Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy
Adeno-associated viruses (AAVs) are common 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. Here we conducted a case study of a child with spinal muscular atrophy type 1 experiencing substantial hepatitis after receiving onasemnogene abeparvovec, undertaking long- and short-read metagenomic sequencing of liver tissue. We identified manufacturing plasmid sequences with complex structures and recombination. Vector genomes had extensive disruption and concatemerization as well as numerous vector-human fusion junctions. We also identified human betaherpesvirus 6B in the liver. Further work and investigation of more patients is needed to establish whether the presence of manufacturing plasmid sequences or helper viruses contribute to the formation of these complex concatemeric DNA structures in the liver, and whether these are a factor in the development of liver toxicity after AAV gene therapy.
Authors
- Oscar Enrique Torres Montaguth (ORCID: https://orcid.org/0000-0003-4234-6037)
- John R. Counsell (ORCID: https://orcid.org/0000-0001-9208-101X)
- A. K. Dhawan
- Sarah Buddle (ORCID: https://orcid.org/0000-0002-4738-9469)
- Leanne M. Kermack
- Rajvinder Karda (ORCID: https://orcid.org/0000-0001-9821-483X)
- Sofia Morfopoulou (ORCID: https://orcid.org/0000-0001-8181-4548)
- Jasmaine Lee
- Hannah L. Macpherson (ORCID: https://orcid.org/0000-0002-9535-4025)
- Judith Breuer (ORCID: https://orcid.org/0000-0001-8246-0534)
- Patawee Asamaphan (ORCID: https://orcid.org/0000-0002-2539-0944)
- R. ORTON
- Georgios Ilia
- Adam D. Hunter
- A Kopeć
- Neil Sebire
- ISARIC4C Investigators
- Giovanni Baranello
- Dee Davis
- Laura Atkinson
- Luis Campos
- Mariacristina Scoto
- Li-An K. Brown
- Simon N. Waddington
- Francesco Muntoni
- J. Kenneth Baillie
- Holly Belfield
- Malcolm Gracie Semple
Institutions
- Roslin Institute (GB)
- University of Liverpool (GB)
- Great Ormond Street Hospital (GB)
- Great Ormond Street Hospital for Children NHS Foundation Trust (GB)
- Edinburgh Royal Infirmary (GB)
- National Institute for Health and Care Research (GB)
- Alder Hey Children's NHS Foundation Trust (GB)
- MRC Prion Unit (GB)
- MRC University of Glasgow Centre for Virus Research (GB)
- Centre for Inflammation Research (GB)
- King's College Hospital (GB)
- Institute of Infection and Immunity (CA)
- University College London (GB)
- Medical Research Council (GB)
- University of Edinburgh (GB)
Publication Details
- Journal
- Nature Medicine
- Published
- 2026-01-16
- DOI
- https://doi.org/10.1038/s41591-025-04073-z
- Citations
- 1
- Primary Topic
- Virus-based gene therapy research
- Type
- article
- Field-Weighted Citation Impact
- 30.93
Funders
- Wellcome Trust
- King's College Hospital NHS Foundation Trust
- Dravet Syndrome UK
- LifeArc
- National Institute for Health and Care Research
- King's College London
- University of Glasgow
- University College London Hospitals NHS Foundation Trust