Stability of transmitted drug-resistant HIV-1 species

Various strategies for developing APOBEC3G protectors to circumvent human immunodeficiency virus type 1

Host restriction factor APOBEC3G (A3G) efficiently restricts Vif-deficient HIV-1 by being packaged with progeny virions and causing the G to A mutation during HIV-1 viral DNA synthesis as the progeny virus infects new cells. HIV-1 expresses Vif protein to resist the activity of A3G by mediating A3G degradation. This process requires the self-association of Vif in concert with A3G proteins, protein chaperones, and factors of the ubiquitination machinery, which are potential targets to discover novel anti-HIV drugs. This review will describe compounds that have been reported so far to inhibit viral replication of HIV-1 by protecting A3G from Vif-mediated degradation.

HIV and Drug-Resistant Subtypes

Acquired Immunodeficiency Syndrome (AIDS) is a human viral infectious disease caused by the positive-sense single-stranded (ss) RNA Human Immunodeficiency Virus (HIV) (Retroviridae family, Ortervirales order). HIV-1 can be distinguished into various worldwide spread groups and subtypes. HIV-2 also causes human immunodeficiency, which develops slowly and tends to be less aggressive. HIV-2 only partially homologates to HIV-1 despite the similar derivation. Antiretroviral therapy (ART) is the treatment approved to control HIV infection, based on multiple antiretroviral drugs that belong to different classes: (i) NNRTIs, (ii) NRTIs, (iii) PIs, (iv) INSTIs, and (v) entry inhibitors. These drugs, acting on different stages of the HIV life cycle, decrease the patient's total burden of HIV, maintain the function of the immune system, and prevent opportunistic infections. The appearance of several strains resistant to these drugs, however, represents a problem today that needs to be addressed as best as we can. New outbreaks of strains show a widespread geographic distribution and a highly variable mortality rate, even affecting treated patients significantly. Therefore, novel treatment approaches should be explored. The present review discusses updated information on HIV-1- and HIV-2-resistant strains, including details on different mutations responsible for drug resistance.

Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana

Background: HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs).  Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure.  Methods: A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared. Results: Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants.  There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing. Conclusion: The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.

Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana

Background: HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs).  Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure.  Methods: A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared. Results: Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants.  There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing. Conclusion: The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.

Estimation of the HIV-1 backward mutation rate from transmitted drug-resistant strains

One of the serious threats facing the administration of antiretroviral therapy to human immunodeficiency virus (HIV-1) infected patients is the reported increasing prevalence of transmitted drug resistance. However, given that HIV-1 drug-resistant strains are often less fit than the wild-type strains, it is expected that drug-resistant strains that are present during the primary phase of the HIV-1 infection are replaced by the fitter wild-type strains. This replacement of HIV-1 resistant mutations involves the emergence of wild-type strains by a process of backward mutation. How quickly the replacement happens is dependent on the class of HIV-1 mutation group. We estimate the backward mutation rates and relative fitness of various mutational groups known to confer HIV-1 drug resistance. We do this by fitting a stochastic model to data for individuals who were originally infected by an HIV-1 strain carrying any one of the known drug resistance-conferring mutations and observed over a period of time to see whether the resistant strain is replaced. To do this, we seek a distribution, generated from simulations of the stochastic model, that best describes the observed (clinical data) replacement times of a given mutation. We found that Lamivudine/Emtricitabine-associated mutations have a distinctly higher, backward mutation rate and low relative fitness compared to the other classes (as has been reported before) while protease inhibitors-associated mutations have a slower backward mutation rate and high relative fitness. For the other mutation classes, we found more uncertainty in their estimates.

