Frequency of Genotypic and Phenotypic Drug-Resistant HIV-1 Among Therapy-Naive Patients of the German Seroconverter Study:

Pre-treatment drug resistance and HIV-1 genetic diversity in the rural and urban settings of Northwest-Cameroon

Background

With the scale-up of antiretroviral therapy (ART), pre-treatment drug resistance (PDR) appears ≥10% amongst ART-initiators in many developing countries, including Cameroon. Northwest region-Cameroon having the second epidemiological burden of HIV infection, generating data on PDR in these geographical settings, will enhance evidence-based decision-making.

Objectives

We sought to ascertain levels of PDR and HIV-1 clade dispersal in rural and urban settings, and their potential association with subtype distribution and CD4-staging.

Methods

A cross-sectional study was conducted from February to May 2017 among patients recently diagnosed with HIV-infection and initiating ART at the Bamenda regional Hospital (urban setting) and the Mbingo Baptist hospital (rural setting). Protease and reverse transcriptase sequencing was performed using an in-house protocol and pre-treatment drug resistance mutations were interpreted using Stanford HIVdb.v8.3. Phylogeny was performed for subtype assignation.

Results

A total of 61 patient sequences were generated from ART initiators (median age: 37 years old; 57.4% female; median CD4 cell count: 184 [IQR: 35–387] in urban vs. 161 [IQR: 96–322] cells/mm³ in rural). Overall, the level of PDR was 9.8% (6/61). Of note, burden of PDR was almost doubled in urban (12.9% [4/31]) compared to rural setting 6.7% (2/30), p = 0.352). Fifteen (15) PDR mutations were found among four patients the urban settings [6 resistance mutations to NRTIs:[M41L (2), E44D (1), K65R (1), K70E (1), M184V/I (2), K219R (1)] and 6 resistance mutations to NNRTIs: K103N (1), E138A/G (2), V179E (1), M230L (1), K238T (1), P225H (1)] against two (02) mutations found in two patients in the rural setting[2 resistant mutations to NNRTIs: E138A (1) and Y188H (1)]. The rural setting showed more genetic diversity (8 subtypes) than the urban setting (5 subtypes), with CRF02_AG being the most prevalent clade (72.1% [44/61]). Of note, level of PDR was similar between patients infected with CRF02_AG and non-CRF02_AG infected (9.1% [4/44]) vs. 11.8% [2/17]), p = 1.000). Moreover, PDR appeared higher in patients with CD4 cell count <200 cells/mm³ compared to those with CD4 cell count ≥200 cells/mm³ (14.7% [5/34]) vs. 3.7% [1/27]), p = 0.214).

Conclusions

PDR is at a moderate rate in the Northwest region of Cameroon, with higher burden within urban populations. CRF02_AG is the most predominant clade in both urban and rural settings. No effect of HIV molecular epidemiology and CD4-staging on the presence of PDR in patients living in these settings was found. Our findings suggest close monitoring, NNRTI-sparing regimens or sequencing for patients initiating ART, especially in urban settings.

Parallel evolution of HIV-1 in a long-term experiment

One of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost 1 year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over 1 year in each evolution line. Many majority mutations appeared in more than one evolution line, that is, our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by phylogenetic methods. We show that one can infer the correct phylogenetic topology by including minority mutations in our analysis. We also find that mutation diversity at the beginning of the experiment is predictive of the frequency of majority mutations at the end of the experiment.

The Pre-clinical Toolbox of Pharmacokinetics and Pharmacodynamics: in vitro and ex vivo Models

Prevention strategies against sexual transmission of human immunodeficiency virus (HIV) are essential to curb the rate of new infections. In the absence of a correlate of protection against HIV infection, pre-clinical evaluation is fundamental to facilitate and accelerate prioritization of prevention candidates and their formulations in a rapidly evolving clinical landscape. Characterization of pharmacokinetic (PK) and pharmacodynamic (PD) properties for candidate inhibitors is the main objective of pre-clinical evaluation. in vitro and ex vivo systems for pharmacological assessment allow experimental flexibility and adaptability at a relatively low cost without raising as significant ethical concerns as in vivo models. Applications and limitations of pre-clinical PK/PD models and future alternatives are reviewed in the context of HIV prevention.

Antiretroviral resistance testing in HIV-positive people

BACKGROUND

Resistance to antiretroviral therapy (ART) among people living with human immunodeficiency virus (HIV) compromises treatment effectiveness, often leading to virological failure and mortality. Antiretroviral drug resistance tests may be used at the time of initiation of therapy, or when treatment failure occurs, to inform the choice of ART regimen. Resistance tests (genotypic or phenotypic) are widely used in high-income countries, but not in resource-limited settings. This systematic review summarizes the relative merits of resistance testing in treatment-naive and treatment-exposed people living with HIV.

OBJECTIVES

To evaluate the effectiveness of antiretroviral resistance testing (genotypic or phenotypic) in reducing mortality and morbidity in HIV-positive people.

SEARCH METHODS

We attempted to identify all relevant studies, regardless of language or publication status, through searches of electronic databases and conference proceedings up to 26 January 2018. We searched MEDLINE, Embase, the Cochrane Central Register of Controlled Trials (CENTRAL), in the Cochrane Library, the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP), and ClinicalTrials.gov to 26 January 2018. We searched Latin American and Caribbean Health Sciences Literature (LILACS) and the Web of Science for publications from 1996 to 26 January 2018.

SELECTION CRITERIA

We included all randomized controlled trials (RCTs) and observational studies that compared resistance testing to no resistance testing in people with HIV irrespective of their exposure to ART.Primary outcomes of interest were mortality and virological failure. Secondary outcomes were change in mean CD4-T-lymphocyte count, clinical progression to AIDS, development of a second or new opportunistic infection, change in viral load, and quality of life.

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed each reference for prespecified inclusion criteria. Two review authors then independently extracted data from each included study using a standardized data extraction form. We analysed data on an intention-to-treat basis using a random-effects model. We performed subgroup analyses for the type of resistance test used (phenotypic or genotypic), use of expert advice to interpret resistance tests, and age (children and adolescents versus adults). We followed standard Cochrane methodological procedures.

MAIN RESULTS

Eleven RCTs (published between 1999 and 2006), which included 2531 participants, met our inclusion criteria. All of these trials exclusively enrolled patients who had previous exposure to ART. We found no observational studies. Length of follow-up time, study settings, and types of resistance testing varied greatly. Follow-up ranged from 12 to 150 weeks. All studies were conducted in Europe, USA, or South America. Seven studies used genotypic testing, two used phenotypic testing, and two used both phenotypic and genotypic testing. Only one study was funded by a manufacturer of resistance tests.Resistance testing made little or no difference in mortality (odds ratio (OR) 0.89, 95% confidence interval (CI) 0.36 to 2.22; 5 trials, 1140 participants; moderate-certainty evidence), and may have slightly reduced the number of people with virological failure (OR 0.70, 95% CI 0.56 to 0.87; 10 trials, 1728 participants; low-certainty evidence); and probably made little or no difference in change in CD4 cell count (mean difference (MD) -1.00 cells/mm³, 95% CI -12.49 to 10.50; 7 trials, 1349 participants; moderate-certainty evidence) or progression to AIDS (OR 0.64, 95% CI 0.31 to 1.29; 3 trials, 809 participants; moderate-certainty evidence). Resistance testing made little or no difference in adverse events (OR 0.89, 95% CI 0.51 to 1.55; 4 trials, 808 participants; low-certainty evidence) and probably reduced viral load (MD -0.23, 95% CI -0.35 to -0.11; 10 trials, 1837 participants; moderate-certainty evidence). No studies reported on development of new opportunistic infections or quality of life. We found no statistically significant heterogeneity for any outcomes, and the I² statistic value ranged from 0 to 25%. We found no subgroup effects for types of resistance testing (genotypic versus phenotypic), the addition of expert advice to interpretation of resistance tests, or age. Results for mortality were consistent when we compared studies at high or unclear risk of bias versus studies at low risk of bias.

