Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors

Significance To develop a cure for HIV-1, it is necessary to understand how infected cells persist despite treatment. Integrated HIV DNA (proviruses) can be distinguished by their sites of integration into the host genome and by their proviral sequence. We applied multiple-displacement amplification (MDA) to single proviruses isolated from blood and lymph nodes to determine their integration sites and full-length sequences. We found that identical subgenomic HIV-1 sequences can result from either clonal expansion or from genetic bottlenecks that occurred with transmission or with the emergence of drug resistance mutations. Furthermore, we show this MDA approach can be used to infer intact ancestral HIV-1 sequences from the archives of defective ones, providing an approach for investigations of HIV-1 evolution in vivo.