MVA/HIV recombinants, pLAS-1 and pLAS-2.
The env gene from Ugandan clade D human immunodeficiency virus (HIV) (isolate AO7412) was then cloned into the new pLW-76 construct. The env containing nucleic acid construct was then transfected into cells, and the cells infected with MVA virus to produce a recombinant MVA virus expressing the HIV ENV protein rMVA/UGDenv(delIIIrst). This virus was then characterized.
When grown in chick embryo fibroblast (CEF) cells, it was observed that infection by rMVA/UGDenv(delIIIrst) resulted in syncytial-type, cytoplasmic effect (CPE). This was due to the deletion of the non-essential A56 hemagglutinin gene during recombination that occurred within the restructured del III site. Normal rMVA had a flay focus (FIG. 28A), whereas infection with rMVA/UGDenv (delIIrt) resulted in foci showing syncytial formation, progressing to condensed syncytial. (FIG. 28B).
rMVA/UGDenv (delIIIrst) was then characterized with regard to the stability of the inserted heterologous nucleic acid sequences. This was done by repeatedly passaging the virus in CEF cells, and testing each generation for the presence of expressed HIV ENV protein. Detection of ENV protein was done by screening viral plaques with monoclonal antibodies to the HIV envelope protein. The stability of rMVA/UGDenv (delIIIrst) was compared to a virus containing the env gene in the del II region, and a virus in which the env gene was inserted into the central conserved region. The results of this comparison are shown in FIG. 29. The level of ENV protein being expressed was also measured by Western blot, using monoclonal antibodies to the HIV ENV protein.
FIG. 29 shows that the MVA/UGDenv(del II) was clearly unstable, due to deletions that occurred within the any and extending into the flanking MVA. Viable deletions were prevented when the UGD env was placed between two VACV essential genes, as in MVA/UGDenv(I8/G1). Finally, integration of the HIV my gene int rMVA/UGDenv(del IIIrst), was observed to be stable at least through 11 passages.
FIG. 30 shows that 11 viral constructs expressed similar amounts of ENV protein.
Thus, the results of these studies suggest that the del III region of the MVA virus genome had been made more stable by restructuring the del III site by removing the non-essential genes.
While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention. All figures, tables, and appendices, as well as patents, applications, and publications, referred to above, are hereby incorporated by reference.

## Claims

1. An isolated nucleic acid construct comprising:
(a) a first nucleic acid sequence derived from, or homologous to, a first essential ORF from a poxvirus genome; and
(b) a second nucleic acid sequence derived from, or homologous to, a second essential ORF from a poxvirus genome;
wherein the first and second essential poxvirus ORFs are separated by at least one non-essential ORF in the parental poxvirus genome, and wherein the first and second nucleic acid sequences are adjacent to each other in the isolated nucleic acid construct.

2. The isolated nucleic acid sequence of claim 1, wherein the first nucleic acid sequence comprises at least 20 contiguous nucleotides from the first essential ORF, and wherein the second nucleic acid sequence comprises at least 20 contiguous nucleotides from the second essential ORF.

3. The isolated nucleic acid construct of claim 1, wherein the first nucleic acid sequence comprises an at least 100 contiguous polynucleotide region that is at least 75% identical to an at least 100 contiguous polynucleotide region in the first essential ORF, and wherein the second nucleic acid sequence comprises an at least 100 contiguous polynucleotide region that is at least 75% identical to an at least 100 contiguous polynucleotide region in the second essential ORF.

4. The isolated nucleic acid construct of claim 1, wherein the first essential ORF is selected from the group consisting of A11R, A12L, A50R, B1R, F10, F12, F13L, F15L, F17R, G1L, H2R, H3L, E1L, E4L, E6L, E8L, E10L, I1L, I3L, I5L, I8R, J1R, J3R, J4R, J5L, D7L, D9L, A24R, and A28R.

