Brief report: primary infection with zidovudine-resistant human immunodeficiency virus type 1

SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs

Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.

Antiviral Activity of Tenofovir Alafenamide against HIV-1 with Thymidine Analog-Associated Mutations and M184V

Tenofovir alafenamide (TAF) and tenofovir disoproxil fumarate (TDF) are prodrugs of the HIV-1 nucleotide reverse transcriptase inhibitor tenofovir (TFV). In vivo, TAF achieves >4-fold-higher intracellular levels of TFV diphosphate (TFV-DP) compared to TDF. Since thymidine analog-associated mutations (TAMs) in HIV-1 confer reduced TFV susceptibility, patients with TAM-containing HIV-1 may benefit from higher TFV-DP levels delivered by TAF. Moreover, the presence of the M184V mutation increases TFV susceptibility during TDF- or TAF-based therapy. The susceptibilities to antiviral drugs of site-directed mutants (SDMs) and patient-derived mutants containing combinations of TAMs (M41L, D67N, K70R, L210W, T215Y, and K219Q) with or without the M184V mutation (TAMs±M184V) were evaluated using either 5-day multicycle (MC; n = 110) or 2-day single-cycle (SC; n = 96) HIV assays. The presence of M184V in TAM-containing HIV-1 SDMs (n = 48) significantly increased TAF sensitivity compared to SDMs without M184V (n = 48). The comparison of TAF and TDF resistance profiles was further assessed in viral breakthrough (VB) experiments mimicking clinically relevant drug concentrations. A total of 68 mutants were assayed at physiological concentration in VB experiments, with 15/68 mutants breaking through with TDF (TFV, the in vitro equivalent of TDF, was used in these experiments), and only 3 of 68 mutants breaking through under TAF treatment. Overall, in the VB assay mimicking the 4-fold-higher intracellular levels of TFV-DP observed clinically with TAF versus TDF, TAF inhibited viral breakthrough of most TAM-containing HIV-1, whereas TDF did not. These results indicate that TAF has a higher resistance threshold than TDF and suggest that higher resistance cutoffs should be applied for TAF compared to TDF in genotypic and phenotypic resistance algorithms.

Analysis of transmitted HIV drug resistance from 2005 to 2015 in Victoria, Australia: a comparison of the old and the new

Background Baseline genotyping is part of standard-of-care treatment. It reveals that transmitted drug resistance (TDR) continues to be important for the management of HIV infection. Attention is typically focused on determining whether resistance to the protease inhibitors (PI) and reverse transcriptase inhibitors (RTI) occurs. However, the increasing use of integrase inhibitors (INIs) raises a concern that TDR to this class of antiretroviral drug may also occur.

METHODS

PI and RTI drug resistance genotyping was performed on blood samples collected between 2005 and 2015 from 772 treatment-naïve Victorian patients infected with HIV within the previous 12 months. Integrase genotyping was performed on 461 of the 485 patient samples collected between 2010 and 2015.

RESULTS

In the period 2005-10, 39 of 343 patients (11.4%) had at least one PI- or RTI-associated mutation, compared with 34 of 429 (7.9%) during the period 2011-15. Compared with 2005-10, during 2011-15 there was a significant decline in the prevalence of the non-nucleoside-associated mutation K103N and the nucleoside-associated mutations at codons M41 and T215. One patient was detected with a major INI resistance mutation, namely G118R. However, this mutation is rare and its effect on susceptibility is unclear. A small number of patients (n=12) was infected with HIV containing accessory resistance mutations in the integrase gene.

CONCLUSIONS

The lack of transmitted resistance to INIs is consistent with a low level of resistance to this class of drugs in the treated population. However, continued surveillance in the newly infected population is warranted as the use of INIs increases.

Increase in transmitted drug resistance in migrants from sub-Saharan Africa diagnosed with HIV-1 in Sweden

OBJECTIVE

To study the trends of transmitted drug resistance (TDR) in HIV-1 patients newly diagnosed in Sweden, 2010-2016.

DESIGN

Register-based study including all antiretroviral therapy-naive patients ≥18 years diagnosed with HIV-1 in Sweden 2010-2016.

METHODS

Patient data and viral pol sequences were extracted from the national InfCareHIV database. TDR was defined as the presence of surveillance drug resistance mutations (SDRMs). A CD4 T-cell decline trajectory model estimated time of infection. Phylogenetic inference was used for cluster analysis. Chi-square tests and logistic regressions were used to investigate relations between TDR, epidemiological and viral factors.

RESULTS

One thousand, seven hundred and thirteen pol sequences were analyzed, corresponding to 71% of patients with a new HIV-1 diagnosis (heterosexuals: 53%; MSM: 34%). The overall prevalence of TDR was 7.1% (95% CI 5.8-8.3%). Nonnucleoside reverse transcriptase inhibitor (NNRTI) TDR increased significantly from 1.5% in 2010 to 6.2% in 2016, and was associated to infection and/or origin in sub-Saharan Africa (SSA). An MSM transmission cluster dating back to the 1990s with the M41L SDRM was identified. Twenty-five (1.5%) patients exhibited TDR to tenofovir (TDF; n = 8), emtricitabine/lamivudine (n = 9) or both (n = 8).

