The prevalence of transmitted antiretroviral drug resistance in treatment-naïve patients and factors influencing firstline treatment regimen selection

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1 DOI: /j x r 2008 Merck & Co., Inc. HIV Medicine (2008), 9, ORIGINAL RESEARCH The prevalence of transmitted antiretroviral drug resistance in treatment-naïve patients and factors influencing firstline treatment regimen selection H-Y Huang, 1 ES Daar, 2 PE Sax, 3 B Young, 4 P Cook, 5 P Benson, 6 C Cohen, 7 A Scribner 8 and H Hu 1 1 Outcomes Research and Management, Merck & Co. Inc., West Point, PA, USA, 2 Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA, 3 Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA, 4 Denver ID Consultants, Denver, CO, USA, 5 Brody School of Medicine, East Carolina University, Greenville, NC, USA, 6 Be Well Medical Center, Berkley, MI, USA, 7 Community Research Initiative of New England, Boston, MA, USA and 8 Diagnostic Clinic of Longview Center for Clinical Research, Longview, TX, USA Objectives To estimate the prevalence of transmitted antiretroviral (ARV) drug resistance, and to assess whether resistance testing influences first-line ARV regimen selection. Methods Data on patients characteristics were collected through questionnaires. ARV drug resistance was tested by genotypic methods and defined by Quest Stanford classification rule. Physicians reported the intended and actual treatments and the factors considered in treatment selection. Results Two hundred and twenty-eight patients were included. The prevalence of ARV drug resistance was 12.1%, with 9.8% for non-nucleoside reverse transcriptase inhibitors (NNRTIs), 4.5% for nucleoside reverse transcriptase inhibitors and 1.8% for protease inhibitors (PIs). Pill burdens, dosing frequency and physicians experience with regimens were the major factors considered in treatment selection. The intended and actual treatment differed for 73 and 44% of the patients with and without ARV drug resistance, respectively [odds ratio (95% confidence interval, CI) ( ), P ]. NNRTI-based regimens were intended for 10 patients with resistance to NNRTIs; these patients were prescribed PI-based regimens after genotypic testing. Conclusions Transmitted ARV drug resistance was detected in 12.1% of treatment-naïve patients, with resistance to NNRTIs the most common. Resistance-testing results played a partial role in first-line treatment selection. However, resistance to NNRTIs pre-empted NNRTI use. Keywords: drug resistance testing, first-line treatment, HIV, transmitted drug resistance Received: 5 November 2007, accepted 31 January 2008 Introduction The use of highly active antiretroviral therapy has made it possible to prolong the life expectancy and reduce the incidence of opportunistic infection in persons with HIV infection or AIDS [1 4]. Current recommended initial regimens employ two nucleoside reverse transcriptase inhibitors (NRTIs) plus either a non-nucleoside reverse Correspondence: Han-Yao Huang, Outcomes Research and Management, Merck & Co. Inc., 770 Sumneytown Pike WP39-166, West Point, PA 19446, USA. Fax: ; transcriptase inhibitor (NNRTI) or a protease inhibitor (PI). Unfortunately, under drug-selective pressure, resistance to these drugs may develop, primarily as a result of mutations in viral reverse transcriptase and protease genes. It has been estimated that approximately 40 80% of chronically HIV-infected, treatment-experienced patients with incomplete virus suppression developed resistance to antiretroviral (ARV) therapy [5], leading to poorer survival and opportunities for transmitted ARV drug resistance [6]. Transmitted resistance to ARV drugs can persist for years [7 9], and hence has implications for treatment strategies. 285

