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

Abstract

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 5-SBGs include the P5 promoters and partial rep gene sequences. The 3-SBGs contains the capsid region. The molecular configuration of 5-SBGs allowed double stranded RNA transcription in their dimer configuration, which in turn regulate AAV rep expression and may improve AAV packaging. In contrast, 3-SBGs at its dimer configuration increased levels of cap protein. The generation and accumulation of 5-SBGs and 3-SBGs appears to be coordinated to balance the viral gene expression level. Therefore, the functions of 5-SBGs and 3-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.