Substitutions at Amino Acid Positions 143, 148 ... - Journal of Virology

Substitutions at Amino Acid Positions 143, 148, and 155 of HIV-1 Integrase Define Distinct Genetic Barriers to Raltegravir Resistance In Vivo Signe Fransen, Soumi Gupta, Arne Frantzell, Christos J. Petropoulos, and Wei Huang Monogram Biosciences, South San Francisco, California, USA

Mutations at amino acids 143, 148, and 155 in HIV-1 integrase (IN) define primary resistance pathways in subjects failing raltegravir (RAL)-containing treatments. Although each pathway appears to be genetically distinct, shifts in the predominant resistant virus population have been reported under continued drug pressure. To better understand this dynamic, we characterized the RAL susceptibility of 200 resistant viruses, and we performed sequential clonal analysis for selected cases. Patient viruses containing Y143R, Q148R, or Q148H mutations consistently exhibited larger reductions in RAL susceptibility than patient viruses containing N155H mutations. Sequential analyses of virus populations from three subjects revealed temporal shifts in subpopulations representing N155H, Y143R, or Q148H escape pathways. Evaluation of molecular clones isolated from different time points demonstrated that Y143R and Q148H variants exhibited larger reductions in RAL susceptibility and higher IN-mediated replication capacity (RC) than N155H variants within the same subject. Furthermore, shifts from the N155H pathway to either the Q148R or H pathway or the Y143R pathway were dependent on the amino acid substitution at position 148 and the secondary mutations in Y143R- or Q148R- or H-containing variants and correlated with reductions in RAL susceptibility and restorations in RC. Our observations in patient viruses were confirmed by analyzing site-directed mutations. In summary, viruses that acquire mutations defining the 143 or 148 escape pathways are less susceptible to RAL and exhibit greater RC than viruses containing 155 pathway mutations. These selective pressures result in the displacement of N155H variants by 143 or 148 variants under continued drug exposure.

R

altegravir (RAL) is the first-in-class antiretroviral inhibitor of HIV-1 that targets the viral integrase (IN) protein. IN is one of three essential enzymes encoded by the pol gene and is necessary for viral DNA integration and replication. IN catalyzes two main steps of integration: the excision of two nucleotides from the 3= ends of the double-stranded viral DNA (3= end processing) and the subsequent joining of the 3= ends of the viral DNA to the 5= ends of the host genomic DNA at the site of proviral integration (strand transfer) (1, 2). RAL specifically inhibits the strand transfer activity of IN in a manner similar to that of several predecessor compounds (14, 30). The approval of RAL by the Food and Drug Administration (FDA) for the treatment of antiretroviral (ARV) drug-experienced and ARV drug-naïve HIV-1-infected patients has added a potent new drug to the armament of ARV drugs used to control HIV-1 replication (4, 18). The development of resistance to antiretroviral drugs has been demonstrated across all drug classes, including IN inhibitors. The majority of IN inhibitor resistance mutations selected by earlier compounds such as the diketo acids and naphthyridines, as well as newer agents, including RAL, elvitegravir (EVG), and dolutegravir (DLG), occur in the catalytic core domain of IN (7, 10, 13, 14, 16, 17, 31). Primary RAL resistance mutations confer changes in the IN coding region at amino acid positions 143, 148, and 155 (4). Additional resistance mutations resulting in amino acid substitutions V72I, L74I or L74M, E92Q, T97A, F121Y, E138K, G140S or G140A, V151I, E157Q, G163R, I203M, and S230R have also been described (D. Cooper and B. Nguyen, presented at the 14th Conference on Retroviruses and Opportunistic Infections, Los Angeles, CA, 25 to 28 February 2007) (19, 21). Recent studies have reported that the primary resistance mutations N155H and Q148R, Q148H, or Q148K represent mutually exclusive and non-

