US20110201088A1

US20110201088A1 - Production of rAAV in Vero Cells Using Particular Adenovirus Helpers

Info

Publication number: US20110201088A1
Application number: US13/081,169
Authority: US
Inventors: Clifford J. Beall; Kelly R. Clark; Philip R. Johnson, Jr.
Original assignee: Nationwide Childrens Hospital Inc
Current assignee: Nationwide Childrens Hospital Inc
Priority date: 2008-04-30
Filing date: 2011-04-06
Publication date: 2011-08-18
Also published as: US7943379B2; US20090275138A1

Abstract

The present invention relates to methods and materials for recombinant adeno-associated virus production. More particularly, in some embodiments the invention contemplates the use of an adenovirus known as Simian Adenovirus 13 (SAdV-13) and Vero cells for production of recombinant adeno-associated virus (rAAV).

Description

STATEMENT OF GOVERNMENT INTEREST

This invention was made with government support under N01-AI-50008 awarded by The National Institute of Allergy and Infectious Diseases (NIAID). The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to methods and materials for recombinant adeno-associated virus production. More particularly, the invention contemplates the use of an adenovirus known as Simian Adenovirus 13 (SAdV-13) and Vero cells for production of infectious recombinant adeno-associated virus (rAAV).

BACKGROUND

Infectious recombinant AAV are being developed as gene transfer vehicles for an ever-widening array of human applications such as for use as vaccines and gene therapy vectors. The intense interest in rAAV has been fueled by the finding that these simple vectors can efficiently transduce a variety of post-mitotic cells when administered in vivo. Promising data from animal models has resulted in the initiation of several ongoing human clinical trials. While these advances are encouraging, obstacles remain for the general implementation of rAAV as a universal gene transfer vehicle.
Adeno-associated virus (AAV) is a replication-deficient parvovirus, the single-stranded DNA genome of which is about 4.7 kb in length including 145 nucleotide inverted terminal repeat (ITRs). The nucleotide sequence of the AAV serotype 2 (AAV2) genome is presented in Srivastava et al., J. Virol., 45: 555-564 (1983) as corrected by Ruffing et al., J. Gen. Virol., 75: 3385-3392 (1994). Cis-acting sequences directing viral DNA replication (rep), encapsidation/packaging and host cell chromosome integration are contained within the ITRs. Three AAV promoters, p5, p19, and p40 (named for their relative map locations), drive the expression of the two AAV internal open reading frames encoding rep and cap genes. The two rep promoters (p5 and p19), coupled with the differential splicing of the single AAV intron (at nucleotides 2107 and 2227), result in the production of four rep proteins (Rep 78, Rep 68, Rep 52, and Rep 40) from the rep gene. Rep 78 and Rep 68, are respectively expressed from unspliced and spliced transcripts initiating at the p5 promoter, while Rep 52 and Rep 40, are respectively expressed from unspliced and spliced transcripts initiating at the p19 promoter. Rep proteins possess multiple enzymatic properties which are ultimately responsible for replicating the viral genome. Rep 78 and 68 appear to he involved in AAV DNA replication and in regulating AAV promoters, while Rep 52 and 40 appear to be involved in formation of single-stranded AAV DNA. The cap gene is expressed from the p40 promoter and it encodes the three capsid proteins VP1, VP2, and VP3. Alternative splicing and non-consensus translational start sites are responsible for the production of the three related capsid proteins. A single consensus polyadenylation site is located at map position 95 of the AAV genome. The life cycle and genetics of AAV are reviewed in Muzyczka, Current Topics in Microbiology and Immunology, 158: 97-129 (1992).
When wild type AAV infects a human cell in culture, the viral genome can integrate into chromosome 19 resulting in latent infection of the cell. Production of infectious virus does not occur unless the cell is infected with a helper virus (for example, adenovirus or herpesvirus). In the case of adenovirus, genes E1A, E1B, E2A, E4 and VA provide helper functions. Upon infection with a helper virus, the AAV provirus is rescued and amplified, and both AAV and adenovirus are produced.
