Aberrant strand transfer events across multiple stages of reverse transcription shape the heterogeneous landscape of the HIV-1 reservoir

Curative interventions for HIV-1 seek to reduce the size of the replication-competent viral reservoir. A comprehensive understanding of the composition of defective proviral sequences is essential for refining the methods used to characterize and measure this replication-competent viral reservoir. An in-depth analysis of proviral sequences with a single internal deletion was performed to better understand the mechanisms behind their origin. An in-house full-length individual proviral sequencing technique was adopted for HIV-1 sequencing. This sequence dataset was further supplemented with sequences from two published studies, adding up to 395 proviral sequences. Based on the deletion junction profile of each individual provirus, six hypothetical mechanisms of aberrant strand transfer during reverse transcription were modelled. Our findings show that proviral sequences with deletions do not exclusively result from erroneous strand transfer events during minus-strand synthesis but emerge through distinct mechanisms throughout the reverse transcription process.