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overlapping pathways (8, 20). With the exception of T66I, viruses that acquire resistance to EVG exhibit similar mutation profiles (N155H, Q148R, H, or K, as well as E92Q); thus, EVG-resistant viruses generally exhibit cross-resistance to RAL and vice versa (10, 11, 28). For the most part, RAL- and EVG-resistant variants remain susceptible to DLG (S/GSK1349572), which, in vitro, selects for a distinct mutation profile that includes L101I, T124A, and S153F or Y (16). A notable exception may be viruses containing mutations at position 148, which in vitro can exhibit reduced susceptibility to DLG when they also contain specific secondary mutations (16) (M. Underwood and W. Spreen, 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention, Cape Town, South Africa, 19 to 22 July 2009). However, in early phase IIb studies, all patients with high-level RAL resistance, including subjects with mutations at position 148, achieved complete suppression of HIV-1 replication while on DLG (J. Eron and J. Yeo, 18th Conference on Retroviruses and Opportunistic Infections, Boston, MA, 27 February to 2 March 2011). Studies evaluating sequential virus samples have reported shifts in primary IN inhibitor resistance mutation patterns in subjects remaining on RAL following virologic treatment failure (3, 5, 9, 20, 22, 23). Specifically, in RAL phase II and III clinical trials, investigators noted that N155H variants detected at the first fail-

Received 27 October 2011 Accepted 20 April 2012 Published ahead of print 2 May 2012 Address correspondence to Wei Huang, [email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.06618-11

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ure time point were frequently replaced by Q148H, K, or R variants at later time points in the presence of ongoing RAL exposure (22, 23). Other groups have also reported shifts from N155H to Q148H (3, 21, 24), as well as shifts from N155H to Y143R (5). To better understand the selective pressures driving shifts in RAL resistance mutation profiles, we performed phenotypic and genotypic analyses on sequential patient virus populations harboring more than one primary resistance mutation, and we confirmed our findings using an isogenic panel of viruses containing specific site-directed mutations in integrase. Our study describes distinct evolutionary pathways that culminate in the selection of virus populations that exhibit large reductions in RAL susceptibility and high IN-mediated replication capacity (RC). MATERIALS AND METHODS Sample selection. Patient viruses from 200 subjects containing at least one IN mutation at position 143, 148, or 155 were studied. These included viruses from 10 subjects enrolled in the SCOPE cohort (12), 68 subjects from the RAL BENCHMRK phase III studies (29), and 122 patient samples submitted to the Monogram Clinical Reference Laboratory for routine integrase inhibitor resistance testing. More than one RAL primary resistance mutation was detected in 18 patient virus populations. Clonal analysis was performed on sequential sample collections to detail changes in the composition of virus populations from 3 of these 18 subjects: subject 3, N155N/H and Y143Y/R; subject 17, N155N/H, Y143Y/R, and Q148Q/R; and subject 18, N155N/H, Y143Y/R, and Q148Q/H. RAL susceptibility and IN-mediated replication capacity (RC). The PhenoSense Integrase assay was used to determine RAL susceptibility and IN-mediated RC. This assay was developed to support preclinical and clinical evaluations of candidate integrase inhibitors and ultimately inform the appropriate selection of integrase inhibitor-containing regimes in the clinic. The assay was validated in compliance with CAP (College of American Pathologists) and CLIA (Clinical Laboratories Improvement Amendments) specifications (S. Fransen and N. Parkin, abstr. H-1214, presented at the 48th Annual ICAAC/46th Annual IDSA meeting, Washington, DC, 25 to 28 October 2008) and utilizes a technology platform initially created and widely used today to measure HIV-1 susceptibility to protease (PR) and reverse transcriptase (RT) inhibitors (25). Briefly, resistance test vectors (RTVs) are created by amplifying HIV-1 pol sequences containing the C-terminal and RNase H domains of RT and the complete IN coding region (RHIN). The 1.6-kb amplification products are subsequently introduced into a genomic indicator vector containing a luciferase reporter gene in the env region. Pseudovirus stocks containing patient-derived IN sequences are produced by cotransfecting human embryonic kidney (HEK 293) cells with IN-specific RTVs and an amphotropic murine leukemia virus envelope protein expression vector. HEK 293 cells are inoculated with pseudovirus stocks containing patient-derived RHIN sequences in the absence or presence of serial dilutions of RAL. RAL susceptibility is calculated by plotting the percent inhibition of virus replication (luciferase activity) versus log10 drug concentration to derive the drug concentration required to inhibit virus replication by 50% (IC50). Reductions in RAL susceptibility are expressed as fold change (FC) in IC50, defined as the ratio of the IC50 of the sample virus and the IC50 of a wild-type reference strain (NL4-3). IN-mediated RC is determined and expressed as a percentage of virus infectivity (luciferase activity) in the absence of drug relative to the wild-type reference strain. Virus replication in the presence of RAL is also determined and expressed as the ratio of viral infectivity of the mutant strain relative to the wild-type reference strain at 1 ␮M RAL. IN genotyping. The nucleotide sequences of IN coding regions were determined using the GeneSeq Integrase assay, which is based on conventional dye-dideoxy chain terminator chemistry (ABI, Foster City, CA). Differences in derived IN amino acid sequences were determined relative to the NL4-3 reference sequence.

