Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy

Characterization of residual plasma virus during antiretroviral therapy (ART) is a high priority to improve understanding of HIV-1 pathogenesis and therapy. To understand the evolution of HIV-1 pol and env genes in viremic patients under selective pressure of ART, we performed longitudinal analyses of plasma-derived pol and env sequences from single HIV-1 genomes. We tested the hypotheses that drug resistance in pol was unrelated to changes in coreceptor usage (tropism), and that recombination played a role in evolution of viral strains. Recombinants were identified by using Bayesian and other computational methods. High-level genotypic resistance was seen in ∼ 70% of X4 and R5 strains during ART. There was no significant association between resistance and tropism. Each patient displayed at least one recombinant encompassing env and representing a change in predicted tropism. These data suggest that, in addition to mutation, recombination can play a significant role in shaping HIV-1 evolution.     

Discordant responses to potent antiretroviral treatment in previously naive HIV-1-infected adults initiating treatment in resource-constrained countries: the antiretroviral therapy in low-income countries (ART-LINC) collaboration

OBJECTIVES: To assess the frequency of and risk factors for discordant responses at 6 months on highly active antiretroviral therapy (HAART) in previously treatment-naive HIV patients from resource-limited countries. METHODS: The Antiretroviral Therapy in Low-Income Countries Collaboration is a network of clinics providing care and treatment to HIV-infected patients in Africa, Latin America, and Asia. Patients who initiated therapy between 1996 and 2004, were aged 16 years or older, and had a baseline CD4 cell count were included in this analysis. Responses were defined based on plasma viral load (PVL) and CD4 cell count at 6 months as complete virologic and immunologic (VR(+)IR(+)), virologic only (VR(+)IR(-)), immunologic only (VR(-)IR(+)), and nonresponse (VR(-)IR(-)). Multinomial logistic regression was used to assess the association between therapy responses and clinical and demographic variables. RESULTS: Of the 3111 patients eligible for analysis, 1914 had available information at 6 months of therapy: 1074 (56.1%) were VR(+)IR(+), 364 (19.0%) were VR(+)IR(-), 283 (14.8%) were (VR(-)IR(+)), and 193 (10.1%) were VR(-)IR(-). OF THE 3111 patients eligible for analysis, 1914 had available information at 6 months of therapy: 1074 (56.1%) were VRIR, 364 (19.0%) were VRIR, 283 (14.8%) were (VRIR), and 193 (10.1%) were VRIR. Compared with complete responders, virologic-only responders were older, had a higher baseline CD4 cell count, had a lower baseline PVL, and were more likely to have received a nonstandard HAART regimen; immunologic-only responders were younger, had a lower baseline CD4 cell count, had a higher baseline PVL, and were more likely to have received a protease inhibitor-based regimen. CONCLUSIONS: The frequency of and risk factors for discordant responses were comparable to those observed in developed countries. Longer follow-up is needed to assess the long-term impact of discordant responses on mortality in these resource-limited settings.     

HIV-1 drug resistance evolution among patients on potent combination antiretroviral therapy with detectable viremia

Many patients infected with HIV do not achieve or maintain virologic suppression below levels of detection while on potent combination antiretroviral therapy. The likelihood of emergence of incident mutations conferring reduced antiretroviral drug susceptibility was estimated among patients maintained on a stable regimen with ongoing detectable plasma HIV RNA levels. Ninety-eight HIV-infected patients were identified who had 2 genotypic antiretroviral resistance tests available. Poisson log-linear regression models were used to identify predictors and estimate incidence rates of number of acquired antiretroviral drug resistance mutations per person-year. At the 1st resistance test, 88% of patients had evidence of at least 1 mutation. Sixty percent of patients acquired at least 1 new mutation during a median of 9.3 months between consecutive resistance tests, with an incidence rate of 1.61 acquired mutations per person-year (95% CI: 1.36-1.90). Predictors of resistance evolution included average plasma HIV RNA level, HIV RNA slope, and number of mutations detected at the 1st resistance test. The likelihood of acquiring drug resistance mutations while remaining on potent combination antiretroviral therapy that does not confer complete suppression of HIV replication is relatively low and depends on the level of viral replication and prior resistance.     

HIV-1 RNA viral load monitoring in HIV-infected drug users on antiretroviral therapy: relationship with outpatient care patterns

HIV-1 viral load (VL) testing is a standard component of HIV care. We examined the use and predictors of VL testing in drug users, a group at risk for problematic care. Using 1996 to 1998 New York State (NYS) Medicaid files, we studied drug users who had been enrolled >10 months, had been prescribed antiretroviral agents in 1997 and 1998, and who had undergone any VL testing in 1997. Our outcome was regular VL testing shown by two or more paid claims for this test in 1998. Patterns of care in 1997 were defined as: regular source of medical care (>35% of visits to one provider), and/or regular drug treatment of >6 months, or neither. We counted visits in 1997 to a provider offering HIV-focused care. Adjusted odds ratios (AORs) of VL testing were assessed. Of 3131 drug users, 73.9% had at least one VL test, whereas 56.2% had two or more VL tests in 1998. The AORs of two or more VL tests were increased for those with regular drug abuse care alone (AOR, 1.50; 95% confidence interval [CI], 1.21-1.84) or with regular medical care (AOR, 1.27; 95% CI, 1.03-1.57) versus those with neither. HIV-focused care was positively associated with two or more VL tests (AOR, 1.38; 95% CI, 1.05-1.81 for 1-3 visits; AOR, 1.94; 95% CI, 1.50-2.51 for four or more visits). We found that nearly half this cohort of drug users did not have regular VL testing. Drug users with HIV-focused care or with regular drug treatment are more likely to have regular VL testing.     

