EuroGuidelines Group for HIV Resistance. Clinical and laboratory guidelines for the use of HIV-1 drug resistance testing as part of treatment management: recommendations for the European setting. The EuroGUidelines Group for HIV resistance

Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

Prospective molecular studies of HIV-1 pol region (2253-5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017-2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790-8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.

Machine Learning to Improve the Effectiveness of ANRS in Predicting HIV Drug Resistance

OBJECTIVES

Human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) is one of the major burdens of disease in developing countries, and the standard-of-care treatment includes prescribing antiretroviral drugs. However, antiretroviral drug resistance is inevitable due to selective pressure associated with the high mutation rate of HIV. Determining antiretroviral resistance can be done by phenotypic laboratory tests or by computer-based interpretation algorithms. Computer-based algorithms have been shown to have many advantages over laboratory tests. The ANRS (Agence Nationale de Recherches sur le SIDA) is regarded as a gold standard in interpreting HIV drug resistance using mutations in genomes. The aim of this study was to improve the prediction of the ANRS gold standard in predicting HIV drug resistance.

METHODS

A genome sequence and HIV drug resistance measures were obtained from the Stanford HIV database (http://hivdb.stanford.edu/). Feature selection was used to determine the most important mutations associated with resistance prediction. These mutations were added to the ANRS rules, and the difference in the prediction ability was measured.

RESULTS

This study uncovered important mutations that were not associated with the original ANRS rules. On average, the ANRS algorithm was improved by 79% ± 6.6%. The positive predictive value improved by 28%, and the negative predicative value improved by 10%.

CONCLUSIONS

The study shows that there is a significant improvement in the prediction ability of ANRS gold standard.

Comparison of in-house HIV-1 genotypic drug resistant test with commercial HIV-1 genotypic test kit

Background: The use of combination antiretroviral therapy (cART) has become a standard of care in the treatment of HIV infection. However, antiretroviral drug resistance occurs in a substantial number of patients. In resource-limited settings, genotypic resistance assay using a commercial kit is costly.

Objective: Focus on the validation of an in-house HIV-1 specific genotypic drug resistance assay in Thai patients failing cART.

Materials and methods: Results of HIV-1 genotypic drug resistance assay was evaluated by comparing an inhouse method to a commercial test. The TRUGENE HIV-1 genotyping kit was used in 79 plasma specimens (49 from HIV patients failing cART therapy and 30 from proficiency testing panels).

Results: The results from the in-house assay were comparable to those obtained from the TRUGENE HIV-1 genotyping kit with >99.0% codon-to-codon agreement. The lower limit of detection by the in-house assay was approximately 100 copies/mL of HIV-1 RNA. In addition, this in-house assay would allow testing of samples from patients infected with HIV-1 subtype other than B.

Conclusion: The in-house HIV-1 genotypic drug resistance assay may be used as an alternative to commercial kits, particularly in resource limited settings.

Antiretroviral therapy and mother-to-child transmission of HIV-1

The advent of highly active antiretroviral therapy has facilitated the virtual elimination of mother-to-child transmission of HIV infection in developed countries, reducing transmission rates to approximately 1 to 2%. In these settings, highly active antiretroviral therapy has also transformed pediatric HIV infection into a chronic disease; although there are associated costs in terms of side effects and the heavy pill burden. In less developed settings, easier-to-use adaptations of antiretroviral therapy regimens, such as short-course and single-dose antiretroviral strategies or neonatal postexposure prophylaxis can also substantially prevent mother-to-child transmission, although to a lesser degree than highly active antiretroviral therapy. However, postnatal transmission of infection through breastfeeding significantly reduces the longer-term efficacy of these strategies. Ongoing research is focusing on the use of antiretroviral therapy in the breastfeeding period.

Baseline clinical HIV genotypes are a valid measure of transmitted drug resistance within the treatment-naive population

OBJECTIVE

To examine whether baseline clinical genotypes are equivalent to diagnostic serum genotypes for surveillance of HIV transmitted drug resistance (TDR).

DESIGN

Current HIV TDR surveillance in Canada is conducted through genotyping remnant diagnostic sera from new HIV diagnoses. As part of routine care, baseline genotyping is now conducted on all newly diagnosed HIV infections, with TDR data being generated a second time on the same patients.

METHODS

Surveillance genotyping, on HIV diagnostic serum, was performed on newly diagnosed HIV cases from 2007 to 2010 in Alberta, Canada. All subjects with a baseline clinical genotype result on file, and no evidence of antiretroviral therapy, were studied further. The HIV sequences from diagnosis and from the first clinical genotype were compared according to elapsed time between testing and by evaluating timing of infection based on BED capture enzyme immunoassay (BED-CEIA, abbreviated as BED in this article).

RESULTS

Eighty-seven genotype pairs were available for analysis, most of which were subtype B. The time between genotypes ranged from 0 to 755 days, with a median of 36 days and an interquartile range of 155.25 days. Genetic distance between genotypes varied between 0 and 0.03389 substitutions per site and did not correlate with sampling times. There was a tendency for the genotypes of infections classified as recent by BED to be more similar to their clinical genotypes but this effect was lost when adjusted for elapsed time between tests. There was no difference in the identified drug resistance.

CONCLUSIONS

Baseline clinical genotypes from treatment-naive patients may be used for HIV TDR surveillance.

An in-house HIV genotyping assay for the detection of drug resistance mutations in Southeast Asian patients infected with HIV-1

Genotyping for HIV drug resistance is costly and beyond the means for many Southeast Asian patients, who are self-funded. This prompted the development of a more cost-effective, in-house assay for an ethnically diverse, Southeast Asian population at the National University Hospital in Singapore, using Sanger-based sequencing. Plasma samples from 20 treatment-failure patients with a broad spectrum of HIV drug resistance mutations were used to validate this assay clinically. Blinded testing gave concordant results for 7/7 (100%) protease drug resistance-related mutations, including one major and six minor mutations, and 111/116 (95.7%) reverse-transcriptase (RT) drug resistance-related mutations, including 65 nucleoside RT inhibitors (NRTI) and 46 non-nucleoside RT inhibitors (NNRTI) mutations. There were five discordant results, involving three NRTI- and two NNRTI-resistance-associated mutations. Highly conserved primers designed to have a wide coverage of the HIV pol gene (covering the entire protease and 395 codons of the RT region) enabled efficient multi-ethnic population-based genotyping. Reagents for this in-house test cost around 60% less than those for commercially available assays (SGD150 vs. SGD350 per sample). In addition, this assay also identified mutations located within the C-terminal domain (codons 312-560) of RT that are beyond the reach of most published and commercial GRTs. Currently, most research on C-terminal drug-resistance-related mutations has been conducted on HIV subtype B infections. Therefore this assay enables further study of these C-terminal mutations in Southeast Asian populations, where there is a high prevalence of CRF01_AE and other non-subtype B HIV infections.

Measuring enzymatic HIV-1 susceptibility to two reverse transcriptase inhibitors as a rapid and simple approach to HIV-1 drug-resistance testing

Simple and cost-effective approaches for HIV drug-resistance testing are highly desirable for managing increasingly expanding HIV-1 infected populations who initiate antiretroviral therapy (ART), particularly in resource-limited settings. Non-nucleoside reverse trancriptase inhibitor (NNRTI)-based regimens with an NRTI backbone containing lamivudine (3TC) or emtricitabine (FTC) are preferred first ART regimens. Failure with these drug combinations typically involves the selection of NNRTI- and/or 3TC/FTC- resistant viruses. Therefore, the availability of simple assays to measure both types of drug resistance is critical. We have developed a high throughput screening test for assessing enzymatic resistance of the HIV-1 RT in plasma to 3TC/FTC and NNRTIs. The test uses the sensitive “Amp-RT” assay with a newly-developed real-time PCR format to screen biochemically for drug resistance in single reactions containing either 3TC-triphosphate (3TC-TP) or nevirapine (NVP). Assay cut-offs were defined based on testing a large panel of subtype B and non-subtype B clinical samples with known genotypic profiles. Enzymatic 3TC resistance correlated well with the presence of M184I/V, and reduced NVP susceptibility was strongly associated with the presence of K103N, Y181C/I, Y188L, and G190A/Q. The sensitivity and specificity for detecting resistance were 97.0% and 96.0% in samples with M184V, and 97.4% and 96.2% for samples with NNRTI mutations, respectively. We further demonstrate the utility of an HIV capture method in plasma by using magnetic beads coated with CD44 antibody that eliminates the need for ultracentifugation. Thus our results support the use of this simple approach for distinguishing WT from NNRTI- or 3TC/FTC-resistant viruses in clinical samples. This enzymatic testing is subtype-independent and can assist in the clinical management of diverse populations particularly in resource-limited settings.