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FIG 1 Frequency of RAL resistance mutations at IN amino acid positions 155, 148, and 143 among 200 patient-derived HIV-1 isolates. Viruses isolated from subjects failing a RAL-containing regimen and containing at least one primary RAL resistance mutation were analyzed. The frequencies of mutations at position N155H only, Q148R, H, or K only, or Y143R or C only, or a combination of more than one of these primary mutations, are shown.

Clonal analysis. Molecular clones were isolated from the virus populations at different time points for three subjects (subjects 3, 17, and 18) described above. Briefly, RTV plasmid DNA containing representative viral IN sequences was used to retransform competent bacteria and plasmid DNA was prepared from the cultures of 24 to 96 bacterial colonies per time point. The IN coding region of each clone was determined using the GeneSeq Integrase assay, and a subset of clones from each virus population was evaluated for RAL susceptibility and IN-mediated RC using the PhenoSense integrase assay. Site-directed mutants. Single or double mutations were introduced into the IN coding region of HIV-1 IIIB using site-directed mutagenesis (27). HIV-1 IIIB sequences containing the mutations Y143R, N155H, Q148R or H, Y143R⫹T97A, N155H⫹E92Q, Q148R⫹G140S, and Q148H⫹G140S were used to assemble IN RTVs. RAL susceptibility and IN-mediated RC of each site-directed mutant (SDM) were determined using the PhenoSense integrase assay.

RESULTS

A majority of patient viruses that exhibit reductions in RAL susceptibility contain primary mutations at amino acid positions 143, 148, and/or 155 of integrase. To determine the frequency of resistance mutations at codons 143, 148, and 155 of IN among patient viruses exhibiting notable reductions in RAL susceptibility, we surveyed the IN sequences of viruses isolated from 200 patients containing at least one RAL primary resistance mutation (Fig. 1). Among the viruses isolated from these 200 subjects, 46% (n ⫽ 92) contained Q148R, Q148H, or Q148K, 33% (n ⫽ 66) contained N155H, and 12% (n ⫽ 24) contained Y143R or Y143C. In addition, 9% (n ⫽ 18) of the virus populations contained more than one primary mutation; details of the mutation profiles of these 18 viruses are described in Table 1. The virus populations in 16 of these 18 subjects contained two mutations, either at positions 148 and 155 (n ⫽ 10), 143 and 155 (n ⫽ 5), or 143 and 148 (n ⫽ 1), while the virus populations in the remaining two subjects contained mutations at all three positions (143, 148, and 155). RAL resistance pathways shift under sustained drug pressure. To further evaluate the evolution of RAL resistance under sustained drug pressure, we characterized virus populations in plasma samples collected sequentially over time from 3 of the 18