AUTHORS' CONCLUSIONS

Resistance testing probably improved virological outcomes in people who have had virological failure in trials conducted 12 or more years ago. We found no evidence in treatment-naive people. Resistance testing did not demonstrate important patient benefits in terms of risk of death or progression to AIDS. The trials included very few participants from low- and middle-income countries.

Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors

BACKGROUND

Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs).

METHODS

We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006. Shannon entropy was calculated to determine the variability at each amino acid position. Time trends in the frequency of amino acid variants were identified by linear regression. Direct coupling analysis was applied to detect covarying sites.

RESULTS

Twenty-two time trends in the frequency of amino acid variants demonstrated either single amino acid exchanges or variation in the degree of polymorphy. Covariation was observed for 17 amino acid variants with a temporal trend. Some minor INSTI resistance mutations (T124A, V151I, K156 N, T206S, S230 N) and some INSTI-selected mutations (M50I, L101I, T122I, T124 N, T125A, M154I, G193E, V201I) were identified at overall frequencies >5%. Among these, the frequencies of L101I, T122I, and V201I increased over time, whereas the frequency of M154I decreased. Moreover, L101I, T122I, T124A, T125A, M154I, and V201I covaried with non-resistance-associated variants.

CONCLUSIONS

Time-trending, covarying polymorphisms indicate that long-term evolutionary changes of the HIV-1 integrase involve defined clusters of possibly structurally or functionally associated sites independent of selective pressure through INSTIs at the inter-patient level. Linkage between polymorphic resistance- and non-resistance-associated sites can impact the selection of INSTI resistance mutations in complex ways. Identification of these sites can help in improving genotypic resistance assays, resistance prediction algorithms, and the development of new integrase inhibitors.

Multiscale Systems-Pharmacology Pipeline to Assess the Prophylactic Efficacy of NRTIs Against HIV-1

While HIV-1 continues to spread, the use of antivirals in preexposure prophylaxis (PrEP) has recently been suggested. Here we present a modular systems pharmacology modeling pipeline, predicting PrEP efficacy of nucleotide reverse transcriptase inhibitors (NRTIs) at the scale of reverse transcription, target-cell, and systemic infection and after repeated viral exposures, akin to clinical trials. We use this pipeline to benchmark the prophylactic efficacy of all currently approved NRTIs in wildtype and mutant viruses. By integrating pharmacokinetic models, we find that intracellular tenofovir-diphosphate builds up too slowly to halt infection when taken "on demand" and that lamivudine may substitute emtricitabine in PrEP combinations. Lastly, we delineate factors confounding clinical PrEP efficacy estimates and provide a method to overcome these. The presented framework is useful to screen and optimize PrEP candidates and strategies and to understand their clinical efficacy by integrating the diverse scales which determine PrEP efficacy.

Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker for identification of recent infections in HIV-1 incidence studies

An increase in the proportion of ambiguous base calls in HIV-1 pol population sequences during the course of infection has been demonstrated in different study populations, and sequence ambiguity thresholds to classify infections as recent or nonrecent have been suggested. The aim of our study was to evaluate sequence ambiguities as a candidate biomarker for use in an HIV-1 incidence assay using samples from antiretroviral treatment-naive seroconverters with known durations of infection (German HIV-1 Seroconverter Study). We used 2,203 HIV-1 pol population sequences derived from 1,334 seroconverters to assess the sequence ambiguity method (SAM). We then compared the serological incidence BED capture enzyme immunoassay (BED-CEIA) with the SAM for a subset of 723 samples from 495 seroconverters and evaluated a multianalyte algorithm that includes BED-CEIA results, SAM results, viral loads, and CD4 cell counts for 453 samples from 325 seroconverters. We observed a significant increase in the proportion of sequence ambiguities with the duration of infection. A sequence ambiguity threshold of 0.5% best identified recent infections with 76.7% accuracy. The mean duration of recency was determined to be 208 (95% confidence interval, 196 to 221) days. In the subset analysis, BED-CEIA achieved a significantly higher accuracy than the SAM (84.6 versus 75.5%, P < 0.001) and results were concordant for 64.2% (464/723) of the samples. Also, the multianalyte algorithm did not show better accuracy than the BED-CEIA (83.4 versus 84.3%, P = 0.786). In conclusion, the SAM and the multianalyte algorithm including SAM were inferior to the BED-CEIA, and the proportion of sequence ambiguities is therefore not a preferable biomarker for HIV-1 incidence testing.

First line treatment response in patients with transmitted HIV drug resistance and well defined time point of HIV infection: updated results from the German HIV-1 seroconverter study

Background

Transmission of drug-resistant HIV-1 (TDR) can impair the virologic response to antiretroviral combination therapy. Aim of the study was to assess the impact of TDR on treatment success of resistance test-guided first-line therapy in the German HIV-1 Seroconverter Cohort for patients infected with HIV between 1996 and 2010. An update of the prevalence of TDR and trend over time was performed.

Methods

Data of 1,667 HIV-infected individuals who seroconverted between 1996 and 2010 were analysed. The WHO drug resistance mutations list was used to identify resistance-associated HIV mutations in drug-naïve patients for epidemiological analysis. For treatment success analysis the Stanford algorithm was used to classify a subset of 323 drug-naïve genotyped patients who received a first-line cART into three resistance groups: patients without TDR, patients with TDR and fully active cART and patients with TDR and non-fully active cART. The frequency of virologic failure 5 to 12 months after treatment initiation was determined.

Results

Prevalence of TDR was stable at a high mean level of 11.9% (198/1,667) in the HIV-1 Seroconverter Cohort without significant trend over time. Nucleotide reverse transcriptase inhibitor resistance was predominant (6.0%) and decreased significantly over time (OR = 0.92, CI = 0.87–0.98, p = 0.01). Non-nucleoside reverse transcriptase inhibitor (2.4%; OR = 1.00, CI = 0.92–1.09, p = 0.96) and protease inhibitor resistance (2.0%; OR = 0.94, CI = 0.861.03, p = 0.17) remained stable. Virologic failure was observed in 6.5% of patients with TDR receiving fully active cART, 5,6% of patients with TDR receiving non-fully active cART and 3.2% of patients without TDR. The difference between the three groups was not significant (p = 0.41).

Conclusion

Overall prevalence of TDR remained stable at a rather high level. No significant differences in the frequency of virologic failure were identified during first-line cART between patients with TDR and fully-active cART, patients with TDR and non-fully active cART and patients without TDR.

Trends in prevalence of HIV-1 drug resistance in Thailand 2009-2010

BACKGROUND

Treatment failure of antiretroviral therapy in HIV-1 infection is increasing due to development of viral resistance. Trends of resistance-associated mutation lead to the ineffective treatment in HIV-infected individuals.

METHODS

Extracted viral RNA from HIV-infected subjects in 2009 to 2010 was performed. The genotypic resistance testing was investigated for HIV-1 drug resistance in RT and PR genes. Frequencies of mutation were compared by a Fischer's exact test.