CONCLUSION

NNRTI TDR has increased from 2010 to 2016 in HIV-1-infected migrants from SSA diagnosed in Sweden, mirroring the situation in SSA. TDR to tenofovir/emtricitabine, used in preexposure prophylaxis, confirms the clinical and epidemiological need for resistance testing in newly diagnosed patients.

HIV drug resistance in HIV positive individuals under antiretroviral treatment in Shandong Province, China

The efficacy of antiretroviral drugs is limited by the development of drug resistance. Therefore, it is important to examine HIV drug resistance following the nationwide implementation of drug resistance testing in China since 2009. We conducted drug resistance testing in patients who were already on or new to HIV antiretroviral therapy (ART) in Shandong Province, China, from 2011 to 2013, and grouped them based on the presence or absence of drug resistance to determine the effects of age, gender, ethnicity, marital status, educational level, route of transmission and treatment status on drug resistance. We then examined levels of drug resistance the following year. The drug resistance rates of HIV patients on ART in Shandong from 2011 to 2013 were 3.45% (21/608), 3.38% (31/916), and 4.29% (54/1259), per year, respectively. M184V was the most frequently found point mutation, conferring resistance to the nucleoside reverse transcriptase inhibitor, while Y181C, G190A, K103N and V179D/E/F were the most frequent point mutations conferring resistance to the non-nucleoside reverse transcriptase inhibitor. In addition, the protease inhibitor drug resistance mutations I54V and V82A were identified for the first time in Shandong Province. Primary resistance accounts for 20% of the impact factors for drug resistance. Furthermore, it was found that educational level and treatment regimen were high-risk factors for drug resistance in 2011 (P<0.05), while treatment regimen was a high risk factor for drug resistance in 2012 and 2013 (P<0.05). Among the 106 drug-resistant patients, 77 received immediate adjustment of treatment regimen following testing, and 69 (89.6%) showed a reduction in drug resistance the following year. HIV drug resistance has a low prevalence in Shandong Province. However, patients on second line ART regimens and those with low educational level need continuous monitoring. Active drug resistance testing can effectively prevent the development of drug resistance.

Commonly Transmitted HIV-1 Drug Resistance Mutations in Reverse-Transcriptase and Protease in Antiretroviral Treatment-Naive Patients and Response to Regimens Containing Tenofovir Disoproxil Fumarate or Tenofovir Alafenamide

Background

The presence of transmitted drug resistance mutations (TDRMs) in antiretroviral treatment (ART)-naive patients can adversely affect the outcome of ART.

Methods

Resistance testing was conducted in 6704 ART-naive subjects predominantly from the United States and Europe in 9 clinical studies conducted by Gilead Sciences from 2000 to 2013.

Results

The presence of TDRMs increased during this period (from 5.2% to 11.4%), primarily driven by an increase in nonnucleoside reverse-transcriptase (RT) inhibitor (NNRTI) resistance mutations (from 0.3% to 7.1%), particularly K103N/S (increase from 0.3% to 5.3%). Nucleoside/nucleotide RT inhibitor mutations were found in 3.1% of patients. Only 1 patient had K65R (0.01%) and 7 had M184V/I (0.1%), despite high use of tenofovir disoproxil fumarate (TDF), emtricitabine, and lamivudine and potential transmission of resistance to these drugs. At least 1 thymidine-analogue mutations was present in 2.7% of patients with 0.07% harboring T215Y/F and 2.7% harboring T215 revertant mutations (T215rev). Patients with the combination of M41L + L210W + T215rev showed full human immunodeficiency virus RNA suppression while receiving a TDF- or tenofovir alafenamide-containing regimen.

Conclusions

There was an overall increase of TDRMs among patients enrolling in clinical trials from 2000 through 2013, driven primarily by an increase in NNRTI resistance. However, the presence of common TDRMs, including thymidine-analogue mutations/T215rev, showed no impact on response to TDF- or tenofovir alafenamide-containing regimens.

Pharmacokinetic Modeling of Lamivudine and Zidovudine Triphosphates Predicts Differential Pharmacokinetics in Seminal Mononuclear Cells and Peripheral Blood Mononuclear Cells

The male genital tract is a potential site of viral persistence. Therefore, adequate concentrations of antiretrovirals are required to eliminate HIV replication in the genital tract. Despite higher zidovudine (ZDV) and lamivudine (3TC) concentrations in seminal plasma (SP) than in blood plasma (BP) (SP/BP drug concentration ratios of 2.3 and 6.7, respectively), we have previously reported lower relative intracellular concentrations of their active metabolites, zidovudine triphosphate (ZDV-TP) and lamivudine triphosphate (3TC-TP), in seminal mononuclear cells (SMCs) than in peripheral blood mononuclear cells (PBMCs) (SMC/PBMC drug concentration ratios of 0.36 and 1.0, respectively). Here, we use population pharmacokinetic (PK) modeling-based methods to simultaneously describe parent and intracellular metabolite PK in blood, semen, and PBMCs and SMCs. From this model, the time to steady state in each matrix was estimated, and the results indicate that the PK of 3TC-TP and ZDV-TP in PBMCs are different from the PK of the two in SMCs and different for the two triphosphates. We found that steady-state conditions in PBMCs were achieved within 2 days for ZDV-TP and 3 days for 3TC-TP. However, steady-state conditions in SMCs were achieved within 2 days for ZDV-TP and 2 weeks for 3TC-TP. Despite this, or perhaps because of it, ZDV-TP in SMCs does not achieve the surrogate 50% inhibitory concentration (IC50) (as established for PBMCs, assuming SMC IC50 = PBMC IC50) at the standard 300-mg twice-daily dosing. Mechanistic studies are needed to understand these differences and to explore intracellular metabolite behavior in SMCs for other nucleoside analogues used in HIV prevention, treatment, and cure.

