ReviewHIV-1 drug resistance and resistance testing
Introduction
The world has embarked on a fast-track strategy to achieve the Joint United Nations Programme on HIV/AIDS 90-90-90 target and reduce the number of new HIV infections to 500,000 per year by 2020. Achieving the 90-90-90 target requires that 90% of all people living with HIV will have been diagnosed, 90% of all people with known HIV infection will be receiving antiretroviral (ARV) therapy (ART), and 90% of all people receiving ART will have a suppressed viral load. To meet the targeted reduction in new infections, the incidence must decline over four-fold from 2.1 million in 2015 (UNAIDS, 2014, UNAIDS, 2016). To help achieve these goals, the World Health Organization (WHO) in 2016 recommended that all HIV-infected individuals should begin ART as soon after diagnosis as possible (Treat All) and that pre-exposure prophylaxis (PrEP) should be considered for persons at high risk of HIV infection (World Health Organization, 2016b). While the successful implementation of these recommendations will reduce the number of new HIV infections, the dramatic increase in ARV use will likely increase the prevalence of acquired drug resistance (ADR) in treated individuals and transmitted drug resistance (TDR) in newly infected individuals (Phillips et al., 2014b).
Whereas the principles of drug resistance are similar in all populations, differences in access to diagnostic testing and to many ARVs in low- and middle-income countries (LMICs) necessitate different approaches to the management of TDR and ADR. In most LMICs, HIV drug resistance (HIVDR) testing is neither feasible nor routinely recommended for patients receiving ART. Nonetheless, understanding the principles and mechanisms of HIVDR is useful to developing appropriate surveillance, informing treatment algorithms, and managing particularly difficult clinical cases. In high-income countries where drug resistance testing is part of routine care, such an understanding can also help clinicians prevent virological failure (VF) and accumulation of further HIVDR by selecting the most efficacious regimens for individual patients infected with drug-resistant viruses.
Although twenty-seven ARVs belonging to six classes have been approved for HIV-1 treatment, eleven of these ARVs are no longer available, no longer recommended, or rarely used, and thus will not be reviewed. We will instead focus on the 16 more commonly used ARVs belonging to 5 drug classes: 5 nucleoside reverse transcriptase inhibitors (NRTIs), 4 non-nucleoside reverse transcriptase inhibitors (NNRTIs), 3 protease inhibitors (PIs), 3 integrase strand transfer inhibitors (INSTIs) and one CCR5 antagonist (Table 1). In this review, we will not distinguish between ritonavir (RTV) and cobicistat pharmacoenhancement nor between the tenofovir prodrugs, tenofovir alafenamide fumarate (TAF) and tenofovir disoproxil fumarate (TDF), as their patterns of cross-resistance are similar (Gallant et al., 2015, Margot et al., 2015). Additionally, specific fixed dose combinations (FDCs) will not be addressed due to the rapid evolution of generic ARV formulations that currently dominate the ARV marketplace in LMICs (Waning et al., 2010).
Section snippets
Mechanisms of HIV-1 drug resistance
HIV-1 genetic variability results from the high rate of HIV-1 reverse transcriptase (RT) processing errors, recombination when more than one viral variants infect the same cell, and the accumulation of proviral variants during the course of infection (Abram et al., 2010, Coffin, 1995, Levy et al., 2004, Mansky, 1996). Although most HIV-1 infections are initiated by a single viral variant (Keele et al., 2008), innumerable variants (or quasispecies) related to the initial transmitted virus emerge
HIV-1 drug resistance testing
HIV-1 drug resistance testing can be performed phenotypically or genotypically. Phenotypic in vitro susceptibility assays measure ARV susceptibility in cell culture. Susceptibility is usually reported as the ARV concentration that inhibits HIV-1 replication by 50% (IC50). The IC50 of a patient's virus is compared to that of a drug-susceptible reference strain, and expressed as a ratio, referred to as fold change, of the IC50 of the patient's virus relative to the reference control. Nearly all
Drug resistance test interpretation
Understanding the results of drug resistance tests is one of the most difficult tasks facing HIV care providers. There are many DRMs and they arise in complex patterns that cause varying levels of drug resistance. Some DRMs are responsible for just low levels of resistance to a drug but would not be a contraindication to using that drug if the remaining components of a patient's regimen were fully active. Further complicating genotypic resistance test interpretation is the recognition that SGRT
NRTI resistance mutations