AAV possesses unique features that make it attractive for delivering DNA to cells in a clinical application, for example, as a gene therapy vector or an immunization vector. AAV infection of cells in culture is noncytopathic, and natural infection of humans and other animals is silent and asymptomatic. Moreover, AAV infects many mammalian cells allowing the possibility of targeting many different tissues in vivo. The AAV proviral genome is infectious as cloned DNA in plasmids which makes construction of recombinant genomes feasible. Furthermore, because the signals directing AAV replication, genome encapsidation and integration are contained within the ITRs of the AAV genome, some or all of the internal approximately 4.3 kb of the genome (encoding replication and structural capsid proteins, rep-cap) may be replaced with foreign DNA such as a gene cassette containing a promoter, a DNA of interest and a polyadenylation signal. The rep and cap proteins may be provided in trans. Another significant feature of AAV is that it is an extremely stable and hearty virus. It easily withstands the conditions used to inactivate adenovirus (56° to 65° C. for several hours), making cold preservation of AAV-vectors less critical. AAV may even be lyophilized. Finally, AAV-infected cells are not resistant to superinfection.
Production of rAAV requires the AAV rep78/68, rcp52/40 and capsid genes and expression of their gene products, a DNA of interest flanked by AAV ITRs, helper functions provided by an adenovirus or herpesvirus helper virus, and a cell line comprising these components that is permissive for AAV replication. Examples of helper virus functions are adenovinis genes E1a, E1b, E2A, E4 and VA RNA [Carter, Adeno-associated virus helper functions in “Handbook of Parvoviruses” Vol I (P. Tjissen, Ed.) CRC Press, Boca Raton, pp 255-282 (1989)]. Wild type AAV (wt AAV) has one of the largest burst sizes of any virus following infection of cells with AAV and adenovirus. This may be well in excess of 100,000 particles per cell [Aitken et al., Hum Gene Therapy, 12:1907-1916 (2001)], while some rAAV production systems have been reported to achieve greater than 10³particles per cell. Rep proteins are absolutely required for both wt AAV and rAAV replication and assembly of intact infectious particles, as summarized in Carter et al., AAV vectors for gene therapy, in “Gene and Cell Therapy: Therapeutic Mechanisms and Strategies”, Second Edition (Ed. N. Templeton-Smith), pp 53-101, Marcel Dekker, New York (2004).
A requirement for the clinical use of recombinant AAV for DNA delivery is a highly efficient scheme for production of infectious recombinant virus that is reproducible and commercially scalable. One popular mechanism of producing rAAV is to transiently transfect cells with one or more plasmids containing adenoviral helper genes, rep and cap genes, and a recombinant AAV genome. Such transfection methods are difficult to scale up, which has lead to development of stable cell line methods.
Two types of stable cell lines have been developed. In one type (producer cells), both the rAAV genome and the rep-cap genes are stably integrated into the cell DNA, while helper functions are provided by a wild-type adenovirus. As used herein, “producer cells” are those cells that are stably transformed with a rAAV genome and AAV rep/cap genes. In the second type (packaging cells), the rep and cap genes are integrated, while the rAAV genome is provided by infection with a recombinant adenovirus or herpes virus containing the rAAV genome (termed herein a “rAd/AAV hybrid” or “rHerpes/AAV hybrid”), and the helper functions are provide by a wild type adenovirus. As used herein, “packaging cells” are those cells that are stably transformed with AAV rep/cap genes.
The most common forms of these scalable systems use HeLa cells. Other cell substrates have also been used to produce AAV. One such cell substrate is a Vero cell. See, for example, U.S. Patent Application US20040224411 published Nov. 11, 2004; Handa et al., Journal of Biological Chemistry 254(14): 6603-6610 (1979); Richardson et al., Proc Natl Acad Sci USA 77(2): 931-935 (1980); and Liu et al., Journal of Virology 80(4): 1672-1679 (2006). Vero cells are derived from African green monkey kidney cells, and were identified as a cell line substrate for viral vector production. Vero cells have been used as a cell line substrate for the production of numerous human vaccines, including poliovirus (both oral and inactivated) and rabies. The safety of the cell line is attested to by pharmacovigilance of more than 20 million doses of rabies vaccine and more than 1 billion of OPV.
Vero cells have been readily adapted for growth in bioreactors on microcarriers and provide consistently high yields of viruses such as polio and rabies viruses. This allows for vaccine purity (less contaminating cell debris), large lots of vaccine (i.e., greater vaccine availability), and more economic production of vaccine. The issues of yield and adaptability to growth in bioreactors are grounds for use of Vero cells that have been provided to the Center for Biologics Evaluation and Research (CBER) division of the FDA by most manufacturers who propose to use them for vaccine production.
There remains a need in the art for new methods for scalable high titer production of rAAV from mammalian nontransformed cancer cells.

