Defective HIV DNA genomes provide ancestral relevance critical for phylogenetic inference of reservoir dynamics

During the course of infection, human immunodeficiency virus (HIV) maintains a stably integrated reservoir of replication-competent viruses within the host genome that are unaffected by antiretroviral therapy. Curative advancements rely heavily on targeting the anatomical reservoirs, though determinants of their evolutionary origins through phyloanatomic inference remain ill-supported through current sequencing and sequence analysis strategies. The vast replication-defective genomic landscape that comprises the HIV DNA population is often discarded in these evolutionary endeavors, despite key information regarding competent ancestry that can be gained from captured genomic regions outside the historically used viral envelope gene. Here, we describe the application of small-amplicon, single-cell DNA sequencing to blood and lymph node samples from a treatment-interrupted S[imian]IV-infected animal model and evaluate the contribution of genome coverage and inclusion on phylogenetic resolution and phyloanatomic inference. Findings from this study point to incomplete genomes as a significant source of phylogenetic information on movement of virus between tissue reservoirs during therapy.