Surveillance of transmitted antiretroviral drug resistance among HIV-1 infected women attending antenatal clinics in Chitungwiza, Zimbabwe

The rapid scale-up of highly active antiretroviral therapy (HAART) and use of single dose Nevirapine (SD NVP) for prevention of mother-to-child transmission (pMTCT) have raised fears about the emergence of resistance to the first line antiretroviral drug regimens. A cross-sectional study was conducted to determine the prevalence of primary drug resistance (PDR) in a cohort of young (<25 yrs) HAART-naïve HIV pregnant women attending antenatal clinics in Chitungwiza, Zimbabwe. Whole blood was collected in EDTA for CD4 counts, viral load, serological estimation of duration of infection using the BED Calypte assay and genotyping for drug resistance. Four hundred and seventy-one women, mean age 21 years; SD: 2.1 were enrolled into the study between 2006 and 2007. Their median CD4 count was 371cells/µL; IQR: 255–511 cells/µL. Two hundred and thirty-six samples were genotyped for drug resistance. Based on the BED assay, 27% were recently infected (RI) whilst 73% had long-term infection (LTI). Median CD4 count was higher (p<0.05) in RI than in women with LTI. Only 2 women had drug resistance mutations; protease I85V and reverse transcriptase Y181C. Prevalence of PDR in Chitungwiza, 4 years after commencement of the national ART program remained below WHO threshold limit (5%). Frequency of recent infection BED testing is consistent with high HIV acquisition during pregnancy. With the scale-up of long-term ART programs, maintenance of proper prescribing practices, continuous monitoring of patients and reinforcement of adherence may prevent the acquisition and transmission of PDR.

High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity

The ViroSeq HIV-1 genotyping system is used in many African countries for drug resistance testing. In this study, we used a panel of diverse HIV-1 group M isolates circulating in Cameroon to show that the performance of this assay can be altered by the sequence variation of non-B HIV-1 strains that predominate in African settings.

HIV-1 proviral resistance mutations: usefulness in clinical practice

OBJECTIVES

Transmitted HIV strains may harbour drug resistance mutations. HIV-1 drug resistance mutations are currently detected in plasma viral RNA. HIV-1 proviral DNA could be an alternative marker, as it persists in infected cells.

METHODS

This was a prospective study assessing the prevalence and persistence of HIV-1 drug resistance mutations in DNA from CD4 cells before and after protease inhibitor (PI)- or nonnucleoside reverse transcriptase inhibitor (NNRTI)-based therapy initiation in 69 drug-naïve patients.

RESULTS

Before therapy, 90 and 66% of detected mutations were present in CD4 cells and plasma, respectively. We detected seven key mutations, and four of these (M184M/V, M184M/I, K103K/N and M46M/I) were only found in the cells. When treatment was started, 40 patients were followed; the mutations detected at the naïve stage remained present for at least 1 year. Under successful treatment, new key mutations emerged in CD4 cells (M184I, M184M/I and Y188Y/H).

CONCLUSIONS

The proportion of mutations detected in the DNA was statistically significantly higher than that detected in standard RNA genotyping, and these mutations persisted for at least 1 year irrespective of therapy. The pre-existence of resistance mutations did not jeopardise treatment outcome when the drug concerned was not included in the regimen. Analysis of HIV-1 DNA could be useful in chronic infections or when switching therapy in patients with undetectable viraemia.

The association of HIV susceptibility testing with survival among HIV-infected patients receiving antiretroviral therapy: a cohort study

BACKGROUND

HIV-1 genotypic and phenotypic susceptibility testing (GPT) optimizes antiretroviral selection, but its effect on survival is unknown.

OBJECTIVE

To evaluate the association between GPT and survival.

DESIGN

Cohort study.

SETTING

10 U.S. HIV clinics.

PATIENTS

2699 HIV-infected patients eligible for GPT (plasma HIV RNA level >1000 copies/mL) seen from 1999 through 2005.

MEASUREMENTS

Demographic characteristics, clinical factors, GPT use, all-cause mortality, and crude and adjusted hazard ratios (HRs) for the association of GPT with survival.

RESULTS

Patients were followed for a median of 3.3 years; 915 (34%) had GPT. Patients who had GPT had lower mortality rates than those who did not (2.0 vs. 2.7 deaths per 100 person-years). In standard Cox models, GPT was associated with improved survival (adjusted HR, 0.69 [95% CI, 0.51 to 0.94]; P = 0.017) after controlling for demographic characteristics, CD4+ cell count, HIV RNA level, and intensity of clinical follow-up. In subgroup analyses, GPT was associated with improved survival for the 2107 highly active antiretroviral therapy (HAART)-experienced patients (2.2 vs. 3.2 deaths per 100 person-years for patients who had GPT vs. those who did not have GPT; adjusted HR, 0.60 [CI, 0.43 to 0.82]; P = 0.002) and for the 921 triple antiretroviral class-experienced patients (2.1 vs. 3.1 deaths per 100 person-years; adjusted HR, 0.61 [CI 0.40 to 0.93]; P = 0.022). Marginal structural models supported associations between GPT and improved survival in the overall cohort (adjusted HR, 0.54; P = 0.001) and in the HAART-experienced group (adjusted HR, 0.56; P = 0.003).

LIMITATIONS

Use of GPT was not randomized. Residual confounding may exist.

CONCLUSION

Use of GPT was independently associated with improved survival among HAART-experienced patients.

PRIMARY FUNDING SOURCE

Centers for Disease Control and Prevention.

Interpretation systems for genotypic drug resistance of HIV-1

Genotypic assays are widely used tools for determining human immunodeficiency virus type 1 (HIV-1) drug resistance and for guiding treatment changes in patients failing antiretroviral therapy. Several systems have been developed to interpret the complex influence of key amino acid substitutions of the enzymes targeted by therapy on the phenotypic susceptibility or clinical response to available antiretroviral agents. This overview identifies 21 systems giving an interpretation on how amino acid substitutions affect phenotypic drug susceptibility or clinical activity of anti-HIV-1 agents. There was substantial variability in the mechanisms underlying the interpretations, the nature of the systems, their intended use, the source type of their knowledge base, and their update and output. Most of the systems could be accessed for free on the internet, functioned as rule-based algorithms updated by experts and at least partially based on literature evidence, and offered an automated report through a software. Nevertheless, the rule base was not always clarified. An update of the rules and the clinical validation of the systems are presented to help in the critical evaluation of their possible use. Importantly, only 8 systems were intended for clinical use and 5 of these had at least partially undergone clinical validation.

Cost-effectiveness analysis of using antiretroviral drug resistance testing

Human immunodeficiency virus (HIV)-infected patients failing highly active antiretroviral therapy (HAART) have a substantially lower chance of clinical success than naive patients given their first antiretroviral therapy. This suggests that HAART failure is a determinant for an increase in the cost of treatment. A review of the literature regarding cost and impact of antiretroviral drug-resistance testing was performed. Examination of existing methods to execute a cost-effectiveness analysis on the use of these tests in clinical practice was also undertaken. The cost of treatment failure in HIV-infected patients has been quantified in several retrospective studies. The cost of care for patients with virological suppression was significantly lower than those with a single virological failure. Moreover, the latter group had lower costs than patients with multiple failures. The result of the cost-effective analysis based on a specific model application using genotypic resistance assays to guide the choice of a subsequent therapy in HIV disease, is cost-effective under a wide range of assumptions regarding effectiveness and costs. The available studies on the cost-effective evaluation of genotypic tests are limited, and the respective studies supply important indications on cost-effective evaluations. Despite its demonstrated benefits, antiretroviral drug resistance testing presents features and limitations that also restrict the cost-effectiveness analysis.