RESULTS

Three hundred and sixty-nine samples (147 in 2009 and 222 in 2010) were genotyped. At least one mutation was found in 90.8% (335/369) in PR gene and 87.0% (321/369) in RT gene. Three sequences in PR gene, M36I, H69K, and L90M, were decreased significantly in 2010 when compared to 2009. Mutations associated with resistance to nucleoside analogue reverse transcriptase inhibitors (NRTI's) were found in 61.0% and 64.2% in nonnucleoside analogue reverse transcriptase inhibitors (NNRTI's). A total of 49.6% was found in combined NRTI and NNRTI. In 2010, M41L was increased significantly from 7.5% to 14.9%. However, there was a decrease in the frequency of the mutations at position 67, 70, and 184 between 2009 and 2010.

CONCLUSIONS

In 2010, three mutations in PR gene, M36I, H69K, and L90M, were decreased significantly. However, only one mutation in RT gene, M41L was significantly increased.

Prevalence of Genotypic Resistance to Nucleoside Analogues and Protease Inhibitors in Antiretroviral-Naive HIV Patients in Campania, Italy

The aim of our study was to determine the prevalence of genotypic resistance to nucleoside analogues and protease inhibitors before and after 1997, the year of introduction of Highly Active Antiretroviral Therapy (HAART) in Campania (Italy). Forty-eight plasma HIV-RNA positive patients who had not been previously treated for HIV infection (naïve) were enrolled in two Divisions of Infectious Diseases. The main demographic characteristics were collected for each subject and the primary mutant genotypes were sought only in HIV-RNA positive patients with viral loads higher than 10,000 copies/ml. The diagnosis of HIV infection dated back to before 1996 for 21 out of 48 patients and to after 2000 for the other 27. INNO-Line Probe Assay (LiPA) HIV-RT and INNO-LiPA HIV protease (Innogenetics, Italy) were used to detect mutations conferring resistance to zidovudine, didanosine, zalcitabine, lamivudine, stavudine, saquinavir, indinavir, rotonavir, nelfinavir and amprenavir. No mutations associated with primary resistance to nucleoside analogues and protease inhibitors were detected in the 21 patients who had acquired HIV infection before 1996, whereas one or more mutations were seen in three of the 27 (11.1%) patients with HIV infection diagnosed after 2000. This study confirms that LiPA is a suitable tool for epidemiological surveys of HIV genotypic primary resistance. Drug-resistant HIV-1 genotypes, resistant both to nucleoside analogues and protease inhibitors, were detected only in subjects who had acquired HIV infection after 2000, most of whom had zidovudine-resistant mutants. These data suggest that the introduction of HAART has brought about the circulation of drug-resistant HIV genotypes.

Preclinical evaluation of the HIV-1 fusion inhibitor L'644 as a potential candidate microbicide

Topical blockade of the gp41 fusogenic protein of HIV-1 is one possible strategy by which microbicides could prevent HIV transmission, working early against infection, by inhibiting viral entry into host cells. In this study, we examined the potential of gp41 fusion inhibitors (FIs) as candidate anti-HIV microbicides. Preclinical evaluation of four FIs, C34, T20, T1249, and L'644, was performed using cellular and ex vivo genital and colorectal tissue explant models. Increased and sustained activity was detected for L'644, a cholesterol-derivatized version of C34, relative to the other FIs. The higher potency of L'644 was further increased with sustained exposure of cells or tissue to the compound. The activity of L'644 was not affected by biological fluids, and the compound was still active when tissue explants were treated after viral exposure. L'644 was also more active than other FIs against a viral escape mutant resistant to reverse transcriptase inhibitors (RTIs), demonstrating the potential of L'644 to be included as part of a multiactive antiretroviral (ARV) combination-based microbicide. These data support the further development of L'644 for microbicide application.

Colorectal microbicide design: triple combinations of reverse transcriptase inhibitors are optimal against HIV-1 in tissue explants

OBJECTIVE

Receptive anal intercourse in both men and women is associated with the highest probability for sexual acquisition of HIV infection. As part of a strategy to develop an effective rectal microbicide, we performed an ex-vivo preclinical evaluation to determine the efficacy and limitation of multiple combinations of reverse transcriptase inhibitors (RTIs).

DESIGN

A nucleotide, PMPA (tenofovir), a nucleoside, FTC (emtricitabine), RTIs and two nonnucleoside RTIs, UC781 and TMC120 (dapivirine), were used in double, triple and quadruple combinations against a panel of CCR5-uing and CXCR4-using clade B HIV-1 isolates and against RTI-escape variants.

METHODS

Indicator cells and colorectal tissue explants were used to assess antiviral activity of drug combinations.

RESULTS

All combinations inhibited the isolates tested in a cellular model and in colorectal explants and produced, for at least one of the compounds, a change in the dose-response curve. Double and triple combinations incrementally augmented activity, even against RTI-escape mutants, whereas quadruple combinations conferred little further advantage.

CONCLUSION

The colorectal explant model may be used to identify the best candidate molecules and their combinations at the preclinical stage. Furthermore, this study demonstrates that combinations based on RTIs with different HIV-1 inhibitory mechanisms have potential as colorectal microbicides.

Evaluation of resistance development and viability recovery by a non-enveloped virus after repeated cycles of aPDT

Nowadays, the emergence of drug resistant microorganisms is a public health concern. The antimicrobial photodynamic therapy (aPDT) has an efficient action against a wide range of microorganisms and can be viewed as an alternative approach for treating microbial infections. The aim of this study was to determine if a model target virus (T4-like bacteriophage), in the presence of the tricationic porphyrin 5,10,15-tris(1-methylpyridinium-4-yl)-20-(pentafluorophenyl)porphyrin tri-iodide (Tri-Py(+)-Me-PF), can develop resistance to aPDT and recover its viability after photodynamic treatments. To assess the development of aPDT resistance after repeated treatments, a suspension of T4-like bacteriophage was irradiated with white light (40 Wm(-2)) for 120 min in the presence of 5.0 μM of Tri-Py(+)-Me-PF (99.99% of inactivation) and new phage suspensions were produced from the surviving phages, after each cycle of light exposure. The procedure was repeated ten times. To evaluate the recovery of viral viability after photoinactivation, a suspension of T4-like bacteriophage was irradiated with white light for 120 min in the presence of 5.0 μM of Tri-Py(+)-Me-PF on five consecutive days. In each day, an aliquot of the irradiated suspension was plated and the number of lysis plaques was counted after 24, 48, 72, 96 and 120 h of dark incubation at 37 °C. The profile of bacteriophage photoinactivation did not change after ten consecutive cycles and no recovery of viability was detected after five accumulated cycles of photodynamic treatment. The results suggest that aPDT represents a valuable and promising alternative therapy to treat viral infections, overcoming the problem of microbial resistance.

Changes in the HIV-1 mutational profile before first-line HAART in the RESINA cohort

Sporadic observations have shown changing patterns of transmitted drug resistance mutations (TDRMs) in HIV infection even without selection pressure by antiretroviral treatment (ART). Repeated genotypic resistance analyses in treatment-naïve patients were performed, in order to analyze intraindividual variances of resistance patterns over time. Between the years 2001 and 2008 two genotypic resistance tests were performed at different time-points in 49 treatment-naïve HIV-positive patients aged >18 years. Wild-type virus was found at baseline and during follow-up in 31 patients (group A, median time between resistance tests 146 days), while resistance mutations were found either at baseline or during follow-up in 18 patients (group B, median time between resistance tests 297 days). In group B, the pattern of resistance changed in eight out of 18 patients over time, with three patients showing decreasing numbers and five patients showing increasing numbers of resistance mutations. The pattern of resistance mutations remained unchanged in 10 out of 18 patients. The mutational pattern in untreated HIV infection may change over time and a single resistance analysis may underestimate the true prevalence of preserved resistance mutations. If these findings can be confirmed in a larger number of patients, it would be prudent to perform genotypic resistance testing both at baseline and prior to the start of ART in order to capture a more complete picture of preserved mutations before initiating ART.