SUMMARY OF THE INVENTION

The present invention provides methods and materials useful for producing infectious recombinant AAV (rAAV). Compared to previous methods and materials, the methods and materials of the invention allow for much higher titers of rAAV to be produced and/or allow for high titer production of rAAV in mammalian cells other than transformed cancer cells.
The present invention achieves scalable high titer rAAV production using Vero cell substrates combined with simian adenovirus 13 (SAdV-13) helper virus. A particular SAdV-13 clone provided by the invention is SAdV-13 PME-12. The sequence of the clone is set out in SEQ ID NO: 16. The invention contemplates that other helper viruses like SAdV-13 or SAdV-13-like helper plasmids may also be used in the methods of the invention. A “SAdV-13-like” helper virus or helper plasmid according to the invention may be a naturally-occurring helper virus (i.e., not made by recombinant DNA techniques), or a recombinant helper virus or recombinant helper plasmid encoding one or more helper virus functions. Techniques to make recombinant helper viruses and helper plasmids are known in the art. Helper viruses of AAV are known in the art and include, for example, viruses from the family Adenoviridae and the family Herpesviridae. In some embodiments of the invention, the “SAdV-13-like” helper virus is from the Adenoviridae family including, but not limited to, a simian or human adenovirus.
In one embodiment of the invention, an “SAdV-13-like” helper virus may be a helper virus, the use of which allows rAAV production in Vero cells at a titer about equal to, equal to, or greater than the titer obtained with SAdV-13 in the assay of Example 2.
In another embodiment of the invention, an “SAdV-I 3-like” helper virus may be a helper virus that induces AAV rep gene amplification in a Vero cell that is about equal to, equal to, or greater than the amplification obtained when SAdV-13 is used. Adenovirus-dependent rep gene amplification can be readily determined by qPCR as previously described [Liu et al., Mol Ther 2:394-403 (2000)].
In yet another embodiment of the invention, an “SAdV-13-like” helper virus may be a helper virus that upregulates the expression of AAV rep, or AAV rep and cap genes, in a Vero cell so that AAV rep gene expression is about equal to, equal to, or greater than that obtained when SAdV-13 is used. Rep gene expression can be measured, for example, with a Western blot assay using anti-rep monoclonal antibody (such as clone 226.7, American Research Products).
In still other embodiment, a “SAdV-13-like” helper virus according to the invention may be a helper virus that exhibits a delayed cytopathic effect (CPE) relative to other helper viruses. These may be identified by carrying out the assay in Example 3 in Vero cells and selecting those helper viruses that take “time to reach maximal CPE about that of SAdV-13” wherein SAdV-13 and the other helper viruses are used at MOI=10. A “time to reach maximal CPE about that of SAdV-13” is a period of greater than 1 day, 2 days, 3 days, 4 days, 5 days or more than the maximal CPE of human adenovirus 5 (M01=10) in the assay. In one embodiment, the “time to reach maximal CPE about that of SAdV-13” is a period of at least 1 day more than the maximal CPE of human adenovirus 5 (MOI-10) in the assay. Alternatively, a “time to reach maximal CPE about that of SAdV-13” may be a period that is at least about 80%, 90%, 95%, 96%, 97%, 98%, 99%, 100% or greater than the time to reach maximal CPE of SAdV-13 in the assay. Other adenovinises that are reported to have delayed cytopathic effect include human Ad-8 and -19 [Schwartz et al., Invest Ophthalmol Vis Sci. 18(9):956-63 (1979)] and mouse adenovirus 1 [Nguyen et al, Gene Therapy 6, 1291-1297 (1999)].
CPE is a change in cellular morphology that occurs following viral infection. The nature of the change varies somewhat between viruses but for adenoviruses is generally recognizable by rounding of the cells and detachment from the substrate in cell culture. This causes the cell boundary to be more refractile when observed by phase contrast microscopy. Maximal CPE can be defined as a state where a vast majority of cells (i.e. >95%) display a rounded shape.
Those of skill in the art will understand that the multiplicity of infection (M01) used in these CPE assays does not necessarily mirror what would be used in method of the invention for production of rAAV. The invention contemplates that variation in host cell, helper virus and culturing conditions may necessitate using a MOI that differs from that utilized in a CPE assay, and would not require undue experimentation by one of ordinary skill in the art to determine. The MOI to be utilized in rAAV production methods of the invention is from about 1 to about 20, or from about 1 to about 100, when a naturally-occurring adenovirus is used as the helper virus. The MOI to be utilized when recombinant adenovirus is used as the helper virus is from about 1 to about 20, about 30, about 40, about 50, or about 70.
In yet another embodiment of the invention, an “SAdV-13-like” helper virus may be a helper virus that, when used in methods of the invention, results in production of a titer of at least about: 2×10⁴DNAse resistant particles (DRP) per cell, 2.5×10⁴DRP per cell, 3×10⁴DRP per cell, 3.5×10⁴DRP per cell, 4×10⁴DRP per cell, 4.5×10⁴DRP per cell, 5×10⁴DRP per cell, 5.5×10⁴DRP per cell, 6×10⁴DRP per cell, 6.5×10⁴DRP per cell, 7×10⁴DRP per cell, 7.5×10⁴DRP per cell, 8×10⁴DRP per cell, 8.5×10⁴DRP per cell, 9×10⁴DRP per cell, 9.5×10⁴DRP per cell, 1×10⁵DRP per cell, 1.5×10) DRP per cell, 2×10⁵DRP per cell, or 2.5×10⁵DRP per cell.
In an embodiment, the invention provides methods for increasing rAAV production in a Vero cell line of at least 2-fold in comparison to use of human adenovirus 5 (HuAdS) helper virus and Vero cells. In other embodiments, the invention provides methods of increasing rAAV production in a Vero cell line of at least 3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least 5-fold, at least 10-fold, at least 20-fold or at least 50-fold.
In an embodiment of the invention, a method of producing rAAV is provided, comprising the steps of infecting a Vero producer cell with SAdV-13 and culturing the cell. See, for example, methods based on stable HeLa cell lines described in Clark et al., Hum. Gene Ther 6:1329-1341 (1995), and Tamayose et al., Hum Gene Ther 7:507-513 (1996).