Detecting primary drug-resistant mutations in Korean HIV patients using ultradeep pyrosequencing

HIV primary resistance, drug resistance in treatment-naïve patients, is an emerging public health issue. The prevalence of HIV primary resistance mutations down to the level of 1% minor variants was investigated using ultradeep pyrosequencing (UDPS) in HIV-positive Korean blood donors and in treatment naïve chronic patients for the comparison. The entire pol region was sequenced from 25 HIV-positive blood donors, and 18 treatment-naïve chronic HIV patients. UDPS was successful in 19 blood donors and 18 chronic patients. In total, 1,011,338 sequence reads were aligned, and 28,093 sequence reads were aligned on average per sample. The prevalence of HIV primary resistance mutations in the HIV-positive blood donors and chronic HIV patients were 63.2% and 44.4% according to UDPS, respectively. Protease inhibitor (PI) drugs demonstrated different patterns in HIV-positive blood donors and chronic HIV patients, whereas non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and integrase inhibitor (INI) drugs showed similar patterns between the two groups. Higher level of primary resistance prevalence was observed mainly because UDPS method could detect mutations in minor variants with 1-10% frequency. The higher resistance prevalence was observed in HIV-positive blood donors than in chronic patients. Considering that treatments for HIV-infected patients were recently amended to start at an earlier stage, information about degree of drug resistance to each drug between the two groups would help to establish future policies, design additional clinical trials, assess HIV patient care in Korea.

HIV type-1 drug resistance in treatment-naive patients monitored using minority species assays: a systematic review and meta-analysis

BACKGROUND

The detection of mutations associated with drug resistance in HIV type-1 might be increased by applying minority species assays capable of identifying low frequency mutations in comparison with the use of population sequencing alone. Because minority species assays are mutation-specific, the benefit of this approach differs depending on the mutation being detected.

METHODS

We performed a systematic review of published data reporting detection of genotypic drug resistance using allele-specific (AS)-PCR minority assays and by standard DNA sequencing in drug-naive populations. We calculated the fold increase of mutation detection for each study and pooled these via meta-analysis, displaying results using Forest plots.

RESULTS

Our studies revealed an increase in detection of 1.9-fold (95% confidence interval [CI] 1.3-2.7; P < 0.0005) for K103N, 4.4-fold (95% CI 1.2-16.6; P = 0.026) for Y181C, 4.8-fold (95% CI 1.5-15.1; P = 0.008) for L90M and 8.7-fold (95% CI 4.0-18.6; P < 0.0005) for M184V. We found no relationship between AS-PCR assay sensitivity and frequency of additional mutation detection.

CONCLUSIONS

Additional detection of drug resistance mutations using AS-PCR minority mutation assays vary significantly depending on the mutation examined; however, the most marked increase in detection of resistance mutations was observed for M184V, a mutation seldom detected by standard techniques in drug-naive patients. We suggest that the presence of drug resistance mutations can be more accurately estimated using a combination of AS-PCR and standard genotyping.

Protection against rectal transmission of an emtricitabine-resistant simian/human immunodeficiency virus SHIV162p3M184V mutant by intermittent prophylaxis with Truvada

Daily preexposure prophylaxis (PrEP) with Truvada (emtricitabine [FTC] and tenofovir disoproxil fumarate [TDF]) is a novel HIV prevention strategy recently found to reduce HIV incidence among men who have sex with men. We used a macaque model of HIV transmission to investigate if Truvada maintains prophylactic efficacy against an FTC-resistant isolate containing the M184V mutation. Five macaques received a dose of Truvada 3 days before exposing them rectally to the simian/human immunodeficiency virus mutant SHIV162p3(M184V), followed by a second dose 2 h after exposure. Five untreated animals were used as controls. Virus exposures were done weekly for up to 14 weeks. Despite the high (>100-fold) level of FTC resistance conferred by M184V, all five treated animals were protected from infection, while the five untreated macaques were infected (P = 0.0008). Our results show that Truvada maintains high prophylactic efficacy against an FTC-resistant isolate. Increased susceptibility to tenofovir due to M184V and other factors, including residual antiviral activity by FTC and/or reduced virus fitness due to M184V, may all have contributed to the observed protection.

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.