Development and customization of a color-coded microbeads-based assay for drug resistance in HIV-1 reverse transcriptase

Background

Drug resistance (DR) of HIV-1 can be examined genotypically or phenotypically. Although sequencing is the gold standard of the genotypic resistance testing (GRT), high-throughput GRT targeted to the codons responsible for DR may be more appropriate for epidemiological studies and public health research.

Methods

We used a Japanese database to design and synthesize sequence-specific oligonucleotide probes (SSOP) for the detection of wild-type sequences and 6 DR mutations in the clade B HIV-1 reverse transcriptase region. We coupled SSOP to microbeads of the Luminex 100 xMAP system and developed a GRT based on the polymerase chain reaction (PCR)-SSOP-Luminex method.

Results

Sixteen oligoprobes for discriminating DR mutations from wild-type sequences at 6 loci were designed and synthesized, and their sensitivity and specificity were confirmed using isogenic plasmids. The PCR-SSOP-Luminex DR assay was then compared to direct sequencing using 74 plasma specimens from treatment-naïve patients or those on failing treatment. In the majority of specimens, the results of the PCR-SSOP-Luminex DR assay were concordant with sequencing results: 62/74 (83.8%) for M41, 43/74 (58.1%) for K65, 70/74 (94.6%) for K70, 55/73 (75.3%) for K103, 63/73 (86.3%) for M184 and 68/73 (93.2%) for T215. There were a number of specimens without any positive signals, especially for K65. The nucleotide position of A2723G, A2747G and C2750T were frequent polymorphisms for the wild-type amino acids K65, K66 and D67, respectively, and 14 specimens had the D67N mutation encoded by G2748A. We synthesized 14 additional oligoprobes for K65, and the sensitivity for K65 loci improved from 43/74 (58.1%) to 68/74 (91.9%).

Conclusions

We developed a rapid high-throughput assay for clade B HIV-1 DR mutations, which could be customized by synthesizing oligoprobes suitable for the circulating viruses. The assay could be a useful tool especially for public health research in both resource-rich and resource-limited settings.

An affordable HIV-1 drug resistance monitoring method for resource limited settings

HIV-1 drug resistance has the potential to seriously compromise the effectiveness and impact of antiretroviral therapy (ART). As ART programs in sub-Saharan Africa continue to expand, individuals on ART should be closely monitored for the emergence of drug resistance. Surveillance of transmitted drug resistance to track transmission of viral strains already resistant to ART is also critical. Unfortunately, drug resistance testing is still not readily accessible in resource limited settings, because genotyping is expensive and requires sophisticated laboratory and data management infrastructure. An open access genotypic drug resistance monitoring method to manage individuals and assess transmitted drug resistance is described. The method uses free open source software for the interpretation of drug resistance patterns and the generation of individual patient reports. The genotyping protocol has an amplification rate of greater than 95% for plasma samples with a viral load >1,000 HIV-1 RNA copies/ml. The sensitivity decreases significantly for viral loads <1,000 HIV-1 RNA copies/ml. The method described here was validated against a method of HIV-1 drug resistance testing approved by the United States Food and Drug Administration (FDA), the Viroseq genotyping method. Limitations of the method described here include the fact that it is not automated and that it also failed to amplify the circulating recombinant form CRF02_AG from a validation panel of samples, although it amplified subtypes A and B from the same panel.

Community HIV-1 drug resistance is associated with transmitted drug resistance

OBJECTIVES

As community viral load (CVL) measurements are associated with the incidence of new HIV-1 infections in a population, we hypothesized that similarly measured community drug resistance (CDR) could predict the prevalence of transmitted drug resistance (TDR).

METHODS

Between 2001 and 2011, the prevalences of HIV-1 drug resistance for patients with established infection receiving HIV care (i.e. CDR) and TDR in recently infected patients were determined in San Diego. At each position in HIV-1 reverse transcriptase (RT) and protease (pro), drug resistance was evaluated both as the overall prevalence of resistance-associated mutations and by weighting each resistance position to the concurrent viral load of the patient and its proportion to the total viral load of the clinic (CVL). The weighting was the proportion of the CVL associated with patients identified with resistance at each residue. Spearman ranked correlation coefficients were used to determine associations between CDR and TDR.

