Molecular impact of the M184V mutation in human immunodeficiency virus type 1 reverse transcriptase

Cytidine deamination induced HIV-1 drug resistance

The HIV-1 Vif protein is essential for overcoming the antiviral activity of DNA-editing apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3 (APOBEC3) cytidine deaminases. We show that naturally occurring HIV-1 Vif point mutants with suboptimal anti-APOBEC3G activity induce the appearance of proviruses with lamivudine (3TC) drug resistance-associated mutations before any drug exposure. These mutations, ensuing from cytidine deamination events, were detected in >40% of proviruses with partially defective Vif mutants. Transfer of drug resistance from hypermutated proviruses via recombination allowed for 3TC escape under culture conditions prohibitive for any WT viral growth. These results demonstrate that defective hypermutated genomes can shape the phenotype of the circulating viral population. Partially active Vif alleles resulting in incomplete neutralization of cytoplasmic APOBEC3 molecules are directly responsible for the generation of a highly diverse, yet G-to-A biased, proviral reservoir, which can be exploited by HIV-1 to generate viable and drug-resistant progenies.

HIV-1 drug resistance mutations: an updated framework for the second decade of HAART

More than 200 mutations are associated with antiretroviral resistance to drugs belonging to six licensed antiretroviral classes. More than 50 reverse transcriptase mutations are associated with nucleoside reverse transcriptase inhibitor resistance including M184V, thymidine analog mutations, mutations associated with non-thymidine analog containing regimens, multi-nucleoside resistance mutations, and several recently identified accessory mutations. More than 40 reverse transcriptase mutations are associated with nonnucleoside reverse transcriptase inhibitor resistance including major primary and secondary mutations, non-polymorphic minor mutations, and polymorphic accessory mutations. More than 60 mutations are associated with protease inhibitor resistance including major protease, accessory protease, and protease cleavage site mutations. More than 30 integrase mutations are associated with the licensed integrase inhibitor raltegravir and the investigational inhibitor elvitegravir. More than 15 gp41 mutations are associated with the fusion inhibitor enfuvirtide. CCR5 inhibitor resistance results from mutations that promote gp120 binding to an inhibitor-bound CCR5 receptor or CXCR4 tropism; however, the genotypic correlates of these processes are not yet well characterized.

Identification of a novel resistance (E40F) and compensatory (K43E) substitution in HIV-1 reverse transcriptase

Background

HIV-1 nucleoside reverse transcriptase inhibitors (NRTIs) have been used in the clinic for over twenty years. Interestingly, the complete resistance pattern to this class has not been fully elucidated. Novel mutations in RT appearing during treatment failure are still being identified. To unravel the role of two of these newly identified changes, E40F and K43E, we investigated their effect on viral drug susceptibility and replicative capacity.

Results

A large database (Quest Diagnostics database) was analysed to determine the associations of the E40F and K43E changes with known resistance mutations. Both amino acid changes are strongly associated with the well known NRTI-resistance mutations M41L, L210W and T215Y. In addition, a strong positive association between these changes themselves was observed. A panel of recombinant viruses was generated by site-directed mutagenesis and phenotypically analysed. To determine the effect on replication capacity, competition and in vitro evolution experiments were performed. Introduction of E40F results in an increase in Zidovudine resistance ranging from nine to fourteen fold depending on the RT background and at the same time confers a decrease in viral replication capacity. The K43E change does not decrease the susceptibility to Zidovudine but increases viral replication capacity, when combined with E40F, demonstrating a compensatory role for this codon change.

Conclusion

In conclusion, we have identified a novel resistance (E40F) and compensatory (K43E) change in HIV-1 RT. Further research is indicated to analyse the clinical importance of these changes.

