Background The advent of near full-length (NFL) HIV-1 proviral genome sequencing greatly expanded our understanding of the quality of the viral reservoir, revealing that only 2-5% of the persistent proviruses in ART-treated individuals can be considered genome-intact. However, current NFL assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. We developed a long-read sequencing assay to characterize many proviral genomes in parallel from bulk DNA. Methods The sensitivity of the long-read assay was determined on a DNA dilution series of J-Lat in uninfected Jurkat ranging from 80,000 to