Laboratory Testing for HIV Tropism. Description

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1 Section: Medicine Effective Date: July 15, 2015 Subject: Laboratory Testing for HIV Tropism Page: 1 of 19 Last Review Status/Date: June 2015 Laboratory Testing for HIV Tropism Description Human immunodeficiency virus (HIV) tropism testing can determine the predominant coreceptor protein used by the HIV to infect target cells. Tropism testing can help select patients for treatment with HIV coreceptor antagonists, such as maraviroc, which block specific co-receptor proteins. Background HIV-1, which causes acquired immunodeficiency syndrome (AIDS), uses co-receptor proteins (either CCR5 or CXCR4) on the surface of target cells to enter and infect the cells. The most commonly transmitted strains of HIV-1 bind to CCR5 and are said to have tropism for CCR5-expressing cells. Dual or mixed (D/M) tropic viruses can bind to either receptor type. It is estimated that around 85% of treatment-naïve patients harbor CCR5-tropic virus only, around 15% harbor D/M virus, and less than 1% are infected with CXCR4-tropic virus alone. CXCR4-tropic virus is associated with immunosuppression and later stages of disease. Coreceptor antagonists, have been designed to interfere with the interaction between HIV-1 and its coreceptors. HIV Coreceptor Antagonists Maraviroc (Selzentry, Pfizer) is the first co-receptor antagonist to be approved by the U.S. Food and Drug Administration (FDA). Maraviroc is a selective, slowly reversible, small-molecule antagonist of the interaction between human cell surface CCR5 and HIV-1 gp120, also necessary for HIV-1 cell infection. Blocking this interaction prevents CCR5-tropic HIV-1 entry into cells. However, CXCR4-tropic HIV-1 entry is not prevented. According to the drug s original label, maraviroc, in combination with other antiretroviral agents, is indicated for adult patients who are infected with only CCR5-tropic detectable HIV-1, who have evidence of viral replications and HIV-1 strains resistant to multiple antiretroviral agents. (1) The currently-approved maraviroc label indicates that maraviroc is indicated for combination antiretroviral treatment for adults infected with only CCR5-tropic HIV-1, without discussion of the presence of viral replication. (2) The FDA-approved full prescribing information for the drug states, Tropism testing must be conducted on a current sample with a highly sensitive tropism assay that has demonstrated the ability to identify patients appropriate for SELZENTRY. This is because efficacy was not demonstrated in a Phase II study of maraviroc in patients with D/M or CXCR4-tropic HIV-1. Due to

2 Subject: Laboratory Testing for HIV Tropism Page: 2 of 20 potential adverse effects (hepatic and cardiac toxicity); maraviroc should only be used in indicated patients. Other HIV coreceptor antagonists are in the drug development pipeline. Cenicriviroc (Tobira Therapeutics) is a small-molecule antagonist of both CCR5 and CCR2, a receptor involved in a number of inflammatory diseases that is currently being investigated for treatment of CCR5-tropic HIV. (3) In January 2015, cenicriviroc was granted fast track designation by FDA for the treatment of nonalcoholic steatohepatitis in patients with liver fibrosis, but the drug does not yet have FDA approval. HIV Tropism Testing HIV tropism testing is available by either phenotypic or genotypic methods. Tropism testing with a phenotypic assay, a cellular-based assay that functionally determines tropism, is available with the enhanced sensitivity Trofile (Monogram Biosciences, South San Francisco, CA) assay (ESTA). This phenotypic assay uses virus stocks pseudotyped with envelope sequences derived from patient plasma to infect cell lines engineered to express CCR5 or CXCR4 HIV-2 co-receptors. Genotypic tropism testing is based on sequencing the third variable (V3) loop of the HIV glycoprotein 120 gene, because the V3 loop interacts with the HIV co-receptor, and mutations in V3 are associated with measurable changes in HIV tropism. Tropism assignment is derived from the sequence data using a bioinformatic algorithm such as geno2pheno (G2P). In the United States, the only commercially available genotypic HIV coreceptor tropism assay is available from Quest Diagnostics, which uses triplicate population sequencing with reflex to ultradeep sequencing if only CCR5-tropic virus is detected. Quest Diagnostics also offers a proviral DNA tropism test (Trofile DNA) which sequences the tropism of HIV-1 DNA that has integrated into the host genome of infected T-lymphocytes via triplicate population sequencing, without the use of ultradeep sequencing. Regulatory Status The FDA-approved full prescribing information for maraviroc (Selzentry, Pfizer) states that Tropism testing must be conducted with a highly sensitive and specific tropism assay that has demonstrated the ability to identify patient s appropriate for [maraviroc] use. (4) Currently-available HIV tropism tests are performed as laboratory developed tests (LDTs). Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; LDTs must meet the general regulatory standards of the Clinical Laboratories Improvement Act (CLIA). Testing for HIV tropism is available under the auspices of CLIA Laboratories that offer LTDs must be licensed by CLIA for high-complexity testing. Policy *This policy statement applies to clinical review performed for pre-service (Prior Approval, Precertification, Advanced Benefit Determination, etc.) and/or post-service claims. HIV tropism testing (see Policy Guidelines for testing methods) may be considered medically necessary for selecting patients for treatment with HIV coreceptor antagonists such as maraviroc when there is an immediate plan to prescribe a co-receptor antagonist.