There are two genetic mechanisms of NRTI resistance: (i) discriminatory mutations that enable RT to distinguish between dideoxy-NRTI chain terminators and the cell's own dNTPs, thus preventing NRTIs from being incorporated into viral DNA; and (ii) primer unblocking mutations that facilitate the phosphorylytic excision of an NRTI-triphosphate from viral DNA. Unblocking mutations are also referred to as thymidine analog mutations (TAMs) because they are selected by the thymidine analogs AZT and
NNRTI resistance mutations
The NNRTIs have a relatively low genetic barrier to resistance. To develop high-level resistance, one DRM in the case of nevirapine (NVP), one to two DRMs in the case of efavirenz (EFV), and two DRMs in the case of etravirine (ETR), are required (Melikian et al., 2014, Sluis-Cremer and Tachedjian, 2008, Vingerhoets et al., 2010). Although rilpivirine (RPV) has a similar structure to ETR, its genetic barrier to clinically significant resistance is lower than ETR because it is administered at a
PI resistance mutations
Boosted lopinavir (LPV/r), boosted atazanavir (ATV/r), and DRV/r are the three most commonly used PIs. ATV/r and DRV/r are the two most commonly recommended PIs in high-income countries (Panel on Antiretroviral Guidelines for Adults and Adolescents, 2016). LPV/r is widely used in second-line regimens in LMICs. LPV/r and DRV/r have high genetic barriers to resistance in that multiple DRMs are required before antiviral activity is compromised (de Meyer et al., 2008, King et al., 2007). LPV/r and
INSTI resistance mutations
Fig. 5 shows the most common INSTI-associated DRMs. More information is known about the DRMs selected by raltegravir (RAL) because it was the first FDA-approved INSTI. RAL resistance occurs by three main, often overlapping mutational pathways with the following signature DRMs: N155H ± E92Q; Q148H/R/K ± G140S/A; and Y143C/R (Blanco et al., 2011, Geretti et al., 2012). The presence of two of these signature DRMs is usually associated with > 150-fold reduced RAL susceptibility. Although each of these
HIV-1 tropism
Maraviroc allosterically inhibits gp120 Env of CCR5 (R5)-tropic HIV-1 strains from binding to the seven-transmembrane G protein-coupled R5 receptor (Tan et al., 2013). Whereas HIV-1 gp120 binds to the N-terminus and second extracellular loop region of R5, maraviroc binds to a pocket formed by the transmembrane helices (Tan et al., 2013). In patients receiving R5 inhibitors, the most common mechanism of VF is the expansion of pre-existing CXCR4 (X4) tropic viruses that are intrinsically
Effect of subtype on HIV-1 drug resistance
Subtype B viruses comprise > 95% of HIV-1 strains in the U.S. and > 60% of strains in Europe but only about 10% of strains worldwide. Subtype B viruses played an outsized role in the earliest ARV development efforts and in the earliest studies of ARV resistance. Nonetheless, existing ARVs are equally effective at treating subtype B and non-subtype B viruses (Bannister et al., 2006, Geretti et al., 2009, Scherrer et al., 2011). Moreover, each of the mutations that cause resistance in subtype B
Transmitted drug resistance
TDR is a type of HIVDR that occurs when primary HIV infection is caused by a DRM-bearing virus. The prevalence of TDR by SGRT is about 12% to 24% in the U.S., and 10% in Europe (Boden et al., 1999, Booth and Geretti, 2007, Kassaye et al., 2016, Li et al., 2016, Little et al., 2002, Parker et al., 2007, Rhee et al., 2015a, Shet et al., 2006, Simon et al., 2002, Weinstock et al., 2000, Weinstock et al., 2004). While limited data suggest that the prevalence is below 5% in most of the LMICs in
Acquired drug resistance
In most studies, > 70–80% of patients with VF develop ADR (Jordan et al., 2016, Kumarasamy et al., 2015, Paton et al., 2014, Prosperi et al., 2011, Schultze et al., 2015, Second-Line Study Group et al., 2013, TenoRes Study, 2016). M184V/I is usually selected as the initial NRTI DRM for cytidine analog (3TC or FTC) containing regimens. Among patients receiving an NNRTI-containing regimen, one or more NNRTI DRMs are also typically seen early in VF. Other NRTI DRMs usually occur after M184V/I and
PrEP and drug resistance
As of September 2015, the World Health Organization has recommended TDF-containing pre-exposure prophylaxis (PrEP) for men who have sex with men, heterosexually-active men and women, and intravenous drug users considered at substantial risk for HIV-1 infection (World Health Organization, 2015c). Although the risk of HIV-1 infection is markedly reduced in patients receiving PrEP, those who become infected are theoretically at high risk of developing drug resistance. In a systematic review and
HIV drug resistance surveillance
Between 2004 and 2013, the World Health Organization recommended the surveillance of TDR among recently infected populations (Bennett et al., 2008, Myatt and Bennett, 2008, Shafer et al., 2008). The WHO-recommended method for surveillance of TDR limited enrollment to ARV-naïve populations likely to have been recently infected, and assessed for the presence of 93 non-polymorphic DRMs found in all subtypes, termed surveillance DRMs (SDRMs) (Bennett et al., 2009, Shafer et al., 2008).