RESULTS

We analysed 1088 resistance tests for 971 clinic patients and baseline resistance tests for 542 recently infected patients. CDR at positions 30, 46, and 88 in pro was associated with TDR between 2001 and 2011. When CDR was weighted by the viral load of patients, CDR was associated with TDR at position 103 in RT. Each of these associations was corroborated at least once using shorter measurement intervals.

CONCLUSIONS

Despite evaluation of a limited percentage of chronically infected patients in San Diego, CDR correlated with TDR at key resistance positions and therefore may be a useful tool with which to predict the prevalence of TDR.

Transmitted resistance to HIV integrase strand-transfer inhibitors: right on schedule

Transmitted drug resistance (TDR), the primary acquisition of an HIV variant already resistant to antiretrovirals, affects approximately 15% of all new infections in the United States. Historically, from the time initial agents in the reverse transcriptase, protease and entry inhibitor classes were introduced, it took 3-5 years before the first case reports of TDR appeared. With the description of the first two cases of transmitted integrase stand-transfer inhibitor resistance, it is only a matter of time before the prevalence of TDR affecting this newest antiretroviral class reaches a level warranting baseline resistance testing for all patients entering care.

Transmission of integrase strand-transfer inhibitor multidrug-resistant HIV-1: case report and response to raltegravir-containing antiretroviral therapy

We report the case of an integrase strand-transfer inhibitor (INI)-resistant and four-drug-class-resistant HIV-1 variant infecting an antiretroviral therapy-naive man. The virus harboured INI drug resistance substitutions (Q148H and G140S) along with multiple reverse transcriptase and protease inhibitor resistance mutations. This case illustrates an emerging need to consider the possibility of acquired INI resistance among newly diagnosed treatment-naive individuals harbouring multidrug-resistant HIV-1.

HIV-1 drug resistance mutations among antiretroviral-naive HIV-1-infected patients in Asia: results from the TREAT Asia Studies to Evaluate Resistance-Monitoring Study

Of 682 antiretroviral-naïve patients initiating antiretroviral therapy in a prospective, multicenter human immunodeficiency virus type 1 (HIV-1) drug resistance monitoring study involving 8 sites in Hong Kong, Malaysia, and Thailand, the prevalence of patients with ≥1 drug resistance mutation was 13.8%. Primary HIV drug resistance is emerging after rapid scaling-up of antiretroviral therapy use in Asia.

Minority variants of drug-resistant HIV

Minor drug-resistant variants exist in every patient infected with human immunodeficiency virus (HIV). Because these minority variants are usually present at very low levels, they cannot be detected and quantified using conventional genotypic and phenotypic tests. Recently, several assays have been developed to characterize these low-abundance drug-resistant variants in the large, genetically complex population that is present in every HIV-infected individual. The most important issue is what results generated by these assays can predict clinical or treatment outcomes and might guide the management of patients in clinical practice. Cutoff values for the detection of these low-abundance viral variants that predict an increased risk of treatment failure should be determined. These thresholds may be specific for each mutation and treatment regimen. In this review, we summarize the attributes and limitations of the currently available detection assays and review the existing information about both acquired and transmitted drug-resistant minority variants.

Primary antiretroviral drug resistance among HIV type 1-infected individuals in Brazil

Infection with drug-resistant human immunodeficiency virus type 1 (HIV-1) has been documented in all countries that have surveyed for it and may result in an unfavorable response to therapy. The prevalence and characteristics of individuals with transmitted resistance to antiretroviral drugs have been scarcely described in Brazil. We performed antiretroviral resistance testing prior to initiation of therapy in 400 subjects enrolled from 20 centers in 13 Brazilian cities between March and September 2007. Genotyping was conducted using PCR-amplified HIV pol products by automated sequencing, and genotype interpretation was done according to the IAS-USA consensus. Of 400 eligible participants, 387 (95.8%) were successfully tested. Seven percent of antiretroviral-naive patients carried viruses with one or more major mutation associated with drug resistance. The prevalence of these mutations was 1.0% for protease inhibitors, 4.4% for nonnucleoside reverse transcriptase inhibitors, and 1.3% for nucleoside reverse transcriptase inhibitors. The frequency of multidrug resistance among the resistant strains was 13.6%. Among subjects infected with drug-resistant virus, the majority were infected with subtype B viruses (91%). Subjects from the city of São Paulo had higher transmitted resistance mutations compared to the rest of the country. Reporting a partner taking antiretroviral medications was associated with a higher chance of harboring HIV variants with major drug resistance mutations [odds ratio = 2.57 (95% confidence interval, 1.07-6.16); p = 0.014]. Resistance testing in drug-naive individuals identified 7% of subjects with mutations associated with reduced susceptibility to antiretroviral drugs. Continued surveillance of drug-resistant HIV-1 in Brazil is warranted when guidelines for HIV prophylaxis and treatment are updated. Resistance testing among drug-naive patients prior to treatment initiation should be considered, mainly directed at subjects whose partners are already on antiretroviral therapy.

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.

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.

