Multiple Infections, Recombination, and Hypermutation During a 12-Month Prospective Study of Five HIV-1 Infected Individuals

The considerable HIV-1 genetic diversity has several implications for viral adaptive and evolutionary capabilities. Its genetic diversity is due to its high mutational rates derived from the error-prone viral reverse transcriptase activity, which generates highly heterogeneous viral populations. Moreover, genetic diversity can also increase due to intra- or intersubtype viral genomic recombination following multiple infections. This study examines HIV-1 intersubtype recombinant viruses and their increased genomic diversity over a 12-month period in five individuals from São Paulo state, Brazil. We collected peripheral blood mononuclear cells once every three months from selected participants at five distinct visits. Molecular clones of 1.15 Kbp fragments of the Pol polyprotein, spanning the protease and a portion of the reverse transcriptase (RT) genes, were generated by bulk PCR. Pol sequences were used for evolutionary analysis, including phylogenetics (using TnT), genetic diversity (using Highlighter), and hypermutation frequency (using Hypermut). Recombination detection experiments were conducted with a jumping profile-hidden Markov model (jpHMM), SimPlot++, and RDP5. We observed great genetic diversity and frequent recombination events in all patients. Furthermore, most of the patients presented hypermutations. These findings highlight the dynamic nature of HIV-1 genetic diversity, driven by frequent recombination and hypermutation, which can accelerate viral adaptation and diversification, underscoring the challenges for treatment, prevention, and disease control.