In another embodiment of the invention, a method of producing rAAV is provided comprising the steps of introducing a rAAV genome into a Vero packaging cell, infecting the cell with SAdV-13 and culturing the cell. The rAAV genome may be introduced by a rAd/AAV hybrid. Vero packaging cell lines may be generated that express rep-cap genes upon adenovirus infection. rAAV is produced by infecting the packaging cell line with a recombinant adenovirus harboring a rAAV vector genome in the adenovirus E1 region or adenovirus E3 region (rAd/AAV hybrid). The corresponding E1 or E3 helper gene products are also provided for robust Ad/AAV hybrid replication. See, for example, Liu et al., Gene Ther. 6:293-299 (1999); Inoue et al., J Virol 72:7024-7031 (1998); Gao et al., Hum Gene Ther 9:2353-2362 (1998); Conway et al., Gene Ther 6:986-993 (1999); Vincent et al., Vaccine 90: 353-359 (1990); Clark et al., Hum Gene Ther 10:1031-1039 (1999); Thrasher et al., Gene Ther 2:481-485 (1995); Fisher et al., Hum Gene Ther 7:2079-2087 (1996); and Gao et al., Mol Ther 5:644-649 (2002). Upon co-infection, the rAAV vector is excised from the adenovirus genome, replicated, and packaged into infectious virions.
In still another embodiment of the invention, a method of producing rAAV is provided comprising the steps of introducing a rAAV genome and AAV rep/cap genes into a Vero cell, infecting the cell with SAdV-13 helper virus and culturing the cell. The introduction of the rAAV genome and AAV rep/cap genes into a Vero cell may occur concurrently with the infection of the cell with helper virus. Alternatively, the Vero cell may be a packaging cell. rAAV is commonly generated in cell culture by plasmid DNA transfection of mammalian cells. The plasmid components are: an AAV vector plasmid, an AAV rep-cap expressing plasmid, and an adenovirus helper plasmid or wild-type adenovirus infection. See, for example, Vincent et al., J Virol 71:1897-1905 (1997); Ogasawara et al., Microbiol Immunol 42:177-185 (1998); Li et al., J Virol 71:5236-5243 (1997); Grimm et al., Hum Gene Ther 9:2745-2760 (1998); Ferrari et al., J Virol 70:3227-3234 (1996); Xiao et al., J Virol 72:2224-2232 (1998); Collaco et al., Gene 238:397-405 (1999); Matsushita et al., Gene Ther 5:938-945 (1998); and Salvetti et al., Hum Gene Ther 9:695-706 (1998). The methods that may be utilized to introduce rep and cap genes into a cell are well known to those of ordinary skill in the art. These may include, e.g., use of a virus that encodes rep and/or cap genes to infect a cell, or use of a plasmid that encodes rep and/or cap genes to transiently transfect a cell.
In an embodiment of the invention, a method of producing rAAV is contemplated comprising the steps of infecting a Vero producer cell with a SAdV-13-like adenovirus helper virus and culturing the cell.
In another embodiment of the invention, a method of producing rAAV is provided comprising the steps of introducing a rAAV genome into a Vero packaging cell, infecting the cell with a SAdV-13-like adenovirus helper virus and culturing the cell. The rAAV genome may be introduced by a rAd/AAV hybrid.
In yet another embodiment of the invention, a method of producing rAAV is provided comprising the steps of introducing a rAAV genome and AAV rep/cap genes into a Vero cell, infecting the cell with a SAdV-13-like helper virus and culturing the cell. The introduction of a rAAV genome and AAV rep/cap genes into a Vero cell may occur concurrently with the infection of the cell with a SAdV-13-like helper virus. Alternatively, the Vero cell may be a packaging cell.
In embodiments of the invention, the rAAV produced by the methods of he invention is isolated.
In a further embodiment of the invention, methods are provided that comprise infecting a Vero packaging cell with helper virus of the invention and then with an Ad/AAV hybrid virus encoding the rAAV genome. In some embodiments, the Vero cell may be infected with the Ad/AAV hybrid virus about 16 to 24 hours after helper virus infection.
In yet another embodiment of the invention, a method is provided for producing infectious recombinant adeno-associated virus (rAAV), the improvement comprising infecting a Vero cell with SAdV-13 helper virus.
In still another embodiment of the invention, a method is provided for producing infectious recombinant adeno-associated virus (rAAV), the improvement comprising infecting a Vero cell with a SAdV-13-like adenovirus helper virus.
In an embodiment of the invention, a method of producing infectious rAAV is provided comprising culturing a Vero producer cell under conditions permissive for rAAV production, wherein the Vero producer cell comprises simian adenovirus 13 (SAdV-13) helper virus.
In another embodiment of the invention, a method of producing infectious rAAV is provided comprising culturing a Vero producer cell under conditions permissive for rAAV production, wherein the Vero producer cell comprises simian adenovirus 13-like (SAdV-13-like) helper virus.
Methods of the invention produce rAAV titers of at least about: 2×10⁴DNAse resistant particles (DRP) per cell, 2.5×10⁴DRP per cell 3×10⁴DRP per cell, 3.5×10⁴DRP per cell, 4×10⁴DRP per cell, 4.5×10⁴DRP per cell, 5×10⁴DRP per cell, 5.5×10⁴DRP per cell, 6×10⁴DRP per cell, 6.5×10⁴DRP per cell, 7×10⁴DRP per cell, 7.5×10⁴DRP per cell, 8×10⁴DRP per cell, 8.5×10⁴DRP per cell, 9×10⁴DRP per cell, 9.5×10⁴DRP per cell, 1×10′ DRP per cell, 1.5×10⁵DRP per cell, 2×10⁵DRP per cell, or 2.5×10⁵DRP per cell. In methods of the invention, Vero cells are cultured under conditions permissive for rAAV production.
The invention contemplates that any rAAV serotype (including, but not limited to, AAV1, AAV2, AAV5, AAV6, AAV7, AAV8, AAV9, and variants thereof), pseudotype or chimera may be produced by methods of the invention.
The invention also contemplates that any rAAV genome that can be packaged in an infectious recombinant AAV (rAAV) may be used in the methods described herein. Numerous appropriate rAAV genomes are described in the art and may be used in the invention. rAAV genomes usually comprise one or more DNAs of interest flanked by AAV ITRs, or comprise an expression cassette (one or more DNAs of interest operatively linked to a promoter and polyadenylation signal for expression) flanked by AAV ITRs. The DNAs of interest may encode a protein or an RNA, as is understood in the art. In embodiments of the invention, there are no AAV rep and cap genes between the AAV ITRs of rAAV genomes.
The present invention provides for a Vero producer cell or Vero cell producer cell substrate (as used interchangeably herein) wherein the Vero producer cell comprises an rAAV ITR flanking a polynucleotide of therapeutic interest (rAAV genome) and AAV rep and cap genes. In some embodiment both the rAAV genome and the rep-cap genes are stably integrated into the Vero cell. In some embodiments either or both the rAAV genome and the AAV rep-cap genes are introduced into the Vero cell via infection with a recombinant adenovirus or recombinant herpes virus wherein the either the rep-cap genes or rAAV genome respectively is a stably integrated into the Vero cell.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts production of rAAV following various helper virus infections of VeroC2 cells. Cells were infected with the indicated virus at MOI=10 and rAAV DRP was quantified by DRP using qPCR. Real time PCR with primer/probe sets detecting the CMV promoter (blue) and the eGFP coding region (red) are shown.