Drug-resistance mutations number and K70R or T215Y/F substitutions predict treatment resumption during guided treatment interruptions

The role of antiretroviral history and genotypic resistance information as predictors of the first treatment interruption (TI) length in a CD4(+) cell count and plasma viremia-guided TI study (GTI) was assessed. Drug-resistance mutations (DRMs) were monitored in chronically HIV-1-infected subjects who underwent GTI. Patients were retrospectively classified into those who received monotherapy or dual therapy prior to HAART (pre-HAART group, n = 44) or directly initiated HAART (HAART group, n = 43). DRMs were assessed by population-based sequencing of proviral DNA at baseline and plasma RNA monthly during TI up to 180 weeks. Univariate and multivariate Cox's proportional hazard models were used to determine time off therapy predictors. The emergence of viruses with DRMs during TI was 5.1-fold more likely in pre-HAART than in HAART patients. The presence of DRMs in proviral DNA or plasma RNA was associated with shorter time off therapy. An accumulation of three or more DRMs duplicated the risk of restarting therapy with respect to having one or two mutations. Regardless of the number of DRMs, the presence of K70R or T215F/Y predicted the shortest TI time. Multivariate analyses adjusted by nadir CD4(+) counts supported the presence of DRMs in plasma HIV-1 RNA, and specifically the K70R or T215F/Y, as potent predictors of time off therapy. A history of monotherapy or dual therapy, accumulation of three or more key DRMs in the HIV-1 polymerase, and/or the presence of substitutions K70R or T215F/Y were associated with shorter time off therapy during GTI. A genotypic profile could provide clinicians with a predictive tool for time off therapy when TI is required in patients with suppressed viremia in whom nadir CD4(+) count is not available.

Combined therapy for tuberculosis and HIV-1: the challenge for drug discovery

Combining drug therapies for dual infection by Mycobacterium tuberculosis and HIV-1 is made complex by high pill burdens, shared drug toxicities, drug-drug and drug-disease interactions, immune reconstitution inflammatory syndrome, co-morbid diseases and drug resistance in both bacillus and virus. Recently, novel anti-tubercular and anti-retroviral drugs have bolstered the tuberculosis-HIV drug pipelines and may help ameliorate these difficulties. This review article discusses the reasons for current problems of therapy for dual infection. It also identifies promising agents, which may significantly improve co-therapy and thus diminish the great morbidity and mortality of these two pandemics.

Antiretroviral drug resistance, HIV-1 tropism, and HIV-1 subtype among men who have sex with men with recent HIV-1 infection

OBJECTIVE

Antiretroviral drug treatment may be complicated in individuals infected with antiretroviral drug-resistant or non-subtype B HIV-1 strains. HIV-1 tropism may also affect disease progression. We analyzed antiretroviral drug resistance, HIV-1 subtype, and HIV-1 tropism among 195 men who have sex with men from six major cities in the United States, using samples collected within 6 months of HIV-1 seroconversion (1999-2003).

METHODS

HIV-1 genotyping was performed using the ViroSeq HIV-1 Genotyping System. HIV-1 tropism was determined using a commercial assay. HIV-1 subtyping was performed by phylogenetic analysis of pol region sequences.

RESULTS

Thirty-one (15.9%) of the men had evidence of antiretroviral drug resistance. Seven (3.6%) men had multi-class resistance, including three (1.5%) with resistance to all three antiretroviral drug classes. We found no statistically significant association of antiretroviral drug resistance with demographic factors, sexual practices, self-reported sexually transmitted infections, use of recreational drugs, or use of antiretroviral drug post-exposure prophylaxis. All samples were HIV-1 subtype B. Four men had CXCR4-using HIV-1 strains. One man with a CXCR4-using strain also had antiretroviral drug resistance.

CONCLUSIONS

Antiretroviral drug resistance is relatively common among recently infected men who have sex with men in the United States. CXCR4-using strains were detected in a small number of these infections, which were all subtype B HIV-1.

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.

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.

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.

Prevalence and predictors of antiretroviral drug resistance in newly diagnosed HIV-1 infection

OBJECTIVES

To determine prevalence and predictors of antiretroviral drug resistance in newly diagnosed individuals with HIV-1 infection, using a systematic approach to avoid selection bias.

METHODS

Plasma samples from all persons diagnosed HIV-1 seropositive at a large London centre between April 2004 and February 2006 underwent sequencing of HIV-1 reverse transcriptase (RT) and protease genes. Subtype was assigned by phylogenetic analysis. Resistance was scored according to the IAS-USA list (2005) modified to include T215revertants and exclude isolated E44D or V118I and minor protease mutations. Recent seroconversion was identified by HIV antibody avidity testing.

RESULTS

The cohort of 239 included 169 (70.7%) males, 126 (52.7%) homosexuals, 118 (49.5%) persons of white ethnicity and 144 (60.0%) persons born outside the UK. Subtypes included B 134 (56.1%), C 46 (19.2%), A 17 (7.1%), other non-B 42 (17.6%). The prevalence of resistance mutations was 17/239 (7.1%; 95% confidence interval 4.5-11.1%), comprising 10/239 (4.2%) nucleoside/nucleotide RT inhibitor (NRTI); 4/239 (1.7%) non-nucleoside RT inhibitor (NNRTI) and 4/239 (1.7%) protease inhibitor (PI) associated mutations. Dual-class (NRTI + PI) resistance mutations were detected in 1/239 (0.4%) person. The prevalence of resistance mutations was 7/85 (8.2%) and 10/154 (6.5%) in persons with recent and established infection, respectively. In multivariate analysis, having been born in the UK and high CD4 count, but not gender, age, risk group, ethnicity or subtype, were independent predictors of resistance.