Prevalence of Drug Resistance Mutations and Non-B Subtypes in Newly Diagnosed HIV-1 Patients in Denmark

The aim of this study was to monitor the prevalence of drug resistance mutations in newly diagnosed HIV-1 positive individuals in Denmark. In addition we assessed the prevalence of non-B subtypes based on phylogenetic analysis of the pol gene. Plasma samples from 104 newly diagnosed HIV-1 positive patients were obtained in the year 2000. The entire protease gene and 320 amino acids of the reverse transcriptase gene were genotyped. Sequences were obtained from 97 patients. No subjects displayed primary resistance mutations in the protease gene, whereas all carried 1 or more secondary mutations. Resistance mutations in the RT-gene associated with NRTI-resistance were found in 1 patient, who was infected with zidovudine resistant HIV-1 harbouring the M41L mutation in combination with T215S and L210S. The T215S mutation has been showed to be associated with reversion of zidovudine resistance. The T215S mutation was found in 1 additional patient. The subtype distribution was subtype B 59%, C 18%, A 8%, CRF02_AG 5%, CRF01_AE 4%, D 3% and G 2%. We found 2 patients (2%) with mutations associated with resistance in the RT-gene and none in the protease gene indicating a low prevalence of resistant HIV-1 in Denmark in the year 2000.

Plasma HIV RNA decline and emergence of drug resistance mutations among patients with multiple virologic failures receiving resistance testing-guided HAART

Early recognition of virologic failure in patients with extensive drug resistance receiving salvage-HAART is essential to avoid exposure to subinhibitory regimens. We studied plasma viral load (PVL) decline and rates of drug-resistance mutation (DRM) accumulation in such patients. A prospective, 48 week study of 38 heavily pretreated patients receiving genotypic resistance testing (GRT)-guided HAART was conducted. The rate of PVL decline was studied by weekly PVL determinations. To assess DRM accumulation, serial GRTs were performed in all nonresponders (never reaching PVL <50 or two PVLs >50 copies/ml after suppression). Over 48 weeks, 10 patients (26%) were nonresponders. Receiving less then two fully active drugs and having an elevated number of PI and NRTI mutations at baseline were strongly associated with virologic failure. There was no evidence of a difference in the change from baseline PVL to week 1 and 2 between responders and nonresponders. By contrast, PVL reductions from week 2 to week 3 and thereafter were significantly greater for responders (p < 0.01). Among nonresponders, the incidence rates per patient-month (95% CI) of emergent DRM were 0.67 (0.13-1.20), 0.40 (0.00-0.74), and 0.37 (0.00-0.75) at weeks 4, 8, and 24, respectively. Having limited baseline resistance, receiving at least two fully active drugs, and showing constant PVL reductions from week 2 to week 3 and thereafter were predictive of virologic response. In contrast, early changes in PVL levels were not. Virologic failure was associated with detection of emergent DRMs. Virologic rebound in patients on salvage-HAART should be addressed aggressively.

The incidence of multidrug and full class resistance in HIV-1 infected patients is decreasing over time (2001-2006) in Portugal

Despite improvements in HIV treatment, the prevalence of multidrug resistance and full class resistance is still reported to be increasing. However, to investigate whether current treatment strategies are still selecting for multidrug and full class resistance, the incidence, instead of the prevalence, is more informative. Temporal trends in multidrug resistance (MDR defined as at most 1 drug fully susceptible) and full class resistance (FCR defined as no drug in this class fully susceptible) in Portugal based on 3394 viral isolates genotyped from 2000 to 2006 were examined using the Rega 6.4.1 interpretation system. From July 2001 to July 2006 there was a significant decreasing trend of MDR with 5.7%, 5.2%, 3.8%, 3.4% and 2.7% for the consecutive years (P = 0.003). Multivariate analysis showed that for every consecutive year the odds of having a new MDR case decreased with 20% (P = 0.003). Furthermore, a decline was observed for NRTI- and PI-FCR (both P < 0.001), whereas for NNRTI-FCR a parabolic trend over time was seen (P < 0.001), with a maximum incidence in 2003–'04. Similar trends were obtained when scoring resistance for only one drug within a class or by using another interpretation system. In conclusion, the incidence of multidrug and full class resistance is decreasing over time in Portugal, with the exception of NNRTI full class resistance which showed an initial rise, but subsequently also a decline. This is most probably reflecting the changing drug prescription, the increasing efficiency of HAART and the improved management of HIV drug resistance. This work was presented in part at the Eighth International Congress on Drug Therapy in HIV Infection, Glasgow (UK), 12-16 November 2006 (PL5.5); and at the Fifth European HIV Drug Resistance Workshop, Cascais (Portugal), 28-30 March 2007 (Abstract 1).

Evaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotyping

INTRODUCTION

The human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) has been considered essential for HIV-1 drug resistance monitoring. However, it is not commonly used in some developing countries in Asia and Africa due to its high running cost.

OBJECTIVE

This study aims to evaluate a new low-cost in-house GRT for both subtype B and non-B HIV-1.

STUDY DESIGN

The in-house GRT sequenced the entire protease and 410 codons of reverse transcriptase (RT) in the pol gene. Its performance on drug resistance interpretation was evaluated against the FDA-approved ViroSeq HIV-1 Genotyping System. Particularly, a panel of 235 plasma samples from 205 HIV-1-infected patients in Hong Kong was investigated. The HIV-1 drug resistance-related mutations detected by the two systems were compared. The HIV-1 subtypes were analyzed through the REGA HIV-1 Genotyping Tool and env phylogenetic analysis.

RESULTS

Among the 235 samples, 229 (97.4%) were successfully amplified by both in-house and ViroSeq systems. All PCR-negative samples harbored viral RNA at <400 copies/mL. The in-house and ViroSeq system showed identical drug resistance-related mutation patterns in 216 out of 229 samples (94.3%). The REGA pol genotyping results showed 93.9% (215/229) concordance with the env phylogenetic results including HIV-1 subtype A1, B, C, D, G, CRF01_AE, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC, CRF15_01B and other recombinant strains. The cost of running the in-house GRT is only 25% of that for the commercial system, thus making it suitable for the developing countries in Asia and Africa.

CONCLUSIONS

Overall, our in-house GRT provided comparable results to those of the commercial ViroSeq genotyping system on diversified HIV-1 subtypes at a more affordable price which make it suitable for HIV-1 monitoring in developing countries.

Human immunodeficiency virus infection and pregnancy

Human immunodeficiency virus infection profoundly affects the medical community and is spreading rapidly in women of childbearing age worldwide. Transmission of HIV from mother to child can occur in utero, during labor, or after delivery through breast-feeding. Most of the infants are infected during delivery. We focus on the factors affecting the transmission of HIV, diagnostic and resistance tests, strategies to prevent mother-to-child transmission with special reference to mode of delivery, infant feeding, and use of antiretroviral therapy. The risk of infection for the infant can be decreased by reducing maternal viral load, by elective cesarean delivery, and by avoidance of breast-feeding. The efficacy of antiretroviral treatment should be balanced against the possibility of embryonic or fetal toxicity. The choice of therapy should be based on the woman's treatment history, the clinical status, and the available prognostic markers, which are related to the progression of disease in the mother and the risk of mother-to-child transmission HIV transmission.

Incorporating drug-resistance measurements into the clinical management of HIV-1 infection

Testing for resistance to antiretrovirals is considered to be standard of care and is widely used in the management of human immunodeficiency virus (HIV)-infected persons. Despite the widespread use of resistance testing, the clinician still faces a number of challenges when applying these technologies in the optimal management of antiretroviral therapy. Both genotype and phenotype tests require interpretation, and available interpretative algorithms for genotypes and resistance cutoffs for phenotypes are incomplete and evolving. Even experts in HIV resistance do not completely agree in their interpretation of genotypes. Moreover, discordant results between genotypes and phenotypes are a common source of confusion when both tests are used to evaluate resistance in a patient. Finally, newer indicators, such as replication capacity, are clinically available and appear to have prognostic value, but how this in vitro measure should be used in the management of antiretroviral therapy remains to be fully defined.

A Randomized Controlled Trial of Genotypic HIV Drug Resistance Testing in HIV-1-Infected Children: The Pera (Penta 8) Trial

Objective

To evaluate the longer-term utility of genotypic resistance testing in HIV-1-infected children with virological failure.

Methods

Children aged 3 months-18 years switching antiretroviral therapy (ART) with HIV-1 RNA >2,000 copies/ml were randomized between genotypic testing (Virtual PhenotypeTM) and no testing at baseline and subsequent virological failures. Children were followed to at least 96 weeks.