Journal of Virology

Genetic Barriers to Raltegravir Resistance

TABLE 1 RAL resistance mutation profiles of 18 patient viruses containing more than one primary mutationa Sample no. 1 2 3b 4 5 6 7 8 9 10 11 12 13 14 15 16 17b 18b

Primary mutation Y143

Q148

Y/R/H/C Y/R Y/R Y/C Y/C

Y/R/H/C Y/R Y/R

Q/K Q/R Q/R Q/R Q/R Q/R Q/R Q/R Q/H Q/H Q/H Q/R Q/H

N155 N/H N/H N/H N/H H N/H N/H N/H N/H N/H N/H N/H N/H N/H N/H N/H N/H

Other resistance-associated mutation(s) [E92Q, T97A, E138K, G140S(A)] T97T/A E92E/Q ND ND E92E/Q, T97T/A E92E/Q, E138E/K T97T/A, G140G/S E138E/K E92E/Q, G140G/A E138E/K G140G/A ND E138E/K G140G/S G140G/S T97T/A, G140G/S E92E/Q, G140G/S G140G/S

a ND, no RAL resistance-associated mutations were detected. /, mixture of wild-type and mutant amino acid. b Virus samples used for sequential analysis.

subjects containing more than one primary resistance mutation (Table 1). (i) N155H to Y143R. The virus from subject 3 was initially characterized at week 16 (W16) of RAL treatment as a mixed population harboring wild-type and resistant codons at positions 155 (N155N/H) and 143 (Y143Y/R) (Table 1). Sequential plasma samples collected at baseline (BL) (pre-RAL treatment), W2, W8, and W24 (open label) were evaluated to further characterize the RAL resistance mutation profiles and RAL susceptibility of virus populations that preceded and followed the W16 virus. The genotypic and phenotypic properties of these virus populations are described in Fig. 2A. No RAL resistance mutations were detected at BL and W2. The N155H mutation was initially detected at W8, and by W16 both the N155H and Y143R mutations were detected as mixtures. At W24, only the Y143R mutation remained. Incremental reductions in RAL susceptibility were observed over time as the RAL resistance mutation profile transitioned initially from wild-type (WT) to N155H and, subsequently, to Y143R. RAL susceptibilities of the BL and W2 virus populations were not different from that of the reference virus (IC50 FC, 0.96 and 0.68, respectively), while RAL susceptibilities of the W8, W16, and W24 virus populations decreased progressively (IC50 FC, 3, 23, and 54, respectively). The IN-mediated RCs were similar among viruses containing resistance mutations: W8, 64%; W16, 86%; and W24, 85%. These RCs were also not significantly different from that of virus isolated at W2 (80%) that lacked resistant mutations. However, the BL virus had a much lower IN-mediated RC (percentage) than that observed at other time points. Sequence analysis indicated that BL virus contained additional mutations at four codons in the IN region (N120N/D, A169A/G, D229D/G, and S283S/G) which were not present in the W2 virus or any of the viruses isolated at subsequent failure time points (W8, W16, and W24).


