Nat. Commun. https://doi.org/10.1038/s41467-019-12449-2 (2019).

Adeno-associated virus (AAV) vectors hold great interest for encoding CRISPR–Cas nucleases for in vivo CRISPR delivery. Yet the potential consequences of long term expression of Cas9 from an AAV vector are largely unknown. Hanlon et al. analyzed the integration events of AAV vectors in differentiated cells of brain, muscle and cochlea. Across the three different organs, they observed similar, high levels of AAV integration at nuclease-induced breaks in therapeutically targeted genes. Detailed AAV mapping in mouse brain shows that the expression of Cas9 does not affect genome-wide integration outside the target locus. To learn the complete integration profiles, the researchers constructed a 465-bp miniature AAV vector for sequencing the entire integration. They observed that the integrants could be fragmented, full-length or concatemers. Therefore, AAV vector integration at target sites should be assessed, especially when clinical applications are considered.