In 2015, WHO
Summary and conclusions
An unprecedented scale-up of ART has been observed in the last 10 years: at the end of 2015, 17 million people were receiving antiretroviral therapy. However, the HIVDR emergence associated with increased ART use can compromise the effectiveness of antiretroviral drugs. Resistance is an inevitable consequence of any interventions that, through the use of ARVs, aim to reduce mortality, morbidity and HIV transmission. While concern for resistance should never limit ARV access for all HIV-infected
Potential conflicts of interest
DSC receives research funding through the Bristol-Myers Squibb Virology Fellows Research Program. RWS is a consultant for Celera, and receives research funding from Roche Molecular, Gilead Sciences, Bristol-Myers Squibb, and Merck. The other authors have no potential conflicts of interest to disclose.
Disclaimer
The opinions and conclusions in this article are those of the authors and do not reflect those of the respective institutions, including the World Health Organization.
Acknowledgments and funding
This work was supported by a KL2 Mentored Career Development Award of the Stanford Clinical and Translational Science Award to Spectrum [grant number NIHKL2 TR 001083 and NIH UL1 TR 001085 to DSC], by the National Institutes of Health [grant number R01 AI068581 to RWS], by CFAR [grant number 1P30A142853 to MRJ] and by the Christine E. Driscoll O'Neill and James M. Driscoll, Driscoll-O'Neill Charitable Foundation [support for MRJ].
References (227)
- et al.
Baseline HIV-1 resistance, virological outcomes, and emergent resistance in the SECOND-LINE trial: an exploratory analysis
Lancet HIV
(2015) - et al.
Single-dose tenofovir and emtricitabine for reduction of viral resistance to non-nucleoside reverse transcriptase inhibitor drugs in women given intrapartum nevirapine for perinatal HIV prevention: an open-label randomised trial
Lancet
(2007) - et al.
Rilpivirine versus efavirenz with two background nucleoside or nucleotide reverse transcriptase inhibitors in treatment-naive adults infected with HIV-1 (THRIVE): a phase 3, randomised, non-inferiority trial
Lancet
(2011) - et al.
Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease
Structure
(2007) - et al.
Virological monitoring and resistance to first-line highly active antiretroviral therapy in adults infected with HIV-1 treated under WHO guidelines: a systematic review and meta-analysis
Lancet Infect. Dis.
(2009) - et al.
Global trends in antiretroviral resistance in treatment-naive individuals with HIV after rollout of antiretroviral treatment in resource-limited settings: a global collaborative study and meta-regression analysis
Lancet
(2012) - et al.
Effect of pretreatment HIV-1 drug resistance on immunological, virological, and drug-resistance outcomes of first-line antiretroviral treatment in sub-Saharan Africa: a multicentre cohort study
Lancet Infect. Dis.
(2012) - et al.
Nucleotide substitution patterns can predict the requirements for drug-resistance of HIV-1 proteins
Antivir. Res.
(1996) - et al.
Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication
J. Virol.
(2010) - et al.
Impact of primary elvitegravir resistance-associated mutations in HIV-1 integrase on drug susceptibility and viral replication fitness
Antimicrob. Agents Chemother.
(2013)