Analysis of individual molecular clones isolated from each time point (n ⫽ 42 to 72 per time point) revealed the detailed composition of each virus population and discerned the functional distinctions between RAL-resistant variants that result in shifts from one RAL resistance profile to another under sustained RAL pressure (Fig. 2B). Only WT clones were detected in the BL and W2 virus populations; however, by W8 71% of clones contained the N155H mutation while 29% remained WT. By W16 all evaluated clones contained a RAL primary resistance mutation: 68% N155H and 32% Y143R. At W24 the viral population was comprised solely of Y143R clones, and 28% of these clones also contained the RAL selected secondary mutation T97A. (ii) N155H/Q148R to Y143R. The virus from subject 17 was initially characterized at W11 as a mixed population containing the RAL primary resistance mutations Y143R, Q148R, and N155H. RAL susceptibility and IN-mediated RC of BL, W11, and W28 viral populations are shown in Fig. 2C. RAL resistance mutations at all three primary positions were present as mixtures at W11, including Y143Y/R, Q148Q/R, and N155N/H, as well as secondary mutations E92E/Q and G140G/S. Both W11 and W28 virus populations exhibited large reductions in RAL susceptibility (⬎150-fold). IN-mediated RC of the W11 (76%) and W28 (72%) viruses was reduced relative to the BL virus (120%). Analysis of multiple clones (n ⫽ 22 to 61 per time point) from each virus population revealed the detailed changes in virus composition under sustained RAL drug pressure (Fig. 2D). All clones isolated at BL lacked RAL resistance mutations, yet by W11 only 11% of the clones remained WT while 21% contained E92Q⫹N155H, 11% contained E92Q⫹Y143R, and 56% contained G140S⫹Q148R. By W28 all clones contained Y143R (90% Y143R⫹T97A, 5% Y143R⫹E92Q, and 5% Y143R alone). (iii) N155H/Y143R to Q148H. The virus from subject 18 was first characterized at W11 as a mixed population containing the RAL resistance mutations Y143R, Q148H, and N155H. RAL susceptibility and IN-mediated RC of virus populations collected at BL, W11, W16, and W24 are summarized in Fig. 2E. RAL resistance mutations were detected as mixtures at all three primary positions by W11, including N155N/H, Y143Y/R, and Q148Q/H, as well as the secondary mutation G140G/S. By W16 the N155H mutation was no longer detected, and by W24 only the Q148H primary and G140S secondary mutation remained. Large reductions in RAL susceptibility (FC, ⬎150) were observed at W11 and persisted through W24. The IN-mediated RC of the W11 virus was reduced relative to that of the BL virus (30% versus 78%) and remained low through W16 and W24 (21% and 17%, respectively). Clonal analysis (41 to 47 clones per time point) was performed on the virus populations at all time points to detail temporal changes in RAL-resistant variants in response to ongoing RAL exposure (Fig. 2F). All clones generated from the BL virus population lacked RAL resistance mutations. At W11 the virus population was comprised of variants containing RAL mutations at Y143R (72%), Q148H⫹G140S (23%), or N155H (5%). By week 16, N155H clones were absent and the virus population was limited to Q148H⫹G140S (85%) and Y143R (15%) variants. By W24, only clones containing Q148H⫹G140S were observed. The changes in the clonal composition of virus populations from subjects 3, 17, and 18 described here are consistent with the sequential replacement of WT virus populations by RAL-resistant virus populations containing the N155H primary mutation, which are subsequently replaced in the face of continued RAL

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FIG 2 Phenotypic, genotypic, and clonal characterization of sequential viral populations from subjects 3, 17, and 18. (A, C, and E) RAL susceptibility (filled squares; diamonds represent FC ⬎150) and IN-mediated RC (open squares) were assessed at different time points. RAL resistance mutations detected at each time point are indicated, samples without resistance mutations are labeled WT. (B, D, and F) The percentage of clones lacking resistance mutations (WT) or containing specific combinations of RAL resistance mutations is shown at each time point for each subject. A range of 22 to 72 clones were evaluated for each time point.

pressure by virus populations containing either the Y143R or Q148H primary mutations. RAL susceptibility and IN-mediated RC of clones derived from subjects that displayed shifts in RAL resistance pathways. To further confirm the selective forces that drive shifts in RAL resistance mutation profiles from N155H to Y143R or Q148H, we examined the RAL susceptibility and IN-mediated RC of representative clones derived from the virus populations of subjects 3, 17, and 18 (Table 2). In subject 3, clones that contained resistance mutations Y143R alone or Y143R⫹T97A displayed larger reduc-

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tions in RAL susceptibility (FC, 56 and ⬎150, respectively) and higher IN-mediated RC (RC, 78% and 86%, respectively) than clones containing N155H (FC, 29; RC, 56%). In subject 17, all resistant clones isolated at W11 (E92Q⫹N155H, E92Q⫹Y143R, and G140S⫹Q148R) exhibited large reductions in RAL susceptibility (FC, ⬎150) and similar IN-mediated RC (RC, 65, 42, and 46%, respectively). Interestingly, clones containing Y143R⫹T97A or Y143R alone that predominated at W28 (90% and 5%, respectively) displayed higher IN-mediated RC (RC, 97% and 86%, respectively) than the resistant clones detected at W11 (RC, 42 to

