Checklist for studies of HIV drug resistance prevalence or incidence: rationale and recommended use.

HIV drug resistance (HIVDR) is a major challenge to the effectiveness of antiretroviral therapy. Global efforts in addressing HIVDR require clear, transparent, and replicable reporting in HIVDR studies. We describe the rationale and recommended use of a checklist that should be included in reports of HIVDR incidence and prevalence. After preliminary consultations with experts on HIVDR and establishing the need for guidance on HIVDR reporting, we used a sequential, explanatory, mixed methods approach to create the checklist; together with the accompanying articles, the checklist was reviewed by the authors and validated externally. The checklist for studies on HIVDR prevalence or incidence (CEDRIC-HIV) includes 15 recommended items that would enhance transparency and facilitate interpretation, comparability, and replicability of HIVDR studies. CEDRIC-HIV will help authors of HIVDR studies prepare research reports and assist reviewers and editors in assessments of completeness of reporting. The checklist will also facilitate statistical pooling and interpretation of HIVDR data.

The S230R Integrase Substitution Associated With Virus Load Rebound During Dolutegravir Monotherapy Confers Low-Level Resistance to Integrase Strand-Transfer Inhibitors.

Background: Dolutegravir (DTG) is an integrase strand-transfer inhibitor (INSTI) used for treatment of human immunodeficiency virus (HIV)-infected individuals. Owing to its high genetic barrier to resistance, DTG has been clinically investigated as maintenance monotherapy to maintain viral suppression and to reduce complication and healthcare costs. Our study aims to explain the underlying mechanism related to the emergence of a S230R substitution in patients who experienced virologic failure while using DTG monotherapy. Methods: We evaluated the effect of the S230R substitution in regard to integrase enzyme activity, viral infectivity, replicative capacity, and susceptibility to different INSTIs by biochemical and cell-based assays. Results: The S230R substitution conferred a 63% reduction in enzyme efficiency. S230R virus was 1.29-fold less infectious than wild-type virus but could replicate in PM1 cells without significant delay. Resistance levels against DTG, cabotegravir, raltegravir, and elvitegravir in tissue culture were 3.85-, 3.72-, 1.52-, and 1.21-fold, respectively, in virus with the S230R substitution. Conclusions: Our data indicate that the S230R substitution is comparable to the previously reported R263K substitution in some respects. Virologic failure during DTG monotherapy can occur through the development of the S230R or R263K mutation, without the need for high-level DTG resistance.

Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data.

OBJECTIVE: To reconstruct dates of HIV infection by the coalescent analysis of longitudinal next-generation sequencing (NGS) data. DESIGN: The coalescent predicts the time that has elapsed since the most recent common ancestor (MRCA) of a population. Because HIV tends to undergo severe bottlenecks upon transmission, the MRCA may be a good predictor of the time of infection. NGS provides an efficient means for performing large-scale clonal sequencing of HIV populations within patients, and the ideal raw material for coalescent analysis. METHODS: Baseline and follow-up plasma samples were obtained from 19 individuals enrolled into the Montréal Primary HIV Infection cohort. Dates of infection were initially estimated at baseline from nongenetic data (clinical and serological markers and patient questionnaires). HIV RNA was extracted and seven regions of the genome were amplified, subjected to parallel-tagged 454 pyrosequencing, and analyzed using the software package BEAST. RESULTS: Mean estimates of the time to the MRCA per patient were significantly correlated with nongenetic estimates (Spearman's ρ = 0.65, P = 4.4 × 10(-3)). The median absolute difference between coalescent and nongenetic date estimates was smallest (median 29.4 days) for highly variable regions of the HIV genome such as env V3, and greater (median 114.9 days) for more conserved regions such as pol. CONCLUSION: This application of NGS represents an important advancement, not only because accurate estimates of dates of infection can be derived retrospectively from archived specimens, but also because each analysis is patient-specific and, therefore, robust to variation in rates of HIV evolution.

Isolation of drug-resistant mutant HIV variants using tissue culture drug selection.

The life cycle of HIV-1 can be affected in different manners by the various classes of antiviral agents. Genetic heterogeneity is a characteristic of this virus, which contributes significantly to the ability of the virus to generate mutations which overcome the efficacy of the drug therapy. The selection of drug resistant mutants in vitro can be readily accomplished by maintaining the virus in a state of sub-optimal growth, regulated by slowly increasing the amount of drug pressure applied. This technique is thought to mimic the consequences of drug therapy in patients. Therefore, in this way, novel compounds can be assessed for their selection profile in order to preview the likelihood of emergence of HIV-1 drug resistance in future clinical trials. In addition, combinations of drugs can be investigated in the same manner.

HIV-1 genetic diversity in antenatal cohort, Canada.

We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylogenetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned. Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin. These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup.

[HIV drug resistance and optimization of antiviral treatment in resource-poor countries]. / Résistance du VIH aux antirétroviraux: conséquences pour les pays à faibles revenus.

HIV drug resistance has been associated with treatment failure in Western countries but the lessons learned can be useful in optimization of highly active antiretroviral treatment (HAART) in resource-poor settings. There is a need to improve access to HAART in such regions, but appropriate strategies must be rapidly implemented, such as adapted programs to facilitate adherence to therapy, rational use of genotypic drug resistance monitoring in specific situations, and use of alternative treatment regimens. The implications of HIV genetic diversity must also be considered in management of drug resistance.

The influence of protease inhibitor resistance profiles on selection of HIV therapy in treatment-naive patients.

Although protease inhibitors (PIs) have dramatically improved outcomes in HIV-infected patients, half still fail treatment with PI-based combination therapy. Genetic pressure from incomplete viral suppression rapidly selects for HIV variants with protease gene mutations that confer reduced susceptibility to PI drugs. A number of specific amino acid substitutions have been associated with PI resistance. However, high-level resistance to individual PIs requires the accumulation of several primary and secondary mutations, developing along drug-specific, step-wise pathways. HIV variants resistant to saquinavir and ritonavir usually contain L90M and V82A substitutions, respectively. Indinavir resistance may be linked to substitutions at positions 46 or 82. Resistance to nelfinavir is primarily associated with D30N but may alternatively be found with L90M. Resistance during exposure to amprenavir can follow development of I50V, which also may confer resistance to lopinavir. Failure during treatment with atazanavir is closely linked to 150L. The overlapping of these pathways can lead to multiple-PI resistance, limiting therapeutic options in antiretroviral-experienced patients. Reduced susceptibility to more than one PI is most likely to be associated with amino acid substitutions at six positions: 10, 46, 54, 82, 84 and 90. Other mutations (D30N, G48V, I50V or I50L) are relatively specific for particular PIs and are less likely to produce cross resistance. Certain resistance mutations selected by exposure to one PI may actually increase susceptibility to others. Patients newly diagnosed with HIV infection are increasingly found to harbour virus that is resistant to the more commonly used drugs. Newer PIs may select for mutations that result in less cross resistance with older agents.