Prevalence of transmitted drug resistance and impact of transmitted resistance on treatment success in the German HIV-1 Seroconverter Cohort

BACKGROUND

The aim of this study is to analyse the prevalence of transmitted drug resistance, TDR, and the impact of TDR on treatment success in the German HIV-1 Seroconverter Cohort.

METHODS

Genotypic resistance analysis was performed in treatment-naïve study patients whose sample was available 1,312/1,564 (83.9% October 2008). A genotypic resistance result was obtained for 1,276/1,312 (97.3%). The resistance associated mutations were identified according to the surveillance drug resistance mutations list recommended for drug-naïve patients. Treatment success was determined as viral suppression below 500 copies/ml.

RESULTS

Prevalence of TDR was stable at a high level between 1996 and 2007 in the German HIV-1 Seroconverter Cohort (N = 158/1,276; 12.4%; CI(wilson) 10.7-14.3; p(for trend) = 0.25). NRTI resistance was predominant (7.5%) but decreased significantly over time (CI(Wilson): 6.2-9.1, p(for trend) = 0.02). NNRTI resistance tended to increase over time (NNRTI: 3.5%; CI(Wilson): 2.6-4.6; p(for trend)= 0.07), whereas PI resistance remained stable (PI: 3.0%; CI(Wilson): 2.1-4.0; p(for trend) = 0.24). Resistance to all drug classes was frequently caused by singleton resistance mutations (NRTI 55.6%, PI 68.4%, NNRTI 99.1%). The majority of NRTI-resistant strains (79.8%) carried resistance-associated mutations selected by the thymidine analogues zidovudine and stavudine. Preferably 2NRTI/1PIr combinations were prescribed as first line regimen in patients with resistant HIV as well as in patients with susceptible strains (susceptible 45.3%; 173/382 vs. resistant 65.5%; 40/61). The majority of patients in both groups were treated successfully within the first year after ART-initiation (susceptible: 89.9%; 62/69; resistant: 7/9; 77.8%).

CONCLUSION

Overall prevalence of TDR remained stable at a high level but trends of resistance against drug classes differed over time. The significant decrease of NRTI-resistance in patients newly infected with HIV might be related to the introduction of novel antiretroviral drugs and a wider use of genotypic resistance analysis prior to treatment initiation.

Surveillance of HIV drug resistance transmission in Iran: experience gained from a pilot study

We performed a pilot surveillance study on transmitted HIV drug resistance (TDR) in Iran, with specimens collected and stored as dried blood spots (DBS). The protease region and relevant positions in the reverse transcriptase region of the pol gene were sequenced to detect mutations known to be associated with resistance to drugs in standard first-line regimens. Seventy-three specimens were collected, with 39 (53%) specimens yielding sequence from both protease and at least part of RT. Specimens were almost exclusively HIV-1 subtype CRF 35_A1D based on pol sequencing. Mutations were restricted to RT, with D67DG and V75AV each seen in a single specimen. An atypical protease inhibitor mutation, I47M, appeared at a resistance-associated position in protease from a single specimen. These preliminary data showed that the rate of transmitted drug resistance in Iran, within the areas sampled, was 5.1% (2/39). However, the small sample size makes this figure only an approximation. Due to the sampling strategy and resulting small sample size, we were unable to accurately calculate TDR rates for individual areas using the WHO HIV drug resistance threshold survey method. Increasing the sample size and improving the yield from DBS would improve the accuracy of drug resistance surveillance and facilitate wider application of this methodology in Iran.

German-Austrian recommendations for HIV1-therapy in pregnancy and in HIV1-exposed newborn, update 2008

In Germany during the last years about 200-250 HIV1-infected pregnant women delivered a baby each year, a number that is currently increasing. To determine the HIV-status early in pregnancy voluntary HIV-testing of all pregnant women is recommended in Germany and Austria as part of prenatal care. In those cases, where HIV1-infection was known during pregnancy, since 1995 the rate of vertical transmission of HIV1 was reduced to 1-2%. - This low transmission rate has been achieved by the combination of anti-retroviral therapy of pregnant women, caesarean section scheduled before onset of labour, anti-retroviral post exposition prophylaxis in the newborn and refraining from breast-feeding by the HIV1-infected mother. To keep pace with new results in research, approval of new anti-retroviral drugs and changes in the general treatment recommendations for HIV1-infected adults, in 1998, 2001, 2003 and 2005 an interdisciplinary consensus meeting was held. Gynaecologists, infectious disease specialists, paediatricians, pharmacologists, virologists and members of the German AIDS Hilfe (NGO) were participating in this conference to update the prevention strategies. A fifth update became necessary in 2008. The updating process was started in January 2008 and was terminated in September 2008. The guidelines provide new recommendations on the indication and the starting point for HIV-therapy in pregnancies without complications, drugs and drug combinations to be used preferably in these pregnancies and updated information on adverse effects of anti-retroviral drugs. Also the procedures for different scenarios and risk constellations in pregnancy have been specified again. - With these current guidelines in Germany and Austria the low rate of vertical HIV1-transmission should be further maintained.

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.

Monitoring HIV drug resistance in treatment-naive individuals: molecular indicators, epidemiology and clinical implications

Transmitted drug resistance (TDR) has been documented to occur soon after the introduction of HAART. The purpose of this review is to summarize the current knowledge regarding the epidemiology, the clinical implications and the trends in the research field of TDR. Until now, there have been different approaches for monitoring TDR, however, the surveillance drug resistance-associated mutations list seems fairly advantageous for TDR surveillance compared with other methods. The prevalence of TDR is approximately 10% in Europe and North America among recently or newly infected individuals sampled over the last few years. TDR was found to be higher among patients infected in Europe and North America compared with those in geographic areas with a high prevalence of HIV-1, reflecting the differences in the access to HAART in the two populations. Resistant viruses show different reversal rates to wild-type depending on the fitness cost of particular mutations. TDR in treatment-naive individuals is of major importance in HIV clinical practice and for this reason British–European and USA guideline panels recommend drug-resistance testing prior to treatment.

Reverse transcriptase inhibitors as potential colorectal microbicides

We investigated whether reverse transcriptase (RT) inhibitors (RTI) can be combined to inhibit human immunodeficiency virus type 1 (HIV-1) infection of colorectal tissue ex vivo as part of a strategy to develop an effective rectal microbicide. The nucleotide RTI (NRTI) PMPA (tenofovir) and two nonnucleoside RTI (NNRTI), UC-781 and TMC120 (dapivirine), were evaluated. Each compound inhibited the replication of the HIV isolates tested in TZM-bl cells, peripheral blood mononuclear cells, and colorectal explants. Dual combinations of the three compounds, either NRTI-NNRTI or NNRTI-NNRTI combinations, were more active than any of the individual compounds in both cellular and tissue models. Combinations were key to inhibiting infection by NRTI- and NNRTI-resistant isolates in all models tested. Moreover, we found that the replication capacities of HIV-1 isolates in colorectal explants were affected by single point mutations in RT that confer resistance to RTI. These data demonstrate that colorectal explants can be used to screen compounds for potential efficacy as part of a combination microbicide and to determine the mucosal fitness of RTI-resistant isolates. These findings may have important implications for the rational design of effective rectal microbicides.