Journal of Virology


TABLE 2 Genotype, phenotype, and IN-mediated replication capacity of infectious molecular clones containing primary RAL resistance mutationsa Subject

Resistant genotype

No. of clones

FCb

RCc

3

N155H Y143R T97A⫹Y143R

3 3 3

29 56 ⬎150

56 78 86

17

E92Q⫹N155H E92Q⫹Y143R G140S⫹Q148R Y143R* T97A⫹Y143R

3 3 3 1 3

⬎150 ⬎150 ⬎150 94 82

65 42 46 86 97

N155H* Y143R G140S⫹Q148H

2 3 3

55 26 ⬎150

2 63 55

18

crease, followed by Y143R⫹T97A, Q148R⫹G140S, and N155H⫹ E92Q (MT/WT ratio, 130, 59, 42, and 25, respectively) (Fig. 3C). These observations are consistent with the phenotypic data obtained using patient clones, and they serve to explain why certain variants exhibit selective advantages over others and thus come to dominate the virus population under continued RAL drug pressure. DISCUSSION

Previously, we demonstrated that IN inhibitor resistance mutations N155H and Q148R, H, or K are independently selected by RAL and were not linked within the same viral genome among treatment failures in the BENCHMRK phase III RAL studies (8). We showed that the secondary mutation E92Q is preferentially selected in N155H viruses, while G140S is selected by viruses containing mutations at IN codon 148. We also reported that the

a RC and FC values represent the average result for three clones with two exceptions designated by asterisks. b FC, fold change in RAL IC50 relative to wild-type control. c RC, IN-mediated replication capacity expressed as a percentage of viral infectivity of the patient clone relative to the wild-type reference in the absence of drug.

65%) but not larger reductions in RAL susceptibility (FC, 82 and 94, respectively). Lastly, in subject 18, resistant clones with Q148H⫹G140S and Y143R that emerged at later time points displayed much higher RC (RC, 63% and 55%, respectively) compared to clones with N155H (RC, 2%). Furthermore, Q148H⫹ G140S clones that predominated at W24 also exhibited greater reductions in RAL susceptibility (FC, ⬎150) than the Y143R (FC, 26) or N155H (FC, 55) clones. RAL susceptibility and IN-mediated RC of viruses containing site-directed mutations N155H, Y143R, and Q148H. To confirm the selective advantage of mutations at position 143 and 148 relative to mutations at position 155, we engineered and evaluated viruses containing mutations at positions 143, 148, or 155 alone and in combination with secondary mutations. Susceptibilities to RAL and IN-mediated RC in the absence or presence of RAL of these viruses are shown in Fig. 3. Viruses with single mutations Y143R, Q148H or R, and N155H exhibited comparable reductions in RAL susceptibility (Y143R FC, 24; Q148R FC, 34; Q148H FC, 18; N155H FC, 16). The addition of secondary mutation E92Q, T97A, or G140S together with a primary mutation resulted in larger reductions in susceptibility: RAL FC, ⬎150 for N155H⫹E92Q, Q148R⫹G140S, Q148H⫹G140S; RAL FC, 127 for Y143R⫹T97A (Fig. 3A). The IN-mediated RC of all viruses with single primary mutations was notably reduced relative to that of the WT reference virus, with the exception of Y143R (N155H, 69%; Q148R, 59%; Q148H, 43%; Y143R, 90%). The RC of the double mutants varied depending on the specific combination of mutations (Fig. 3B). The addition of E92Q to N155H and T97A to Y143R further reduced RC relative to N155H or Y143R alone (69% versus 49% and 90% versus 50%, respectively). The addition of G140S to Q148R had no effect on RC, whereas G140S combined with Q148H increased RC. Viral replication in the presence of RAL (1 ␮M) was determined and expressed as a ratio of mutant (MT) replication relative to WT replication (Fig. 3C). All single primary mutations displayed slightly greater replication than the WT (MT/WT ratio: N155H, 4; Q148R, 14; Q148H, 2; Y143R, 10), and double mutants exhibited higher replication than single mutants, with Q148H⫹G140S displaying the largest in-


