Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cells

Cell therapies have yielded durable clinical benefits for patients with cancer, but the risks associated with the development of therapies from manipulated human cells are still being understood. For example, we currently lack a comprehensive understanding of the mechanisms of neurotoxicity observed in patients receiving T cell therapies, including recent reports of encephalitis caused by human herpesvirus 6 (HHV-6) reactivation[1][1]. Here, via petabase-scale viral RNA data mining, we examine the landscape of human latent viral reactivation and demonstrate that HHV-6B can become reactivated in human CD4+ T cells in standard in vitro cultures. Using single-cell sequencing, we identify a rare population of HHV-6 ‘super-expressors’ (~1 in 300-10,000 cells) that possess high viral transcriptional activity in chimeric antigen receptor (CAR) T cell culture before spreading to infect other cells in vitro . Through the analysis of single-cell sequencing data from patients receiving cell therapy products that are FDA-approved[2][2] or used in clinical studies[3][3],[4][4], we identify the presence of CAR+, HHV-6 super-expressor T cells in vivo . Together, our study implicates cell therapy products as a source of lytic HHV-6 reported in clinical trials[1][1],[5][5]–[7][6] and has broad implications for the design, production, and monitoring of cell therapies. ### Competing Interest Statement A.T.S. is a founder of Immunai and Cartography Biosciences and receives research funding from Allogene Therapeutics and Merck Research Laboratories. C.A.L. is a consultant to Cartography Biosciences. N.J.H. is a consultant for Constellation Pharmaceuticals. C.J.W. holds equity in BioNTech Inc and receives research funding from Pharmacyclics. G.G. receives research funds from IBM and Pharmacyclics. G.G. is a founder, consultant and privately held equity in Scorpion Therapeutics. M.V.M. is also an inventor on patents related to CAR-T cell therapies held by the University of Pennsylvania (some licensed to Novartis). M.V.M. holds equity in TCR2, Century Therapeutics, Genocea, Oncternal, and Neximmune, and has served as a consultant for multiple companies involved in cell therapies. M.J.K. has received research funding from Kite, BMS/Celgene, and Roche as well as honoraria from Mundipharama, Novartis, Takeda, Miltenyi, and Adicet. S.G. is a co-inventor on patent applications in the fields of cell or gene therapy for cancer. He is a consultant of TESSA Therapeutics, a member of the Data and Safety Monitoring Board (DSMB) of Immatics, and has received honoraria from Tidal, Catamaran Bio, Sanofi, and Novartis within the last 2 years. JCC and PGT have patent applications in the fields of T cell or gene therapy for cancer. G.Y., J.P., R.S., W.L., A.S., A.M., R.A., T.P., and H.D. are employees and shareholders of Allogene Therapeutics. A.K. is scientific co-founder of Ravel Biotechnology Inc., is on the scientific advisory board of PatchBio Inc., SerImmune Inc., AINovo Inc., TensorBio Inc. and OpenTargets, is a consultant with Illumina Inc. and owns shares in DeepGenomics Inc., Immunai Inc. and Freenome Inc. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-4 [5]: #ref-5 [6]: #ref-7