Identification of adeno-associated virus contamination in cell and virus stocks by PCR

AAV Vectors Pseudotyped with Capsids from Porcine and Bovine Species Mediate In Vitro and In Vivo Gene Delivery

Adeno-associated virus (AAV) vectors are among the most widely used delivery vehicles for in vivo gene therapy as they mediate robust and sustained transgene expression with limited toxicity. However, a significant impediment to the broad clinical success of AAV-based therapies is the widespread presence of pre-existing humoral immunity to AAVs in the human population. This immunity arises from the circulation of non-pathogenic endemic human AAV serotypes. One possible solution is to use non-human AAV capsids to pseudotype transgene-containing AAV vector genomes of interest. Due to the low probability of human exposure to animal AAVs, pre-existing immunity to animal-derived AAV capsids should be low. Here, we characterize two novel AAV capsid sequences: one derived from porcine colon tissue and the other from a caprine adenovirus stock. Both AAV capsids proved to be effective transducers of HeLa and HEK293T cells in vitro. In vivo, both capsids were able to transduce the murine nose, lung, and liver after either intranasal or intraperitoneal administration. In addition, we demonstrate that the porcine AAV capsid likely arose from multiple recombination events involving human- and animal-derived AAV sequences. We hypothesize that recurrent recombination events with similar and distantly related AAV sequences represent an effective mechanism for enhancing the fitness of wildtype AAV populations.

Multi-attribute analysis of adeno-associated virus by size exclusion chromatography with fluorescence and triple-wavelength UV detection

Adeno-associated virus (AAV) is the leading platform for in vivo gene therapy to treat numerous genetic diseases. Comprehensive analysis of the AAV particles is essential to ensure desired safety and efficacy. An array of techniques is required to evaluate their critical quality attributes. However, many of these techniques are expensive, time-consuming, labour-intensive, and varying in accuracy. Size exclusion chromatography coupled with fluorescence and triple-wavelength ultraviolet detection (SEC-FLD-TWUV) and incorporating an aromatic amino acid of tryptophan as an internal standard offers a simple, rapid, and reliable approach for simultaneous multi-attribute analysis of AAVs. In the current study, we demonstrate its capability for AAV characterization and quantification, that includes capsid concentration, empty to full capsid ratio, vector genome concentration, and the presence of aggregates or fragments. All were performed in 20-min chromatographic runs with minimal sample handling. Data analysis involves the assessment of intrinsic fluorescence and UV absorbance of samples at three wavelengths that can be utilised to determine the content of the capsid protein and genome copy number. The separation efficiency using SEC columns with different pore sizes, and elution buffers of varying compositions, ionic strength, and pH values was also evaluated. This SEC-FLD-TWUV method may serve as a powerful yet cost-effective tool for responsive quality evaluation of AAVs. This may enhance performance, robustness, and safety of bioprocessing for AAV vectors to be used in gene therapy.

A quantitative PCR screening method for adeno-associated viral vector 2-mediated gene doping

Gene therapy is currently prohibited in human and equine athletes and novel analytical methods are needed for its detection. Most in vivo products use non-integrating, recombinant viral vectors derived from adeno-associated virus (AAV) to deliver transgenes into cells, where they are transcribed and translated into functional proteins. Although the majority of wild-type AAV (WTAAV) DNA is removed from recombinant AAV (rAAV) vectors, some sequences are conserved. The goal of this study was to develop a quantitative polymerase chain reaction (QPCR) screening test targeting conserved AAV sequences to enable theoretical detection of all rAAV gene therapy products, regardless of encoded transgenes while excluding the presence of WTAAV DNA in horses. Primer sets were developed and validated to target an AAV2 sequence highly conserved across rAAV viral vectors and a sequence only found in wild type AAV2 (WTAAV2). Six horses were administered an intra-articular injection of rAAV. Plasma and synovial fluid were collected on days 0, 1, 2, 4, 7, 14, 28, 56, and 84. Using QPCR, rAAV was detected in plasma for up to 2-4 days in all horses. rAAV DNA was detected for 28 days in synovial fluid from two horses for which synovial fluid samples were available. No WTAAV2 DNA was detected in any sample. This is the first study to develop a QPCR test capable of screening for rAAV vectors that may be used for gene doping in horses.

Parvoviruses: structure and infection

Parvoviruses package a ssDNA genome. Both nonpathogenic and pathogenic members exist, including those that cause fetal infections, encompassing the entire spectrum of virus phenotypes. Their small genomes and simple coding strategy has enabled functional annotation of many steps in the infectious life cycle. They assemble a multifunctional capsid responsible for cell recognition and the transport of the packaged genome to the nucleus for replication and progeny virus production. It is also the target of the host immune response. Understanding how the capsid structure relates to the function of parvoviruses provides a platform for recombinant engineering of viral gene delivery vectors for the treatment of clinical diseases, and is fundamental for dissecting the viral determinants of pathogenicity. This review focuses on our current understanding of parvovirus capsid structure and function with respect to the infectious life cycle.

Recombinant adeno-associated viral vector production and purification

Gene delivery vectors based on recombinant adeno-associated virus (AAV) are powerful tools for studying myogenesis in normal and diseased conditions. Strategies have been developed to use AAV to increase, down-regulate, or modify expression of a particular muscle gene in a specific muscle, muscle group(s), or all muscles in the body. AAV-based muscle gene therapy has been shown to cure several inherited muscle diseases in animal models. Early clinical trials have also yielded promising results. In general, AAV vectors lead to robust, long-term in vivo transduction in rodents, dogs, and non-human primates. To meet specific research needs, investigators have developed numerous AAV variants by engineering viral capsid and/or genome. Here we outline a generic AAV production and purification protocol. Techniques described here are applicable to any AAV variant.

