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Adeno-associated virus type 2 preferentially integrates single genome copies with defined breakpoints

Tyler Janovitz123, Michel Sadelain3 and Erik Falck-Pedersen2*

Author Affiliations

1 Tri-Institutional MD-PhD Program, Weill Medical College of Cornell University, New York, NY 10065, USA

2 Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA

3 Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA

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Virology Journal 2014, 11:15  doi:10.1186/1743-422X-11-15

Published: 27 January 2014



Adeno-associated virus (AAV) serotype 2 prevalently infects humans and is the only described eukaryotic virus that integrates site-preferentially. In a recent high throughput study, the genome wide distribution of AAV-2 integrants was determined using Integrant Capture Sequencing (IC-Seq). Additional insight regarding the integration of AAV-2 into human genomic DNA could be gleaned by low-throughput sequencing of complete viral-chromosomal junctions.


In this study, 140 clones derived from Integrant-Capture Sequencing were sequenced. 100 met sequence inclusion criteria, and of these 39 contained validated junction sequences. These unique sequences were analyzed to investigate the structure and location of viral-chromosomal junctions.


Overall the low-throughput analysis confirmed the genome wide distribution profile gathered through the IC-Seq analysis. We found no unidentifiable sequence inserted at AAV-2 chromosomal junctions. Assessing both left and right ends of the AAV genome, viral breakpoints predominantly occurred in one hairpin of the inverted terminal repeat and AAV genomes were preferentially integrated as single copies.

AAV-2; Integration; Virus chromosomal junctions; Viral breakpoints