2 286 H-Y Huang et al. In 2001, the World Health Organization established the Global HIV Drug Resistance Surveillance Programmes to respond to the emergent threat of viral resistance to ARV drugs. It was recommended that surveillance should target treatment-naïve individuals newly or recently infected with HIV [10]. The existence of transmitted drug resistance has been documented in several studies, mostly of small sample size. The reported prevalence varied ranging from 1 to 25% [11] because of variation in study patients, availability and types of ARV drugs used by patients who were the origin of viral transmission, time points of resistance testing during the infection course, resistance assay sensitivity and algorithms used to define resistance, among other factors. According to the International AIDS Society-USA and the US Department of Health and Human Services guidelines, resistance testing is recommended for patients with acute or recent infection (o6 12 months), and is recommended or should be considered for treatment-naïve patients with chronic infection (1 year or longer) [12,13]. Recently, the use of HIV susceptibility testing was shown to be associated with enhanced survival even after adjusting for stages of HIV disease, demographics and age [14]. However, little is known about how ARV drug resistance testing guides clinical decisions on the selection of firstline treatment regimens. In this setting, we conducted a study in HIV-infected, treatment-naïve but treatment-ready patients to assess the prevalence of ARV drug resistance and its associated factors, and to examine the factors considered by study physicians in first-line treatment regimen selection. Patients and methods Study design This cross-sectional study with repeated measurements examined treatment regimen selection and factors considered in regimen selection pre- and post-genotypic testing as well as HIV resistance to ARV drugs. The study was conducted at 19 HIV clinics located in Florida (six sites), Massachusetts (four sites), California (two sites), Colorado (one site), Michigan (one site), North Carolina (one site), New York (one site), Texas (one site), New Jersey (one site) and Nevada (one site) from August 2005 to January Study population Patients were eligible for study enrolment if they met all of the following criteria: 19 or more years of age; documented laboratory evidence of HIV infection; most recent viral load of 4600 HIV-1 RNA copies/ml of plasma prior to the baseline clinical visit; never used an ARV drug; decided to initiate ARV treatment in consultation with his/her doctor; was expected by the study physicians to start an ARV regimen once genotype resistance test results from the baseline visit are available; and provided informed consent to study participation. Patients were ineligible if they had participated in any HIV-related trials of investigational drugs or were in need of ARV drug treatment (as determined by study physicians) before a genotype resistance test result became available. The study protocol was approved by the Schulman Associates Institutional Review Board Inc. and the local institutional review boards at each study site. Data collection Patients visited the study physicians clinics, where their eligibility for participating in the study was confirmed. Patients then provided written informed consent and filled out a questionnaire that inquired about their demographic information, education, employment status, sexual orientation, HIV clinical history, HIV risk factors and payment methods for HIV medication. Plasma samples were aliquoted into vials, stored at 20 1C or colder on site, and shipped to a central laboratory within 24 h on dry ice. Before the genotypic test result for a patient became available, the patient s physician recorded the patient s most recent CD4 cell counts and HIV viral load, history of an AIDS-defining illness (opportunistic infections, disease affecting the central and peripheral nervous system, malignancies or wasting syndrome), current presentation of any severe symptoms of HIV infection (i.e. unexplained fever or diarrhoea 42 4 weeks, oral candidiasis or 410% unexplained weight loss), intended treatment regimens and factors influencing the regimen selection (including genotypic testing, low pill burdens, dosing frequency, prior experience with the regimens, clinical guidelines, fewer side effects, recent CD4 and/or viral load, patient had AIDS symptoms, intent to avoid future resistance, patient s preference, drug drug interaction, cost of regimens, patient was of child-bearing age, patient was pregnant, contradiction to another regimen, recently acquired new information about this regimen or one of its components, and insurance formulary restrictions). When a genotypic test result became available (typically, 2 weeks after blood sample collection), the study physicians filled out a second questionnaire on the actual treatment regimens he/she prescribed and the factor(s) that influenced the selection of treatment regimens.