Development and evaluation of an oligonucleotide ligation assay for detection of drug resistance-associated mutations in the human immunodeficiency virus type 2 pol gene

Human immunodeficiency virus type 2 (HIV-2) is naturally resistant to several antiretroviral drugs, including all of the non-nucleoside reverse transcriptase inhibitors and the entry inhibitor T-20, and may have reduced susceptibility to some protease inhibitors. These resistance properties make treatment of HIV-2 patients difficult, with very limited treatment options. Therefore, early detection of resistance mutations is important for understanding treatment failures and guiding subsequent therapy decisions. With the Global Fund Initiative, a substantial number of HIV-2 patients in West Africa will receive antiretroviral therapy. Therefore, development of cheaper and more sustainable resistance assays, such as the oligonucleotide ligation assay (OLA), is a priority. In this study, we designed oligonucleotide probes to detect the Q151M mutation, associated with phenotypic resistance to zidovudine, didanosine, zalcitabine, and stavudine, and the M184V mutation, associated with phenotypic resistance to lamivudine and emtricitabine, in HIV-2. The assay was successfully developed and evaluated with 122 samples from The Gambia, Guinea Bissau, The Netherlands, and Sweden. The overall sensitivity of the assay was 98.8%, with 99.2% for Q151M and 98.4% for M184V. OLA results were compared with sequencing to give high concordances of 98.4% (Q151M) and 97.5% (M184V). OLA demonstrated a higher sensitivity for detection of minor variants as a mixture of wild-type and mutant viruses in cases when sequencing detected only the major population. In conclusion, we have developed a simple, easy-to-use, and economical assay for genotyping of drug resistance in HIV-2 that is more sustainable for use in resource-poor settings than is consensus sequencing.

Is HIV drug resistance a limiting factor in the development of anti-HIV NNRTI and NRTI-based vaginal microbicide strategies?

Antiviral drugs that act at specific sites within the HIV life cycle have important rationale for development as anti-HIV microbicides. However, to be effective, such drugs must act by directly interfering with viral enzymatic function and eliminate the ability of HIV to mediate infection. Compounds that are developed as microbicides must have high potency, and should ideally not be well absorbed from the vaginal cavity in order to minimize any potential problems of drug resistance. Such compounds should also be active over long periods of time and should be able to be combined with other active agents, in order to promote the concept of synergy, such as that which has been demonstrated in HIV therapeutic studies.

Challenges for the Clinical Development of New Nucleoside Reverse Transcriptase Inhibitors for HIV Infection

There is a need for new antiretroviral drugs with activity against HIV isolates resistant to currently available agents and improved short and long-term tolerability profiles. Clinical trial designs for nucleotide and nucleoside reverse transcriptase inhibitors (NRTIs) are restricted by the characteristics of these agents (for example, their cross-resistance, resistance threshold and interaction profiles), the ethical need to ensure that patients are not maintained on suboptimal regimens, and regulatory requirements (for example, with regards to trial designs and patient populations). For example, consideration of cross-resistance profiles must influence the way in which an NRTI in development is sequenced to minimize any impact on future treatment options. The resistance threshold is determined by the number of mutations required to diminish sensitivity to a given drug. Pharmacokinetic or pharmacodynamic interactions restrict how NRTIs may be combined during clinical development. Doses may be selected on the basis of results from short-term monotherapy studies in treatment-naive patients, but such studies cannot establish the long-term efficacy or tolerability of new agents used in combination regimens. Confirmatory studies in treatment-naive populations do not meet the medical and regulatory needs for clinical data in treatment-experienced populations, while studies in treatment-experienced populations are subject to numerous clinical and logistical difficulties. Intensification, switch and hybrid study designs all offer suitable approaches to the evaluation of NRTIs with novel resistance profiles. Switch studies are particularly useful for agents with resistance profiles that suggest a specific sequencing approach in treatment and for those with the potential, based on pharmacokinetic data, for interactions with other agents. The successful development of new NRTIs will depend upon a thorough appreciation of these many and complex issues, not only among those involved in the design of clinical studies, but also those contributing to their review and conduct.

Inhibition of HIV-1 reverse transcription: basic principles of drug action and resistance

Nucleoside and non-nucleoside analog inhibitors of HIV Type 1 reverse transcriptase are currently used in the clinic to treat infection with this retrovirus. Following their intracellular activation, nucleoside analogs act as chain terminators, while non-nucleoside analog reverse transcriptase inhibitors bind to a hydrophobic pocket in close proximity to the active site and inhibit the catalytic step. Compounds that belong to the two different classes of drugs are frequently administered in combination to take advantage of the different mechanisms of drug action. However, the development of drug resistance may occur under conditions of continued, residual viral replication, which is a major cause of treatment failure. This review addresses the interaction between different inhibitors and resistance-conferring mutations in the context of combination therapy with drugs that target the reverse transcriptase enzyme. Focus is placed on biochemical mechanisms and the development of future approaches.