Results

One hundred and seventy eligible children, from 24 clinical centres in six countries, were randomized to resistance testing ( n=87) or no testing ( n=83) between June 2000-July 2003. At baseline, mean HIV-1 RNA and CD4+ T-cell percentage were 4.7 log10 copies/ml and 20%, respectively. Children had taken ART for a mean of 5 years; 24% had received all three classes, 53% nucleoside reverse transcriptase inhibitors (NRTIs)+protease inhibitors (PIs), 9% NRTIs+non-nucleoside reverse transcriptase inhibitors (NNRTIs) and 14% NRTIs only. There was no difference between the arms in the drug classes or the individual PIs/NNRTIs prescribed. However, 49% in the resistance test arm (RT) versus 19% in the no-test arm (NT) continued at least one NRTI from their failing regimen; 56% versus 19% were prescribed didanosine+stavudine as their NRTI backbone. Adjusting for baseline HIV-1 RNA, mean reductions in HIV-1 RNA at 48 weeks were 1.51 log10 copies/ml in the RT arm and 1.23 in the NT arm ( P=0.3); the difference between the arms was smaller at week 96 (RT: 1.50, NT: 1.47; P=0.9).

Conclusion

In this first paediatric trial of resistance testing, we observed a substantial difference in NRTI-prescribing behaviour across arms. However statistically significant evidence of a long-term virological or immunological benefit was not observed. This trial is registered as an International Standard Randomised Controlled Trial, number ISRCTN14367816.

A randomised trial comparing genotypic and virtual phenotypic interpretation of HIV drug resistance: the CREST study

Objectives:

The aim of this study was to compare the efficacy of different HIV drug resistance test reports (genotype and virtual phenotype) in patients who were changing their antiretroviral therapy (ART).

Design:

Randomised, open-label trial with 48-week followup.

Setting:

The study was conducted in a network of primary healthcare sites in Australia and New Zealand.

Participants:

Patients failing current ART with plasma HIV RNA > 2000 copies/mL who wished to change their current ART were eligible. Subjects were required to be > 18 years of age, previously treated with ART, have no intercurrent illnesses requiring active therapy, and to have provided written informed consent.

Interventions:

Eligible subjects were randomly assigned to receive a genotype (group A) or genotype plus virtual phenotype (group B) prior to selection of their new antiretroviral regimen.

Outcome Measures:

Patient groups were compared for patterns of ART selection and surrogate outcomes (plasma viral load and CD4 counts) on an intention-to-treat basis over a 48-week period.

Results:

Three hundred and twenty seven patients completing > one month of followup were included in these analyses. Resistance tests were the primary means by which ART regimens were selected (group A: 64%, group B: 62%; p = 0.32). At 48 weeks, there were no significant differences between the groups for mean change from baseline plasma HIV RNA (group A: 0.68 log copies/mL, group B: 0.58 log copies/mL; p = 0.23) and mean change from baseline CD4+ cell count (group A: 37 cells/mm³, group B: 50 cells/mm³; p = 0.28).

Conclusions:

In the absence of clear demonstrated benefits arising from the use of the virtual phenotype interpretation, this study suggests resistance testing using genotyping linked to a reliable interpretive algorithm is adequate for the management of HIV infection.

Background: Antiretroviral drugs are used to treat patients with HIV infection, with good evidence that they improve prognosis. However, mutations develop in the HIV genome that allow it to evade successful treatment—known as drug resistance—and such mutations are known against every class of antiretroviral drug. Resistance can cause treatment failure and limit the treatment options available. Different types of tests are often used to detect resistance and to work out whether patients should switch to a different drug regimen. Currently, the different types of tests include genotype testing (direct sequencing of genes from virus samples infecting a patient); phenotype testing (a test that assesses the sensitivity of a patient's HIV sample to different drugs), and virtual phenotype testing (a way of interpreting genotype data that estimates the likely viral response to different drugs). The researchers of this study did a trial to find out whether providing an additional virtual phenotype report would be beneficial to patients, as compared with a genotype report alone. The main outcome was HIV viral load after 12 months of treatment, but the researchers also looked at differences in drug regimens prescribed, number of treatment changes in the study, and changes in CD4+ (the type of white blood cell infected by HIV) counts.

What this trial shows: The researchers found that the main endpoint of the trial (HIV viral load after 12 months) was no different in patients whose clinicians had received a virtual phenotype report as well as a genotype report, compared with those who had received a genotype report alone. In addition, the average number of drugs prescribed was no different between patients in the two different arms of the trial, and there was no difference in number of drug regimen changes, and no change in immune response (measured using CD4+ cell levels). However, more drugs predicted to be sensitive were prescribed by clinicians who got both a genotype and virtual phenotype report, as compared with clinicians who received only the genotype report.

Strengths and limitations: The size of the trial (338 patients recruited) was large enough to properly test the hypothesis that providing a virtual phenotype report as well as a genotype report would result in lower HIV viral loads. Randomization of patients to either intervention ensured that the comparison groups were well-balanced, and the researchers also tested whether selection bias had affected the results (i.e., testing for the possibility that clinicians could predict which intervention participants would receive, and change recruitment into the trial as a result). They found no evidence for selection bias occurring within the trial. However, interpreting the results is difficult because the trial did not directly compare the two different testing platforms, but rather looked at whether providing a virtual phenotype report as well as a genotype report was better than providing a genotype report alone. The investigators also acknowledge that since the trial was conducted, the cutoffs for interpreting genotype information as resistant have been lowered. The findings may therefore not translate precisely to the current situation.

Contribution to the evidence: Other cohort studies and clinical trials have shown that patients offered resistance testing respond better to antiretroviral therapy compared with those who were not, but the clinical effectiveness of different resistance testing methods is not known. This study provides additional data on the respective benefits of genotype testing versus genotype plus provision of virtual phenotype. Another trial comparing genotype versus virtual phenotype has also found that the different interpretation methods perform similarly.

Drug-Class-Wide Resistance to Antiretrovirals in HIV-Infected Patients Failing Therapy: Prevalence, Risk Factors and Virological Outcome

Background

Drug-class-wide resistance (DCWR) to anti-retrovirals substantially reduces treatment options.

Methods

A database of 602 patients failing highly active antiretroviral therapy (HAART) undergoing genotypic resistance test (GRT) was analysed. DCWR was defined according to the International AIDS Society consensus. A multiple logistic regression model was built to define factors significantly associated with DCWR and to assess virological response to salvage regimens.

Results

NRTI DCWR was observed in 28.5% of 592 NRTI-exposed patients, NNRTI DCWR in 57.7% of 284 NNRTI exposed patients, PI DCWR in 19.9% of 412 PI exposed patients, and three-class resistance in 21.4% of 112 three-class-exposed patients. The prevalence of NRTI and PI DCWR increased significantly by year of exposure to the same class from 8.9% (<1 year) to 35.3% (>4 years) and from 1.2% (<1 year) to 34.8% (>4 years), respectively ( P<0.001, for trend). The risk of developing NRTI and PI DCWR increased by 25% (95% confidence interval [CI]: 1.6%–51.3%) and by 53% (20.5%–94.3%) for each year of treatment, and by 17% (95% CI: 5.6%–29.3%) and by 32% (17.7%–50.3%) for each previous failing NRTI- and PI-containing regimen, respectively. NRTI DCWR due to at least four nucleoside analogues mutations (NAMs) increased by year of NRTI exposure from 8.9% (<1 year) to 32.6% (>4 years; P<0.001, for trend). After adjustment for confounding factors, the probability of achieving plasma viral load <500 copies/ml was significantly reduced in patients with NRTI (OR: 0.750; 95% CI: 0.574–0.979), NNRTI (OR: 0.746; 95% CI: 0.572–0.975), PI (OR: 0.655; 95% CI: 0.456–0.941), three-class (OR: 0.220; 95% CI: 0.082–0.593) resistance.

Conclusions

The probability of developing NRTI and PI DCWR increased with length of class exposure and with the number of previously failing regimens. By contrast, high levels of NNRTI DCWR were observed within 1 year in NNRTI-failing patients, with a steady prevalence over time. The increase in prevalence with time of NRTI DCWR was due to the accumulation of NAMs. DCWR to NRTIs, NNRTIs, PIs or all the three together was associated with an increased probability of virological failure to subsequent HAART regimens.