3 HIV antiretroviral drug resistance and treatment 287 Table 1 Patients characteristics Characteristics n (%) Age, mean (SD) 37.1 (9.2) Sex Female 45 (19.7) Male 183 (80.3) Race or ethnicity White 85 (37.3) Black/African American 92 (40.4) Hispanic 39 (17.1) Asian/Pacific Islander 4 (1.8) Others 6 (2.6) Missing 2 (0.9) Employment status Employed full-time 98 (43.0) Employed part-time 38 (16.7) Retired 2 (0.9) Unemployed 89 (39.0) Missing 1 (0.4) Years of school education o12 47 (20.6) (78.5) Unknown 2 (0.9) Payment method for HIV medicines Completely by a health insurance company 34 (14.9) Partially by a health insurance company 30 (13.0) Completely by a state or federal government programme 69 (30.3) Partially by a state or federal government programme 12 (5.3) Completely with personal finance 3 (1.3) Unknown 77 (33.8) None of the above 3 (1.3) Sexual orientation Heterosexual 80 (35.1) Homosexual 127 (55.7) Bisexual 19 (8.3) Missing 2 (0.9) HIV sub-type A 2 (0.9) AG 2 (0.9) B 217 (96.9) C 3 (1.3) Self-reported duration between the diagnosis of HIV infection and the present study visit (years) Median (interquartile range) 1 (0, 3) Range (0, 22) Being part of a high-risk group* Sex partner is an injection drug user 8 (3.5) Male male sexual partner 109 (47.8) Sex partner of a person who has sex with men 45 (19.7) Sex partner of a person who has HIV/AIDS 89 (39.0) Commercial sex worker 6 (2.6) Injection drug users who shared needles or equipment 14 (6.1) Latest CD4 counts (cells/ml) o50 20 (8.8) (17.5) (33.3) (21.5) (16.2) Not recorded 6 (2.6) Latest viral load (HIV-1 RNA copies/ml) (15.8) (45.2) (36.0) Missing 7 (3.1) Diagnosis with AIDS No 196 (86.0) Yes 21 (9.2) Table 1. (Contd.) Characteristics n (%) Unknown 11 (4.8) Severe symptoms of HIV infection No 192 (84.2) Yes 32 (14.0) Missing 4 (1.8) *Categories are not mutually exclusive. SD, standard deviation. Laboratory analysis HIV-1 RNA was extracted from patients plasma samples and reverse-transcribed into DNA. Polymerase chain reaction was applied to amplify the sequence of the protease gene and the amino-terminal 400 amino acids of the reverse transcriptase gene. The minimal viral load required for successful genotyping analyses was 600 copies/ml. The Quest Stanford classification rule was used to define drug resistance [15]. Statistical analysis Patients demographic and clinical characteristics were summarized by frequency for categorical variables and by means and standard deviations (SDs) for continuous variables. The prevalence of resistance to each ARV drug and to drug classes of NRTIs, NNRTIs and PIs, alone or combined, was estimated. Logistic regression models were used to explore the associations between patients characteristics and presence of drug resistance, the association between genotypic test results (yes or no for resistance) and changes in ARV prescription (yes or no for a change), and the association between resistance test results (yes or no for resistance) and changes in factors considered in treatment selection (yes or no for a change). Results A total of 228 participants were recruited. Mean (SD) age of the patients was 37.1 (9.2); 80% were men; 37% were White, 40% were Black; and 78% of the patients reported to have contracted HIV through sexual exposure (Table 1). The median of self-reported time since diagnosis of HIV infection was 1 year [interquartile range (IQR) 0 3). With the exception of one patient whose CD4 cell counts and viral load were measured about 1.5 years prior to the clinical visit, patients CD4 cell counts and viral loads were

4 288 H-Y Huang et al. Percent (%) % 4.5% 1.8% 8.9% 2.2% 1.0% NNRTIs NRTIs PIs 1 class 2 classes 3 classes Fig. 1 Prevalence of transmitted resistance to antiretroviral drugs by drug classes and by number of drug classes. Table 2 Prevalence of resistance to antiretroviral drugs Drug class Drug NRTIs Zidovudine 4.5 Abacavir 0.45 Didanosine 1.4 Lamivudine 0.9 Emtricitabine 0.45 Stavudine 2.7 Zalcitabine 0.94 Tenofovir 0.45 NNRTIs Delavirdine 7.7 Efavirenz 9.0 Nevirapine 9.5 PIs Amprenavir 0.9 Fosamprenavir 0.9 Indinavir 1.35 Nelfinavir 1.35 Ritonavir 1.35 Saquinavir 0.9 Lopinavir 0 Atazanavir 0.45 Tipranavir 0 Darunavir 0 Patients with resistance (%) NNRTIs, non-nucleoside reverse transcriptase inhibitors; NRTIs, nucleoside reverse transcriptase inhibitors; PIs, protease inhibitors. measured within 1 year [median (IQR) 20 (7 42) days]. Approximately one-quarter of the patients had CD4 counts o200 cells/ml, and one third of the patients had CD4 counts between 200 and 350 cells/ml. Nine per cent of the patients had a history of an AIDS-defining illness and 14% of the patients had severe symptoms of HIV infection at the time of clinical visit (Table 1). The prevalence of detected ARV resistance was 12.1% (9.8% for NNRTI, 4.5% for NRTI and 1.8% for PI) (Fig. 1). Among the study patients, 8.9, 2.2 and 1.0% had HIV-1 strains resistant to one, two or three classes of ARV drugs, respectively (Fig. 1). In the NRTI class, zidovudine (ZDV) was the drug to which a higher proportion of patients were resistant (Table 2). In the NNRTI class, the prevalence of Table 3 Associations between patients characteristics and viral resistance to