FIG. 2 depicts infectious rAAV titers produced by VeroC2 cells upon infection with various helper viruses. Lysates were produced as described and then used for co-infection of HeLa C12 cells with human Ad5. Lysates produced with SAdV-2, 3, 10, 11, 16 or mock-infected did not produce any detectable infectious rAAV (<100 IU/ml).

FIG. 3 depicts the BamHI restriction pattern of four fosmid clones compared to SAdV-13 infected cell Flirt DNA showing an identical banding pattern consistent with isolation of an SAdV-13 molecular clone.

FIG. 4 depicts phylogenetic trees for hexon and penton protein sequences from various simian (SAdV) and human (HuAdV) adenoviruses. Bovine adenovirus sequence (BoAdA) was used to root the tree and the position of SAdV-13 is marked with arrows.

DETAILED DESCRIPTION

The present invention is illustrated by the following examples relating to the production of increased titers of rAAV using a VeroC2 cell line and SAdV-13. Example 1 describes experiments in which VeroC2 cells are infected with simian adenoviruses. Example 2 describes the level of production of rAAV as measured by a DNAse-resistant particle (DRP) assay. Example 3 describes a CPE assay used to determine the maximal CPE of various adenovirus helper viruses. Example 4 describes the production of rAAV in Vero cells. Example 5 demonstrates the development of Vero lines that could be used to produce rAAV by an alternative, scalable method. Example 6 describes rAAV production using Vero packaging cells and the Ad/AAV hybrid system with SAdV-13 helper virus. Example 7 describes the cloning and sequencing of a particular SAdV-13 helper virus named SAdV-13 (PME12). Example 8 describes the development of a qPCR assay to quantitate SAdV-13.

Example 1

The effect of use of various simian adenovirus helper viruses on rAAV expression of a heterologous gene in Vero cells was examined.
Simian adenoviruses were obtained from the American Type Culture Collection (ATCC, Manassas, Va.) and propagated by infecting LLC-MK2 cells (ATCC) in DMEM with 2% supplemented calf serum (Cosmic Calf Serum, HyClone, Logan Utah). Cleared cell lysates were prepared by four rounds of freezing and thawing followed by centrifugation to remove particulates. Virus samples were checked for the presence of wild type AAV by a PCR assay with degenerate primers as described in Chen et al., J Virol 79: 14781-14792 (2005). Viral samples that showed the presence of contaminating wild type AAV were processed by plaque purifying virus in the presence of anti-AAV1 rabbit antiserum. The PCR assay was then repeated on the new viral stocks. Viruses were titered by the TCID_5omethod on LLC-MK2 cells as described in the Adeno-X expression system 1 User Manual, pages 46-47 (August 2007 version, protocol PT3414, version PR7823350), Clontech Laboratories, Inc. (Mountain View, Calif.).
A producer AAV cell line was derived from the standard Vero line distributed by ATCC (Cat #CCL-81) by methods generally described in U.S. Pat. No. 5,658,785. The producer cell line named VeroC2 has three elements stably integrated in the genomic DNA: (1) the rep and cap genes of AAV2; (2) a recombinant AAV genome with a green fluorescent protein (GFP) gene; and (3) the neomycin resistance gene. The cell line was plated at 20,000 cells per well in a 24 well plate. After one day the cells were infected with a panel of monkey adenoviruses. The adenovirus was used at a multiplicity of infection (MOI) of 10. The cells were examined 1-2 days later using a fluorescent microscope that detects GFP expression as a result of recombinant genome replication and transgene expression. Simian adenoviruses that were tested were SAdV-2, 3, 5, 8, 10, 11, 13, 16, 19 and 20.
Results showed highest GFP expression in VeroC2 cells infected with SAdV-13. Lower GFP expression was noted for VeroC2 cells infected with SAdV-5, -8, and -19. GFP expression was barely detectable for VeroC2 cells infected with SAdV-2, 3, 10, 11, 16 and 20.

Example 2

The effect of use of various simian adenovirus helper viruses on rAAV particle production in Vero cells was also examined.
The level of production of rAAV was measured by the DNAse-resistant particle (DRP) assay. Vero C2 cells were infected at an MOI of 10 with SAdV-2, -3, -5, -8, -10, -11, -0.13, -16, -19, or -20. When infected cells showed maximal cytopathic effect (CPE) (evidenced by rounding and detachment) they were harvested and subjected to 4 freeze thaw cycles to lyse the cells and release the virus. Heat treatment was used to inactivate residual Ad5 (55° C. for 30 min). The samples were then diluted 1:1,000 in 50 mM KCl, 10 mM Tris pH 8.0, 5 mM MgCl₂and 50 μl of the diluted lysate was treated with DNAse I for 30 min at 37° C. The DNAse was heat inactivated at 95° C. for 10 minutes and 10 rig of Proteinase K was added and allowed to digest the rAAV capsid for 1 hr at 50° C. and then the Proteinase K was inactivated by heating at 95° C. for 20 minutes. The net effect of the two treatments is to first remove any DNA that is not packaged into viral particles, and then to degrade the viral capsid proteins and release the encapsidated viral genomes. Viral DNA was quantified by real-time qPCR using “Taqman” chemistry in a ABI 7000 real time instrument (Applied Biosystems). Two primer/probe sets were utilized, one set that detects the CMV promoter, and a second set that detects the eGFP gene. A complete list of primer/probe sets that are used in this disclosure arc shown in Table 1. The probes were labeled with 6-FAM at the 5′ end and TAMRA at the 3′ end. The Ad5 E4 sequences used were taken from Sagawa et al., 2004, Mol. Therapy 10, 1043.

