Adeno-associated virus vector genome integration site (AAV integration site)

Adeno-associated virus (AAV) vector genome integration sites are the specific locations in the host cell's chromosomal DNA where AAV-derived genetic material is incorporated. While recombinant AAV (rAAV) vectors are designed to persist primarily as episomes, a small fraction of the vector genomes (0.1% to 1%) can integrate into the host genome, typically at sites of DNA damage or double-strand breaks (Deyle & Russell, 2009; PMID: 19363492). This integration is a critical safety consideration in gene therapy because it can lead to insertional mutagenesis, potentially activating oncogenes or disrupting tumor suppressor genes (Nault et al., 2015; PMID: 25825441). In wild-type AAV, integration is targeted to the AAVS1 safe harbor locus on chromosome 19 by the viral Rep protein, but therapeutic rAAV vectors lack this protein and integrate more stochastically (Kotin et al., 1990; PMID: 2160169). Monitoring these integration sites through high-throughput sequencing is essential for evaluating the long-term safety and genotoxic potential of AAV-based therapies such as Zolgensma and Hemgenix (Nguyen et al., 2021; PMID: 33571567). Understanding the preference of AAV for certain genomic features, such as transcriptionally active regions or CpG islands, helps in predicting and mitigating genotoxic risks (Gil-Farina et al., 2016; PMID: 27501105).

Other names

AAVS1AAV integration locusProviral integration siterAAV integration siteGenomic safe harbor

Recombinant AAV (rAAV) vectors primarily persist as episomal concatemers in the nucleus of transduced cells. However, a small fraction (0.1% to 1%) of the vector genomes can integrate into the host chromosomal DNA. This integration typically occurs at sites of pre-existing double-strand breaks (DSBs) and is mediated by the host cell's non-homologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ) pathways (Deyle & Russell, 2009; PMID: 19363492). In contrast to wild-type AAV, which utilizes the viral Rep protein to integrate site-specifically into the AAVS1 locus on chromosome 19, rAAV vectors lack the Rep gene and integrate in a more stochastic manner, often showing a preference for transcriptionally active regions, CpG islands, and ribosomal DNA (Kotin et al., 1990; PMID: 2160169; Gil-Farina et al., 2016; PMID: 27501105).