antiretroviral drugs Characteristics Drug resistance (%) OR (95% CI) Sex Female Male (0.5, 4.5) Race or ethnicity White Black/African American (0.3, 1.9) Hispanic (0.5, 4.3) Asian/Pacific Islander 0 American Indian/Alaskan native 0 Others 0 Years of school education o (0.6, 7.7) Duration since HIV diagnosis (years)* o (0.3, 2.5) 41, (0.4, 4.4) (0.3, 2.5) Sexual orientation Heterosexual Homosexual (0.6, 4.7) Bisexual (1.2, 17.4) Being part of a high-risk group (yes/no) Sex partner is an injection drug user 0.0/12.4 Male male sexual partner 15.7/ (0.9, 4.5) Sex partner of a person who has sex with men 4.4/ (0.06, 1.1) Sex partner of a person who has HIV/AIDS 11.4/ (0.4, 2.1) Commercial sex worker 0.0/12.3 Injection drug users who shared 8.3/ (0.08, 5.2) needles or equipment Latest CD4 counts (cells/ml) (0.4, 34.6) (0.2, 18.0) (0.2, 16.0) o (0.4, 31.3) Latest viral load (HIV-1 RNA copies/ml) (0.4, 4.4) (0.2, 2.4) Diagnosis with AIDS No Yes (0.3, 4.5) Unknown 0.0 Severe symptoms of HIV infection No Yes (0.7, 5.3) *Self-reported duration between the diagnosis of HIV infection and the present study visit. CI, confidence interval; OR, odds ratio. resistance was similar for delavirdine, efavirenz (EFV) and nevirapine (Table 2). Of the 27 patients who had HIV resistance to any of the three drug classes, 22 patients were first diagnosed with HIV infection 2 years prior to the clinical visits; the other five patients were first diagnosed 4 6 years prior to the clinical visits. There was no association between drug resistance and

5 HIV antiretroviral drug resistance and treatment 289 Table 4 Treatment regimens pre- and post-genotypic testing, stratified by resistance test results With any detected resistance Without any detected resistance Antiretroviral regimens Intended (n 5 27) (%) Actual (n 5 26)* (%) Intended (n 5 197) (%) Actual (n 5 194)* (%) NRTIs Emtricitabine Lamivudine Zalcitabine Zidovudine Didanosine Tenofovir Stavudine Abacavir NNRTIs w Delavirdine Efavirenz w Nevirapine PIs Amprenavir Tipranavir Indinavir Saquinavir Lopinavir Fosamprenavir Ritonavir Atazanavir Nelfinavir Fusion Enfuvirtide Fixed combinations Combivir (lamivudine 1 zidovudine) Epzicom (lamivudine 1 abacavir) Trizivir (abacavir 1 lamivudine 1 zidovudine) Truvada (emtricitabine 1 tenofovir) Atripla (emtricitabine 1 tenofovir 1 efavirenz) NRTIs 1 1 NNRTI w NRTIs 1 1 PI NRTIs 1 2 PIs z NNRTI 1 1PI *Data on actual regimens were not available from one patient who had resistance and three patients who did not have resistance because the patients did not make a second clinic visit. w Po0.001 for the association between resistance test results and changes in regimen selection from intended to actual prescription. z P for the association between resistance test results and changes in regimen selection from intended to actual prescription. Po0.01 for the association between resistance test results and changes in regimen selection from intended to actual prescription. NNRTIs, non-nucleoside reverse transcriptase inhibitors; NRTIs, nucleoside reverse transcriptase inhibitors; PIs, protease inhibitors. self-reported years since HIV diagnosis (Table 3). Men with male sexual partner(s) or persons with CD4 counts o500 cells/ml were twofold or higher more likely to have viral resistance. However, in both univariate and multivariate analyses, bisexual orientation was the only variable that was significantly associated with viral resistance (Table 3). Prior to genotypic drug resistance testing, pill burdens, dosing frequency, physicians prior experience with treatment regimens, clinical guidelines, side effects, CD4 cell counts/viral load and intent to avoid future resistance were the factor(s) considered in treatment selection for 71, 68, 58, 47, 33, 26 and 12% of the patients, respectively. Each of the other factors was considered for o15% of the patients (range 0 13%). Among the 27 cases whose genotypic test results indicated ARV drug resistance, the actual treatment regimen was not prescribed for one patient because of loss to follow-up. Overall, the intended and actual treatment differed in 73% of the 26 patients with ARV drug resistance, and in 44% of those without resistance [odds ratio (OR) (95% confidence interval, CI) ( ), P for changes after positive results compared to changes after negative results]. However, none of the changes in specific drug selections was associated with resistance test results, with the exception of efavirenz [OR (95% CI) ( ), P ] (Table 4). Eighty-four per cent of the study participants were prescribed fixed combinations of ARV drugs,