5. The isolated nucleic acid construct of claim 1, wherein the second essential ORF is selected from the group consisting of A11R, A12L, A50R, B1R, F10, F12, F13L, F15L, F17R, G1L, H2R, H3L, E1L, E4L, E6L, E8L, E10L, I1L, I3L, I5L, I8R, J1R, J3R, J4R, J5L, D7L, D9L, A24R, and A28R.

6. The isolated nucleic acid construct of claim 1, wherein the first essential ORF is A50R and the second essential ORF is B1R.

7. The isolated nucleic acid construct of claim 1, wherein adjacent ends of the first and second nucleic acid sequences are separated by a third nucleic acid sequence comprising at least one nucleotide sequence selected from the group consisting of (a) an intergenic region, and (b) a restriction enzyme recognition site.

8. The isolated nucleic acid construct of claim 1, wherein adjacent ends of the first and second nucleic acid sequences are separated by a heterologous nucleic acid sequence.

9. The isolated nucleic acid construct of claim 8, wherein the heterologous nucleic sequence comprises at least one coding sequence under the transcriptional control of a transcriptional control element.

10. The isolated nucleic acid construct of claim 1, wherein the poxvirus genome is from a poxvirus in the subfamily Chordopoxvirinae.

11. The isolated nucleic acid construct of claim 1, wherein the poxvirus genome is from a poxvirus in the genus Orthopoxvirus.

12. A method for producing a stable, recombinant poxvirus, the method comprising:
(a) transfecting a cell with a nucleic acid construct comprising:
i. a first nucleic acid sequence derived from, or homologous to, a first essential ORF from a poxvirus genome; and,
ii. a second nucleic acid sequence derived from, or homologous to, a second essential ORF from a poxvirus genome;

wherein the first and second essential poxvirus ORFs are separated by at least one non-essential ORF in the parental poxvirus genome, and wherein the first and second nucleic acid sequences are adjacent to each other in the isolated nucleic acid construct;
(b) infecting the transfected cell with a poxvirus;
(c) culturing the infected cell under conditions suitable to allow homologous recombination between the nucleic acid construct and the poxvirus genome.

13. The method of claim 12, wherein the first nucleic acid sequence comprises at least 20 contiguous nucleotides from the first essential ORF, and wherein the second nucleic acid sequence comprises at least 20 contiguous nucleotides from the second essential ORF.

14. The method of claim 12, wherein the first nucleic acid sequence comprises an at least 100 contiguous polynucleotide region that is at least 75% identical to an at least 100 contiguous polynucleotide region in the first essential ORF, and wherein the second nucleic acid sequence comprises an at least 100 contiguous polynucleotide region that is at least 75% identical to an at least 100 contiguous polynucleotide region in the second essential ORF.

15. The method of claim 12, wherein the first essential ORF is selected from the group consisting of A11R, A12L, A50R, B1R, F10, F12, F13L, F15L, F17R, G1L, H2R, H3L, E1L, E4L, E6L, E8L, E10L, I1L, I3L, I5L, I8R, J1R, J3R, J4R, J5L, D7L, D9L, A24R, and A28R.

16. The method of claim 12, wherein the second essential ORF is selected from the group consisting of A11R, A12L, A50R, B1R, F10, F12, F13L, F15L, F17R, G1L, H2R, H3L, E1L, E4L, E6L, E8L, E10L, I1L, I3L, I5L, I8R, J1R, J3R, J4R, J5L, D7L, D9L, A24R, and A28R.

17. The method of claim 12, wherein the first essential ORF is A50R and the second essential ORF is B1R.

18. The method of claim 12, wherein adjacent ends of the first and second nucleic acid sequences are separated by a third nucleic acid sequence comprising at least one nucleotide sequence selected from the group consisting of (a) an intergenic region, and (b) a restriction enzyme recognition site.

19. The method of claim 12, wherein adjacent ends of the first and second nucleic acid sequences are separated by a heterologous nucleic acid sequence.

20. The method of claim 19, wherein the heterologous nucleic sequence comprises at least one coding sequence under the transcriptional control of a transcriptional control element.