A frequent functional toll-like receptor 7 polymorphism is associated with accelerated HIV-1 disease progression

OBJECTIVES

Toll-like receptors (TLRs) play an important role in the innate immune response to pathogens. TLR7 recognizes RNA of various viruses including HIV. The objective of this study was to examine the influence of individual genetic variations of TLR7 on the susceptibility to and progression of HIV disease.

METHOD

We genotyped a population of 734 HIV-positive adults and 545 healthy controls for three TLR7 single nucleotide polymorphisms. The frequency of TLR7 genetic variations was assessed and related to HIV disease progression. Furthermore, we analyzed peripheral blood mononuclear cells obtained from healthy individuals differing in their TLR7 genotype and assessed their response to a TLR7-specific ligand ex vivo.

RESULTS

Presence of the most frequent TLR7 polymorphism, TLR7 Gln11Leu, was associated with higher viral loads and accelerated progression to advanced immune suppression in HIV patients. Furthermore, in women this polymorphism may be associated with increased HIV-1 susceptibility as it was found more frequently among patients as compared with controls. Peripheral blood mononuclear cells from polymorphism carriers secreted significantly less IFN-alpha following TLR7 activation, whereas IL-6 production remained unaltered.

CONCLUSION

This is the first report of a functional TLR7 variant to be associated with susceptibility to and a more severe clinical course of HIV-1 disease. These results may have implications for the risk assessment of individual patients as well as for HIV-1 therapy and vaccination strategies in the future.

Understanding transmitted HIV resistance through the experience in the USA

Transmitted drug resistance is an emerging phenomenon with important clinical and public health implications. It has been reported in 3.4% to 26% of HIV-infected persons in the USA. Most cases affect non-nucleoside reverse transcriptase inhibitors or nucleos(t)ide reverse transcriptase inhibitors. Transmitted protease inhibitor or multi-class resistance is uncommon, occurring in <5% of cases. The genital tract may function as a reservoir of transmissible drug-resistant variants or a site for low-level viral replication at a time plasma HIV is suppressed. Transmitted drug-resistant HIV variants, including those that exist in very low titers (minority populations), are associated with suboptimal virologic response to initial antiretroviral therapy. Baseline resistance testing, preferably genotype, appears to be cost-effective and is recommended for all treatment-naïve patients in the USA, although prospective trials have not been performed. It appears transmitted drug resistance is still relatively low in developing countries, but there is a dearth of information.

Phylogenetic investigation of transmission pathways of drug-resistant HIV-1 utilizing pol sequences derived from resistance genotyping

OBJECTIVES

To investigate the nature of transmission links existing between patients recently infected with HIV strains containing transmitted drug resistance (TDR) mutations.

METHODS

Virus from 63 individuals recently infected with HIV-1 containing TDR mutations was analyzed phylogenetically to determine virological links. Phylogenetic trees were reconstructed using maximum likelihood and distance-based methods. Monophyletic clusters detected on the basis of pol sequences were confirmed using env and gag sequences. Potential bias caused by the presence of drug resistance mutations was assessed by reanalyzing the pol sequence set after the omission of 16 drug resistance codons identified in the TDR population.

RESULTS

Phylogenetic analysis revealed 9 apparent transmission clusters involving 24 of the 63 (38%) TDR patients. Each cluster was supported by high bootstrap values and low intracluster genetic distances. The 9 transmission clusters were confirmed in separate analyses using env and gag sequences and in pol sequences after the removal of codons associated with drug resistance.

CONCLUSIONS

Pol sequences generated during baseline resistance genotyping for newly HIV-infected patients provide the opportunity for real-time phylogenetics to identify sources of multiple HIV transmission events. This study demonstrated the existence of several distinct clusters of patients whose TDR strains were linked. Several discrete clusters involving transmission of K103N- and/or M41L-resistant virus to multiple recipients were detected, suggesting that multiple transmission pathways can exist for viruses with the same resistance mutations.

CCR5Delta32 genotypes in a German HIV-1 seroconverter cohort and report of HIV-1 infection in a CCR5Delta32 homozygous individual

Background

Homozygosity (Δ32/Δ32) for the 32 bp deletion in the chemokine receptor 5 (CCR5) gene is associated with strong resistance against HIV infection. Heterozygosity is associated with protection of HIV-1 disease progression.

Methodology/Principal Findings

We genotyped a population of 737 HIV-positive adults and 463 healthy controls for the CCR5Δ32 deletion and found heterozygous frequencies of 16.2% (HIV-negative) and 17.5% (HIV-positive) among Caucasian individuals. Analysis of CCR5Δ32 influence on disease progression showed notably lower viral setpoints and a longer time to a CD4 count of <200 µl⁻¹ in seroconverters heterozygous for the deletion. Furthermore, we identified one HIV-positive man homozygous for the Δ32 deletion.

Conclusions/Significance

The protective effect of CCR5 Δ32 heterozygosity is confimed in a large cohort of German seroconverters. The HIV-infected CCR5 Δ32 homozygous individual, however, displays extremely rapid disease progression. This is the 12th case of HIV-infection in this genotype described worldwide.

Comparison of the human immunodeficiency virus (HIV) type 1-specific immunoglobulin G capture enzyme-linked immunosorbent assay and the avidity index method for identification of recent HIV infections

The sensitivity and specificity of the human immunodeficiency virus (HIV) type 1-specific immunoglobulin G capture enzyme-linked immunosorbent assay (BED-CEIA) were compared with those of the avidity index method to identify recent HIV infection using a panel of 148 samples (81 patients) representing durations of infection ranging from 0 to 222 weeks. The results from the two tests were similar (sensitivity of 80% versus 74% [P = 0.53]; specificity of 86% versus 82% [P = 0.67]).

Antiretroviral Treatment Strategies and Immune Reconstitution in Treatment-naive HIV-Infected Patients with Advanced Disease

Treatment-naïve advanced HIV-infected patients have a lower life expectancy than those treated early with highly active antiretroviral therapy (HAART). Early treatment allows greater immunological recovery, a reduction of AIDS progression, a reduced risk of related illnesses, and lower mortality compared with HAART initiation in advanced disease. Given the numbers with advanced disease worldwide and the high cost of care, strategies encouraging early detection may be life saving and cost effective. Factors associated with increased clinical progression include higher baseline HIV viral load and older age, emphasizing the need for early viral load suppression. HAART initiation faces many challenges; interactions between antiretroviral agents and drugs used to treat life-threatening opportunistic infections may cause subtherapeutic antiretroviral exposure and the development of resistance or supratherapeutic levels resulting in adverse effects. Immune reconstitution inflammatory syndrome can be another cause of suboptimal outcomes. The management of patients with advanced HIV infection should include rapid short-term immune reconstitution to limit the risk of disease progression plus aggressive antiviral treatment to achieve rapid virological suppression. Clear evidence on the optimal regimen and agents to use to target advanced HIV disease is lacking. Therefore, antiretroviral treatment for these patients has to be carefully tailored to the individual according to many variables.

Transmitted Resistance: An Overview and Its Potential Relevance to the Management of HIV-Infected Persons in Resource-Limited Settings

Transmitted resistance has become an important clinical problem in developed countries with long histories of antiretroviral use. In resource-limited settings, it is a foreseeable, if not insidiously emerging, issue. Any transmission route or currently approved antiretroviral drug may be involved. The clinical relevance of polymorphisms that commonly occur at sites known to be associated with resistance, and peculiarities of the non-B subtypes, are incompletely understood. Adverse clinical consequences that have been demonstrated with transmitted resistance include an increased risk of failing initial therapy and further development of resistance. Although treatment outcomes can be optimized by baseline resistance testing and virologic monitoring, these are impractical in most resource-limited settings at this time. The scale and impact of transmitted resistance can probably be reduced by comprehensive prevention and management strategies. Equally germane are epidemiological and clinical studies to extend understanding of the dynamics, clinical implications, and management of transmitted resistance.