Self-reported adherence to antiretroviral therapy for HIV-1 infection and virologic treatment response: a meta-analysis

BACKGROUND: Adherence to highly active antiretroviral therapy (HAART) for HIV-1 infection is essential for plasma HIV-1 RNA suppression. Self-report is the most frequently used measure of adherence to HAART, but its validity is controversial. Studies on the relation between self-reported adherence and virologic treatment response have shown inconsistent results. We investigated whether this variability between studies about the effect of self-reported adherence on virologic treatment response could be attributed to study design features. METHODS: We searched for studies reporting on adult nonpregnant patients prescribed antiretroviral therapy for chronic HIV-1 infection using a self-reported adherence measure and providing information about the relation between adherence and plasma HIV-1 RNA concentrations. Meta-analysis with random effects modeling was used to pool data and to investigate sources of heterogeneity. RESULTS: Sixty-five studies fulfilled inclusion criteria, containing data from 15,351 patients. The pooled odds ratio (95% confidence interval) of detectable plasma viral load in nonadherent patients was 2.31 (1.99-2.68). There was significant heterogeneity among studies (P < 0.001). Not ascertaining confidentiality of responses, use of actual viral load measurements, an adherence threshold lower than 95%, higher percentages of patients on their initial antiretroviral regimen, and higher percentages of patients with a history of intravenous drug use within a study were associated with higher point estimates. CONCLUSIONS: Overall, we observed that self-reported adherence measures can distinguish between clinically meaningful patterns of medication-taking behavior. Distinct study characteristics were significantly associated with the relation between adherence and virologic response. These characteristics should be taken into consideration when interpreting results from studies on self-reported adherence.     

Efficient monitoring of HIV-1 vertically infected children in Kenya on first-line antiretroviral therapy

Background

Worldwide access to antiretroviral therapy (ART) in low- and middle-income countries has significantly increased. Although this presents better treatment options for HIV-infected individuals, the challenge of monitoring ART in these settings still remains.

Objective

To investigate efficient and cost-effective criteria for assessing ART failure among HIV-1-infected children on first-line ART in resource-limited settings.

Study design

Retrospective analysis of 75 HIV-1 vertically infected Kenyan children with a follow-up period of 24 months after initiating ART. Plasma viral load, peripheral CD4⁺T-cell counts and HIV-1 drug-resistance mutations were monitored biannually.

Results

Plasma viral load (VL) was suppressed to undetectable level or more than 1.5 log₁₀ from baseline levels in 53 (70.7%) children within 24 months. VL in the remaining 22 (29.3%) children was not suppressed significantly. Of the 22 children, 21 were infected with HIV-1 strains that developed drug-resistance mutations; 9 within 12 months and 12 between 12 and 24 months. Among the 53 who were successfully treated, VL was suppressed in 33 within 12 months and in 20 between 12 and 24 months. There was no significant difference in VL at baseline and the change of CD4⁺T-cell counts after initiating ART between those treated successfully and the failure groups.

Conclusion

After initiating ART, children may require longer times to achieve complete viral suppression. Plasma viral load testing 24 months after initiating ART could be used to differentiate ART failures among HIV-1 vertically infected children in resource-limited settings. Additionally, drug resistance testing, if affordable, would be helpful in identifying those failing therapy and in choosing second-line regimens.     

Reservoirs of HIV-1 in vivo: implications for antiretroviral therapy

The eradication of HIV-1 from infected individuals remains the ultimate goal of all anti-HIV therapeutics. Although highly active antiretroviral therapy (HAART) has led to a profound decrease in morbidity and mortality in infected people by suppressing HIV replication, the virus continues to evolve slowly during therapy even when patients achieve below detectable levels of HIV in plasma. HIV-1 persists in latently infected memory CD4+ T cells and there is minimal decay of HIV in this compartment despite prolonged HAART. Various other reservoirs and sanctuary sites harboring HIV are also established in vivo during antiretroviral therapy. Collectively these sites represent a major impediment to the eradication of HIV-1. This review presents a detailed overview of various reservoir sites in vivo, and discusses their impact on the success and failure of HAART for HIV patients. In addition, it addresses the effect of sub-optimal drug concentrations on reservoir establishment and outlines future therapeutic strategies to counteract these reservoirs and sanctuaries.     