Regional Changes Over Time in Initial Virologic Response Rates to Combination Antiretroviral Therapy Across Europe

BACKGROUND

Changes in virologic response to initial combination antiretroviral therapy (cART) over calendar time may indicate improvements in cART or emergence of primary resistance. Regional variations may identify differences in available antiretroviral drugs or patient management.

METHODS

Virologic response (viral load < 500 copies/mL) 6 to 12 months after starting cART was analyzed in antiretroviral-naive EuroSIDA patients. Analyses were stratified by region (south, central west, north, east) or time started cART (early, 1996-1997; mid, 1998-1999; late, 2000-1904).

RESULTS

Virologic suppression was achieved by 60% of 2102 patients: 57% south (n = 560), 61% central west (n = 466), 63% north (n = 606), 58% east (n = 470) (P = 0.091). An increase was observed over time: 52% early cART, 56% mid cART, 69% late cART (P < 0.001). Overall, there were significant effects of region (P = 0.026) and time (P < 0.001) on virologic response after adjustment for confounders. Stratified by period, regional differences were less evident (early cART, P = 0.967; mid cART, P = 0.291; late cART, P = 0.163). Stratified by region, temporal changes were observed (south, P = 0.061; central west, P < 0.001; north: P = 0.070; east, P = 0.001).

CONCLUSIONS

There was some evidence of regional differences in initial virologic response to cART. Improvements over time were observed, suggesting that so far, the effect of primary resistance has not been of sufficient magnitude to prevent increasing suppression rates.

A Longitudinal Analysis of Healthcare Costs after Treatment Optimization following Genotypic Antiretroviral Resistance Testing: Does Resistance Testing pay off?

Objective

To assess the impact of antiretroviral therapy optimized by genotypic antiretroviral resistance testing (GRT) on healthcare costs over a 2-year period in patients after antiretroviral treatment failure.

Study design

Non-randomized, prospective, tertiary care, clinic-based study.

Patients

One-hundred and forty-two HIV patients enrolled in the ‘ZIEL’ study and the Swiss HIV Cohort Study who experienced virological treatment failure.

Methods

For all patients GRT was used to optimize the antiretroviral treatment regimen. All healthcare costs during 2 years following GRT were assessed using micro-costing. Costs were separated into ART medication costs and healthcare costs other than ART medication (that is, non-ART medication costs, in-patient costs and ambulatory [out-patient] costs). These cost estimates were then split into four consecutive 6-month periods (period 1–4) and the accumulated cost for each period was calculated. Univariate and multivariate regression modelling techniques for repeated measurements were applied to assess the changes of healthcare costs over time and factors associated with healthcare costs following GRT.

Results

Overall healthcare costs after GRT decreased over time and were significantly higher in period 1 (32%; 95% confidence interval [CI]: 18–47) compared with period 4. ART medication costs significantly increased by 1,017 (95% CI: 22–2,014) Swiss francs (CHF) from period 1–4, whereas healthcare costs other than ART medication costs decreased substantially by a factor of 3.1 (95% CI: 2.6–3.7) from period 1 to period 4. Factors mostly influencing healthcare costs following GRT were AIDS status, costs being 15% (95% CI: 6–24) higher in patients with AIDS compared with patients without AIDS, and baseline viral load, costs being 12% (95% CI: 6–17) higher in patients with each log increase in plasma RNA.

Conclusions

Optimized antiretroviral treatment regimens following GRT lead to a reduction of healthcare costs in patients with treatment failure over 2 years. Patients in a worse health state (that is, a positive AIDS status and high baseline viral load) will experience higher overall costs.

Net benefits of resistance testing directed therapy compared with standard of care in HIV-infected patients with virological failure: A meta-analysis

BACKGROUND

We incorporated the latest available information to evaluate the net benefit of using resistance testing in HIV-infected patients with virological failure.

METHODS

Meta-analysis of randomized controlled trials comparing the clinical impact of selecting antiretroviral therapy according to results of resistance testing (phenotype or genotype) or according to the standard of care. The population studied included HIV-infected patients with virological failure. The outcome measures were the proportion of patients with HIV-RNA below the detection limit, and the decline in HIV-RNA and increase in CD4 lymphocyte count at the end of follow-up (< or = 24 weeks). Clinical trials were identified through searches in MEDLINE, EMBASE and proceedings from major infectious diseases meetings.

RESULTS

Eight trials including a total of 1810 patients were eligible. Therapy guided by resistance testing resulted in a higher percentage of patients with HIV-1 RNA below the detection limit at the end of follow-up (< or = 24 weeks) as compared with the standard of care (40.2% vs. 32.9%). The pooled risk ratio was 1.23; 95% CI 1.09-1.40, p = 0.0009; test for heterogeneity I(2)=0%; p = 0.46). The number needed to treat [NNT] was 13 (95% CI: 9-25). Subgroup analysis showed greater benefits in therapy guided by genotype testing with expert interpretation, when compared with standard of care (NNT: 5; 95% CI: 3-9; p = 0.06). The heterogeneity among trials for evaluating HIV-1 RNA decline and CD4 lymphocyte cell count increase made unfeasible pooling the results across studies.

CONCLUSION

Genotype testing with expert interpretation showed the greatest benefit for guiding therapy in patients with HIV infection and virological failure.

Durable efficacy of enfuvirtide over 48 weeks in heavily treatment-experienced HIV-1-infected patients in the T-20 versus optimized background regimen only 1 and 2 clinical trials

BACKGROUND

The T-20 Versus Optimized Background Regimen Only (TORO) 1 and TORO 2 clinical trials are open-label, controlled, parallel-group, phase 3 studies comparing enfuvirtide plus an optimized background (OB) of antiretrovirals (n = 661) with OB alone (n = 334) in treatment-experienced HIV-1-infected patients.

METHODS

The primary objective at week 48 was to investigate durability of efficacy, as measured by the percentage of patients maintaining their week 24 response or improving. Efficacy analyses used the intent-to-treat population.

RESULTS

A total of 73.7% of patients randomized to the enfuvirtide group remained on treatment through week 48 versus 21.3% originally randomized to the control group. At week 48, a higher proportion of week 24 responders maintained their response or were new responders in the enfuvirtide group than in the control group in each responder category: HIV-1 RNA level > or =1.0 log(10) change from baseline, <400 copies/mL and <50 copies/mL (37.4%, 30.4%, and 18.3% in the enfuvirtide group vs. 17.1%, 12.0%, and 7.8% in the control group, respectively; P < 0.0001 for all comparisons). CD4 cell count increases from baseline were twice as great in the enfuvirtide group as in the control group.

CONCLUSION

These data demonstrate durable efficacy of enfuvirtide plus OB over 48 weeks.

Comparative performance evaluation of the HIV-1 LiPA protease and reverse transcriptase resistance assay on clinical isolates

BACKGROUND

Assays that provide information regarding HIV-1 resistance to antiretroviral drugs are widely used to help manage antiretroviral treatment. The most commonly used HIV genotypic resistance assays are based on DNA sequencing (TRUGENE, ViroSeq, and home-brew) or reverse hybridization (LiPA).

OBJECTIVES

This study compares the results from clinical specimens using two assay methods: the LiPA HIV-1 protease (PR) and reverse transcriptase (RT) resistance assay and DNA sequencing.

STUDY DESIGN

Operators at each of three sites tested 10-20 randomly selected clinical specimens using LiPA (three strips total with probes for PR codons 30, 46, 48, 50, 54, 82, 84, and 90, and RT codons 41, 69, 70, 74, 75, 103, 106, 151, 181, 184, and 215) and DNA sequencing (TRUGENE) HIV-1 Genotyping Assay or home-brew methodology). Results from the two methods were categorized for each codon as follows: (i) concordant (LiPA and sequencing having the same result for wild-type (WT), mutant, and mixture); (ii) partially concordant (mixture by one method and not by the other); (iii) indeterminate (no result by LiPA); and (iv) discordant (LiPA and sequencing detecting different amino acids).