6 290 H-Y Huang et al. predominantly Truvadat (emtricitabine and tenofovir). The most common intended treatment regimens were two NRTIs combined with one NNRTI or PI, but a significant decrease in prescribing NNRTIs occurred for patients with viral resistance to ARV drugs (Table 4). Specifically, before genotypic testing, NNRTI-based regimens were intended for 10 of the 21 patients who were found subsequently to have viral resistance to NNRTIs. All of these patients were prescribed PI-based regimens after review of resistance test results. For the three patients who had resistance to one or more drugs in the PI class, one was prescribed lopinavir, to which the patient was not resistant. The other two patients were prescribed Truvadat and EFV without a PI. Among the 10 patients who had resistance to a particular drug within the NRTI class, seven patients were prescribed regimens that included another drug in the same class or regimens that included the drug to which patients had resistance. Specifically, one patient was prescribed lamivudine (3TC), abacavir (ABC) and saquinavir when resistant to ZDV; another patient was prescribed 3TC, tenofovir, ABC and atazanavir when resistant to ZDV; the other five patients were prescribed Truvadat-based regimens (one of them was resistant to tenofovir). Among these 10 patients, two who were intended to receive one NNRTI 1 two NRTIs were changed to receive two NRTIs 1 one PI and two NRTIs 1 two PIs, respectively. There was no indication that PI was prescribed more to provide a more robust genetic barrier. After resistance testing, pill burdens, dosing frequency and physicians prior experience with treatment regimens remained to be the major reasons for treatment selection. None of the changes in treatment consideration factors (excluding genotypic testing) was associated with resistance test results, overall or when limited to those whose prescriptions were changed. Discussion In the USA, the prevalence of ARV drug resistance in HIVinfected, treatment-naïve patients has been reported to range from 10 to 25% during the period from 2003 to 2006 [16 20]. Similarly to a surveillance study from 2003 to 2006 [16] where transmitted drug resistance was observed in 10.4% of HIV-1 infected, treatment-naïve patients, we observed a prevalence rate of 12.1%. Although the prevalence of transmitted drug resistance does not seem to have increased in the USA and Europe in recent years [21 23], preventative, monitoring and containment measures remain indispensable. It has been shown that thymidine analogue mutations linked to resistance to NRTIs and M184V are the most common mutations in ARV treatment-experienced patients [5]. In contrast, mutations associated with resistance to NNRTIs are relatively common in treatment-naïve patients, suggesting that these mutations may have better fitness and transmissibility than the mutations that cause resistance to other classes of drugs. We found that persons with transmitted drug resistance had lower CD4 cell counts than those without transmitted drug resistance. Interestingly, one previous study found that CD4 cell counts declined more rapidly in the first year of infection in persons with HIV resistant to ARV drugs than those with HIV of no resistance, but the declines slowed down thereafter [24,25]. The impact of transmitted drug resistance on clinical presentation and prognosis are uncertain and are complicated by the possibilities that viruses with resistant mutations may be archived in lymphoid tissue and cellular reservoir, cross-resistance may exist, some mutations may enhance drug sensitivity, mutated strains may revert to wild-types and host factors may play a role in determining treatment responses [8,26]. To date, data have been very sparse on whether patients with transmitted drug resistance would have poorer prognosis if left untreated or treated. One recent study showed that the time to viral suppression was longer in patients with transmitted resistance to PI or NRTIs [27]. Most of the previous studies have been of small sample size and brief in exploring factors associated with transmitted ARV drug resistance in treatment-naïve patients. To this end, two findings from the present study merit discussion. Firstly, in contrast to one previous study [28] but consistent with others [29,30], we did not find higher prevalence of viral resistance in non-hispanic White individuals. Disparities in healthcare-seeking behaviour, access to and adherence to treatment regimens and sampling errors may have accounted for any discrepancy in prevalence of drug resistance by race/ethnic groups. Secondly, consistent with one [30] but not another [28] previous study, we found that persons with bisexual orientation were more likely to have viral resistance to ARV drugs. In this study, only one woman had bisexual orientation: bisexual-oriented persons were predominantly male. It is unknown whether the association between bisexual orientation and ARV drug resistance was attributed to sexual risk behaviour, transmitters poor adherence to treatment regimens or transmitters better access to treatments. Nonetheless, this finding suggests that prevention and containment measures to limit the emergence and spread of HIV drug resistance can be targeted at individuals with bisexual preference. While it appeared peculiar that physicians changed regimens for 44% of the patients without resistance, this finding reflected the fact that several treatment regimens were available for selection. Because none of the changes