3 Subject: Laboratory Testing for HIV Tropism Page: 3 of 20 HIV tropism testing without immediate plans to prescribe HIV coreceptor antagonists such as maraviroc is not medically necessary. Repeat HIV tropism testing during co-receptor antagonist treatment or after failure with co-receptor antagonists is investigational. HIV tropism testing to predict disease progression (irrespective of co-receptor antagonist treatment) is investigational. Policy Guidelines Testing should be conducted immediately prior to intended prescribed use of maraviroc to obtain the most accurate prediction of tropism at the start of treatment. Either phenotypic or V3 population genotypic testing may be used to determine HIV tropism; both are not necessary. V3 population genotypic testing may be conducted by either standard V3 sequencing via Sanger methods (amplification and population sequence analysis of patient-derived V3 region) OR V3 deep sequencing methods (synonyms: ultra-deep sequencing; pyrosequencing; next-generation sequencing). In the U.S., the only currently commercially available plasma HIV DNA coreceptor genotypic test (requires HIV viral load greater than or equal to 1000 copies/ml) includes step-wise testing, with an initial standard sequencing with reflex to V3 deep sequencing if standard sequencing detects only CCR5-tropic virus. Rationale This literature review first discusses the evidence for the role of HIV tropism testing in clinical practice in 3 settings: in conjunction with the use of HIV coreceptor antagonist therapy, for monitoring response to therapy, and for prognosis of HIV infection. Subsequently, aspects of the technical performance of different types of HIV tropism testing are reviewed. The Role of HIV Tropism Testing in Clinical Practice The primary use of HIV tropism testing is to identify candidate patients for HIV coreceptor antagonist therapy. The approval by the U.S. Food and Drug Administration (FDA) of maraviroc is based on safety and effectiveness data from 3 studies in adult subjects infected with CCR5-tropic HIV-1: A and A in antiretroviral treatment-experienced adult patients; and A in treatment-naïve patients. Clinical Studies of HIV Coreceptor Antagonist Therapy in Treatment-Experienced Patients The Maraviroc versus Optimized Therapy in Viremic Antiretroviral Treatment-Experienced Patients (MOTIVATE) 1 and 2 trials assessed the efficacy of maraviroc in patients previously treated or resistant to 3 antiretroviral drug classes and with HIV-1 RNA levels exceeding 5,000 copies/ml. (5) MOTIVATE- 1 was conducted in Canada and the United States, and MOTIVATE-2 in Australia, Europe, and the

4 Subject: Laboratory Testing for HIV Tropism Page: 4 of 20 United States, using identical study designs. A total of 1075 patients were randomized to 3 trial arms, and 1049 received at least one dose of study drug: placebo (n=209), maraviroc once daily (n=414), or maraviroc twice daily (n=426). Selected subjects had only CCR5-tropic HIV-1as determined by the original Trofile assay for HIV tropism (see Tropism Testing section below). At 48-weeks follow-up in an intention-to-treat analysis, 16% in the placebo group and 45% in both maraviroc-treated groups had HIV-1 RNA levels less than 50 copies/ml. The mean increase in CD-4 count from baseline was 60 in placebo group compared to 120 in the maraviroc groups. Based on the early trial results and review by the FDA Antiviral Drugs Advisory Committee, the FDA concluded that, compared to placebo, maraviroc significantly reduced HIV RNA copy number, and significantly increased CD4 cells, both validated markers of improved health outcomes. (6) At nearly 2 years of follow-up (96 weeks), 81% to 87% of maraviroc-treated patients maintained these responses with no new or unexpected events impact safety. (7) At 5-year follow up, 46 deaths were reported, with ongoing low rates of hepatic failure, malignancy, and myocardial infarction. (8) In contrast, in a trial of 167 patients infected with dual- or mixed-tropic HIV-1, randomized to receive optimal therapy plus maraviroc or placebo, there was no difference in outcomes between treatment groups, indicating maraviroc treatment failure in patients harboring assay-detectable CXCR4-tropic HIV-1 populations. (9) Clinical Studies of HIV Coreceptor Antagonist Therapy in Treatment-Naïve Patients The MERIT (Maraviroc versus Efavirenz in Treatment-Naïve Patients) study is a randomized, doubleblind, multicenter study in subjects infected with CCR5-tropic HIV-1 according to the original Trofile assay. Patients had plasma HIV-1 RNA levels of at least 2000 copies/ml and did not have: 1) prior antiretroviral therapy for longer than 14 days, 2) an active or recent opportunistic infection or primary HIV-1 infection, or 3) resistance to zidovudine, lamivudine, or efavirenz. Subjects were randomized to 2 doses of either maraviroc or efavirenz, each in combination with zidovudine/lamivudine. In a preplanned interim analysis, the lower dose of maraviroc failed to meet prespecified efficacy criteria and was discontinued. Patients were stratified by screening HIV-1 RNA levels and by geographic region. The median CD4 cell counts and mean HIV-1 RNA at baseline were similar for both treatment groups. At 96 weeks, after reanalysis using results from the enhanced sensitivity Trofile assay (ESTA; see Tropism Testing section below), virologic response rates in both treatment arms were approximately equal, and there were fewer discontinuations due to adverse events in the maraviroc arm. (10) Although most newly infected patients harbor CCR5-tropic virus alone, a study of 150 individuals from 2 recent seroconverter cohorts documented 4% infection with detectable CXCR4-tropic virus (either mixed or, rarely, CXCR4-only), indicating that tropism analysis is necessary, even for the recently infected. (11) Tropism Testing for Treatment Monitoring and at Virologic Failure Viral strains transmitted in vivo are usually CCR5-tropic.(12) Over time and more often after antiretroviral treatment, detectable CXCR4-tropic virus emerges in about half of patients and is associated with rapid CD4 cell depletion and clinical disease progression.(13, 14) However, patients whose infection remains predominately CCR5-tropic can also experience disease progression. HIV-1 viral load is a strong prognostic indicator of HIV disease progression and suppression of viral load is a

5 Subject: Laboratory Testing for HIV Tropism Page: 5 of 20 critical goal of antiretroviral therapy. (15) Viral rebound (virologic failure) is typically followed by a reduction in CD4 cell count (immunologic failure), and if not adequately addressed by changes in treatment, by HIV-related events (clinical progression). Thus, success of any antiretroviral treatment regimen is monitored by measuring HIV-1 RNA level and CD4 cell count; significant changes direct patient management. The prominent reason for individual treatment failure in the clinical studies was outgrowth of a minor CXCR4-tropic virus population not detected at screening. However, treatment failure with CCR5-tropic virus alone also occurred, indicating that resistance to CCR5 antagonists occurs independent of tropism. In vitro studies have provided extensive information on resistance; mechanisms may involve the ability of HIV to bind the CCR5 inhibitor-receptor complex. Resistance to CCR5 antagonists has been associated with increased affinity for CCR5, changes in the gp 120 V3 loop, and with other gp 120 (or other envelope) changes. A concern regarding treatment with CCR5 co-receptor antagonists is that small, undetectable populations of CXCR4-tropic virus would be enriched and accelerate disease progression. However, in a randomized, placebo-controlled phase II study of maraviroc treatment of patients with dual or mixed (D/M)-tropic infections, there was no evidence that this was the case. (16) The association of CXCR4 tropism (defined with the original Trofile assay) with clinical progression has been shown to be independent of CD4 cell count and HIV-1 RNA level (adjusted hazard ratio 3.82, 95% confidence interval [CI], 1.69 to 8.60, p=0.001, vs patients with CCR5-tropic infection only). (17) Fatkenheuer et al performed a post-hoc analysis of the virologic response according to tropism at baseline and at treatment failure (18) using pooled data from the MOTIVATE 1 and 2 trials. Virologic failure occurred in 53% of placebo-treated patients and in 22% to 23% in the maraviroc treatment arms. However, of the 133 treatment failures in the maraviroc groups, 76 (57%) had CXCR4 or D/M tropism compared to 6 of 95 (6%) in the placebo group, (18) raising concerns that maraviroc treatment could lead