Resistance to antiretroviral agents in individuals with HIV-1 non-B subtypes

Naturally occurring polymorphisms at positions involved in resistance to antiretroviral agents are frequently seen in HIV-1 non-B subtypes. Although they do not seem to affect significantly the susceptibility to antiretroviral drugs in vitro, they may facilitate the selection of different pathways and/or a more rapid emergence of drug resistance and treatment failure under not fully suppressive treatment regimens.     

我国HIV-1感染者耐药突变的流行性研究

目的 掌握我国大规模用药前耐药突变在我国HIV-1感染者中流行情况的本底资料。方法 在第二次全国HIV流行病调查2002年样本中随机选取20％，对于蛋白酶(PR)基因区全长和逆转录酶(RT)20～230氨基酸位点进行PCR扩增、测序并使用HIVdb-Drug Resistance Algorithm软件进行分析，检测耐药相关突变。结果 分别得到164份PR基因区样本和138份RT基因区样本。PR基因区样本中发现1份(0．61％)样本存在蛋白酶抑制剂(PI)主要相关突变，163份(99．39％)样本存在P1次要耐药相关突变。RT基因区样本中发现8份(5．80％)具有核苷类逆转录酶抑制剂(NRTI)耐药相关突变，2份(1．45％)存在非核苷类逆转录酶抑制剂(NNRTI)耐药相关突变。结论 我国未用药HIV感染者中耐药相关突变尚处于低流行状态，应当在用药过程中定期监控以减少耐药突变的产生与传播。     

HIV-1 viral load and phenotypic antiretroviral drug resistance assays based on reverse transcriptase activity in comparison to amplification based HIV-1 RNA and genotypic assays

BackgroundAmplification based HIV-1 viral load and genotypic resistance assays are expensive, technologically complex and may be difficult to implement in resource limited settings. Inexpensive, simpler assays are urgently needed.ObjectivesTo determine the suitability of the ExaVir? Load and ExaVir? Drug assays for use in patient monitoring.Study designSpecimens from 108 adults were used to compare ExaVir? Load HIV-1 RT to Amplicor HIV-1 Monitor^® HIV-1 RNA, and ExaVir? Drug phenotype to HIV GenoSure? genotype.ResultsHIV-1 RT and HIV-1 RNA levels were comparable (Pearson correlation coefficient 0.83). Most (94%) had detectable results in both assays. The mean difference (HIV-1 RT minus HIV-1 RNA) was ?0.21 log₁₀ cps/mL equiv. Relationship between HIV-1 RT and HIV-1 RNA was not affected by RT mutations, CD4 cell count, or efavirenz (EFV) or nevirapine (NVP) use. Phenotypes were generally consistent with genotype findings for EFV, but not for NVP. Most patients (93.9%) with phenotypic EFV resistance had at least one EFV mutation, while 78.0% of patients with phenotypic NVP resistance had at least one NVP mutation. Eleven of 49 samples tested for EFV susceptibility were found resistant (n = 2) or with reduced susceptibility (n = 9) despite the absence of genotypic resistance. Eleven of 45 samples tested for NVP susceptibility were found resistant (n = 9) or with reduced susceptibility (n = 2) with no evidence of genotypic mutations.ConclusionsThe ExaVir? Load assay performed well and may be an alternative to amplification based techniques for HIV-1 RNA quantification. The ExaVir? Drug assay for phenotypic resistance testing requires further evaluation, especially for NVP.     

Adherence to antiretroviral therapy assessed by drug level monitoring and self-report in cameroon

OBJECTIVES: To compare adherence to antiretroviral therapy using drug level monitoring and self-report and to explore the relation between these 2 methods and viral load measurements. METHODS: Sixty patients received a fixed-dose combination of nevirapine, stavudine, and lamivudine in a clinical study in Cameroon. Adherence was assessed every 6 months until month 36 by nevirapine minimal plasma concentration and self-report. Plasma HIV-1 viral load was determined at the same time. Analyses included 159 complete observations. RESULTS: The proportion of patients labeled as "adherent" was significantly lower using nevirapine monitoring (88.7%, 95% confidence interval [CI]: 82.7 to 93.2) than self-report (97.5%, CI: 93.7 to 99.3; P = 0.002). Virologic failure was associated with the nevirapine concentration (adjusted odds ratio [aOR] = 4.43; P = 0.018) but not with the self-reported adherence (aOR = 0.84; P = 0.9). As compared with the virologic outcome, the sensitivity of nevirapine level monitoring for predicting inadequate adherence was 20.5%, the specificity was 91.7%, the positive predictive value was 44.4%, and the negative predictive value was 78.0%. For self-report, the respective values were 2.6%, 97.5%, 25.0%, and 75.5%. CONCLUSIONS: Drug level monitoring provided a more reliable estimate of adherence than self-report. This method could be used in research settings. Operational research is required to define how to improve the accuracy of the self-report method because it is the most feasible method in clinical practice.