TABLE 1

Sequence	Primer	1	Primer 2	Probe
detected	sequence	sequence	sequence

CMV-IE	TGGAAATCCC	CATGGTGATGC	CCGCTATCCACG
promoter	CGTGAGTCAA	GGTTTTGG	CCCATTGATG
	SEQ ID NO 1	SEQ ID NO 2	SEQ ID NO 3

eGFP	CCACTACCTG	TCCAGCAGGA	TGAGCAAAGACCC
	AGCACCCAGTC	CCATGTGATC	CAACGAGAAGCG
	SEQ ID NO 4	SEQ ID NO 5	SEQ ID NO 6

Beta gal	TGGCTGGAGT	CGTGCATCTG	TGAGGCCGATAC
	GCGATCTTC	CCAGTTTGA	TGTCGTCGTCCC
	SEQ ID NO 7	SEQ ID NO 8	SEQ ID NO 9

Ad5E4	GGAGTGGAGC	ACTACGTCCG	TGGCATGACACTAC
	CGAGACAAC	GCGTTCCAT	GACCAACACGATCT
	SEQ ID NO 10	SEQ ID NO 11	SEQ ID NO 12

By comparing the results for unknown samples with a standard curve generated with known quantities of plasmid DNA, the number of copies of a sequence in the sample were determined. The numbers were converted to the numbers of rAAV genomes produced per cell (FIG. 1).
The overall results indicated that SAdV-13 was the best helper virus tested. Importantly, using SAdV-13 as the helper levels of rAAV per cell were generated that were comparable to levels attainable with HeLa-based lines. Although vector yields depend on a number of factors, the highest producing HeLa lines for any given construct tend to produce 10⁴-10⁵particles per cell.

Example 3

The CPE of various helper viruses was examined.
The time to reach maximum CPE was examined for various viruses by infecting cells at MOI 10, then examining their morphology daily by phase contrast microscopy with an inverted microscope. The time to maximal CPE was defined as the first day at which at least 95% of the cells show definite rounding.
For simian adenoviruses 1, 2, 3, 5, 7, 8, 10, 11, 16, 19, and 20 on Vero cells, the time to maximal CPE was 2-3 days. For HuAd5 on Vero cells the time to maximal CPE was 3-4 days, while for HuAd5 on HeLa cells it was 2 days. For SAdV-13 on Vero cells the time to maximal CPE was 5 days.

Example 4

Recombinant AAV was produced in Vero cells.
Vero cell lysates (from Vero cells infected with SAdV-5, -8, -13, -19 and -20) were applied to HeLa-derived C12 cells that had simultaneously been infected with Ad5. HeLa C12 cells are an “indicator” line that contains the AAV2 rep and cap genes. Upon co-infection with rAAV and Ad5, the rAAV genome is massively amplified (10⁴-10⁵logs) due to the presence and activity of the rep gene. Therefore, vector genome and transgene amplification arc sensitive readouts for rAAV infection. Accordingly, serial dilutions (10⁻¹to 10⁻⁸) of VeroC2 cell lysates infected with various adenoviruses were generated and used to infect C12 cells also infected with Ad5 to stimulate rep dependent rAAV vector genome replication. Twenty hr. post-infection the wells were examined in the inverted fluorescent microscope. The total number of green cells were counted in wells with fewer than 50, and those numbers were used to generate an infectious rAAV titer (FIG. 2).
These data further confirm that SAdV-13 was the most effective helper to produce functional rAAV from the VeroC2 cell line.

Example 5

Vero lines were also developed that could be used to produce rAAV by an alternative, scalable method. In this system, AAV rep and cap genes are integrated into the Vero cellular DNA, but the rAAV genome is delivered by an adenovirus-AAV hybrid, where an rAAV genome is integrated into the E1 region of an adenovirus vector and packaged in the adenovirus capsid. The cells are also concurrently infected with a wild type adenovirus that provides helper functions for rAAV production and also allows for replication of the Ad/AAV hybrid by providing E1 gene products that are deleted in the Ad/AAV hybrid virus. Control experiments (not shown) had demonstrated that E1 products from SAdV-13 could allow replication by an E1 deleted HuAd5 in Vero cells.
To adapt such an Ad/AAV hybrid packaging system to Vero cells, cell lines were first selected that contained the AAV rep and cap genes. All these lines were derived from the World Health Organization (WHO) certified stock of Vero cells, which was provided by the ATCC with a release from the FDA. Two constructs were used to make the stable cell lines. Both have neomycin resistance genes for selection and the rep gene from AAV2, while one has the cap gene from AAV1 (rep2cap1neo) and the other has the cap gene from AAV2 (rep2cap2neo). The two constructs were transfected into WHO Vero cells and selected for stable integration with 600 μg/ml G418. A total of 387 rep2cap1 lines and 338 rep2cap2 lines were selected. Previous experience with rAAV producer cell lines indicated that robust rep gene amplification was key to high-titer cell line. Since this is amenable to high throughput screening, an initial screen based on this property was performed. Cells were infected with SAdV-13, then after 5 days, they were lysed by the addition of 1/10th volume of 4 M NaOH, 50 mM EDTA, and 10 μg/ml herring sperm DNA. The denatured cell lysate was transferred to a positively charged nylon membrane by using a “dot blot” filtration device. The level of rep DNA amplification was determined by using a rep radiolabeled hybridization probe. The cell lines corresponding to the most highly radioactive spots were selected for further analysis. There were ten rep2cap1 and 8 rep2cap2 lines that were subjected to further characterization. These were co-infected with SAdV-13 and an Ad/AAV hybrid virus to determine rAAV vector yields using this second production platform.
Five rep2cap1 packaging cell lines and five rep2cap2 cell lines were co-infected with SAdV-13 and an Ad/AAV hybrid virus (Ad/AAV β-gal) that contained a rAAV genome harboring the β-galactosidase gene integrated into the E1 region of human Ad5. The test packaging cell lines were infected with SAdV-13 at a MOI of 1 and 20 hr later infected with Ad/AAV β-gal at a MOI of 3. After 5 days, cells were lysed by 4 rounds of rapid freezing and thawing and clarified lysates generated by centrifugation and heat treatment to inactivate residual adenovirus. A DRP assay was performed using a primer/probe combination that is specific to the β-galactosidase transgene (Table 1). The productivity for the highest producing cell lines identified in this experiment. rAAV production by Vero rep2cap 1 and rep2cap2 cell lines co-infected with SAdV-β and Ad/AAV β-gal hybrid virus are shown in Table 2.