CONCLUSIONS

In an unselected UK cohort, subtypes other than B accounted for 43.9% of new HIV-1 diagnoses. The prevalence of resistance mutations was 7.1% and highest in those born in the UK.

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.

Primary HIV drug resistance and efficacy of first-line antiretroviral therapy guided by resistance testing

BACKGROUND

Primary HIV drug resistance has been associated with poor treatment outcome of first-line highly active antiretroviral therapy (HAART) in several trials. The aim of the study was to assess the efficacy of first-line HAART guided by resistance testing.

METHODS

In a prospective multicenter study in the state of Nordrhein-Westfalen, Germany, chronically HIV-infected patients underwent genotypic resistance testing and were monitored for 48 weeks after initiation of HAART.

RESULTS

Primary drug resistance was found in 30 of 269 patients entering the study between January 2001 and December 2003 [11.2%; 95% confidence interval, 7.4-14.9]. In intent-to-treat analysis, the proportion of patients with viral load below 50 copies/mL after 24 and 48 weeks was 70.0% and 66.7%, respectively, in patients with resistance and 74.1% and 73.6%, respectively, in patients without (P = 0.66 and 0.51). In on-treatment analysis, the proportions were 80.8% and 83.3%, respectively, in patients with resistance and 81.9% and 85.0%, respectively, in patients without (P= 0.79 and 0.77). These results were also valid considering a detection limit of 400 copies/mL.

CONCLUSIONS

The prevalence of primary drug resistance was 11.2% in chronically HIV-infected patients. HAART guided by resistance testing had similar efficacy in patients with primary drug resistance as compared with patients with wild-type virus. Based on these facts, resistance-adapted first-line HAART is suggested as routine practice.

Prevalence of transmitted HIV-1 drug resistance and the role of resistance algorithms: data from seroconverters in the CASCADE collaboration from 1987 to 2003

OBJECTIVES

To examine factors influencing the rate of transmitted drug resistance (TDR) among seroconverters, with particular emphasis on 3 widely used genotypic drug resistance algorithms.

METHODS

The study used data from CASCADE (Concerted Action on Seroconversion to AIDS and Death in Europe), a collaboration of seroconverter cohorts in Europe and Canada. Genotypic resistance data were derived within 18 months of the last seronegative test or date of laboratory evidence of acute infection and before the initiation of antiretroviral therapy. The Stanford algorithm was used to analyze each individual's nucleotide sequence. A multivariate logistic model was used to assess independent relationships between the presence of TDR and exposure category, sex, age at seroconversion, and year of seroconversion. The paper also describes 3 alternative definitions of resistance: the Stanford algorithm, the key resistance mutations defined by the International AIDS Society, and the Agence Nationale de Recherches sur le Sida (ANRS) algorithm.

RESULTS

Forty-five of 438 patients (10.3%) seroconverting between 1987 and 2003 were infected with a drug-resistant HIV-1 variant. Forty patients (9.1%) showed resistance mutations to only 1 class of antiretroviral drugs, 2 (0.5%) to 2 classes, and 3 (0.7%) to 3 classes of antiretroviral therapy. It was suggested that individuals seroconverting later in calendar time were more likely to have TDR (relative risk 3.89 and 95% CI: 0.84 to 18.02, and relative risk 4.69 and 95% CI: 1.03 to 21.31, for 1996-1999 and 2000-2003, respectively, compared with pre-1996; P trend = 0.08). This trend was apparent regardless of the definition of TDR used. The total estimated proportion of individuals with TDR varied between 10.3% and 15.5% according to which definition was used.

CONCLUSIONS

Evidence was found for the rise of TDR over time. A specific definition of what constitutes TDR rather than a simple list of mutations is needed.

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.

Snapshot of HIV pathogenesis in China

Several reviews have focused on the nature of HIV infection and its spread in various geographical regions of China. In contrast, this review provides a comprehensive update on the prevalence of multiple HIV-1 subtypes, consequent emergence of recombinant and novel forms of HIV-1 in China, and the implications this may have on HIV diversity and the development of effective vaccines. In addition it also examines the dissemination of primary drug resistance in therapy naïve patients, as well as co-infections with two other important viruses-hepatitis B and C. The main purpose of this review is to provide a current snapshot of HIV-1 pathogenesis in China and possibly shed some light on the future of HIV evolution, and potential challenges for future vaccine and anti-retroviral therapeutics against HIV strains in this area.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Confronting the emergence of drug-resistant HIV type 1: impact of antiretroviral therapy on individual and population resistance