to emergence of CXCR4-tropic subpopulations and more rapid development of clinical progression. This was not the case, as the CXCR4 maraviroc treatment failures were not associated with declines in CD4 cell counts nor with disease progression. There currently is no recommended management change based on a CCR5 to CXCR4 tropism switch during treatment with maraviroc. Treatment failure is detected by increased viral load and decreased CD4 cell count, (15) indicating that maraviroc treatment can be discontinued. The most common mechanism of maraviroc treatment failure is emergence of a CXCR4-tropic viral population. However, this is not necessarily correlated with rapid clinical progression. (19) Tropism testing for HIV prognosis Aside from the specific situation of maraviroc treatment failure, CXCR4-tropic virus infection has been associated with more rapid disease progression, compared to CCR5 infection, in several studies (e.g., see Wilkin et al. (17)) but current management recommendations are based on monitoring CD4 cell count and viral load, rather than viral tropism.

6 Subject: Laboratory Testing for HIV Tropism Page: 6 of 20 Tropism Testing for HIV Prognosis Aside from the specific situation of maraviroc treatment failure, CXCR4-tropic virus infection has been associated with more rapid disease progression, compared with CCR5 infection, in several studies (eg, Wilkin et al (20), Almeida et al (21), and Visseaux et al (22). However, other studies have demonstrated no independent association between the HIV tropism and HIV-related outcomes, including short term risk of AIDS and death (23) and hepatic fibrosis in HIV/hepatitis C virus-coinfected patients. (24) Current management recommendations are based on monitoring CD4 cell count and viral load, rather than viral tropism. Tropism Testing For the clinical studies of patients with treatment failure, tropism at enrollment and again at baseline was determined using the original phenotypic Trofile assay for 2560 potential enrollees; 56% were CCR5-tropic only and were eligible for the clinical trials. Most other patients had dual/mixed HIV infection; CXCR4-infection alone is rare. Of the patients enrolled, 90% had CCR5-tropic virus at baseline, 4% had dual-mixed tropic virus, and 5% had non-typable virus infection. The original phenotypic Trofile assay had a turnaround time of 14 to 18 days, failed to work in 3% to 7% of patients, and required at least 1000 copies/ml of HIV RNA. (25) The assay was 100% effective in detecting model CXCR4-tropic or dual/mixed HIV present in a 10% mixture, and 83% effective at a 5% mixture. Validation studies also indicated 100% accuracy of results for 38 samples with known tropism, and 100% reproducibility including repeat assays using multiple operators, instrumentation, reagent lots, and conducted over a 14-day period. No false-positive results were obtained on samples that were HIVnegative but positive for either hepatitis B or C virus. An enhanced sensitivity Trofile assay (ESTA) has replaced the original Trofile. The ESTA can detect CXCR4-tropic virus present at levels less than 0.3% of the total virus population, and at that level of virus or higher, the assay is stated to be 100% sensitive. (26) Total viral concentration of at least 1,000 copies/ml is required. However, ESTA remains limited by long turnaround time and the relatively high minimum level of viremia required, making it not useful in patients in virological failure with low viremia. Additionally, a small proportion of samples cannot be successfully phenotyped with either generation of the Trofile assay. (15) The MERIT study of treatment-naïve patients was retrospectively reanalyzed using ESTA; approximately 15% of the subjects originally identified as CCR5-tropic had dual/mixed- or CXCR4- tropic virus by ESTA. Removing these from the analysis resulted, as already noted, in similar responses in both trial arms, indicating that maraviroc in a combination regimen is at least as good as another well-accepted combination regimen for treatment-naïve patients. (10) Wilkin et al used ESTA to reanalyze samples from 4 large cohort studies that had originally been evaluated for HIV tropism with the original Trofile assay. (20) Nine percent to 26% of patients with CCR5-tropic virus by the original Trofile assay had CXCR4-using virus by ESTA.

