Adeno-associated virus
Adeno-associated virus (AAV) is a small virus which infects humans and some other primate species. AAV is not currently know to cause disease and consequently the virus causes a very mild immune response. AAV can infect both dividing and non-dividing cells and may incorporate its genome into that of the host cell. These features make AAV a very attractive candidate for creating viral vectors for gene therapy.

# Overview
Dependovirus adeno-associated virus belongs to the Parvoviridae.  The virus is a small (20 nm) replication-defective, nonenveloped virus of mammals (including humans), which has not been associated with any known diseases.  AAV is being extensively researched as a potential vector for gene therapy as it possesses many advantages in this regard.

# Gene Therapy Vector

## Advantages and drawbacks
Wild-type AAV has attracted considerable interest from gene therapy researchers due to a number of features. Chief amongst these is the viruses apparent lack of pathogenicity. It can also infect non-dividing cells and has the ability to stably integrate into the host cell genome at a specific site (designated AAVS1) in the human 19th chromosome. The feature makes it somewhat more predictable than retroviruses, which present threat of a random insertion and of mutagenesis, which is sometimes followed by development of a cancer. The AAV genome integrates most frequently into the site mentioned, while random incorporations into the genome take place with a negligible frequency. AAVs also present very low immunogenicity, seemingly restricted  to generation of neutralizing antibodies, while they induce no clearly-defined cytotoxic response. This feature, along with the ability to infect quiescent cells present their dominance over adenoviruses as vectors for the human gene therapy.
Use of the virus does present some disadvantages. The cloning capacity of the vector is relatively limited and most therapeutic genes require the complete replacement of the virus's 4.8 kilobase genome. It is accordingly unclear if the site-specific integration can be preserved in a usable vector since it appears to be partially dependent on products of the Rep open reading frame. The humoral immunity instigated by infection with the wild type is thought to be a very common event. The asscoiated neutralising activity limits the usefulness of the most commonly used serotype AAV2 in certain applications.

## Clinical trials
To date, AAV vectors have been used for first- and second-phase clinical trials for treatment of cystic fibrosis and first-phase trials for hemophilia. Promising results have been obtained from phase I trials for Parkinson's disease, showing good tolerance of an AAV2 vector in the central nervous system. Other trials have begun, concerning AAV safety for treatment of Canavan disease, muscular dystrophy and late infantile neuronal ceroid lipofuscinosis.
Trials for the treatment of prostate cancer have reached phase III, however these ex vivo studies do not involve direct administration of AAV to patients.

# AAV structure

## AAV genome, transcriptome and proteome
The AAV genome is built of single-stranded deoxyribonucleic acid (ssDNA), either positive- or negative-sensed, which is about 4.7 kilobase long. The genome comprises inverted terminal repeats (ITRs) at both ends of the DNA strand, and two open reading frames (ORFs): rep and cap. The former is composed of four overlapping genes encoding Rep proteins required for the AAV life cycle, and the latter contains overlapping nucleotide sequences of capsid proteins: VP1, VP2 and VP3, which interact together to form a capsid of an icosahedral symmetry.

### ITR sequences
The Inverted Terminal Repeat (ITR) sequences comprise 145 bases each. They were named so because of their symmetry, which was shown to be required for efficient multiplification of the AAV genome.  Another property of these sequences is their ability to form a hairpin, which contributes to so-called self-priming that allows primase-independent synthesis of the second DNA strand. The ITRs were also shown to be required for both integration of the AAV DNA into the host cell genome (19th chromosome in humans) and rescue from it, as well as for efficient encapsidation of the AAV DNA combined with generation of a fully-assembled, deoxyribonuclease-resistant AAV particles.
With regard to gene therapy, ITRs seem to be the only sequences required in cis next to the therapeutic gene: structural (cap) and packaging (rep) genes can be delivered in trans.  With this assumption many methods were established for efficient production of recombinant AAV (rAAV) vectors containing a reporter or therapeutic gene.  However, it was also published that the ITRs are not the only elements required in cis for the effective replication and encapsidation.  A few research groups have identified a sequence designated cis-acting Rep-dependent element (CARE) inside the coding sequence of the rep gene.  CARE was shown to augment the replication and encapsidation when present in cis.

