Resistance to HIV Integrase Strand Transfer Inhibitors Among Clinical Specimens in the United States, 2009–2012

MAJOR ARTICLE HIV/AIDS Resistance to HIV Integrase Strand Transfer Inhibitors Among Clinical Specimens in the United States, 2009–2012 Christopher B. Hurt,1 Joseph Sebastian,2 Charles B. Hicks,3 and Joseph J. Eron1 1 Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, 2Laboratory Corporation of America, Research Triangle Park, and 3Division of Infectious Diseases, Duke University, Durham, North Carolina Background. Data on integrase inhibitor resistance come primarily from clinical trials and in vitro studies. We examined results of all clinically indicated integrase genotypic resistance tests (GRTs) performed at a US national referral lab from 2009 through 2012. Methods. Integrase sequences and demographic data were compiled with paired protease–reverse transcriptase (PR-RT) GRT results, when available. Analyses utilized the Stanford HIV Drug Resistance Database. “Major” integrase mutations included T66AIK, E92QV, F121Y, Y143CHR, S147G, Q148HKR, and N155H; multiple accessory mutations were also assessed. Results. Among 3294 sequences from 3012 patients, 471 patients had viruses with ≥1 raltegravir or elvitegravir resistance mutation (15.6%). Q148 and N155 pathways were equally represented (both n = 197); 84 had Y143 mutations. Q148 rarely occurred without accessory mutations (n = 3). Among 224 patients with serial integrase GRTs, 22 with baseline wild-type acquired a major mutation, after a median 224 days between tests (interquartile range, 148– 335 days). Major mutations were observed to persist up to 462 days. Most (62%) had paired PR-RT results. Patients with integrase-resistant viruses were older and more likely to have PR-RT mutations (both P < .001). Among those with PR-RT data, 42 patients had 4-class resistance (2.3%). Sex, geographic region, and test year were not associated with integrase resistance. High-level dolutegravir resistance was predicted in 12% of patients with raltegravir- or elvitegravir-resistant viruses (2% of all patients). Conclusions. Approximately 1 in 6 US patients undergoing integrase GRT for clinical decision making harbors significant resistance, with Q148 and N155 pathways equally common. Dolutegravir is likely to have full or partial activity against most variants observed. Keywords. human immunodeficiency virus; antiretroviral resistance; raltegravir; elvitegravir; dolutegravir. As the newest class of antiretrovirals (ARVs), integrase strand transfer inhibitors (INSTIs) have assumed an important role in treating human immunodeficiency virus (HIV) infection. Raltegravir became part of a Received 20 August 2013; accepted 7 October 2013; electronically published 21 October 2013. Presented in part: 20th Conference on Retroviruses and Opportunistic Infections, Atlanta, Georgia, 3–6 March 2013. Abstract 591. Correspondence: Christopher B. Hurt, MD, University of North Carolina at Chapel Hill, 130 Mason Farm Road, CB7030, Chapel Hill, NC 27599–7030 (. edu). Clinical Infectious Diseases 2014;58(3):423–31 © The Author 2013. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: . DOI: 10.1093/cid/cit697 preferred initial regimen in the United States for HIVinfected adults [1] within 2 years of Food and Drug Administration (FDA) approval [2], owing to its demonstrated efficacy and favorable safety profile in treatmentexperienced [3] and -naive patients [4]. The second drug in the class, elvitegravir [5, 6], is a component of an alternative INSTI-based regimen for treatment-naive patients [7], in a fixed-dose combination tablet with tenofovir disoproxil fumarate, emtricitabine, and the pharmacologic booster cobicistat [8]. Dolutegravir, a second-generation INSTI, was approved by the FDA in August 2013 [9]. Despite the potency, tolerability, and durability of first-generation INSTIs, resistance mutations are detected in up to 60% of patients with virologic failure in HIV/AIDS • CID 2014:58 (1 February) • 423 clinical trials studying highly treatment-experienced patients, and up to 8% in studies of initial therapy [10, 11]. Three principal mutation pathways reduce susceptibility to raltegravir: Y143CHR, Q148HKR, and N155H. These codons are located in close proximity to integrase’s active site, and each mutation significantly reduces viral fitness [12]. Certain compensatory mutations can partially or fully restore viral replicative capacity: T97A rescues catalytic function in the presence of Y143 mutants, similar to G140ACS or E138AK for Q148 mutants [13]. In the case of N155H, its main accessory mutation, E92QV, further reduces susceptibility without restoring fitness—a fact that helps explain why N155 mutants are frequently replaced by Q148 ± G140 [14] in vivo. Interestingly, E92Q is the most common initial mutation to arise during failure of elvitegravirbased regimens, followed by N155H and Q148R [15]. Due to unique interactions between active site residues and raltegravir, substitutions at Y143 unaccompanied by additional mutations have no effect on in vitro susceptibility to dolutegravir [16] and little [17] to no [18] effect on elvitegravir. Indeed, dolutegravir retains activity against all single-mutation variants [16, 19, 20]. Patients continued on failing raltegravir-containing regimens may accumulate multiple mutations over time [21]—a scenario that can reduce susceptibilities to other INSTIs, including dolutegravir. In 2 studies of dolutegravir among patients who failed raltegravir (VIKING-2 and -3), the greatest reduction in dolutegravir susceptibility occurred when Q148 was accompanied by ≥2 other major mutations. However, a reduced but measurable antiretroviral effect was still observed in most patients [19, 20]. Two recently identified mutations, G118R and R263K, each confer low-level resistance to dolutegravir [22, 23]. Both have been reported in vivo [24, 25]. Although much is known about the mutation pathways affecting INSTIs, all such data come from in vitro experiments or clinical trials. In this report, we focus on integrase genotypic resistance tests (GRTs) sent to a US national referral laboratory, in order to characterize the profile of INSTI resistance among specimens obtained for clinical decision making. Our principal aims were to (1) describe the prevalence of INSTI resistance and the patterns of mutations resulting from INSTI failures in a clinical population; (2) determine the association between integrase and protease–reverse transcriptase (PR-RT) mutations among patients with paired GRTs; and (3) assess the frequency of mutation patterns likely to impact dolutegravir susceptibility among patients harboring viruses with resistance to firstgeneration INSTIs. METHODS Study Population and Data Collection Integrase and PR-RT GRTs require 2 separate amplifications, each sequencing distinct areas of the HIV genome and 424 • CID 2014:58 (1 February) • HIV/AIDS reporting mutations on (...truncated)