LVV SMRTcap reveals extensive proviral variation in lentiviral vector-transduced CAR T cells

Abstract Lentiviral vectors are commonly used to introduce chimeric antigen receptor transgenes into T cells, but routine assays quantify vector copy number or integration sites without sequencing full-length integrated vectors. HIV-1 proviruses often acquire large deletions and cytidine deaminase-driven hypermutation; whether similar variation occurs in therapeutic lentiviral vectors is unclear. We adapted a novel long-read capture approach to enrich long fragments spanning vector DNA and adjacent human sequence, enabling simultaneous integration-site mapping and proviral integrity analysis with single-molecule resolution. In research-grade CAR T cells produced with an experimental, transient-transfection lentiviral vector workflow, 40% of integrated vectors carried recurrent deletions that removed the internal promoter or parts of the chimeric antigen receptor cassette. The dominant promoter deletion was present in the viral stock. In clinical chimeric antigen receptor T cell products, promoter deletions were less frequent, but detectable pre-infusion and post-infusion. Across datasets we observed widespread G-to-A substitutions consistent with restriction factor editing, including changes predicted to introduce premature stop codons within the transgene open reading frame. Our method reveals proviral variants invisible to standard quality-control assays and provides a framework to improve vector production and monitor transgene integrity in clinical products. Competing Interest Statement M.L.S is co-founder and Chief Executive Officer (CEO) of Clareo Biosciences, Inc.; however, the work presented here is unrelated to Clareo Biosciences. J.A.F.: Patents and intellectual property in T-cell-based cancer immunotherapy with royalties; funding from Tmunity Therapeutics and Danaher Corporation; consultancy with Retro Biosciences; scientific advisory board memberships with Cartography Bio, Shennon Biotechnologies Inc., CellFe Biotech, OverT Bio, Inc., and Tceleron Therapeutics, Inc.