Resistance to antiretroviral agents, and in particular the increasing levels of transmitted resistant virus could offset the substantial gains won with potent antiretroviral therapy. Primary and acquired antiretroviral resistance rates reflect the relative usage of different antiretroviral drugs in the population, as well as the inherent genetic barrier to the development of resistance associated with individual drugs. Data on antiretroviral resistance rates, gleaned from the growing HIV-1-infected population treated with a continuously increasing number of antiretroviral drugs and drug combinations, provide insights into patient management approaches for delaying the emergence of resistance and minimizing the degree of resistance. Evolving data suggest that the relative ease by which HIV-1 escapes the selective pressure of chronic drug exposure varies for the different antiretroviral drug classes and individual antiretroviral drugs. The development of resistance in vivo can be anticipated based on these data, in conjunction with the individuals treatment history and resistance testing results. These in turn can guide the judicious use of antiretroviral drugs to attain optimal treatment responses and to preserve therapeutic options for the time when antiretroviral-resistant strains emerge. The recent developments of new antiretroviral drugs, including the use of boosted protease inhibitors, suggest that treatment strategies can limit the development of resistance.

Correlation of a Brief Perceived Stress Measure With Nonadherence to Antiretroviral Therapy Over Time

Adherence to antiretroviral medications has proven to be a challenge for individuals diagnosed with HIV infection. Nonadherence can lead to treatment failure, HIV resistance, and poor health outcomes. Many published studies have described factors associated with poor adherence, yet few have presented validated scales that could practically be applied in treatment settings to identify individuals at higher risk of nonadherence. This article explores the relationship between a revised version of the Perceived Stress Scale and nonadherence to antiretroviral therapy. The scale consists of the following items: How often in the past month have you felt that you were unable to control the important things in your life; confident in your ability to handle your personal problems; that things were going your way; and difficulties were piling up so high you could not handle them? Response options were "never or rarely," "sometimes," "often," and "mostly or always." In multivariate analysis, clients who scored in the highest quartile of perceived stress were more than twice as likely to be nonadherent at baseline and follow-up 1 and more than 5 times as likely to be nonadherent at follow-up 2 than clients in the lowest quartile of perceived stress scores.

HIV-1 chemotherapy and drug resistance

BACKGROUND

Therapy with inhibitors of human immunodeficiency virus type 1 (HIV-1) replication has had only transient clinical benefit to date. It has been speculated that drug-resistant virus mutants may contribute to therapeutic failure.

OBJECTIVE

To extrapolate from the biology of drug-resistant HIV-1 to improve antiretroviral chemotherapeutic strategies.

STUDY DESIGN

The literature was reviewed in regard to clinical and virologic correlates of HIV-1 drug resistance, methodology for detection of resistant virus, and chemotherapeutic strategies for prolonging suppression of virus replication.

RESULTS

HIV-1 isolates resistant to different nucleoside reverse transcriptase (RT) inhibitors, nonnucleoside RT inhibitors, and protease inhibitors have been implicated to different extents with virologic or clinical failure of therapeutic effectiveness. The in vivo antiviral effect of certain nonnucleoside RT inhibitors as monotherapy is lost coincident with emergence of a dominant population of resistant virus. Disease progression is more rapid among patients at advanced stages of HIV-1 disease with highly zidovudine (AZT)-resistant virus (50% inhibitory concentration 1.0 muM AZT) and is not attributable to effects of other baseline predictors of progression studied to date. However, there is no definitive evidence that high level AZT resistance causes the loss of therapeutic benefit of AZT. Several of the research methods used for detection of drug-resistant mutants could be developed for future use as screening assays in clinical virology laboratories.

CONCLUSIONS

Strategies for individualizing therapy based on switching, or adding, drugs at first detection of drug-resistant HIV-1 aim to minimize replication of viruses that are drug-resistant, as well as those that remain susceptible to the drug. If clinical investigation reveals that such approaches extend duration of antiretroviral therapeutic benefit, HIV-1 drug-resistance assessment may be increasingly requested from clinical virology laboratories. Monitoring antiviral suppression by quantifying plasma HIV-1 RNA appears more practical at present, however. Different combination regimens are also being studied to see if some regimens delay emergence of resistant virus longer than others. In the future, sequential empiric changes to new combination regimens every few months may also bear investigation to attempt to "pre-empt" HIV-1 resistance development.

Viral resistance patterns selected by antiretroviral drugs and their potential to guide treatment choice

Massive viral turnover and reverse transcriptase's high error rate create the potential for drug-resistant viral variants to appear rapidly under the selective pressure of antiretroviral therapy. Loss of antiviral effect in treatment-adherent persons is most commonly coincident with the appearance of viral mutants with reduced drug sensitivity. Thus, detection of viral resistance may represent an early marker of therapy failure. Similarly, control of viral replication in the plasma compartment, as defined by plasma viral load below the levels of assay quantification, is associated with a sustained therapeutic response and delayed development of viral resistance. Information on patterns of resistance to and cross-resistance between antiretroviral agents is increasingly well characterised and represents an important consideration when deciding how to combine and/or sequence antiretrovirals to achieve optimal antiviral effects. Given the limited number of antiretrovirals presently available or in advanced development, it is important not to limit future therapeutic options by using therapies early in the treatment sequence which may select for cross-resistant viral variants and hence potentially reduce the magnitude of therapeutic response when treatment is changed to another member of that drug class. However, no studies using resistance to guide clinical decision making have been reported to date and available sequencing studies have focused largely on switching or adding therapies to patients experienced with zidovudine monotherapy. Thus, no resistance driven treatment algorithm is currently available.

