Multiplex viral tropism assay in complex cell populations with single-cell resolution

Gene therapy constitutes one of the most promising mode of disease treatments. Two key properties for therapeutic delivery vectors are the transduction efficiency (how well the vector delivers therapeutic cargo to desired target cells) and specificity (how well it avoids off-target delivery into the other unintended cells within the body). Here we developed a novel technology that enables multiplex measurement of transduction efficiency and specificity, particularly by measuring how libraries of delivery vectors transduce libraries of diverse cell types. We demonstrated that pairing high-throughput measurement of AAV identity with high-resolution single-cell RNA transcriptomic sequencing maps how natural and engineered AAV variants transduce individual cells within human cerebral and ocular organoids. This library-on-library technology is important for determining the safety and efficacy of therapeutic delivery vectors.