RESULTS

A total of 50 clinical specimens were tested using the LiPA PR strip; 40 of these were also tested using the LiPA RT strip. For PR, 91.3% of the codon results were concordant, 3.0% were partially concordant, 4.5% were indeterminate by LiPA, and 1.3% were discordant. For RT, 88.0% of the codon results were concordant, 5.9% were partially concordant, 5.2% were indeterminate, and 0.9% were discordant. LiPA detected 3.0% (PR) and 6.4% (RT) WT/mutant mixtures, compared to 0.5% (PR) and 3.2% (RT) mixtures by sequencing.

CONCLUSIONS

More WT/mutant mixtures were detected using LiPA, possibly indicating increased sensitivity. Relatively high concordance and low discordance rates were observed between LiPA and DNA sequencing. The indeterminate rate for LiPA was moderately high and may limit the clinical utility of this assay.

Genotypic and phenotypic resistance testing of HIV-1 in routine clinical care

Data on genotypic and phenotypic resistance testing of HIV-1 in the routine clinical setting are lacking. In a retrospective single-center study, all patients (n = 102) for whom genotypic resistance typing (GRT) and phenotypic resistance typing (PRT) were performed during the calendar year 2002 were examined. GRT and PRT results were concordant for 79% of the drugs, being highest for nevirapine (92%) and lowest for didanosine (57%). Concordance of results for protease inhibitors was lowest for lopinavir (78%) and highest for indinavir (88%). Discordant results for lamivudine were observed in 16% of patients; 90% of these results corresponded to high-level resistance by PRT and susceptibility by GRT. Overall, HIV loads were lower and CD4+ cell counts higher after therapy following resistance testing, but a significant association with the number of active drugs as predicted by GRT or PRT could not be identified. In a subgroup of 43 patients with virological failure under antiretroviral therapy and sufficient follow-up data, HIV loads were significantly lower after 3 and 6 months. More patients with HIV loads <400/ml had 2 or more active drugs according to PRT (21/29 [75%]) than according to GRT ([15/29 [52%]; p = 0.109. This was also found for HIV loads <50/ml (PRT 16/22 [72%], GRT 10/22 [42%]; p = 0.103), although the differences were not statistically significant. There was no discernable difference between GRT and PRT in the clinic-based population, but the numbers of resistance tests performed are not sufficient to draw definitive conclusions.

Drug-resistance mutations in antiretroviral-naive patients with established HIV-1 infection in Mexico

OBJECTIVES

To describe the prevalence of baseline drug-resistance mutations, resistance to antiretroviral drugs, and the subsequent virological response to therapy in treatment-naïve patients from Mexico with established HIV-1 infection.

METHODS

Resistance testing was performed on plasma samples from antiretroviral-naïve patients. Data on mutations associated with antiretroviral drug resistance were obtained using Stanford software (http://hivdb.stanford.edu).

RESULTS

Ninety-six treatment-naïve individuals were enrolled in the study during 2002-2003. Of these, 83 patients (86%) had at least one resistance mutation and 15 (16%) had drug resistance. At baseline, the mean plasma viral load was 299 834 HIV-1 RNA copies/mL, and at follow-up it was 37 620 copies/mL (P<0.0001). Primary mutations in the reverse transcriptase region were observed in 15% of patients. For nucleoside inhibitors, mutations T215Y/C and F77L (3%) and D67N/S, T69N and M184V (2%), were detected. For nonnucleoside inhibitors, mutations K103N/R (6%), Y181C (3%) and G190A (2%) were detected. Overall, 6% of patients showed resistance to delavirdine and nevirapine, 4% to efavirenz, and 2% to lamivudine and nelfinavir. Twelve patients showed no response to treatment and three of these patients had antiretroviral drug resistance.

CONCLUSIONS

The prevalence of baseline drug-resistance mutations found in this study was similar to that found in previous reports for newly HIV-infected individuals, although access to and management of antiretrovirals in Mexico are different.

A direct comparison of drug susceptibility to HIV type 1 from antiretroviral experienced subjects as assessed by the antivirogram and PhenoSense assays and by seven resistance algorithms

HIV-1 drug resistance methodologies are being increasingly utilized to guide treatment decisions; however, information comparing the various assays is limited. Duplicate plasma samples from 70 ART-experienced subjects were analyzed by both the Antivirogram and PhenoSense phenotypic assays and the results compared. HIV genotypes were also obtained and analyzed using seven different resistance algorithms. These results were also compared with the phenotypic assay results. Concordances between the phenotypic tests and between each algorithm, and between the two phenotypic assays were calculated and kappa coefficients (KC) determined. Overall agreement between the two phenotypic assays was good (86.9% concordance; KC 0.621). The highest concordance by drug class was seen for protease inhibitors (93.4%; KC 0.679) and the lowest (79.8%; KC 0.549) for nucleoside reverse transcriptase inhibitors. Concordance between the two phenotypic assays, when evaluating individual drugs, was good for all drugs tested except for abacavir, zalcitabine, and indinavir. Agreement between the seven algorithms and each phenotypic assay was variable, though most had good or excellent agreement. The highest overall level of agreement for an individual drug was observed when comparing lamivudine susceptibility to either assay. Concordance for abacavir, didanosine, zalcitabine, and saquinavir was generally problematic when comparing one or more phenotypic assays to the drug resistance predictive algorithms. In conclusion, results comparing these two phenotypic tests were mostly similar, but comparisons of the predictive resistance algorithms for specific drugs, as well as to specific phenotypic assays, were more inconsistent.

Genotyping of B and non-B subtypes of human immunodeficiency virus type 1

Current HIV-1 genotyping assays were developed using subtype B viruses prevalent in Western countries. It is not clear whether these assays are appropriate for use among African patients, who are likely to be infected with non-B subtypes. We evaluated the Bayer TRUGENE HIV-1 genotyping (TG) assay using prospectively collected samples from HIV-1-infected individuals who acquired infection in either sub-Saharan Africa or the West (Europe, North America, and Australia). Plasma samples from 208 individuals with an HIV-1 viral load of >1,000 copies/ml were tested using version 1 primers supplied with the TG assay. If these failed, an alternative primer set version 1.5 was used. Of the 208 individuals, the likely origin of infection was Africa (n = 104), Western (n = 87) and "Others" (i.e., all other geographic locations or origin not certain; n = 17). Among the three groups, the version 1 primers were successful in 85 (82%), 77 (89%), and 13 (76%) individuals, respectively (P = 0.1). Of the remaining 32 samples, 30 were successfully amplified by using the version 1.5 primers. HIV-1 subtypes deduced from the reverse transcriptase sequences correlated with the likely origin of infection: Africa (28A, 3B, 33C, 13D, 6G, 4J, 2K, 5CRF01_AE, and 10CRF02_AG), Western (86B and 1K), and Others (1A and 16B). The success of the version 1 primers correlated with viral load (P < 0.014) and not with HIV-1 subtypes. A protocol based on version 1 primers, followed by 1.5 primers, was successful in sequencing 99% of the samples in this cohort.

Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes

Genotypic assays are used often to guide clinicians in decisions concerning the treatment of patients. An optimized sequence-based genotypic assay was used to determine the whole protease and reverse transcriptase (RT) gene, including the gag cleavage site region and RNase H region. Since non-B subtypes are increasing in countries where subtype B was the most prevalent subtype, and treatment becomes more available in developing countries where the epidemic is characterized by a high prevalence of non-B subtypes, it was important that the genotypic test was evaluated using a panel of different subtypes. Amplification was successful for different subtypes: A, B, C, D, F, G, H, J, CRF01_AE, CRF02_AG, CRF11_cpx, CRF13_cpx and an uncharacterized recombinant sample. The detection limit of the PCR was 1000 copies/ml, except for 1 subtype C sample (PL3) and 1 CRF02_AG sample (PL8). The detection limit for these samples was 5000 copies/ml. A sequence could be obtained in both directions for most of the samples.

In vitro synthesis of enzymatically active HIV-1 protease for rapid phenotypic resistance profiling

BACKGROUND

Given the expanding antiretroviral therapy, inexpensive and fast HIV drug resistance assays are urgently needed. In this view, we have developed a novel phenotypic resistance test for HIV-1 protease inhibitors (PIs) based on recombinant expression of patient-derived HIV PR in Escherichia coli and subsequent enzymatic testing in a fluorescent readout.

OBJECTIVES

To facilitate and expedite the test procedure, we have introduced coupled in vitro transcription/translation using a commercially available technology called RTS for producing enzymatically active HIV-1 protease (PR).