7 HIV antiretroviral drug resistance and treatment 291 in treatment consideration factors (other than genotypic testing) was associated with a presence or absence of drug resistance, it is possible that physicians did not consider differently when changing regimens for patients with resistance and those without resistance except in the consideration on genotypic test results. It is also possible that different physicians interpreted and responded differently to the question on their reasons for regimen selection. Some physicians might have checked the item genotypic testing for patients who had no resistance because resistance was not a concern based on the genotypic testing results, whereas other physicians might not have checked the item because resistance was not a concern. Therefore, to understand whether physicians considered resistance-testing results, we relied on the data of changes from intended to actual regimens, rather than on the data of whether genotypic testing was checked. Only one out of the 26 patients who had resistance was prescribed a drug to which he or she had resistance. This finding suggests that physicians avoided prescribing drugs to which patients were resistant. In particular, resistance to NNRTI pre-empted the use of NNRTI. It is noteworthy that in assessing the association between resistance test results and changes in drug selection, the statistical significance relies on the number of patients with resistance to individual drugs. Therefore, it is not surprising that resistance test results were not significantly associated with changes in drugs in the NRTI or PI classes, to which fewer patients were resistant compared to NNRTIs. As shown in Table 4, efavirenz was the only NNRTI drug intended for the patients who were subsequently found to have resistance to NNRTI. With few choices within the NNRTI class, these patients were prescribed other classes of drugs after a review of resistance test results. We examined changes in physicians prescriptions to see whether M184V was assumed, even though it was not detected, in the presence of other mutations. An intended regimen that included 3TC was changed to other drugs after genotypic testing for four out of the 18 patients (22%) who had resistance to drugs other than 3TC. Actual treatment regimens were not changed from the intended regimens for all seven patients who were not intended to receive 3TC. An intended regimen that included FTC was changed to other drugs after genotypic testing for three out of eight patients (37.5%) who had resistance to drugs other than FTC. Actual treatment regimens for two of 16 patients (12.5%) were changed to include FTC when they had resistance to drugs other than FTC. However, because changes also occurred for patients who had no resistance, and none of the changes in specific drug selections was associated with resistance test results (except EFV), we were unable to differentiate physicians prescription pattern for individual drug switch by genotypic testing results. In this study, pill burdens, dosing frequency and physicians prior experience with the regimens are the factors considered most frequently in treatment regimen selection. Although side effects were not reported to be a primary consideration in treatment regimen selection, it is possible that physicians prior experiences pertain to consideration on side effects. A recent study on the prescription patterns for HIV patients receiving care in the US Department of Veterans Affairs from 1992 to 2004 showed that physicians prescription was better correlated with clinical guidelines on strategies to avoid adverse drug reactions than with the guidelines on strategies to enhance efficacy [31]. ARV drug resistance testing is recommended for patients newly or recently infected with HIV and for patients with treatment failures [12,13,32]. However, there have been difficulties in the methodology and use of resistance testing. The sensitivity of genotypic testing may not be sufficient for detecting mixed resistant viral populations. While phenotypic testing provides direct and quantitative information on how HIV may respond to a particular drug, it is also limited by the inability to detect minor variants, is expensive and often impractical for routine use in clinical settings, and does not detect mixtures of wild type and resistant virus. Furthermore, interpretation of testing results requires renewed knowledge of genetic mutations and associated treatment implications. The complexity and uncertainties of interpreting resistance-testing results could have compromised their use in clinical settings. Future studies should look into the need and the design of user-friendly tools that can incorporate clinical guidelines and interpretation of resistance-testing results into clinical practices and assess how the tools facilitate informed treatment decision-making. In conclusion, transmitted ARV drug resistance was detected in 12% of patients who were ARV-naïve, with resistance to NNRTIs the most common finding. Pill burdens, dosing frequency and physicians prior experience were the major factors influencing initial treatment selection. ARV drug resistance testing, intent to prevent future drug resistance and clinical guidelines played a partial role in guiding treatment selection. However, resistance to NNRTIs pre-empted the use of NNRTIs. Acknowledgements This study was supported by a research fund of Merck & Co. Inc. The authors thank Mr Larry Ma for his assistance with data management.