7 Subject: Laboratory Testing for HIV Tropism Page: 7 of 20 V3 Population Genotyping to Determine Tropism The Trofile assay is a cell-based, functional (phenotypic) assay. Genotypic assays are based on the sequencing of the patient-derived HIV-1 gp 120 V3 domain, which determines the protein amino acid sequence for the major determinant of coreceptor binding. This sequencing method results in a V3 sequence that represents the average or dominant viral population sequence for each patient. The patient-derived HIV V3 sequence is used to predict HIV-1 tropism using web-based bioinformatic interpretation tools developed from prior data. These are most often the support vector machine-based geno2pheno co-receptor (G2P; available online at: (27) and position-specific scoring matrices (PSSM; available online at: (28) Newer genotypic assays have incorporated additional components of the HIV envelope genotype (eg, gp41) and/or components of the gp120 gene other than the V3 domain. (29) Genotyping can be conducted on either viral RNA samples (plasma) or on proviral DNA (peripheral blood mononuclear cells), the latter allowing tropism determination in the context of undetectable viremia. (30) Other potential advantages of genotypic assays are reduced cost, shorter turnaround time, and fewer sample failures. (31) Early genotyping studies with comparisons to original Trofile assay results reached contradictory conclusions regarding the adequacy of genotyping for predicting CXCR4 coreceptor usage. Some of the variability in genotype-phenotype assay correlation may have been due to the lower sensitivity of the original Trofile assay, and some variability may have accrued from inclusion of samples containing HIV subtypes other than B (the dominant form in Europe, the Americas, Japan, Thailand, and Australia). Ultimately, the best indication against which tropism assay results should be compared is the virological outcome of patients who receive CCR5-antagonist medication. (32) Table 1 summarizes the results of studies comparing V3 genotyping results to virologic outcomes after maraviroc treatment. Because most studies use G2P for interpretation, only these results are presented. Where reported, results of original Trofile and enhanced-sensitivity Trofile assay results are also shown. Only the study reported by Gonzalez-Serna was prospective; for the others, V3 genotyping was conducted retrospectively on banked samples. McGovern (2010) likely includes data reported by Harrigan (2009). Results depend on the false-positive rate (FPR) cutoff value chosen for the G2P algorithm. If the result provided by G2P for a specific V3 sequence is higher than the chosen cut-off, the prediction of HIV-1 co-receptor tropism is CXCR4. Because the G2P distributions for CCR5- and CXCR4-tropic viruses overlap, no cutoff value allows perfect classification. Using a higher cutoff value is considered a conservative choice because predictions of CXCR4-tropism are more likely to be true predictions; the trade-off is that some true CXCR4-tropic HIV infections will be falsely identified as CCR5- tropic. For example, a cutoff value of 5.75% was optimized retrospectively for the MOTIVATE trial data, (33) but for routine clinical practice, the European guidelines on HIV-1 tropism testing recommend a cut-off of 10% for sequencing of samples in triplicate, or a cut-off of 20% when only a single sequence is generated. (34) The data in Table 1 indicate that, depending on the G2P cutoff value chosen, V3 sequencing results can be generated that are very similar in their ability to predict response to maraviroc to both the original Trofile and the enhanced sensitivity Trofile assays. The Gonzalez-Serna study reports somewhat different results, with lower sensitivity and higher specificity for maraviroc response using

