Contaminating manufacturing plasmids and disrupted vector genomes present in liver tissue following adeno-associated virus gene therapy

Adeno-associated viruses (AAVs) are the most used vectors in gene therapy but can frequently cause liver complications in patients. The mechanisms underlying AAV-related liver toxicity remain poorly understood, posing challenges for effective prevention and intervention. We undertook long and short read metagenomic sequencing of liver tissue from a child with spinal muscular atrophy type 1 experiencing significant hepatitis after receiving onasemnogene abeparvovec. We identified manufacturing plasmid sequences, with evidence of complex structures and recombination. Vector genomes had extensive disruption and concatemerisation. We also identified the presence of human betaherpesvirus 6B in the liver. It is possible that presence of the manufacturing plasmid sequences or helper viruses allow replication of the vector within cells, contributing to the development of complex concatemeric structures and associated hepatitis.