Generation and mucosal transmissibility of emtricitabine- and tenofovir-resistant SHIV162P3 mutants in macaques

Transmission of drug-resistant HIV has been widely documented. We generated tenofovir (TFV)- and emtricitabine (FTC)-resistant SHIV162P3 mutants that can be used to investigate the transmission efficiency of drug-resistant viruses and their impact on the efficacy of pre-exposure prophylaxis. Both SHIV162p3(M184V) and SHIV162p3(K65R) replicated in vitro at high titers. Drug resistance profiles were similar to those seen in HIV. Virus infectivity to virion particle ratios were 4- and 10-fold lower in SHIV162p3(M184V) and SHIV162p3(K65R), compared to a concurrently generated WT SHIV162p3, respectively. Mucosal transmissibility studies using a repeat low-dose macaque model of rectal and vaginal transmission showed that both mutants were able to efficiently infect macaques only after the dose was increased to adjust for fitness reductions due to K65R and M184V. Our results in limited number of macaques suggest that the reduction in fitness due to M184V and K65R decreases virus transmissibility, and identify in vitro infectivity parameters that associate with mucosal transmissibility.

Increased detection of the HIV-1 reverse transcriptase M184V mutation using mutation-specific minority assays in a UK surveillance study suggests evidence of unrecognized transmitted drug resistance

OBJECTIVES

The aim of the study was to estimate the levels of transmitted drug resistance (TDR) in HIV-1 using very sensitive assays to detect minority drug-resistant populations.

METHODS

We tested unlinked anonymous serum specimens from sexual health clinic attendees, who had not received an HIV diagnosis at the time of sampling, by both standard genotyping and using minority detection assays.

RESULTS

By standard genotyping, 21 of 165 specimens (12.7%) showed evidence of drug resistance, while, using a combination of standard genotyping and minority mutation assays targeting three commonly observed drug resistance mutations which cause high-level resistance to commonly prescribed first-line antiretroviral therapy (ART), this rose to 32 of 165 (19.4%). This increase of 45% in drug resistance levels [95% confidence interval (CI) 15.2-83.7%; P=0.002] was statistically significant. Almost all of this increase was accounted for by additional detections of the M184V mutation.

CONCLUSIONS

Future surveillance studies of TDR in the United Kingdom should consider combining standard genotyping and minority-specific assays to provide more accurate estimates, particularly when using specimens collected from chronic HIV infections in which TDR variants may have declined to low levels.

Transmission of triple-class, drug-resistant HIV-1 in Australia

We report the first two cases of transmitted triple-class, drug-resistant HIV-1 in Australia. Baseline testing of a newly diagnosed man showed four reverse transcriptase resistance mutations (affecting two drug classes) and six protease resistance mutations. A source patient was identified, and a likely second case newly infected 1 year later, suggesting sequential transmission. This raises therapeutic implications for the individual patients, as well as public health concerns.

The effect of transmitted HIV-1 drug resistance on pre-therapy viral load

BACKGROUND

Reduced replication capacity of viruses expressing drug resistant mutations implies that patients with transmitted drug resistance (TDR) could have lower HIV RNA viral load than those infected with wild-type virus.

METHODS

We performed analysis using data from the UK HIV Drug Resistance Database and the UK CHIC study. Eligible patients had a resistance test performed between 1997 and 2007 while naive to antiretroviral therapy, were 16 years or older, and had a viral load and CD4 cell count measurement within 6 months of this test. Models were adjusted for CD4 cell count, viral subtype, ethnicity, risk group, sex, age, calendar year, clinical centre, and viral load assay.

RESULTS

Of a total of 7994 patients included, 709 (9%) had TDR: 604 (85%) had resistance to one drug class only [350 nucleos(t)ide reverse transcriptase inhibitors (NRTIs), 164 non-nucleos(t)ide reverse transcriptase inhibitors (NNRTIs), 90 protease inhibitors (PIs)], 77 (11%) to two classes (42 NRTIs/NNRTIs, 31 NRTIs/PIs, 4 NNRTIs/PIs), and 28 (4%) had resistance to all three classes. The overall mean (SD) viral load at the time of resistance testing was 4.60 (0.82) log(10) copies/ml, and did not differ by class of TDR. However, patients harbouring M184V/I (n = 61) had a significantly lower viral load [adjusted mean difference -0.33 log10 copies/ml (95% CI -0.54 to -0.11), 53% lower (95% CI 22 to 71%), P = 0.002] compared to wild-type virus.