STUDY DESIGN

We expressed one wild type PR and one highly resistant mutant starting from molecular clones as well as three patient-derived PRs. The amplified PR gene was either ligated into an expression vector or directly used as a template for the in vitro transcription/translation reaction. Enzymatic susceptibility data derived from in vitro expressed PRs were correlated to the respective results from E. coli expression and genotypic evaluation.

RESULTS

All tested enzymes were obtained in sufficient quantities for complete resistance profiling to five PIs. The PRs required no purification prior to the enzymatic assay. Inhibition constants and enzymatic resistance factors compared well to corresponding data from PRs expressed in parallel in E. coli. Enzymatic resistance was in good agreement with the respective PR genotype.

CONCLUSION

The presented in vitro transcription/translation system represents a novel approach for HIV PR expression starting from molecular clones or patient samples. Coupled with the enzyme-kinetic PR assay recently developed in our group it allows to sensitively quantify resistance to PIs. The test system is significantly less laborious and faster than currently available phenotypic drug resistance assays.

RNA extraction prior to HIV-1 resistance detection using Line Probe Assay (LiPA): comparison of three methods

BACKGROUND

Genotyping testing has been accepted as a guidance in the therapeutic management of Human Immunodeficiency virus 1 (HIV-1). However, optimization of the available routine techniques for such purpose has not been fulfilled.

OBJECTIVE

To evaluate the use of three RNA extraction methods in order to be applied in the genotypic HIV-1 resistance testing by LiPA.

STUDY DESIGN

Comparative prospective study of three HIV-1 RNA extraction methods. Forty-eight plasma samples were tested for the determination of viral load (VL) by means of Cobas Amplicor HIV-1 Monitor (Roche Diagnostics. Branchburg, NJ, USA), preserving the obtained RNA extracts. RNA was also extracted using two other techniques: "SV Total RNA Isolation System" (Promega Corporation. Madison, WI, USA) and "QIAamp Viral RNA" (QIAGEN Inc., Valencia, CA, USA). The three RNA extracts were processed in parallel for the detection of HIV resistance by LiPA, and bands were recorded comparatively.

RESULTS

Results obtained by Roche extraction method were superior, followed by those of Qiagen and Promega, in the several studied parameters. First, proportion of amplified samples (75.0% by Promega versus 95.8 by Qiagen and 97.9% by Roche for LiPA RT and 97.7% by Promega versus 100.0% by Roche and Qiagen for LiPA P); second, percentage of combined mutations patterns, and third, differences in band intensity. Thus, for LiPA RT 51.4% and 54.3% of the samples showed greater intensity after Roche and Qiagen extractions, respectively. These percentages dropped to 12.8 and 19.1 for LiPA P.

CONCLUSIONS

The outcome obtained by LiPA after RNA extraction by Roche methodology was remarkably superior to those of Promega and Qiagen. LiPA technique needs further optimization, especially the sample amplification phase of LiPA RT.

Comparison between sequence analysis and a line probe assay for testing genotypic resistance of human immunodeficiency virus type 1 to antiretroviral drugs

The purpose of this study was to compare a line probe assay (LiPA) with sequence analysis for the detection of mutations conferring resistance to nucleoside and non-nucleoside inhibitors in human immunodeficiency reverse transcriptase and protease inhibitors. The limitations for interpreting LiPA make it unacceptable for routine clinical practice.

High sequence conservation of human immunodeficiency virus type 1 reverse transcriptase under drug pressure despite the continuous appearance of mutations

To define the extent of sequence conservation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) in vivo, the first 320 amino acids of RT obtained from 2,236 plasma-derived samples from a well-defined cohort of 1,704 HIV-1-infected individuals (457 drug naïve and 1,247 drug treated) were analyzed and examined in structural terms. In naïve patients, 233 out of these 320 residues (73%) were conserved (<1% variability). The majority of invariant amino acids clustered into defined regions comprising between 5 and 29 consecutive residues. Of the nine longest invariant regions identified, some contained residues and domains critical for enzyme stability and function. In patients treated with RT inhibitors, despite profound drug pressure and the appearance of mutations primarily associated with resistance, 202 amino acids (63%) remained highly conserved and appeared mostly distributed in regions of variable length. This finding suggests that participation of consecutive residues in structural domains is strictly required for cooperative functions and sustainability of HIV-1 RT activity. Besides confirming the conservation of amino acids that are already known to be important for catalytic activity, stability of the heterodimer interface, and/or primer/template binding, the other 62 new invariable residues are now identified and mapped onto the three-dimensional structure of the enzyme. This new knowledge could be of help in the structure-based design of novel resistance-evading drugs.

Comparison of HIV type 1 protease inhibitor susceptibility results in viral samples analyzed by phenotypic drug resistance assays and by six resistance algorithms: an analysis of a subpopulation of the CHORUS cohort

Drug resistance testing is increasingly used to guide treatment decisions in patients infected with HIV-1. A number of rules-based algorithms have been designed to predict drug resistance profiles based on the HIV-1 genotypic data. Drug-resistance mutations in 206 viral samples from protease inhibitor (PI)-experienced subjects with HIV-1 infection were assessed, and the level of susceptibility of the samples predicted using seven unique algorithms. kappa scores were used to compare agreement of results obtained using each of the predictive algorithms with the phenotypic assay results. Good overall agreement between the different algorithms and the phenotypic results was observed. Good or excellent agreement was observed between the results obtained by the predictive algorithms and the phenotypic assay results for ritonavir, indinavir, saquinavir, and nelfinavir. For amprenavir and lopinavir, there were marked differences between the different algorithms, with poor agreement (kappa < 0.40) obtained with four of the seven algorithms for amprenavir. For lopinavir, poor agreement was obtained with three of seven algorithms using the 2.5-fold biological cut-off and four of seven with the clinical cut-off of 10. Atazanavir susceptibility was evaluated for concordance among six algorithms, with a range of 23-50% of the samples maintaining susceptibility. Although this cohort of patients included many who were highly antiretroviral experienced, predictive algorithms demonstrated good agreement with phenotype for several Pls. For those where discordance among algorithms existed, further improvement will likely occur as drug resistance pathways for the more recently approved PIs are elucidated.

Multiple drug class-wide resistance associated with poorer survival after treatment failure in a cohort of HIV-infected patients

OBJECTIVE

To evaluate the effect of drug class-wide resistance (CWR) on survival in HIV-infected individuals who underwent genotypic resistance test after antiretroviral failure.

DESIGN

Observational, longitudinal cohort study.

METHODS

HIV-infected individuals experiencing treatment failure were enrolled at first genotypic resistance test. End-points were death for any cause, AIDS-related death and AIDS-defining event/death. CWR was defined according to the International AIDS Society consensus. Survival analysis was performed with Cox's model.

RESULTS

Among 623 patients enrolled and followed for a median of 19 months (interquartile range, 12-29), Kaplan-Meier analyses for end-points at 48 months in patients with no CWR, one CWR, two CWR or three CWR were 8.9, 11.7, 13.4 and 27.1%, respectively, for death; 6.1, 9.9, 13.4 and 21.5%, respectively, for AIDS-related death; and 16.0, 17.7, 19.3 and 35.9%, respectively, for new AIDS event/death. In a multivariate Cox's model, higher HIV RNA level, previous AIDS and detection of three CWR (hazard ratio, 5.34; 95% confidence interval, 1.76-16.24) were all significantly associated with increased risk of death, while higher CD4 cell count and use of a new boosted protease inhibitor drug after identifying genotypic resistance were associated with reduced risk. Detection of three CWR was also significantly associated with higher risk of AIDS-related death and new AIDS event/death.

CONCLUSIONS

Even in the late era of highly effective antiretroviral treatments, detection of CWR, particularly if extended to all three drug classes is related to poorer clinical outcome and represents a risk-marker of disease progression and death.

Antiretroviral recommendations may influence the rate of transmission of drug-resistant HIV type 1

BACKGROUND

Human immunodeficiency virus (HIV) treatment guidelines have evolved, shifting from more-aggressive to more-conservative approaches. The potential impact of these shifts on the transmission of drug-resistant virus is unknown.