FIG 3 RAL susceptibility and replicative capacity (RC) in the presence and absence of RAL for site-directed mutant viruses containing RAL resistance mutations. (A) RAL susceptibility (IC50 FC). (B) Percentage of IN-mediated RC (RC in the absence of RAL). (C) Ratio of mutant infectivity (relative light units [RLU]) to wild-type infectivity in the presence of 1 ␮M RAL (highest concentration evaluated).

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selection of both primary and secondary RAL resistance mutations was driven by the ability to maximize replication at high RAL concentrations and retain or restore replication in the absence of drug (8). In this report, we extend these findings by investigating the selection dynamics of RAL-resistant virus populations and by temporally characterizing the emergence of IN mutations in sequential virus samples obtained from patients failing a RAL-containing regimen. Our analysis demonstrates that the mutation profiles that predominate early in treatment failure differ from those observed at later time points. The three cases studied here illustrate distinct evolutionary pathways that confer large reductions in RAL susceptibility: shifts from N155H to Y143R (subject 3), from N155H/Q148R to Y143R (subject 17), and from N155H/ Y143R to Q148H (subject 18). RAL susceptibility and IN-mediated RC data suggest that phenotypic characteristics conferred by specific resistance mutations drive the viral evolution during continued treatment pressure. The eventual predominance of 143 mutations or 148 mutations over 155 mutations is dependent on the selective advantage of the emerging variants. Specifically, both the Y143R and Q148H variants conferred stronger selective advantages than the N155H variants in all three subjects. The Q148H variant was preferentially selected over the Y143R and N155H variants in subject 18, while the Y143R variant was preferentially selected over the N155H variant in subject 3 and the Q148R and N155H variants in subject 17. Clonal analysis indicated that resistant mutations at codons 143 and 148 emerged independently from mutations at codon 155, since mutations at 143 and 155 or at 148 and 155 were not observed in the same virus clones isolated from these patients. These data are consistent with our previous observations (8). It is important to note that secondary mutations selected by RAL play a critical role in the evolutionary pathways of RALresistant virus populations. For example, the W11 virus population of subject 18 was comprised of Y143R, Q148H⫹G140S, and N155H clones, while the W24 population was comprised solely of Q148H⫹G140S variants. Analysis of patient clones and SDMs indicate that the double mutant Q148H⫹G140S exhibited greater reductions in RAL susceptibility than either single mutant N155H or Y143R and also exhibited equivalent or higher IN-mediated RC relative to the N155H and Y143R variants. Based on SDM data, the addition of the secondary mutation G140S to the primary mutation Q148H resulted in much higher replication than with mutants Y143R or N155H in the presence of RAL. In subjects 3 and 17, variants with Y143R⫹T97A mutations outcompeted other variants that coexisted in the population, including N155H and Y143R variants in subject 3 and Y143R, Q148R⫹G140S, Y143R⫹E92Q, and N155H⫹E92Q variants in subject 17. The fact that individual clones with Y143R⫹T97A mutations isolated from subjects 3 and 17 exhibited higher levels of IN-mediated RC compared to these other variants is consistent with the reported emergence of this variant at later time points in patients. The evaluation of SDMs also demonstrated and confirmed that the Y143R⫹T97A double mutant replicated at a higher level in the presence of RAL compared to other mutants, including Y143R, N155H, N155H⫹Q92E, Q148R, and Q148R⫹G140S. Conversely, Y143R⫹T97A variants were not preferentially selected over Q148H⫹G140S variants in subject 18, which is also consistent with data we have generated using SDMs; i.e., the double mutant Q148H⫹G140S exhibited larger reductions in susceptibility and higher levels of replication in the absence and presence of RAL, compared to the Y143R⫹T97A mutant. In addition, we