DISCUSSION

Our study provides clear evidence of an in-vivo fitness cost associated with the M184V/I mutation independent of drug effects which select for this mutation. This was not observed for any other mutation, but true effects may have been obscured by reversion of initially resistant viruses to wild-type.

HIV, transmitted drug resistance, and the paradox of preexposure prophylaxis

The administration of antiretrovirals before HIV exposure to prevent infection (i.e., preexposure prophylaxis; PrEP) is under evaluation in clinical trials. Because PrEP is based on antiretrovirals, there is considerable concern that it could substantially increase transmitted resistance, particularly in resource-rich countries. Here we use a mathematical model to predict the effect of PrEP interventions on the HIV epidemic in the men-who-have-sex-with-men community in San Francisco. The model is calibrated using Monte Carlo filtering and analyzed by constructing nonlinear response hypersurfaces. We predict PrEP interventions could substantially reduce transmission but significantly increase the proportion of new infections caused by resistant strains. Two mechanisms can cause this increase. If risk compensation occurs, the proportion increases due to increasing transmission of resistant strains and decreasing transmission of wild-type strains. If risk behavior remains stable, the increase occurs because of reduced transmission of resistant strains coupled with an even greater reduction in transmission of wild-type strains. We define this as the paradox of PrEP (i.e., resistance appears to be increasing, but is actually decreasing). We determine this paradox is likely to occur if the efficacy of PrEP regimens against wild-type strains is greater than 30% and the relative efficacy against resistant strains is greater than 0.2 but less than the efficacy against wild-type. Our modeling shows, if risk behavior increases, that it is a valid concern that PrEP could significantly increase transmitted resistance. However, if risk behavior remains stable, we find the concern is unfounded and PrEP interventions are likely to decrease transmitted resistance.

Primary drug resistance and transmission analysis of HIV-1 in acute and recent drug-naïve seroconverters in Singapore

OBJECTIVES

The aim of the study was to elucidate primary drug resistance and transmission of HIV-1 in acute and recent drug-naïve seroconverters in Singapore.

METHODS

Acute and recent HIV-1 seroconverters were enrolled in the study. The HIV-1 polymerase (pol) gene was sequenced and used for genotypic drug resistance analysis and phylogenetic analysis. HIV-1 transmission clusters were inferred from phylogenetic clustering analysis.

RESULTS

Of the 60 subjects analysed, 95% were men, and 73.3% were men who have sex with men (MSM). Six HIV-1 subtypes were identified, including CRF01_AE (46.7%), subtypes B (30%), B' (15%) and G (1.7%), CRF33_01B (1.7%) and CRF34_01B (5%). Primary genotypic resistance was detected in only one (1.7%) subtype B variant. Thirty-one patients (51.7%) were phylogenetically clustered, of whom 90% reported having local risk exposure, compared with 59% of the patients who were not phylogenetically clustered [odds ratio (OR) 6.35, 95% confidence interval (CI) 1.65-23.95]. MSM (OR 5.63, 95% CI 1.17-27.15), high viral load (OR 4.28, 95% CI 1.37-13.36) and young age (OR 0.92, 95% CI 0.85-0.99) were independently associated with clustered individuals.

CONCLUSIONS

In Singapore, HIV-1 primary resistance is insignificant; individuals with seroconversion account for about half of onward transmission among recently infected seroconverters. MSM, high viral load and young age are factors that facilitate transmission. Early detection of these individuals is of paramount importance for the prevention of HIV-1 transmission.