METHODS

Drug-resistance genotypes were examined in all consecutive patients with recent HIV type 1 (HIV-1) seroconversion (hereafter, "HIV-1 seroconverters") seen at 10 Spanish hospitals since 1997. During the same period, the proportion of patients with chronic HIV-1 infection having undetectable viremia was examined, to estimate the extent and effectiveness of antiretroviral therapy.

RESULTS

A total of 141 recent HIV-1 seroconverters were identified, 67.4% of whom were men who have sex with men. The rate of primary drug-resistance mutations, by year of infection, was 33.3% for 1997, 29.4% for 1998, 20% for 1999, 14.3% for 2000, 3.4% for 2001, 15.4% for 2002, and 10.9% for 2003. On the other hand, the proportion of 8388 persons with chronic HIV-1 carriage who had an undetectable virus load was 33.4% for 1997, 34.6% for 1998, 39.7% for 1999, 47.5% for 2000, 52.9% for 2001, 39.7% for 2002, and 58.1% for 2003. A significant inverse correlation between transmission of drug-resistant HIV-1 and undetectable virus load was found (r=-0.955, by Spearman's test; P=.001). The lowest rate of transmission of drug-resistant HIV-1 was seen in 2001, when relatively "aggressive" treatment guidelines were used. Transmission of drug-resistant HIV-1 increased in 2002, in parallel with a reduction in the number of patients with chronic HIV-1 carriage and undetectable virus load, reflecting the popularity of drug holidays or treatment interruptions.

CONCLUSION

The rate of drug resistance in recent HIV-1 seroconverters inversely correlates with the proportion of chronically HIV-1-infected individuals who have undetectable virus loads in the same region, which indirectly reflects antiretroviral treatment rules at any given time.

A randomized controlled trial of the value of phenotypic testing in addition to genotypic testing for HIV drug resistance: evaluation of resistance assays (ERA) trial investigators

OBJECTIVES

To assess the clinical utility of phenotypic resistance testing in addition to genotypic resistance testing among HIV-1-infected patients experiencing virologic failure and with limited therapeutic options.

DESIGN

Multicenter randomized trial.

METHODS

Patients were eligible if a decision had been made to switch antiretroviral therapy, the most recent HIV-1 RNA plasma viral load (VL) exceeded 2000 copies/mL, and the clinician was unable to select a potent regimen of 3 or more drugs without access to a resistance test. Subjects were randomized to genotypic resistance testing alone (G arm) or to genotypic plus phenotypic testing (G + P arm). Patients had access to resistance testing at any time during follow-up (minimum of 1 year) according to the original allocation. The primary end point was change in plasma VL from baseline at 12 months.

RESULTS

Three hundred eleven patients were recruited between February 2000 and July 2001. At baseline, mean VL and CD4 count were 4.23 log10 copies/mL and 275 cells/mm, respectively, and subjects had previous exposure to a mean of 7.7 antiretroviral drugs. There was no appreciable difference between the study arms in the drug regimens prescribed after randomization. Mean reduction in VL load at 12 months was similar in the 2 arms (G: 1.37 log10 reduction, G + P: 1.28 log10 reduction; P = 0.77), as was the proportion of subjects with VL <50 copies/mL (G: 35%, G + P: 27%).

CONCLUSION

The study did not demonstrate added value of phenotypic resistance testing in conjunction with genotypic resistance testing in patients with limited therapeutic options.

Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: an international comparison (The GUESS Study)

BACKGROUND

Resistance testing is considered standard of care in HIV medicine, but there is no standard interpretation system for genotype tests. We sought to determine how much agreement exists within a group of experts in the interpretation of complex genotypes.

METHODS

Genotypes from clinical specimens were sent to an international panel of 12 resistance experts. Phenotypic susceptibility testing of these clinical isolates was performed with antivirogram. Experts predicted phenotype fold change category (<2.5-fold change, 2.5-4.0-fold change, >4.0- to 7.0-fold change, >7.0- to 10-fold change, >10- to 20-fold change, or >20-fold change) and predicted expected drug activity for each of 16 antiretroviral drugs. Experts were also asked to make treatment recommendations on the basis of the genotype.

RESULTS

The experts predicted the exact phenotype fold change category correctly 44% of the time, but they varied widely by antiretroviral drug (range, 25%-74%). The highest accuracy was observed for lamivudine (74%) and the nonnucleoside reverse transcriptase inhibitors (66%-69%). Experts generally predicted higher levels of resistance to the remaining nucleoside reverse transcriptase inhibitors than what was found by phenotypic testing. Agreement among experts in predicting phenotype fold change category ranged widely depending on the drug (median agreement, 42% [range, 28%-74%]); the same pattern was observed in predicting expected drug activity (median agreement, 45% [range, 32%-87%]). Experts agreed on treatment recommendations in a median of 79% of instances, and recommendations were consistent over time, with blinded retesting.

CONCLUSIONS

Although their ability to predict phenotype from a genotype varied for individual antiretroviral drugs, this expert panel had a high degree of agreement in deriving treatment recommendations from the genotype.

Resistencias genotípicas en pacientes con infección por el virus de la inmunodeficiencia humana. Correlación con las pautas terapéuticas empleadas en su tratamiento

BACKGROUND AND OBJECTIVE

Our goal was to establish the different therapeutic regimens used in our clinical setting, and to determine the prevalence of genotypic resistances in patients under antiretroviral therapy, analyzing the relationship between the appearance of mutations and treatments along with other HIV related variables.

MATERIAL AND METHOD

191 samples from the same number of patients who were on antiretroviral therapy and virological failure were analyzed. Samples were processed by means of the genotypic technique LiPA in order to study the presence of mutations in the reverse transcriptase (RT) and the protease (P) genes. Prescribed therapeutic regimens and epidemiological variables relevant in HIV infection were also analyzed.

RESULTS

Overall resistance prevalence was 72.32%. By LiPA, RT mutations were detected in 71.43% of patients, being M184V, T215Y and L41M the most frequent ones. Moreover, P mutations were detected in 59.38% of cases, being V82A, L90M and I84V the most frequent ones. 61.02% of the patients presented one or more mutations against the reverse transcriptase inhibitors included in their treatment. With regard to protease inhibitors, this fact was documented in 28.81% of cases, and in 23.73% of patients receiving both reverse transcriptase inhibitors and protease inhibitors.

CONCLUSIONS

Although the analysis of the mutation patterns by LiPA has known limitations, the prevalence of resistances in our study was different from that reported by other authors, being lower in the P gene and higher in the RT one. Of note, a high proportion of patients showed mutations against the drugs included in their prescribed treatment.

Rare mutations at codon 103 of HIV-1 reverse transcriptase can confer resistance to non-nucleoside reverse transcriptase inhibitors

BACKGROUND

The K103N mutation in HIV-1 reverse transcriptase (RT) confers high-level resistance to current non-nucleoside reverse transcriptase inhibitors (NNRTI). The prevalence and resistance profile of HIV-1 with other substitutions at RT codon 103 is less well documented.

METHODS

K103 substitutions among over 70,000 clinical samples submitted for routine antiretroviral resistance testing at two independent centres were examined. Phenotypic resistance profiles of isolates harboring rare K103 variants in the absence of known NNRTI-associated resistance mutations were retrieved from Virco's correlative genotype/phenotype database. Genotyped samples with known treatment histories were retrieved from the British Columbia Centre for Excellence in HIV/AIDS database. Site-directed mutants containing K103 variants were constructed and phenotyped.

RESULTS

K103N, R and S were observed in 29, 1.8, and 0.9% of Virco isolates and in 16, 1.5 and 0.4% of British Columbia isolates. K103T/Q/H substitutions were observed only rarely (<0.2%). The prevalence of unusual codon 103 substitutions remained stable over 5 years, except K103S, which increased over fourfold in both datasets. K103R/Q-containing clinical isolates remained phenotypically susceptible to NNRTI, whereas K103S/T/H-containing isolates showed over 10-fold decreased NNRTI susceptibility. Among patients with a known treatment history, K103S/T/H were observed primarily in individuals failing NNRTI-containing regimens. Site-directed mutants confirmed decreased susceptibility to NNRTI in K103S/T/H-containing recombinants.

CONCLUSION

Variants at HIV RT codon 103 other than K103N are observed relatively rarely in clinical isolates, but K103 S, T and H confer decreased susceptibility to NNRTI. These data are relevant for interpretive genotype algorithms and in the design of assays specific to RT codon 103 mutations.