Verlauf der HIV-Epidemie in Deutschland

The course of the HIV epidemic in Germany can be modelled by back calculation until the beginning of the nineties. The recent course of the epidemic can only be derived from surveillance data of newly diagnosed HIV infections in conjunction with other data sources. Based on these surveillance data HIV incidence in Germany can be estimated to have been stable with 2000 to 2500 new infections per year since the early nineties, after having peaked in the early eighties. The most affected group are men who have sex with men followed by persons infected by heterosexual contact and migrants from high prevalence countries. The number of intravenous drug users has declined over the years and is now in fourth place. There are indications that increased risk behaviour and rising numbers of other sexually transmitted infections together with a change towards later initiation of antiretroviral therapy has led to an increase in new HIV infections in Germany in recent years. An improvement of the epidemiological surveillance for "indicator" STIs in combination with the assessment of risk behaviours in high risk groups would be desirable steps towards a second generation surveillance in Germany.

Prevalence of X4 tropic viruses in patients recently infected with HIV-1 and lack of association with transmission of drug resistance

BACKGROUND

HIV-1 co-receptor usage may play a critical role in AIDS pathogenesis. Information on viral tropism in HIV-1 seroconverters is scarce, as is the relationship with transmission of drug-resistant viruses.

METHODS

All consecutive HIV-1 seroconverters seen between January 1997 and December 2005 in 17 Spanish hospitals were retrospectively analysed. V3 loop amino acid sequences derived from plasma RNA at the time of initial diagnosis were used to predict co-receptor usage. Major drug resistance mutations, plasma HIV RNA, CD4 counts and HIV subtype were considered for subsequent analyses.

RESULTS

A total of 296 HIV-1 seroconverters were identified (84% male; median age 30 years; 61% homosexual men). Median estimated time from infection was 7 months (interquartile range, 3-11). Primary drug resistance mutations were seen in 12.5%, being 9.5% for nucleoside reverse transcriptase inhibitors (NRTI), 4.4% for non-NRTI (NNRTI) and 3% for protease inhibitors (PI). Twenty-four (8.1%) carried non-B subtypes. HIV tropism could be characterized in 203 seroconverters (69%). X4 viruses (either pure or dual/mixed R5/X4) were recognized in 35 (17.2%). There was no association between HIV tropism and mean plasma HIV RNA (4.5 versus 4.4 log copies/mL in R5 versus X4, respectively; P = 0.45) or mean CD4 counts (594 versus 554 cells/mm(3), respectively; P = 0.48). The proportion of X4 viruses did not differ in patients infected with wild-type or drug-resistant viruses (17% versus 18%, P = 1). Intravenous drug users tended to show X4 viruses more frequently than individuals infected by sexual relationships (35.7% versus 16.5%, respectively; P = 0.073). After 12 months of follow-up in 78 seroconverters who did not start antiretroviral therapy, more pronounced increases in plasma HIV RNA (+5056 versus -3430) and declines in CD4 cell counts (-126 versus -60) were seen in X4 compared with R5 carriers.

CONCLUSIONS

A significant proportion of recent HIV-1 seroconverters harbour X4 viruses (17.2%), without any evidence of association between co-receptor usage, transmission of drug-resistant viruses and HIV subtype.

Human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns among treatment-naive patients in different stages of infection in Rio de Janeiro, Brazil

The presence of genetic mutations in HIV-1-positive untreated individuals and its contribution to treatment failure, either in an individual or on a population basis, remains an important concern. The goal was to analyze and compare HIV-1 reverse transcriptase (RT) and protease (PR) genes of untreated individuals with chronic and recent infections. Fifty-one chronic infected individuals for whom initiation of antiretroviral treatment had been recommended and 20 individuals with recent documented HIV-1 seroconversion had their plasma viral RNA extracted and the PR and RT genes sequenced in order to determine subtype, presence of genetic polymorphisms and mutations associated with resistance to antiretroviral drugs. All 20 recent seroconvertors were infected with subtype B viruses. Of the 51 chronically infected patients, 40 (78.4%), 7 (13.7%), and 2 (3.9%) were infected with subtypes B, F, and C, respectively. Two (3.9%) hybrid forms were also observed in two individuals with chronic infection: D/B and D/F. Despite seroconversion stage, type and quantity of mutations were similar to both groups (P = 0.961). This group also presented the only (1.4%) drug-resistance mutation (M184V) among all samples investigated. In summary, the present study shows a high occurrence of equivalent polymorphisms unrelated to drug resistance in samples collected from untreated HIV-1- infected individuals in different seroconversion status, and suggests low primary resistance mutations. Results also indicate that non-B subtypes circulating in Rio de Janeiro have specific Brazilian non-synonymous mutations.

Anti-retroviral drug resistance-associated mutations among non-subtype B HIV-1-infected Kenyan children with treatment failure

Recently increased availability of anti-retroviral therapy (ART) has mitigated HIV-1/AIDS prognoses especially in resource poor settings. The emergence of ART resistance-associated mutations from non-suppressive ART has been implicated as a major cause of ART failure. Reverse transcriptase inhibitor (RTI)-resistance mutations among 12 non-subtype B HIV-1-infected children with treatment failure were evaluated by genotypically analyzing HIV-1 strains isolated from plasma obtained between 2001 and 2004. A region of pol-RT gene was amplified and at least five clones per sample were analyzed. Phylogenetic analysis revealed HIV-1 subtype A1 (n = 7), subtype C (n = 1), subtype D (n = 3), and CRF02_AG (n = 1). Before treatment, 4 of 12 (33.3%) children had primary RTI-resistance mutations, K103N (n = 3, ages 5-7 years) and Y181C (n = 1, age 1 year). In one child, K103N was found as a minor population (1/5 clones) before treatment and became major (7/7 clones) 8 months after RTI treatment. In 7 of 12 children, M184V appeared with one thymidine-analogue-associated mutation (TAM) as the first mutation, while the remaining 5 children had only TAMs appearing either individually (n = 2), or as TAMs 1 (M41L, L210W, and T215Y) and 2 (D67N, K70R, and K219Q/E/R) appearing together (n = 3). These results suggest that "vertically transmitted" primary RTI-resistance mutations, K103N and Y181C, can persist over the years even in the absence of drug pressure and impact RTI treatment negatively, and that appearing patterns of RTI-resistance mutations among non-subtype B HIV-1-infected children could possibly be different from those reported in subtype B-infected children.

Human immunodeficiency virus-1 subtypes and antiretroviral drug resistance profiles among drug-naïve Brazilian blood donors

BACKGROUND

Human immunodeficiency virus-1 (HIV-1) genetic variability and its implication on the development of new reagents were investigated by correlating time of infection and resistance to antiretroviral drugs.

STUDY DESIGN AND METHODS

Seventy-four plasma samples from Brazilian drug-naïve blood donors were assayed to further develop a panel of biologic reagents to be used in serology and molecular tests. After viral RNA extraction, cDNA was generated and used in nested polymerase chain reaction protocols with primers for the ENV (C2-V3 and gp41), protease (PR), and reverse transcriptase (RT) of HIV-1. Genomic sequencing was conducted to define HIV-1 subtypes and drug resistance mutations.