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and others have shown, using site-directed mutagenesis, that the single mutation Q148H does not confer a selective advantage over other primary resistance mutations (at positions 143 and 155) with respect to RAL susceptibility or IN-mediated RC (8, 15). In fact, we observed in this study a selective advantage of N155H over Q148H in the presence of RAL, which is consistent with previous reports (15, 26). At this point, all available data suggest that N155H variants are preferentially selected early in RAL treatment failure but are subsequently replaced by variants containing other primary mutations after the further acquisition of secondary mutations under RAL pressure (26). The later emergence of Q148H variants is also consistent with the observation that this mutation impairs integration which can be rescued by the addition of a G140S mutation (6). Based on our survey of 200 clinical isolates, single substitution Q148H variants were rarely observed in vivo and, when identified, rapidly acquired G140S. Together, the data reported here and in previous studies (8, 20) demonstrate that RAL-resistant viruses emerge via multiple pathways within and among individual patient virus populations. Furthermore, shifts from one pathway to another occur in the presence of continued RAL pressure (23) and are driven by the relative selective advantages conferred by the specific constellation of primary and secondary mutations that emerge within a patient virus population. Recent reports suggest that certain primary RAL resistance mutations do not confer reductions in susceptibility to second-generation IN inhibitors. For example, viruses with mutations at position 143 or 155 retain susceptibility to DLG in in vitro studies (16). The virologic responses observed in phase IIb studies suggest that DLG administered twice daily suppresses the replication of viruses containing RAL resistance mutations, including variants with mutations at position 148 (M. Underwood and W. Spreen, presented at the 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention, 19 to 22 July 2009; A. Sato and B. Johns, presented at the 49th Annual Interscience Conference on Antimicrobial Agents and Chemotherapy, 12 to 15 September 2009; J. Eron and J. Yeo, presented at the 18th Conference on Retroviruses and Opportunistic Infections, 27 February to 2 March 2011). Additionally, in contrast to the single mutant Q148H and double mutant Q148H⫹G140S, we previously demonstrated that viruses containing Q148K⫹G140S are more susceptible to RAL and have increased RC relative to viruses containing Q148K alone (8). These observations further illustrate how specific combinations of mutations differentially alter RAL susceptibility. Based on in vitro passage studies, early IN inhibitor candidates selected for variants that displayed distinct resistance mutation profiles; the diketo acids selected for mutations at positions 66, 153, and 154 of IN, while the naphthyridine carboxamides (specifically L-870,810) selected for mutations at positions 72, 121, 125, and 151 (13), with the exception of mutations at position 155, which reduce susceptibility to both compounds. The distinct resistance mutation profiles exhibited by the early IN inhibitor candidates versus current inhibitors (RAL and EVG) and versus nextgeneration IN inhibitors (DLG) highlight the importance of developing a more comprehensive understanding of the resistance and cross-resistance patterns so that all members of this drug class can be optimally incorporated into regimens that fully suppress HIV-1 replication.

Journal of Virology


ACKNOWLEDGMENTS This study was supported in part by National Institutes of Health (NIH) U.S. National Institute of Allergy and Infectious Diseases (NIAID) Small Business Innovation Research (SBIR) grant R44 AI057074. We thank the Monogram Biosciences Clinical Reference Laboratory for performing the PhenoSense Integrase and GeneSeq Integrase assays, Cynthia Sedik for administrative assistance, Merck Clinical Research for the samples from BENCHMRK studies, and Steven Deeks (UCSF) for providing samples from the SCOPE cohort, which is supported in part by the NIAID (K24AI069994), the UCSF CFAR (PO AI27763), the UCSF CTSI (UL1 RR024131), and the CFAR Network of Integrated Systems (R24 AI067039).

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