8 292 H-Y Huang et al. Conflicts of interest statement: H.-Y. Huang and H. Hu are employees of Merck & Co. Inc. E. S. Daar is a consultant/advisor, receives speakers honoria and/or receives research support from Abbott, Boerhringer Ingelheim, Bristol-Myers Squibb, Gilead, GlaxoSmithKline, Merck, Pfizer, Tibotec and Monogram Biosciences. P. Sax is a consultant to Abbott, Bristol-Myers Squibb, Gilead Sciences and GlaxoSmithKline, and he receives honoraria for teaching from Abbott, Bristol-Myers Squibb, Gilead, GlaxoSmithKline, Merck, Tibotec and Virco, and grant support from Bristol-Myers Squibb, Pfizer and Merck & Co. Inc. B. Young is a consultant to Boehringer Ingelheim Pharmaceuticals, Bristol-Myers Squibb, Cerner Corporation, Gilead Sciences, GlaxoSmithKline, Hoffman-LaRoche, speakers bureaux for Boehringer Ingelheim Pharmaceuticals, Gilead Sciences, GlaxoSmithKline, Hoffman-LaRoche and Merck & Co. Inc., and receives grant/research funds from Bristol-Myers Squibb, Cerner Corporation, Gilead Sciences, GlaxoSmithKline, Hoffman-LaRoche and Merck & Co. Inc. P. Cook receives grants from GlaxoSmithKline, Merck & Co. Inc., Senzyme and Pfizer, and serves on the speakers bureaux for Wyeth and Merck & Co. Inc. C. Cohen receives research funds and speaker honoraria from Virco and Monogram Bioscience. References 1 Schneider MF, Gange SJ, Williams CM et al. Patterns of the hazard of death after AIDS through the evolution of antiretroviral therapy: AIDS 2005; 19: Mocroft A, Ledergerber B, Katlama C et al. Decline in the AIDS and death rates in the EuroSIDA Study: an observational study. Lancet 2003; 362: Grubb JR, Moorman AC, Baker RK, Masur H. The changing spectrum of pulmonary disease in patients with HIV infection on antiretroviral therapy. AIDS 2006; 20: Brodt HR, Kamps BS, Gute P, Knupp B, Staszewski S, Helm EB. Changing incidence of AIDS-defining illnesses in the era of antiretroviral combination therapy. AIDS 1997; 11: Geretti AM. Clinical implications of HIV drug resistance to nucleoside and nucleotide reverse transcriptase inhibitors. AIDS Rev 2006; 8: Hogg RS, Bangsberg DR, Lima VD et al. Emergence of drug resistance is associated with an increased risk of death among patients first starting HAART. PLoS Med 2006; 3: e Fox J, Dustan S, McClure M, Weber J, Fidler S. Transmitted drug-resistant HIV-1 in primary HIV-1 infection; incidence, evolution and impact on response to antiretroviral therapy. HIV Med 2006; 7: Ghosn J, Pellegrin I, Goujard C et al. HIV-1 resistant strains acquired at the time of primary infection massively fuel the cellular reservoir and persist for lengthy periods of time. AIDS 2006; 20: Brenner BG, Routy JP, Petrella M et al. Persistence and fitness of multidrug-resistant human immunodeficiency virus type 1 acquired in primary infection. J Virol 2002; 76: World Health Organization. Guidelines for Surveillance of HIV Drug Resistance. resisguide12_12.pdf Geretti AM. Epidemiology of antiretroviral drug resistance in drug-naïve persons. Curr Opin Infect Dis 2007; 20: Hammer SM, Saag MS, Schechter M et al. Treatment for adult HIV infection: 2006 recommendations of the International AIDS Society USA Panel. JAMA 2006; 296: Department of Health and Human Services. Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents. AdultandAdolescentGL.pdf Palella F Jr, Armon C, Chmiel J et al. Improved survival associated with use of HIV susceptibility testing among HAARTexperienced and therapy-naïve patients in the HIV Outpatient Study. 14th Conference on Retroviruses and Opportunistic Infections. Los Angeles, CA, February 2007 [Abstract 660]. 