RESULTS

Subtype B was found in 83.8 percent of all samples, subtype F in 2.7 percent, and BF mosaics in 11 percent of the cases. B and F different genetic profiles were evidenced: B(PR)B(RT)B(gp120)B(gp41), F(PR)F(RT)F(gp120)F(gp41), F(PR)F(RT)B(gp120)B(gp41), F(PR)B(RT)B(gp120)B(gp41), and B(PR)B(RT)F(gp120)B(gp41). A single sample (1.4%) was characterized as a BC mosaic (B(PR)C(RT)U(gp120)C(gp41)) and an AGH mosaic (AG(PR)G(RT)H(gp120)H(gp41)) was first observed in the country. Antiretroviral resistance to nucleoside RT inhibitor was observed in one sample (1.35%) showing M41L and T215S mutations. Nonnucleoside RT inhibitor and major PR inhibitor resistance mutations were not observed. Previously unseen patterns of resistance to T20 were found among HIV-1-infected drug-naïve individuals in Brazil. Recent infections were characterized in 21.6 percent of the blood donor samples included in this study.

CONCLUSIONS

The availability of characterized plasma samples and HIV isolates will allow the development of biologic reagents necessary to implement quality control programs and to develop, validate, and evaluate the performance of diagnostic kits, considering all HIV-1-circulating variants in the country.

Persistence of a sexually transmitted highly resistant HIV-1: pol quasispecies evolution over 33 months in the absence of treatment

The evolution of a sexually transmitted multiresistant HIV-1 in a linked transmission chain was followed for 33 months to assess its potential to persist in the absence of treatment. The multiresistant HIV reverted slowly to wild type in reverse transcriptase (positions 44, 67, 74, 118) rendering the virus only susceptible to lamivudine/emtricitabine. Persistence of the replication-competent resistant HIV increases its potential to spread further and strengthens the importance of resistance testing in newly infected patients.

HIV drug-resistant strains as epidemiologic sentinels

Observed declines in drug resistance to nucleoside reverse transcriptase inhibitors among persons recently infected with HIV-1 in monitored subpopulations can be interpreted as a positive sign and lead public health officials to decrease efforts towards HIV prevention. By means of a mathematical model, we identified 3 processes that can account for the observed decline: increase in high-risk behavior, decrease in proportion of acutely infected persons whose conditions are treated, and change in treatment efficacy. These processes, singly or in combination, can lead to increases or decreases in disease and drug-resistance prevalence in the general population. We discuss the most appropriate public health response under each scenario and emphasize how further data collection and analyses are required to more reliably evaluate the observed time trends and the relative importance of forces shaping the epidemic. Our study highlights how drug resistance markers can be used as epidemiologic sentinels to devise public health solutions.

Access to highly active antiretroviral therapy for injection drug users: adherence, resistance, and death

Injection drug users (IDUs) continue to comprise a major risk group for HIV infection throughout the world and represent the focal population for HIV epidemics in Asia and Eastern Europe/Russia. HIV prevention programs have ranged from HIV testing and counseling, education, behavioral and network interventions, drug abuse treatment, bleach disinfection of needles, needle exchange and expanded syringe access, as well as reducing transition to injection and primary substance abuse prevention. With the advent of highly active antiretroviral therapy (HAART) in 1996, dramatic clinical improvements have been seen. In addition, the treatment's impact on reducing HIV viral load (and therefore transmission by all routes) provides a stronger rationale for an expansion of the focus on prevention to emphasize early identification and treatment of HIV infected individuals. However, treatment of IDUs has many challenges including adherence, resistance and relapse to high risk behaviors, all of which impact issues of access and ultimately effectiveness of potent antiretroviral treatment. A major current challenge in addressing the HIV epidemic revolves around an appropriate approach to HIV treatment for IDUs.

Long-term persistence of primary genotypic resistance after HIV-1 seroconversion

Primary infection with drug-resistant HIV-1 is well documented. We have followed up patients infected with such viruses to determine the stability of resistance-associated mutations. Fourteen patients who experienced primary infection with genotypic evidence of resistance were followed for up to 3 years. Drug resistance-associated mutations persisted over time in most patients studied. In particular, M41L, T69N, K103N, and T215 variants within reverse transcriptase (RT) and multidrug resistance demonstrated little reversion to wild-type virus. By contrast, Y181C and K219Q in RT, occurring alone, disappeared within 25 and 9 months, respectively. Multidrug resistance in 2 patients was found to be stable for up to 18 months, the maximum period studied. We conclude that certain resistance-associated mutations are highly stable and these data support the recommendation that all new HIV diagnoses in areas where primary resistance may occur should undergo genotyping irrespective of whether the date of seroconversion is known.

Detection of minor populations of drug-resistant HIV-1 in acute seroconverters

OBJECTIVE

The transmission of drug-resistant HIV-1 is a major health concern. To date, most clinical studies have relied on sequencing techniques for genotypic analyses which do not allow quantification of minority viral populations below 25%. As minor populations of drug-resistant HIV-1 could impact the efficiency of antiretroviral therapy, this study was performed to determine the prevalence of minor populations of drug-resistant HIV-1 in acute seroconverters.

DESIGN AND METHODS

Forty-nine acute seroconverters from two clinical centers in Germany were included in the study. Individuals were identified between June 1999 and March 2003, and none had received antiretroviral therapy prior to sampling. Minor populations of drug-resistant variants were detected by quantitative real-time polymerase chain reaction using allele-discriminating oligonucleotides for three key resistance mutations: L90M (protease), K103N and M184V (reverse transcriptase). The approximate discriminative power was between 0.01 and 0.2%.

RESULTS

Drug-resistant variants were detected in 10 of 49 patients (20.4%). The L90M mutation was found in one of 49 (2%), the K103N mutation in five of 49 (10.2%) and the M184V mutation in six of 49 (12.2%) patients, respectively. In five of the 10 individuals with detectable drug-resistant virus (50%), the detected population represented a minor viral quasi-species (< 25% of viruses) and was not detected by direct sequencing.

CONCLUSIONS

The prevalence of minor populations of drug-resistant HIV-1 in acute seroconverters can be frequently detected and may impact the success of antiretroviral therapy.

Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections

OBJECTIVE

To study primary HIV-1 infections (PHI) using molecular and epidemiological approaches in order to assess correlates of transmission in this population.

METHODS

Individuals with PHI were recruited prospectively from a discrete cohort of 1235 individuals under follow-up in a well-defined geographical area between 1999 and 2003. PHI was diagnosed by one of the following: negative HIV antibody test within 18 months, evolving antibody response, or application of the serological testing algorithm for recent HIV seroconversion. The pol gene was sequenced to identify genotypic resistance and facilitate molecular epidemiological analysis. Clinical data were collected and linked in an irretrievable fashion when informed consent was obtained.

RESULTS

A total of 103 individuals with PHI diagnosed between 1999 and 2003 were included in the study; 99 (96%) were male and 90 (91%) were men who have sex with men. Viruses from 35 out of 103 (34%) appeared within 15 phylogenetically related clusters. Significant associations with clustering were: young age, high CD4 cell count, number of sexual contacts, and unprotected anal intercourse (UAI) in the 3 months before diagnosis (P < 0.05 for all). High rates of acute sexually transmitted infections (STI) were observed in both groups with a trend towards higher rates in those individuals with viruses within a cluster (42.9 versus 27.9%; P = 0.13).

CONCLUSION

High rates of partner change, UAI and STI are factors that facilitate onward transmission during PHI. More active identification of individuals during PHI, the management of STI and highly active antiretroviral therapy may all be useful methods to break transmission networks.

