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 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 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. 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 only for their respective pol gene segment(s). We analyzed results from all specimens sent to the referral laboratory (Laboratory Corporation of America, Research Triangle Park, North Carolina) for integrase GRT over the 4-year period beginning on the date this assay became commercially available (1 January 2009) and ending on 31 December 2012. In some cases, multiple specimens were sent during the study period for a given patient; individual results were considered separately in our analyses. In addition to an internal patient identification number and the date of specimen collection, the referral laboratory collected the patient’s age and sex along with the state and postal (ZIP) code of the ordering clinic or provider. The laboratory does not obtain data on the patient’s treatment status (naive or experienced) or history of prior ARV exposures. For this analysis, laboratory data managers searched for PR-RT GRT results available for each patient, and all such records accompanied the final integrase GRT results. We considered integrase and PR-RT GRTs to be paired if specimens were submitted within 30 days of one another. No specimens associated with clinical trials were included in this study. To ensure that we did not duplicate patients or integrase GRT nucleotide sequences in the final data set, we compared sex, specimen dates, clinic location, and specimen tracking numbers. We also created a maximum likelihood phylogenetic tree and examined the same descriptive data elements to identify any potential duplicates in clusters of sequences separated by a genetic distance of ≤0.015. Details of these analyses are included in this article’s Supplementary Data. Genotyping and Analysis of Nucleotide Sequence Data HIV-1 RNA was extracted from each submitted plasma specimen and subjected to RT-PCR to generate complementary DNA. Dideoxynucleotide sequencing was then performed using GenoSure primers spanning sections of the pol gene encoding amino acids 1–288, 1–99, and 1–400 of integrase, PR, and RT, respectively. Integrase and PR-RT sequences were analyzed separately using the Stanford University HIV Drug Resistance Database genotypic resistance interpretation algorithm (HIVdb Program, version 6.3.0, http://hivdb.stanford.edu). Sequence analyses were conducted on 7 June 2013. Definitions of Resistance Mutations After a review of relevant abstracts, published data, and the June 2013 update of the Stanford University HIV Database [13–15, 21, 26–29], we defined a “major” integrase mutation as any of the following: T66AIK, E92QV, F121Y, Y143CHR, S147G, Q148HKR, or N155H. “Accessory” mutations included H51Y, L68IV, L74IM, T97A, E138AK, G140ACS, S153F, E157Q, G163KR, and R263K. We used the 2009 (...truncated)