HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: A view from the clinic and ex vivo
Introduction
In a human immunodeficiency virus (HIV)-infected individual, the rapid turnover, high-mutation rate, and high frequency of recombination result in a diverse viral population. Unlike eukaryotic DNA polymerases, HIV-1 reverse transcriptase (RT) has no proofreading ability, and its error rate has been estimated to be between 10−4 and 10−5 mutations per nucleotide and replication cycle (reviewed in Menéndez-Arias, 2002, Svarovskaia et al., 2003). If one assumes that 109 to 1010 viral particles are produced each day in an infected person, then these particles must be the product of at least 107 to 108 replication cycles. Given the length of the HIV-1 genome (approximately 10,000 nucleotides), it is likely that every possible single point mutation (and probably many double mutations) will occur at least once each day in an infected individual (Coffin, 1995). Although specific combinations of multiple mutations may be rare, it is clear that the degree of potential genetic change drives the diversification of HIV-1 in response to the selective pressure of host immune responses or antiretroviral therapy. When we talk about divergent, rapidly changing HIV-1 variants, we frequently use the term ‘quasispecies.’ This term was originally coined by Eigen (Eigen, 1971, Eigen and Schuster, 1979) to designate closely related but distinguishable genomes that undergo continuous genetic variation, competition, and selection.
The introduction of potent antiretroviral therapy has made an enormous contribution to the control of HIV infection and AIDS. Current treatments target viral enzymes such as RT and protease (PR), as well as the envelope glycoprotein gp41. During 2007 the United States Food and Drug Administration (FDA) approved a pair of first-in-class antiretrovirals for HIV-infected patients with drug-resistant disease: maraviroc is the first chemokine receptor antagonist, and raltegravir is the first integrase inhibitor. Despite the success of potent combination regimens, the development of HIV-1 drug resistance constitutes a major hurdle for the long-term efficacy of current antiretroviral therapy (Menéndez-Arias, 2002). The evolutionary pathways leading to resistance have been widely studied for many antiretroviral drugs. In general, drug resistance mutations confer a fitness cost, in part because the mutations associated with drug resistance may decrease the enzymatic efficiency of the target proteins.
Fitness is a complex parameter that describes the replicative adaptability of an organism to its environment. What Charles Darwin called “natural selection, or the preservation of favored races in the struggle for life” was called “survival of the fittest” by a 19th-century contemporary, Herbert Spencer (Goudsmit, 2004). A specific virus population is fitter than another when it is more able to multiply and spread, given certain conditions. However, those fittest under one set of conditions can quickly be supplanted if a new set of conditions suddenly prevails, such as when the inner environment of an HIV-infected person changes as a result of taking (or changing) antiretroviral drugs. In this case, the drug-resistant virus that prevails might not have survived under the old conditions, but it is now in the right place at the right time, while all drug-sensitive viruses will seemingly not survive (Goudsmit, 2004). Thus, viruses change as fast as conditions change. For HIV (and other RNA viruses), an experimentally useful approach to fitness is its relative ability to produce stable infectious progeny in a given environment (e.g., cell culture, bloodstream) (for reviews, see Domingo and Holland, 1997, Domingo et al., 1999). Evolution of resistance to antiretroviral drugs is characterized by significant fitness costs and subsequent repair strategies that include compensatory mutations in the targeted gene, as well as other molecular mechanisms that improve fitness. Recognition of virological and clinical correlates of viral fitness is becoming more and more important in clinical practice, and in this review we discuss the relevant techniques used to measure fitness, focusing on the effect of RT inhibitor resistance mutations in viral fitness and their implications in the management of HIV infection.
Section snippets
Currently used techniques for estimating the fitness of drug-resistant HIV variants
The term viral fitness refers to the ability of a virus to produce infectious progeny under specific environmental circumstances (i.e. a defined host cell system, host, or host population). Viral fitness depends on multiple viral and host factors. First, all events involved in the virus life cycle could have an impact on replication capacity: (i) target cell entry, (ii) reverse transcription, (iii) integration, (iv) gene expression, (v) assembly, (vi) budding, and (vii) maturation. Second,
Fitness and development of resistance to RT inhibitors
At present, the RT inhibitor family is composed of eight nucleoside/nucleotide and three nonnucleoside inhibitors that bind to distinct sites within the polymerase. Nucleoside analogue inhibitors were the first drugs capable of fighting HIV-1 infection and are still a component of most HAART regimens.