Intranasal administration of adeno-associated virus type 12 (AAV12) leads to transduction of the nasal epithelia and can initiate transgene-specific immune response

A critical aspect in defining the utility of a vector for gene therapy applications is the cell tropism and biodistribution of the vector. Adeno-associated virus type 12 (AAV12) has several unique biological and immunological properties that could be exploited for gene therapy purposes, including a unique cell surface receptor, transduction of epithelial cells, and limited neutralization by pooled human antibodies. However, little is known about its cell tropism and biodistribution in vivo. In vivo biodistribution studies with AAV12 vectors encoding a cytomegalovirus promoted luciferase transgene indicated preferential transduction of the nasal epithelia which was not observed with AAV2-based vectors. Expression peaked 2 weeks postadministration, before decreasing to a persistent level. The level of neutralizing antibodies (Nab) induced was sevenfold lower for AAV12 than for AAV2, an advantage for use in repeat administration. Furthermore, vectors encoding influenza A nucleoprotein (NP), an antigen which has previously been shown to induce immune protection against challenge, resulted in generation of both anti-A/NP antibodies and lung anti-A/NP T cells. Our findings suggest further evaluation of AAV12 as a vector for gene therapy and as a potential nasal vaccine.

Molecular characterization of the heparin-dependent transduction domain on the capsid of a novel adeno-associated virus isolate, AAV(VR-942)

A new adeno-associated virus (AAV), referred to as AAV(VR-942), has been isolated as a contaminant of adenovirus strain simian virus 17. The sequence of the rep gene places it in the AAV serotype 2 (AAV2) complementation group, while the capsid is only 88% identical to that of AAV2. High-level AAV(VR-942) transduction activity requires cell surface heparan sulfate proteoglycans, although AAV(VR-942) lacks residues equivalent to the AAV2 R585 and R588 amino acid residues essential for mediating the interaction of AAV2 with the heparan sulfate proteoglycan receptor. Instead, AAV(VR-942) uses a distinct transduction region. This finding shows that distinct domains on different AAV isolates can be responsible for the same activities.

Adeno-associated virus type 12 (AAV12): a novel AAV serotype with sialic acid- and heparan sulfate proteoglycan-independent transduction activity

Recombinant adeno-associated virus (rAAV) is a promising vector for gene therapy. Recent isolations of novel AAV serotypes have led to significant advances by broadening the tropism and increasing the efficiency of gene transfer to the desired target cell. However, a major concern that remains is the strong preexisting immune responses to several vectors. In this paper, we describe the isolation and characterization of AAV12, an AAV serotype with unique biological and immunological properties. In contrast to those of all other reported AAVs, AAV12 cell attachment and transduction do not require cell surface sialic acids or heparan sulfate proteoglycans. Furthermore, rAAV12 is resistant to neutralization by circulating antibodies from human serum. The feasibility of rAAV12 as a vector was demonstrated in a mouse model in which muscle and salivary glands were transduced. These characteristics make rAAV12 an interesting candidate for gene transfer applications.

Identification and characterization of novel adeno-associated virus isolates in ATCC virus stocks

Adeno-associated viruses (AAVs) depend on a helper virus for efficient replication. To identify novel AAV isolates, we screened a diverse set of virus isolates for the presence of AAV DNA. AAVs found in 10 simian adenovirus isolates showed greater than 96% homology to AAV1 and AAV6 but had distinct biological properties. Two representatives of this group, AAV(VR-195) and AAV(VR-355), were studied in more detail. While the novel AAVs had high sequence homologies and required sialic acid for cell binding and transduction, differences were observed in lectin competition, resulting in distinct tropisms in human cancer cell lines.

Cloning and characterization of a bovine adeno-associated virus

To better understand the relationship between primate adeno-associated viruses (AAVs) and those of other mammals, we have cloned and sequenced the genome of an AAV found as a contaminant in two isolates of bovine adenovirus that was reported to be serologically distinct from primate AAVs. The bovine AAV (BAAV) genome has 4,693 bp, and its organization is similar to that of other AAV isolates. The left-hand open reading frame (ORF) and both inverted terminal repeats (ITRs) have the highest homology with the rep ORF and ITRs of AAV serotype 5 (AAV-5) (89 and 96%, respectively). However, the right-hand ORF was only 55% identical to the AAV-5 capsid ORF; it had the highest homology with the capsid ORF of AAV-4 (76%). By comparing the BAAV cap sequence with a model of an AAV-4 capsid, we mapped the regions of BAAV VP1 that are divergent from AAV-4. These regions are located on the outside of the capsid and are partially located in exposed loops. BAAV was not neutralized by antisera raised against recombinant AAV-2, AAV-4, or AAV-5, and it demonstrated a unique cell tropism profile in four human cancer cell lines, suggesting that BAAV might have transduction activity distinct from that of other isolates. A murine model of salivary gland gene transfer was used to evaluate the in vivo performance of recombinant BAAV. Recombinant BAAV-mediated gene transfer was 11 times more efficient than that with AAV-2. Overall, these data suggest that vectors based on BAAV could be useful for gene transfer applications.