TABLE 2

Cell line	AAV Capsid gene source	rAAV DRP/cell

R2C1.SF.1B1	Serotype	1	1706
R2C2.CA.1D3	Serotype	2	2316
R2C2.SF.1B1	Serotype	2	2286

An additional control experiment was done to show that there was no residual adenovirus present that could be making β-gal sequences DNAse resistant. Recombinant adenovirus containing the β-gal transgene should have been denatured by the 56° C. heating step, and to confirm this the DRP assay was repeated but with a human Ad5 E4 primer probe set. The numbers of copies of adenovirus present by using this qPCR primer/probe set were at least 10-fold lower than the β-gal copies present in the lysates, indicating that the vast majority of the DRP values were being contributed by rAAV/β-gal particles.
This initial experiment provided proof of concept that the Ad/AAV hybrid packaging type cell line could be adapted to Vero cells. The approach has been further optimized by selecting a somewhat more productive line (R2C1.CA.8C4) for production of rAAV1. Three other simian adenoviruses were additionally tested that had shown some activity with Vero C2 cells (SAdV-5, 8 and 19) in Example 1. These helper viruses had sub-detectable levels of rAAV production in this rAd/AAV hybrid system. A key aspect of this packaging system as opposed to the producer cells is that one needs only a single cell line to produce multiple different rAAV vectors of the same serotype. This could increase efficiency and reduce cost since it would not be necessary to qualify a new cell line for each rAAV vector produced.

Example 6

An additional rAd/AAV hybrid virus encoding a heterologous protein smaller than β-galactosidase and more similar in size to proteins used for therapeutic purposes was used to optimize production parameters. The rAd/AAV hybrid virus contained the enhanced green fluorescent protein (eGFP) transgene. This gene was contemplated to package more efficiently and yield greater levels of rAAV.
Two Vero derived AAV packaging cell lines were isolated following plasmid DNA transfection. The R2C1.CA.8C3 line contains the rep gene from AAV2 and the cap gene from AAV1, while the R2C2.CA.1D3 line contains both rep and cap from AAV2. To evaluate the packaging ability of Vero-derived cells with the eGFP containing rAd/AAV hybrid, the cell lines were co-infected with the rAd/AAV hybrid virus and SAdV-13 at variable timing. The rAd/AAV hybrid virus was used at 100 vector genomes per cell, while SAdV-13 was used at 1 TCID₅₀per cell.
Timing of infection was varied to look at the effects on rAAV yield. Infection with the rAd/AAV hybrid virus occurred at the following times relative to the SAdV-13: 4 hours before, at the same time, or 4-24 hours after at 4 hour intervals. To determine yield, cells were harvested at maximal cytopathic effect (5 days for SAdV-13), lysed by 4 freeze thaw cycles and the lysates were then diluted 1:2000. They were then treated sequentially with DNAse and Proteinase K, and assayed by real time PCR. rAAV present in the clarified cell lysate was achieved by qPCR to measure DNAse resistant vector genomes as described previously. The levels for SAdV-13 arc shown in Tables 3 and 4.
Table 3 depicts AAV1 GFP production while Table 4 depicts AAV2 eGFP production.

TABLE 3

AAV1 eGFP Production

	Timing of Ad hybrid	SAdV-13
	addition (hours)	DRP/Cell

	−4	3555
	0	9216
	+4	7966
	+8	12427
	+12	11634
	+16	16272
	+20	7262
	+24	8522

TABLE 4

AAV2 eGFP Production

	Timing of Ad hybrid	SAdV-13
	addition (hours)	DRP/Cell

	−4	86561
	0	73977
	+4	58256
	+8	83783
	+12	62963
	+16	60230
	+20	149504
	+24	98333

The data indicates that high levels of rAAV productivity are possible with this system. Up to 150,000 DNAse resistant particles per cell were documented for the rAAV2.eGFP vector. Optimal production conditions for infection varied between cell lines, with the most effective timing being rAd/AAV hybrid virus infection 16-24 hours after SAdV-13 virus infection.

Example 7

A SadV-13 was molecularly cloned and sequenced as follows.
Low molecular weight DNA was isolated from SAdV-13 infected Vero cells by a modified Hirt DNA extraction procedure [Hirt et al., Journal of Molecular Biology, 26(2): 365-369 (1967)], and then the terminal protein was removed by treatment with Klenow fragment in the presence of three of the four dNTPs followed by S1 nuclease [Berkner et al., Nucleic Acids Res 11(17): 6003-20 (1983)]. The SAdV-13 virus genomes were then cloned into a fosmid vector (Epicentre Copy Control System) and resulting clones analyzed by digestion with BamH1 restriction enzyme for an identical restriction pattern as that observed for the bulk Hirt DNA. Four clones were identified with the expected pattern (FIG. 3). Clone #3 (SAdV13-PME12) was subsequently selected for high-throughput 454 deep sequencing.
Several clones were selected and the terminal sequences determined. Sequence of the inverted terminal repeats (ITRs) for six independent clones was obtained and shared significant homology to other published adenovirus ITR sequences. Two kinds of heterogeneity in the clones' ITR sequence was observed that were otherwise identical except for orientation. The first was that there were variable numbers of nucleotides (4-18) missing from the terminal repeat ends. Secondly, in some cases short duplications of 100-400 bp of sequence was appended to intact ITRs.
Clone SAdV13-PME12 was selected for complete sequencing and possessed a 4 bp deletion at the 5′ end and a 12 bp deletion at the 3′ end. A portion of the resulting sequence matched exactly the previously reported VA RNA gene sequence [Kidd et al., Virology 207(1): 32-45 (1995)] supporting that this sequence is SAdV-13. Translation of the virus sequence resulted in the clear delineation of identity between this novel isolate and previously published adenoviral genomes. SAdV-13 is clearly related to other primate adenoviruses without being notably similar to any other previously published adenovirus genomes. Phylogenetic analysis of the deduced amino acid sequences of the hexon and penton proteins is shown in FIG. 4 and the complete virus genome sequence provided as SEQ ID NO: 16. This sequence, along with the putative protein sequences expressed therefrom, are depicted in Table 5 below.