An HIV-1 215V mutant shows increased phenotypic resistance to d4T

Human immunodeficiency virus type 1 (HIV-1) viruses with C/S/D/E at 215 codon of the reverse transcriptase (RT) have been associated with the T215Y/F HIV-1 resistant viruses transmission to naïve patients. The uncommon T215V mutation was detected in DNA proviral samples of a treatment-naïve patient. Virus T215V was obtained after cloning the patient-RT into a molecular clone. Wild-type (T215) and resistant (T215F) clones, were obtained in T215V clone by "in vitro" site-directed mutagenesis. Phenotypic resistance against AZT, ddI and d4T, replication kinetics and the selection of resistance mutations were estimated "in vitro". The T215V virus replicated as efficiently as the wild-type (T215) without antivirals and in the presence of AZT or ddI. The T215V virus showed higher replicative capacity than the wild-type and a 4.3-fold increase in the IC(50) values in cultures with d4T. Selection of resistance mutations was not observed in viral quasispecies of the T215V virus after serial passages in culture in presence of increasing concentrations of AZT, ddI or d4T. This work demonstrates that the T215V mutation decreases the susceptibility of HIV-1 to d4T, and consequently, it could compromise the response to regimens containing this antiviral.

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).

Epidemiology of human immunodeficiency virus in the United States

The human immunodeficiency virus (HIV) epidemic emerged in the early 1980s with HIV infection as a highly lethal disease among men who have sex with men and among frequent recipients of blood product transfusions. Advances in the treatment of HIV infection have resulted in a fundamental shift in its epidemiology, to a potentially chronic and manageable condition. However, challenges in the prevention of this infection remain. In particular, increasing evidence suggests that transmission of drug-resistant virus is becoming more common and that the epidemic is having a profound impact on morbidity and mortality in ethnic and racial minority subgroups in the United States. New population-based data collection systems designed to describe trends in behaviors associated with HIV transmission and better methods for measuring the true incidence of transmission will better elucidate the characteristics of HIV infection in the United States and inform future public health policies.

Evidence of a decline in transmitted HIV-1 drug resistance in the United Kingdom

OBJECTIVE

To examine recent trends in transmitted drug resistance (TDR) in the United Kingdom.

METHODS

Analysis of results of genotypic resistance tests reported to the UK HIV Drug Resistance Database, which includes virtually all tests conducted as part of routine clinical care nationally. Resistance was based on major mutations as defined in the 2005 International AIDS Society-USA guidelines. Analysis was restricted to persons who were antiretroviral treatment-naive at the time of sampling, and a test defined as relating to recent infection if the patient was co-enrolled in the UK Register of HIV Seroconverters and the sample taken within 18 months of a negative HIV antibody test.

RESULTS

A total of 4454 samples from treatment-naive patients between 1996 and 2004 were analysed, including 316 from patients recently infected at the time of the resistance test. After an initial rise, TDR declined from a peak of around 14% in 2001-2002 to around 8% by the end of 2004 (Ptrend < 0.001), largely driven by a decrease in nucleos(t)ide reverse transcriptase inhibitor (NRTI) mutations. Non-NRTI resistance has become increasingly important in relative terms and is now as common as NRTI resistance. Among patients with recent infection, an almost identical pattern was observed but shifted approximately 2 years earlier. A change in the distribution of viral subtypes did not explain these temporal trends.

CONCLUSIONS

This is the first clear evidence of a decrease in TDR at national level. The wider use of regimens that suppress viral concentration to below infectious levels is one of several plausible explanations for this finding.

Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment

Viral recombination has been postulated to play two roles in the development of human immunodeficiency virus (HIV) resistance to antiretroviral drugs. First, recombination has the capacity to associate resistance mutations expressed by distinct viruses, thereby contributing to the development of viruses with improved drug resistance. In addition, recombination could preserve diversity in regions outside those subject to strong selective pressure. In this study, we sought direct evidence for the occurrence of these processes in vivo by evaluating clonal virus populations obtained from the same patient before and after a treatment change that, while unsuccessful in controlling viral replication, led to the emergence of viruses expressing a different profile of resistance mutations. Phylogenetic studies supported the conclusion that the genotype arising after the treatment change resulted from the emergence of recombinant viruses carrying previously existing resistance mutations in novel combinations, whereas alternative explanations, including convergent evolution, were not consistent with observed genotypic changes. Despite evidence for a strong loss of genetic diversity in genomic regions coding for the protease and reverse transcriptase, diversity in regions coding for Gag and envelope was considerably higher, and recombination between the emerging viruses expressing the new pattern of resistance mutations and viral quasispecies in the previously dominant population contributed to this preservation of diversity in the envelope gene. These findings emphasize that recombination can participate in the adaptation of HIV to changing selective pressure, both by generating novel combinations of resistance mutations and by maintaining diversity in genomic regions outside those implicated in a selective sweep.

