To better design therapeutic approaches that prevent the evolution of drug resistance in HIV-1, it is important to understand how drug resistance spreads and establishes within a patient. There is mounting evidence that intrahost viral evolution is a non-homogenous process within the body and therefore must be understood spatially and temporally.
We examined >3300 single-genome sequences from four macaques infected with RT-SHIV, a SIV with an HIV reverse transcriptase (RT). Macaques were given monotherapies to induce the emergence of drug resistance within RT between weeks 12-20 post-infection. Both viral RNA and DNA (vRNA and vDNA) were sampled from four different compartments (lymph node, vagina, gut and PBMC) in addition to plasma vRNA between 13 and 30 weeks post-infection. Compartmentalization was assessed using the variance partitioning statistic ΦST from population genetics.
Acquisition of drug resistance is a highly dynamic process with periods of stasis. Although compartmentalization is observed, both natural selection within and migration between compartments are important for establishing drug resistant lineages. We observe differential dynamics between compartments, with the gut being particularly notable. In all four macaques, gut vRNA has the greatest rate of turnover, both compared to gut vDNA and to vRNA in other tissues. In addition, drug resistance increases in frequency more quickly in gut vDNA compared to vDNA other compartments. We find that RT-SHIV does not acquire detectable drug resistance immediately after treatment initiation, but takes more than one week. Upon treatment removal, plasma vRNA does not change significantly over the following 6 weeks, suggesting that drug resistance can have limited fitness cost.
Drug resistance evolution depends on the interactions between partially independent compartments, some of which have SHIV populations that show more persistence than others or respond more quickly to pressures imposed by treatment. Characterizing the differences and relationships between the compartments could be important in understanding how multidrug resistance emerges, particularly outside of the blood, and could inform the administration of treatment. That many of these findings are reliant on the sampling scheme of both vDNA and vRNA, across compartments and time demonstrates the importance of varied sampling to obtain a more complete picture of how intrahost evolution proceeds.