TABLE 5

SEQ ID NO:	Description

16	SAdV-13 Viral Genome
17	E4 orf 2
18	E4 orf 3
19	E4 orf 4
20	E4 34K
21	Fiber
22	E3 14.7 (15.3)
23	U exon
24	E3 RID-beta
25	E3 RID-alpha
26	E3 CR1 beta1
27	E3 CR1-alpha1
28	E3 12.5K
29	pVIII
30	33K?
31	22K
32	100K
33	DBP
34	Protease
35	Hexon
36	pVI
27	V
38	pX?
39	pVII
40	III (penton base)
41	pTP
42	po1
43	pIIIa
44	52K
45	IVa2 C-terminus
46	IX
47	E1B 55K
48	E1B 19K
49	E1A
50	E4 orf 1

Example 8

The DNA sequence of the SAdV-13 (PME-12) clone enabled the development of a quantitative real-time PCR assay to detect SAdV-13 genomes. This assay is useful for the rapid, sensitive and precise measurement of the SAdV-13 and permits rapid optimization of virus infection conditions for increased rAAV production in this production platform.
Specifically, samples are quantitated by dilution of the sample 100 to 10.000-fold in 50 mM KCl, 10 mM Tris pH 8.0, and 5 mM MgCl₂. Samples are then digested in a 50 μl volume with 175 U of DNAse I at 37° C. for 30 minutes to remove non-encapsidated viral DNA. After heating at 95° C. for 10 minutes to inactivate DNAse I, the sample is treated with 200 μg/ml proteinase K at 50° C. for 1 hour to degrade the viral capsid and other cellular proteins. After treatment at 95° C. for 30 min to inactivate Proteinase K, the viral genomes are quantitated by real time PCR with a Taqman® primer probe set as follows:

	Forward primer:
	(SEQ ID NO: 13)
	5′-CTTGAAGCCACGCAAGTTTA-3′

	Reverse primer:
	(SEQ ID NO: 14)
	5′-TGCAAATAATCCAGCAAAGC-3′

	Probe:
	(SEQ ID NO: 15)
	6-FAM-CATGTTTGCTCATCGCCCGG-TAMRA

Quantitation is carried out by comparison with a plasmid standard curve.
While the present invention has been described in terms of various embodiments and examples, it is understood that variations and improvements will occur to those skilled in the art. Therefore, only such limitations as appear in the claims should be placed on the invention.

Claims

1. A method of producing infectious recombinant adeno-associated virus (rAAV) comprising the steps of:

a) infecting a Vero producer cell with simian adenovirus 13 (SAdV-13) helper virus and

b) culturing the cell to produce rAAV.

2. A method of producing infectious recombinant adeno-associated virus (rAAV) comprising the steps of:

a) introducing a rAAV genome into a Vero packaging cell,

b) infecting the cell with simian adenovirus 13 (SAdV-13) helper virus and

c) culturing the cell to produce rAAV.

3. The method of claim 2 wherein the rAAV genome is introduced by infection with a rAd/AAV hybrid.

4. A method of producing infectious recombinant adeno-associated virus (rAAV) comprising the steps of:

a) introducing a rAAV genome and AAV rep/cap genes into a Vero cell,

b) infecting the cell with simian adenovirus 13 (SAdV-13) helper virus and

c) culturing the cell to produce rAAV.

5. The method of claim 4 wherein steps a) and b) occur concurrently.

6. The method of claim 4 wherein the Vero cell is a packaging cell.

7. A method of producing infectious recombinant adeno-associated virus (rAAV) comprising the steps of:

a) infecting a Vero producer cell with a SAdV-13-like adenovirus helper virus and

b) culturing the cell to produce rAAV.

8. A method of producing infectious recombinant adeno-associated virus (rAAV) comprising the steps of:

a) introducing a rAAV genome into a Vero packaging cell,

b) infecting the cell with a SAdV-13-like adenovirus helper virus helper virus and

c) culturing the cell to produce rAAV.

9. The method of claim 8 wherein the rAAV genome is introduced by infection with a rAd/AAV hybrid.

10. A method of producing infectious recombinant adeno-associated virus (rAAV) comprising the steps of:

a) introducing a rAAV genome and AAV rep/cap genes into a Vero cell,

b) infecting the cell with a SAdV-13-like adenovirus helper virus and

c) culturing the cell to produce rAAV.

11. The method of claim 10 wherein steps a) and b) occur concurrently.

12. The method of claim 10 wherein the Vero cell is a packaging cell.

13. The method of any of claims 1-12 further comprising the step of isolating the rAAV produced by the cell.

14. The method of claim 3 or 9 wherein the Vero cell is infected with the rAd/AAV 16-24 hours after helper virus infection.

15. In a method for producing infectious recombinant adeno-associated virus (rAAV), the improvement comprising infecting a Vero cell with SAdV-13 helper virus.

16. In a method for producing infectious recombinant adeno-associated virus (rAAV), the improvement comprising infecting a Vero cell with a SAdV-13-like adenovirus helper virus.

17. A method of producing infectious rAAV comprising culturing a Vero producer cell under conditions permissive for rAAV production, wherein the Vero producer cell comprises simian adenovirus 13 (SAdV-13) helper virus.

18. A method of producing infectious rAAV comprising culturing a Vero producer cell under conditions permissive for rAAV production, wherein the Vero producer cell comprises simian adenovirus 13-like (SAdV-13-like) helper virus.

19. The method of any of the preceding claims wherein the SAdV-13 helper virus is SAdV-13 PME-12.