Transmitted human immunodeficiency virus type 1 carrying the D67N or K219Q/E mutation evolves rapidly to zidovudine resistance in vitro and shows a high replicative fitness in the presence of zidovudine

Drug-naive patients infected with drug-resistant human immunodeficiency virus type 1 (HIV-1) who initiate antiretroviral therapy show a shorter time to virologic failure than patients infected with wild-type (WT) viruses. Resistance-related HIV genotypes not commonly seen in treated patients, which likely result from reversion or loss of primary resistance mutations, have also been recognized in drug-naive persons. Little work has been done to characterize the patterns of mutations in these viruses and the frequency of occurrence, their association with phenotypic resistance, and their effect on fitness and evolution of resistance. Through the analysis of resistance mutations in 1082 newly diagnosed antiretroviral-naive persons from the United States, we found that 35 of 48 (72.9%) persons infected with HIV-1 containing thymidine analog mutations (TAMs) had viruses that lacked a primary mutation (T215Y/F, K70R, or Q151M). Of these viruses, 9 (25.7%) had only secondary TAMs (D67N, K219Q, M41L, or F77L), and all were found to be sensitive to zidovudine (AZT) and other drugs. To assess the impact of secondary TAMs on the evolution of AZT resistance, we generated recombinant viruses from cloned plasma-derived reverse transcriptase sequences. Two viruses had D67N, three had D67N and K219Q/E, and three were WT. Four site-directed mutants with D67N, K219Q, K219E, and D67N/K219Q were also made in HIV-1(HXB2). In vitro selection of AZT resistance showed that viruses with D67N and/or K219Q/E acquired AZT resistance mutations more rapidly than WT viruses (36 days compared to 54 days; P = 0.003). To investigate the factors associated with the rapid selection of AZT mutations in these viruses, we evaluated fitness differences among HXB2(WT) and HXB2(D67N) or HXB2(D67N/K219Q) in the presence of AZT. Both HXB2(D67N/K219Q) and HXB2(D67N) were more fit than HXB2(WT) in the presence of either low or high AZT concentrations, likely reflecting low-level resistance to AZT that is not detectable by phenotypic testing. In the absence of AZT, the fitness cost conferred by D67N or K219Q was modest. Our results demonstrate that viruses with unique patterns of TAMs, including D67N and/or K219Q/E, are commonly found among newly diagnosed persons and illustrate the expanding diversity of revertant viruses in this population. The modest fitness cost conferred by D67N and K219Q supports persistence of these mutants in the untreated population and highlights the potential for secondary transmission. The faster evolution of these mutants toward AZT resistance is consistent with the higher viral fitness in the presence of AZT and shows that these viruses are phenotypically different from WT HIV-1. Our study emphasizes the need for clinical studies to better define the impact of these mutants on treatment responses and evolution of resistance.

The Role of Baseline HIV-1 Resistance Testing in Patients with Established Infection

Effective long-term treatment of HIV-1 infection is challenging because of several factors, including antiretroviral drug resistance. Antiretroviral resistance testing has short-term benefit for optimizing the choice of a rescue regimen after treatment failure. Resistance testing also is recommended before therapy in pregnancy and acute infection or recent seroconversion. The benefit of routine resistance testing before starting treatment for established infection is less clear. This report summarizes the accumulating evidence of persistence of resistant mutants after initial infection, detectability of resistant virus with standard assays before treatment of established infection, the potential adverse impact of this baseline resistance on effectiveness of therapy, and the increasing prevalence of resistance in treatment-naïve patients. Taken together, these data suggest that pretreatment genotypic resistance testing also may be useful in patients with established infection. Although further study is needed, clinicians are now encouraged to routinely obtain pretreatment resistance testing.

Drug resistance in non-subtype B HIV-1

Treatment of HIV-1 with antiretroviral therapy may select mutations in the pol gene associated with resistance to reverse transcriptase inhibitors and protease inhibitors. To provide durable clinical benefit, emergence of drug resistance is countered by prescription of alternative drug regimens. Data on sequential treatments that are effective after virologic failure and the selection of drug resistance is largely confined to HIV-1 subtype B, the clade that has circulated in North America and Europe. However, HIV-1 subtype B currently accounts for only 12% of the estimated 40 million HIV infected individuals worldwide. The global HIV-1 epidemic includes infection with nine identified HIV-1 group M subtypes (A-K), as well as distinct sub-subtypes and numerous chimerical or recombinant forms. Increasing access to treatment of HIV-1 in the developing world and increasing non-subtype B infection through travel and migration pose new questions about the susceptibility and response of these diverse HIV-1 viruses to antiretroviral drugs. Here we review HIV diversity and the published literature on drug resistance, comparing the known resistance mutations in individuals infected with subtype B to the growing experience in the treatment of non-subtype B HIV-1 worldwide.