Study Links AAV Gene Therapy–Associated Hepatitis to Complex Vector and Plasmid DNA Structures in the Liver

January 16, 2026-A recent landmark study has shed new light on the mechanisms behind severe liver complications following AAV gene therapy, specifically in a case involving onasemnogene abeparvovec (Zolgensma) for Spinal Muscular Atrophy (SMA). While liver inflammation is a known side effect of systemic AAV administration, the underlying cause has long been debated as either an immune response to the viral capsid or a reaction to the transgene. This investigation, however, shifts the focus toward the “genomic instability” of the vector itself and the presence of unintended manufacturing impurities within the patient’s liver cells.

The researchers discovered that DNA sequences from all three manufacturing plasmids—the vector, the packaging, and the helper plasmids—persisted in the patient’s liver tissue seven weeks after the infusion. Notably, the presence of the AAV2 rep gene and adenoviral helper sequences is highly significant. If these “contaminant” genes are expressed, they could potentially allow the therapeutic vector to replicate or rearrange within the liver, leading to the formation of massive, complex DNA structures known as concatemers. These structures are not part of the intended therapeutic design and may trigger a profound inflammatory response.

Beyond simple contamination, the study utilized long-read sequencing to reveal a state of “genomic chaos” within the hepatocytes. The AAV vector genomes did not remain as simple, stable loops of DNA; instead, they underwent extensive disruption, recombining with one another and even fusing with the patient’s own human DNA. These vector-human fusion junctions and large DNA concatemers mimic the behavior of wild-type viral infections, which may explain why the patient’s liver histology showed intense T-cell infiltration and “ballooning” hepatocyte degeneration—features typically seen in acute viral hepatitis.

The study also identified the presence of human betaherpesvirus 6B (HHV-6B) in the liver tissue. HHV-6 is known to function as a “helper virus” that can jump-start the replication of AAV. While it is unclear if the virus was actively replicating, its presence suggests a potential “perfect storm” where a pre-existing viral infection interacts with high-dose AAV therapy to exacerbate liver damage. This finding highlights the importance of screening for co-infections and understanding how environmental viral factors might influence the safety of genetic medicines.

Ultimately, these findings suggest that the industry may need to re-evaluate manufacturing purity and the long-term structural fate of AAV vectors in the body. The persistence of plasmid backbone sequences and the formation of complex DNA rearrangements pose a significant challenge for the safety of high-dose gene therapies. Future regulatory guidelines may require more stringent reporting on these complex structures to help prevent fulminant liver failure and improve the management of patients undergoing these life-changing treatments.