Prevalence and determinants of transmitted antiretroviral drug resistance in HIV-1 infection

Transmission of drug-resistant HIV-1 variants from antiretroviral treatment-experienced persons has been documented to occur through multiple routes, including sexual intercourse, intravenous drug use and vertically from mother to child. Newly infected persons with transmitted drug resistance (TDR) also act as a source for the onward transmission of resistant variants. Rates of virological suppression and behavioural patterns of treated populations and the relative fitness of drug-resistant variants are important determinants of the prevalence of TDR. Current estimates indicate that the prevalence is highest in regions and populations with long-established use of antiretroviral therapy. Limited data suggest that the incidence of TDR is rising in developing countries where access to therapy is increasing. There are methodological variations between studies, however, including those relative to the selection of the study population and the resistance interpretation system, which can skew prevalence estimates. TDR has important implications for the successful management of antiretroviral therapy. Routine resistance testing of drug-naive persons has been widely adopted in affluent countries and shown to effectively guide the selection of first-line regimens. Genotypic resistance tests offer a practical approach for detecting TDR. However, routine methods can only detect resistant mutants within the dominant quasi-species and fail to detect low-frequency resistant variants, which may become important once selective drug pressure is introduced. More sensitive testing methods are being evaluated but remain research tools at present. In addition, factors such as superinfection and possible differences in resistance patterns between plasma and cellular reservoirs and between anatomical compartments should be considered when evaluating TDR.

The fitness cost of mutations associated with human immunodeficiency virus type 1 drug resistance is modulated by mutational interactions

It is generally accepted that the fitness cost of resistance mutations plays a role in the persistence of transmitted drug-resistant human immunodeficiency virus type 1 and that mutations that confer a high fitness cost are less able to persist in the absence of drug pressure. Here, we show that the fitness cost of reverse transcriptase (RT) mutations can vary within a 72-fold range. We also demonstrate that the fitness cost of M184V and K70R can be decreased or enhanced by other resistance mutations such as D67N and K219Q. We conclude that the persistence of transmitted RT mutants might range widely on the basis of fitness and that the modulation of fitness cost by mutational interactions will be a critical determinant of persistence.

Algorithms for the interpretation of HIV-1 genotypic drug resistance information

Drug resistance testing has proven its use to guide treatment decisions in HIV-1 infected patients. Genotyping is the preferred technique for clinical drug resistance testing. Many factors complicate the interpretation of mutations towards therapy response, such that an interpretation system is necessary to help the clinical virologist. No consensus interpretation exists to date and experts often have quite different opinions. As a result, several algorithms for the interpretation of HIV-1 genotypic drug resistance information have been designed. Clinical evaluation of their genotypic interpretation is not always straightforward. We describe a few publicly available systems and their clinical evaluation. We also stress that in addition to drug resistance, for effective management of HIV infection the clinician needs to take into account all potential causes of treatment failure. Successful therapy heavily relies on the expertise of the clinician.

Persistence of drug-resistant HIV-1 and possible implications for antiretroviral therapy

Antiretroviral therapy has significantly reduced the morbidity and mortality of subjects infected with HIV-1. However, the establishment of persistent infection and the development of drug-resistant variants are major obstacles facing the eradication of HIV-1. This review summarizes the current knowledge of the persistence of drug-resistant HIV-1 acquired by transmission, or due to therapy failure and the possible implications for antiretroviral therapeutic strategies.