A superior knowledge of Integrase inhibitor modifications in HIV-1 population genetics with combination antiretroviral treatment (cART) is crucial for Integrase inhibitor planning eradication strategies. The appearance of genetically uniform virus populations and the lack of divergence after prolonged cART and cART interruption provide strong evidence that HIV-1 persists in long-lived cells infected before cART was initiated, that some of these infected cells may be capable of proliferation, and that on-going cycles of viral replication are not evident.
Anti-HIV compounds are highly effective for preventing the onset of AIDS but they do not cure infected individuals. Very low levels of virus remain detectable in the blood of most patients despite antiviral treatment and levels surge if treatment is stopped. It is crucial to understand why current treatments are not equipped to cure HIV infection so that new therapies addressing these shortcomings can be developed. By characterizing genetic sequences of HIV in patients before and during antiviral treatment, we found that the low levels of virus detected in the blood of treated patients did not result from newly infected cells but originated from cells, or the daughters of cells, that were already infected when treatment was initiated. This finding demonstrates that HIV present in blood after prolonged antiviral treatment is derived from cells infected prior to treatment which likely expanded over time through cell division. Such long lived, infected cells are likely the critical target for developing strategies to cure HIV infection.
The HIV-1 lifecycle includes rapid and error prone nucleic acid replication that results in large and genetically diverse virus populations in vivo. The consequences of broad HIV-1 genetic diversity include the presence of viral variants containing mutations that escape immune responses or confer resistance to individual antiretroviral agents. The use of antiretroviral agents in combination results in potent suppression of HIV-1 replication and reverses immune deficiency, at least in part. Despite the ability of cART to inhibit HIV-1 replication, treatment does not eradicate infection and plasma viremia persists at low levels in the majority of patients , . If cART is discontinued, viremia rapidly rebounds to pre-therapy levels. Determining the sources and mechanisms for viral persistence during cART and rebound after interruption is essential for designing strategies to eradicate infection.
The dynamics of HIV-1 decay after initiating cART can be divided into four phases. The first phase, reflecting rapid clearance of ca 90% of productively infected cells with half-life of 1–2 days, is followed by a more gradual clearance of infected cells with a half-life of 2–3 weeks. A study by Palmer, et al. described a third phase consisting of long-lived, perhaps latently-infected, cells with a half-life of 6–44 months as well as a fourth phase having a slope not significantly different from zero. The plateau in the fourth phase suggests that long-term cART fully inhibits HIV-1 replication and that the source of persistent viremia is either long-lived virus-expressing cells or activation of virus expression from latently-infected cells. In this regard, studies by Dinoso et al., McMahon et al., and Gandhi et al.