### rep genes and Rep proteins
On the "left side" of the genome there are two promoters called p5 and p19, from which two overlapping messenger ribonucleic acids (mRNAs) of different length can be produced. Each of these contains an intron which can be either spliced out or not. Given these possibilities, four various mRNAs, and consequently four various Rep proteins with overlapping sequence can be synthesized. Their names depict their sizes in kilodaltons (kDa): Rep78, Rep68, Rep52 and Rep40.  Rep78 and 68 can specifically bind the hairpin formed by the ITR in the self-priming act and cleave at a specific region, designated terminal resolution site, within the hairpin. They were also shown to be necessary for the AAVS1-specific integration of the AAV genome. All four Rep proteins were shown to bind ATP and to possess helicase activity. It was also shown that they upregulate the transcription from the p40 promoter (mentioned below), but downregulate both p5 and p19 promoters.

### cap genes and VP proteins
The right side of a positive-sensed AAV genome encodes overlapping sequences of three capsid proteins, VP1, VP2 and VP3, which start from one promoter, designated p40. The molecular weights of these proteins are 87, 72 and 62 kiloDaltons, respectively.  All three of them are translated from one mRNA. After this mRNA is synthesized, it can be spliced in two different manners: either longer or shorter intron can be excised, which results in formation of two pools of mRNAs: 2.3 kb-, and 2.6 kb-long. Usually, especially in the presence of adenovirus, the longer intron is preferred, so the 2.3-kb-long mRNA represents so-called major splice. In this form the first AUG codon, from which the synthesis of VP1 protein starts, is cut out, resulting in a reduced overall level of VP1 protein synthesis. The first AUG codon, which remains in the major splice, is the initiation codon for VP3 protein. However, upstream of that codon in the same open reading frame lies the ACG sequence, which endcodes threonine, but is surrounded by the optimal Kozak context, that contributes to a low level of synthesis of VP2 protein, which is actually VP3 protein with additional N terminal residues, as is VP1.
Since the bigger intron is preferred to be spliced out, and since in the major splice the ACG codon is a much weaker translation initiation signal, the ratio at which the AAV structural proteins are synthesized in vivo is about 1:1:20, which is the same as in the mature virus particle.  The unique fragment at the N terminus of VP1 protein was shown to possess the phospholipase A2 (PLA2) activity, which is probably required for the releasing of AAV particles from late endosomes. Muralidhar et al. reported that VP2 and VP3 are crucial for correct virion assembly.  More recently, however, Warrington et al showed VP2 to be unnecessary for the complete virus particle formation and an efficient infectivity, and also presented that VP2 can tolerate large insertions in its N terminus, while VP1 can not, probably because of the PLA2 domain presence.
The crystal structure of the VP3 protein was determined by Xie, Bue, et al.

# AAV serotypes, receptors and native tropism
As of 2006 there have been 11 AAV serotypes described, the 11th in 2004.
All of the known serotypes can infect cells from multiple diverse tissue types. Tissue specificity is determined by the capsid serotype and pseudotyping of AAV vectors to alter their tropism range will likely be important to their use in therapy.

## Serotype 2
Serotype 2 (AAV2) has been the most extensively examined so far.  AAV2 presents natural tropism towards e.g. skeletal muscles, neurons, vascular smooth muscle cells and hepatocytes.
Three cell receptors haver been described for AAV2: heparan sulfate proteoglican (HSPG), aV5 integrin and fibroblast growth factor receptor 1 (FGFR-1). The first functions as a primary receptor, while the latter two have a co-receptor activity and enable AAV to enter the cell by receptor-mediated endocytosis.)  These study results have been disputed by Qiu, Handa, et al.  HSPG functions as the primary receptor, though its abundance in the extracellular matrix can scavenge AAV particles and impair the infection efficiency.

### Serotype 2 and cancer
Studies have shown that serotype 2 of the virus (AAV-2) apparently kills cancer cells without harming healthy ones.  "Our results suggest that adeno-associated virus type 2, which infects the majority of the population but has no known ill effects, kills multiple types of cancer cells yet has no effect on healthy cells," said Craig Meyers, a professor of immunology and microbiology at the Penn State College of Medicine in Pennsylvania.  This could lead to a new anti-cancer agent.