The antiretroviral rollout and drug-resistant HIV in Africa: insights from empirical data and theoretical models

The U.S. Government has pledged to spend $15 billion in Africa and the Caribbean on AIDS. A central focus of this plan is to provide antiretroviral treatment (ART) to millions. Here, we evaluate whether the plan to rollout ART in Africa is likely to generate an epidemic of drug-resistant strains of HIV. We review what has occurred as a result of high usage of ART in developed countries in terms of changes in risky behavior, and the emergence and transmission of drug-resistant HIV. We also review how mathematical models have been used to predict the evolution of drug-resistant HIV epidemics. We then show how models can be used to predict the likely impact of the ART rollout on the evolution of drug-resistant HIV in Africa. At currently planned levels of treatment coverage, we predict that (over the next decade) in Africa: (i) the impact of ART on reducing HIV transmission (and prevalence) is likely to be undetectable (unless accompanied by substantial changes in behavior), (ii) the transmission rate of drug-resistant HIV will be below the WHO surveillance threshold of 5%, and (ii) the majority of cases of drug-resistant HIV that will occur will be due to acquired (and not transmitted) resistance. For the next decade, large-scale surveillance for detecting transmitted resistance in Africa is unnecessary. Instead, we recommend that patients should be closely monitored for acquired resistance, and sentinel surveillance (in a few urban centers) should be used to monitor transmitted resistance.

Diversity of human immunodeficiency virus type 1 subtype A and CRF03_AB protease in Eastern Europe: selection of the V77I variant and its rapid spread in injecting drug user populations

To characterize polymorphisms of the subtype A protease in the former Soviet Union, proviral DNA samples were obtained, with informed consent, from 119 human immunodeficiency virus type 1 (HIV-1)-positive untreated injecting drug users (IDUs) from 16 regions. All individuals studied have never been treated with antiretroviral drugs. The isolates were defined as IDU-A (n = 115) and CRF03_AB (n = 4) by using gag/env HMA/sequencing. The pro region was analyzed by using sequencing and original HIV-ProteaseChip hybridization technology. The mean of pairwise nucleotide distance between 27 pro sequences (23 IDU-A and 4 CRF03_AB) was low (1.38 +/- 0.79; range, 0.00 to 3.23). All sequences contained no primary resistance mutations. However, 13 of 23 (56.5%) subtype A isolates bore the V77I substitution known as the secondary protease mutation. V77I was associated with two synonymous substitutions in triplets 31 and 78, suggesting that all V77I-bearing viruses evolved from a single source in 1997. Hybridization analysis showed that 55 of 115 (47.8%) HIV-1 isolates contained V77I, but this variant was not found in any of 31 DNA samples taken from regions, where the HIV-1 epidemic among IDUs started earlier 1997, as well as in any of four CRF03_AB isolates. The results of analysis of 12 additional samples derived from epidemiologically linked subjects showed that in all four epidemiological clusters the genotype of the donor and the recipients was the same irrespective of the route of transmission. This finding demonstrates the transmission of the V77I mutant variant, which is spreading rapidly within the circulating viral pool in Russia and Kazakhstan. The continued molecular epidemiological and virological monitoring of HIV-1 worldwide thus remains of great importance.

Novel patterns of nevirapine resistance-associated mutations of human immunodeficiency virus type 1 in treatment-naïve patients

Several reports have recently shown that drug-resistant human immunodeficiency virus type 1 (HIV-1) is often isolated from treatment-naïve patients. We phenotypically analyzed HIV-1 strains isolated from 44 treatment-naïve individuals and found two strains highly resistant (69- and >310-fold) against nevirapine (NVP). Direct sequencing showed these two isolates had a novel mutation, K238S, in reverse transcriptase (RT), but did not have any reported NVP resistance-associated mutation. A 48-h culture in the presence of NVP, however, selected HIV-1 carrying NVP resistance-associated mutations, V106A, V108I, or both, suggesting that minor viral populations of these two isolates had harbored these mutations. Replication kinetic studies of recombinant HIV-1 clones suggested that K238S conferred a significant resistance against NVP, especially when accompanied with V106A (530-fold) or V108I (56-fold). Our study identified a novel NVP resistance-associated mutation, K238S, which could be persistently detected by genotypic assay longer than V106A and V108I during off-treatment period.

Updated European Recommendations for the Clinical Use of HIV Drug Resistance Testing

In most European countries, HIV drug resistance testing has become a routine clinical tool. However, its practical implementation in a clinical context is demanding. The European HIV Drug Resistance Panel was established to make recommendations to clinicians and virologists on this topic and to propose quality control measures. The panel recommends resistance testing for the following indications: i) drug-naive patients with acute or recent infection; ii) therapy failure, including suboptimal treatment response, when treatment change is considered; iii) pregnant HIV-1-infected women and paediatric patients with detectable viral load when treatment initiation or change is considered; and iv) genotype source patient when post-exposure prophylaxis is considered. In addition, for drug-naive patients with chronic infection in whom treatment is to be started, the panel suggests that resistance testing should be strongly considered and recommends testing the earliest sample for drug resistance if suspicion of resistance is high or prevalence of resistance in this population exceeds 10%. The panel does not favour genotyping over phenotype, however it is anticipated that genotyping will be used more often because of its greater accessibility, lower cost and faster turnaround time. For the interpretation of resistance data, clinically validated systems should be used to the greatest extent possible. It is mandatory that laboratories performing HIV resistance tests take regular part in quality assurance programs. Similarly, it is necessary that HIV clinicians and virologists take part in continuous education and meet regularly to discuss problematic clinical cases. Indeed, resistance test results should be used in the context of all other clinically relevant information for predicting therapy response. The panel also encourages the timely collection of epidemiological information to estimate the impact of transmission of resistant HIV and the prevalence of HIV-1 non-B subtypes in the different European countries.

Current Patterns in the Epidemiology of Primary HIV Drug Resistance in North America and Europe

Despite numerous studies in recent years, it is still difficult to draw general conclusions about the extent to which drug-resistant HIV-1 is transmitted. In addition to the highly stratified nature of primary resistance itself, true epidemiological surveillance has been rare and studies to date have suffered from wide variability in their designs, definitions and datasets. In the absence of consensus standards, this has resulted in a large number of isolated ‘snapshots’ with little scope for data-pooling and comparison.

This brief review examines some of the major confounding factors that restrict the utility of individual studies and prevent the combination of studies to increase statistical power. Despite these limitations, data from North America and Europe lead to the tentative conclusion that transmission rates in these areas have generally fallen or remained stable in the past 2–3 years. However, data for the UK seem to indicate an ongoing rise in the transmission of drug resistance mutations, currently present in up to 20% of new infections.

Transmission of resistant HIV represents a clinically important phenomenon, although the scale and relevance are being obscured by methodological variations and non-clinical definitions of resistance. Those of us with an interest in the epidemiology of drug resistance, whether in primary transmission or on-treatment, must learn to speak the same language if we are to establish meaningful correlations between survey datasets and the HIV-infected population as a whole.

Prevalence of human immunodeficiency virus drug resistance mutations and subtypes in drug-naive, infected individuals in the army health service of Rio de Janeiro, Brazil

The prevalence of mutations that confer resistance to antiretroviral drugs was examined in 56 drug-naive, human immunodeficiency virus type 1 (HIV-1)-infected individuals from the Army Health Service in Rio de Janeiro, Brazil. No primary protease inhibitor mutations were found, but secondary mutations were observed in 51.2% of the samples. Fourteen percent of the viruses had reverse transcriptase inhibitor-associated mutations. Comparative analysis of protease secondary mutations from four different time periods in drug-naive patients in the city of Rio de Janeiro has indicated constant rates for particular mutations. Changes in CD4 cell counts and HIV viral load over time in subtype B- and non-B-infected drug-naive patients were not significantly different.