It is widely accepted that, in general terms, mutations conferring resistance to RT inhibitors do not reduce fitness to the same extent as those conferring resistance to PR inhibitors. This may
Molecular mechanisms leading to recovery of fitness during treatment with RT inhibitors
In general, initial or primary mutations modify the active sites of the viral enzymes, followed by stepwise accumulation of secondary or compensatory mutations leading to restored enzyme functionality (Gallant, 2005). Given the extreme plasticity of the HIV-1 genome, genetic changes at a distance from the target domains could contribute to the process of drug resistance. Similarly, mutations in genomic regions outside the RT may compensate for reductions in replication capacity conferred by
The role of viral fitness in HIV pathogenesis
The development of clinical symptoms and progression in HIV-1-infected patients is the manifestation of the effects of the pathogenic viral life cycle of HIV-1. Individual variants of HIV-1 vary widely in features that determine viral fitness and virulence. It might seem reasonable to infer that the greater the viral fitness, the greater the pathogenicity.
In the absence of drug pressure, the HIV-1 env gene may be under the greatest selective pressure due to the humoral immune response (Richman
The challenge of drug-resistant HIV: is there any possible clinical advantage?
This has remained an intriguing question for many years, and has been only partially answered by scattered data. One set of data refers to HIV-1 harboring the lamivudine- and emtricitabine-resistant mutation M184V. This substitution has been shown to have favorable effects on the susceptibility of some other NRTIs and can delay clinical and immunologic progression by decreasing viral fitness. Although it is always better not to have any drug resistance so that lamivudine and emtricitabine are
Conclusions
All currently available antiretroviral drugs select for genotypic mutations that confer reduced phenotypic drug susceptibility. There is substantial in vitro and in vivo evidence that antiretroviral therapy selects for mutations that impair the inherent ability of HIV to replicate. Throughout this review, we have documented the impact that mutations associated with resistance to RT inhibitors have on viral fitness. Most of the replication capacity data has been obtained in vitro by using pol
Acknowledgments
We thank S. Elena for his critical review of the manuscript and M.C. Puertas for her help with the illustrations. Work in the laboratory of J.M.-P. is supported by the Spanish Ministry of Education and Science through grants SAF2004-06991 and SAF2007-64696, the Spanish AIDS network “Red Temática Cooperativa de Investigación en SIDA” (RD06/0006), and the Fundación para la Investigación y Prevención del Sida en España (FIPSE) through grants 36356/05, 36523/05, and 36621/06. MAM was supported by
References (190)
- et al.
A novel small reporter gene and HIV-1 fitness assay
J. Virol. Methods
(2006) - et al.
Drug-resistant mutants of HIV-1 in patients exhibiting increasing CD4 cell count despite virological failure of highly active antiretroviral therapy
AIDS
(2001) - et al.
Cross-resistance among nonnucleoside reverse transcriptase inhibitors limits recycling efavirenz after nevirapine failure
AIDS Res. Hum. Retroviruses
(2002) - et al.
Mutants of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase resistant to nonnucleoside reverse transcriptase inhibitors demonstrate altered rates of RNase H cleavage that correlate with HIV-1 replication fitness in cell culture
J. Virol.
(2000) - et al.
Sorting out the complexities of HIV-1 fitness
AIDS
(2003) - et al.
Reduced replication of 3TC-resistant HIV-1 variants in primary cells due to a processivity defect of the reverse transcriptase enzyme
EMBO J.
(1996) - et al.
Adherence-resistance relationships for protease and non-nucleoside reverse transcriptase inhibitors explained by virological fitness
AIDS
(2006) - et al.
The role of viral fitness in HIV pathogenesis
Curr. HIV/AIDS Rep.
(2005) - et al.
Evolution of phenotypic drug susceptibility and viral replication capacity during long-term virologic failure of protease inhibitor therapy in human immunodeficiency virus-infected adults
J. Virol.
(2002) - et al.
Wide variation in pro/pol replication capacity in recently transmitted HIV-1 is conferred in part by protease inhibitor resistance mutations
Antivir. Ther.
(2003)