15 Stanford University. HIV Drug Resistance Database. resistanceestimator.cgi Wheeler W, Mahle K, Bodnar U et al. Antiretroviral drug resistance mutations and subtypes in drug naïve persons newly diagnosed with HIV-1 infection, United States, March 2003 October th Conference on Retroviruses and Opportunistic Infections. Los Angeles, CA, February 2007 [Abstract 648]. 17 Smith D, Moini N, Pesano R et al. Clinical utility of HIV standard genotyping among antiretroviral-naïve individuals with unknown duration of infection. Clin Infect Dis 2007; 44: Truong HH, Grant RM, McFarland W et al. Routine surveillance for the detection of acute and recent HIV infections and transmission of antiretroviral resistance. AIDS 2006; 20: Shet A, Berry L, Mohri H et al. Tracking the prevalence of transmitted antiretroviral drug-resistant HIV-1: a decade of experience. J Acquir Immune Defic Syndr 2006; 41: Grubb JR, Singhatiraj E, Mondy K, Powderly WG, Overton ET. Patterns of primary antiretroviral drug resistance in antiretroviral-naïve HIV-1-infected individuals in a midwest university clinic. AIDS 2006; 20: Pillay D. Current patterns in the epidemiology of primary HIV drug resistance in North America and Europe. Antivir Ther 2004; 9:

9 HIV antiretroviral drug resistance and treatment Bannister WP, Kirk O, Gatell JM et al. Regional changes over time in initial virologic response rates to combination antiretroviral therapy across Europe. J Acquir Immune Defic Syndr 2006; 42: Weinstock HS, Zaidi I, Heneine W et al. The epidemiology of antiretroviral drug resistance among drug-naïve HIV-1-infected persons in 10 US cities. J Infect Dis 2004; 189: Bhaskaran K, Pillay D, Walker AS et al. Do patients who are infected with drug-resistant HIV have a different CD4 cell decline after seroconversion? An exploratory analysis in the UK Register of HIV Seroconverters. AIDS 2004; 18: Pillay D, Bhaskaran K, Jurriaans S et al. Theimpactof transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS 2006; 20: Hirsch MS, Brun-Vezinet F, Clotet B et al. Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society USA Panel. Clin Infect Dis 2003; 37: Little S, Frost S, Smith D, May S, Parkin N, Richman D. Transmission of HIV drug resistance and treatment response. 14th Conference on Retroviruses and Opportunistic Infections. Los Angeles, CA, February 2007 [Abstract 60]. 28 Novak RM, Chen L, MacArthur RD et al. Prevalence of antiretroviral drug resistance mutations in chronically HIV-infected, treatment-naïve patients: implications for routine resistance screening before initiation of antiretroviral therapy. Clin Infect Dis 2005; 40: Shet A, Berry L, Mohri H et al. Tracking the prevalence of transmitted antiretroviral drug-resistant HIV-1: a decade of experience. J Acquir Immune Defic Syndr 2006; 41: Jayaraman GC, Archibald CP, Kim J et al. A population-based approach to determine the prevalence of transmitted drugresistant HIV among recent versus established HIV infections: results from the Canadian HIV Strain and Drug Resistance Surveillance Program. J Acquir Immune Defic Syndr 2006; 42: Holodniy M, Hornberger J, Rapoport D et al. Relationship between antiretroviral prescribing patterns and treatment guidelines in treatment-naïve HIV-1-infected US veterans ( ). J Acquir Immune Defic Syndr 2007; 44: Vandamme AM, Sonnerborg A, Ait-Khaled M et al. Updated European recommendations for the clinical use of HIV drug resistance testing. Antivir Ther 2004; 9:

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