Satellite subgenomic particles are key regulators of adeno-associated virus life cycle

Historically, AAV defective interfering particles (DI) were known as abnormal virions arising from natural replication and encapsidation errors. Through single virion genome analysis, we revealed that a major category of DI particles contains a double stranded DNA genome in a “snapback” configuration (SBG). The 59-SBGs include the P5 promoters and partial rep gene sequences. The 39-SBGs contains the capsid region. The molecular configuration of 59-SBGs allowed double stranded RNA transcription in their dimer configuration, which in turn regulate AAV rep expression and may improve AAV packaging. In contrast, 39-SBGs at its dimer configuration increased levels of cap protein. The generation and accumulation of 59-SBGs and 39-SBGs appears to be coordinated to balance the viral gene expression level. Therefore, the functions of 59-SBGs and 39-SBGs may help maximize the yield of AAV progenies. We postulate that AAV virus population behaved as a colony and utilizes its subgenomic particles to overcome the size limit of viral genome and encodes additional essential functions.