Direct Nanopore Sequencing Data for Single-stranded, Self-complementary rAAV and Parental Plasmids

Quality control strategies for rAAV vectors fall short in detecting contaminants and truncated genomes. These unwanted materials, which include viral and human DNA fragments related to the production process, can impact the efficacy and safety of these therapies. For this study, we used both MinION R9 and R10 flow cells to: 1) evaluate differences in sequencing ssAAV and scAAV genomes, 2) validate whether reads accurately reflect the vector genome population in preparations, and 3) assess the accuracy of nanopore sequencing across the inverted terminal repeats (ITRs). We find that the ONT platform excels in detecting vector heterogeneity and can serve as a rapid and lower cost alternative for analyzing rAAV vector genomes.