## Other Serotypes
Although AAV2 is the most popular serotype in various AAV-based research, it has been shown that other serotypes can be more effective as gene delivery vectors. For instance AAV6 appears much better in infecting airway epithelial cells, AAV7 presents very high transduction rate of murine skeletal muscle cells (similarly to AAV1 and AAV5), AAV8 is superb in transducing hepatocytes and AAV1 and 5 were shown to be very efficient in gene delivery to vascular endothelial cells.  AAV6, a hybrid of AAV1 and AAV2, also shows lower immunogenicity than AAV2.
Serotypes can differ with the respect to the receptors they are bound to. For example AAV4 and AAV5 transduction can be inhibited by soluble sialic acids (of different form for each of these serotypes), and AAV5 was shown to enter cells via the platelet-derived growth factor receptor.

# AAV immunology
AAV is of particular interest to gene therapists due to its apparent limited capacity to induce immune responses in humans, a factor which should positively influence vector transduction efficiency while reducing the risk of any immune-associated pathology.

## Innate
The innate immune response to the AAV vectors has been characterised in animal models. Intravenous administration in mice causes transient production of pro-inflammatory cytokines and some infiltration of neutrophils and other leukocytes into the liver, which seems to sequester a large percentage of the injected viral particles. Both soluble factor levels and cell infiltration appear to return to baseline within six hours. By contrast, more aggressive viruses produce innate responses lasting 24 hours or longer.

## Humoral
The virus is known to instigate robust humoral immunity in animal models and in the human population where up to 80% of individuals are thought to be seropositive for AAV2. Antibodies are known to be neutralising and do impact on vector transduction efficiency via some routes of administration. As well as persistent AAV specific antibody levels, it appears from both prime-boost studies in animals and from clinical trials that the B-cell memory is also strong.

## Cell-mediated
The cell-mediated response to the virus and to vectors is poorly characterised and has been largely ignored in the literature as recently as 2005. Clinical trials using an AAV2-based vector to treat haemophilia B seem to indicate that targeted destruction of transduced cells may be occurring. Combined with data that shows that CD8+ T-cells can recognise elements of the AAV capsid in vitro, it appears that there may be a cytotoxic T lymphocyte response to AAV vectors. However, the data is incomplete as the role of T-helper cells and evidence of targeted cytoxicity has not been fully explored.

# AAV infection cycle
There are several steps in the AAV infection cycle, from infecting a cell to producing new infectious particles:
- attachment to the cell membrane
- endocytosis
- endosomal trafficking
- escape from the late endosome or lysosome
- translocation to the nucleus
- formation of double-stranded DNA replicative form of the AAV genome
- rep genes expression
- genome replication
- cap genes expression, synthesis of progeny ssDNA particles
- assembly of complete virions, and
- release from the infected cell.
Some of these steps may look different in various types of cells, which, in part, contributes to the defined and quite limited native tropism of AAV. Replication of the virus can also vary in one cell type, depending on the cell's current cell cycle phase.
The characteristic feature of the adeno-associated virus is a deficiency in replication and thus its inability to multiply in unaffected cells.  The first factor that was described as providing successful generation of new AAV particles, was the adenovirus, from which the AAV name originated. It was then shown that AAV replication can be facilitated by selected proteins derived from the adenovirus genome, by other viruses such as HSV, or by genotoxic agents, such as UV irradiation or hydroxyurea.
The minimal set of the adenoviral genes required for efficient generation of progeny AAV particles, was discovered by Matsushita, Ellinger et al.  This discovery allowed for new production methods of recombinant AAV, which do  not require adenoviral co-infection of the AAV-producing cells.  In the absence of helper virus or genotoxic factors, AAV DNA can either integrate into the host genome or persist in episomal form. In the former case integration is mediated by Rep78 and Rep68 proteins and requires the presence of ITRs flanking the region being integrated. In mice, the AAV genome has been observed persisting for long periods of time in quiescent tissues, such as skeletal muscles, in episomal form (a circular head-to-tail conformation).

# Notes
-  Template:Harvard reference
-   Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 6.0 6.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 11.0 11.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 17.0 17.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 25.0 25.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 32.0 32.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 48.0 48.1 Template:Harvard reference
-  Jump up to: 49.0 49.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 54.0 54.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Jump up to: 58.0 58.1 Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference
-  Template:Harvard reference