Adeno-associated viral genome
The AAV genome is small (about 5 kb) and comprises a central region containing rep (replicase) and cap(capsid) genes flanked by 145 base inverted terminal repeats (ITRs). The rep gene is involved in viral replication and integration whereas cap gene encodes viral capsid proteins. ITRs are required for replication, transcription, proviral integration and rescue.

In earlier AAV vectors, foreign DNA replaced the cap region and was expressed under the control of an endogenous AAV promoter. The transgene expression was inefficient using heterologous promoters due to inhibition of their activity by Rep protein.

Rep interference with endogenous promoters resultedin cytotoxic effects of the virus. To overcome the above limitations, such vectors in which both genes were deleted and the transgene was expressed from either an endogenous or a heterologous promoter, were developed.

In vitro manipulation of AAV is facilitated by cloning the inverted terminal repeats in a plasmid vector and inserting the transgene between them. Transfection of this construct into cells along with a helper plasmid produced recombinant viral particles.

Figure 5-1.4.2(b): AAV Genome, Vector genome and Packaging coil.
(Adapted from Somia N, Verma IM. 2000. Gene therapy: trials and tribulations. Nature Reviews Genetics, 1: 91-99)