8 Subject: Laboratory Testing for HIV Tropism Page: 8 of 20 similar G2P cutoff values. This study prospectively enrolled patients attending the infectious disease service of a university hospital, as opposed to the other retrospective studies of carefully selected clinical trial participants, but was also much smaller. Sequencing in this study was not done in triplicate as it was in the other studies. Table 1. Performance of HIV V3 Genotyping, Trofile, and ESTA Assays With Reference to Maraviroc Treatment Outcomes Characteristics McGovern (2012)35 Harrigan (2009) Gonzalez-Serna McGovern (2010)38 (Abs)36 (2011)37 Sample size Patients Drug-naive patients from MERIT trial Treatmentexperienced patients from MOTIVATE and 1029 studies Patients with persistent viral load and on treatment hiatus RT-PCR replicates Virologic response <50 copies/ml at definition week 48 <50 copies/ml or reduction 2 log at week 8 <50 copies/ml or reduction 1 log on day 8 Treatment-experienced patients from MOTIVATE and 1029 studies <50 copies/ml or reduction 2 log at week 8 V3 genotyping algorithm G2P, FPR=5.75% G2P, FPR=5% G2P clonal FPR=5% FPR=10% G2P, FPR=5% V3 genotyping vs virologic response to MVC Sens=94% Spec=13% Sens=85% Spec=36% Sens=58% Spec=89% Sens=68% Spec=83% NR Sens=89% Spec=24% Original Trofile vs virologic response to MVC NR Sens=90% Spec=31% Sens=92% Spec=20% ESTA vs virologic Sens=91% NR NR NR response to MVC Spec=22% ESTA: enhanced sensitivity Trofile assay; FPR: false-positive rate (used as cutoff value); G2P: geno2pheno coreceptor system; MERIT: (Maraviroc versus Efavirenz Regimens as Initial Therapy trial; MOTIVATE: Maraviroc Plus Optimized Therapy in Viremic Antiretroviral Treatment-Experienced Patients trials; MVC: maraviroc; NR: not reported; RT-PCR: reversetranscriptase polymerase chain reaction; Sens: sensitivity; Spec: specificity. Newer bioinformatics algorithms continue to be developed, some of which incorporate clinical variables such as HIV-1 viral load and nadir CD4+ count, into their prediction modeling. (39) Some studies, such as one reported by Ceresola et al in a cohort of 67 subjects with HIV, suggest that the G2P algorithm may be more likely to overestimate the frequency of CCX4-tropic viruses compared with other methods. (40) Table 2 summarizes studies that evaluated the results of V3 sequencing using ESTA as the reference standard; treatment outcomes were not considered in these analyses. All studies sequenced HIV V3 RNA from plasma (standard assay); 2 additionally sequenced HIV V3 DNA from whole blood, which targets proviral DNA (useful for patients with low plasma levels of virus). These studies are much smaller than the studies in Table 1, and largely, where it could be determined, did not test samples in triplicate. It is important to remember that the test performance characteristics reported in Table 2 cannot be compared to those reported in Table 1, as the reference standards differ. In general, the sensitivity results indicate that V3 genotyping detects somewhat fewer CXCR4-tropic viral samples than

9 Subject: Laboratory Testing for HIV Tropism Page: 9 of 20 does ESTA; the specificity results indicate that the FPR is not high, ie, few CCR5-tropic samples are identified as CXCR4-tropic. Assay concordance is relatively high. Where reported, genotyping results for proviral DNA appear very similar to those for RNA in paired samples from the same patient population. (see also, Tropism Testing in Patients with Undetectable Viral Load section). In a prospective, phase 3 trial which randomized treatment-naïve patients with HIV to genotypic or phenotypic (Trofile) testing showed no significant differences in treatment response. (41) Previously presented results of European cohort studies have shown maraviroc virologic extended response rates of 69% to 82% in those patients in which HIV variants were genotypically classified CCR5-tropic. (42) Overall and based largely on the studies of tropism assays with reference to maraviroc treatment outcome (Table 1), the evidence suggests that HIV V3 genotyping classifies patients as well as Trofile assays. Genotyping has additional advantages of shorter turnaround time, ability to generate results for patients who cannot be assayed by Trofile, and more access to assay providers. Table 2. Performance of HIV V3 Genotyping with Reference to Enhanced Sensitivity Trofile Assay Study N Patients RT-PCR V3 Genotyping Algorithm V3 Genotyping vs ESTA Replicates Sens Spec Conc Prosperi 2010 (31) Switcher 2010 (30) Sanchez 2010 (43) Strang 2009 (Abs) (44) 55 Patients failing antiretroviral treatment % treatmentexperienced patients 119 Naïve and treatmentexperienced patients 79 Patients evaluated for maraviroc therapy 31 Banked samples, 1x 1x 1x (?) G2P clonal, FPR=5.75% G2P clonal, FPR=10% G2P clonal, FPR=5.75% G2P clonal, FPR=10% G2P clonal, FPR=5% G2P clonal, FPR=10% G2P clonal, FPR=5% G2Pclonal, FPR=10% RNA: 55% 55% DNA: 68% 67% 49% 55% RNA: 96% 79% DNA: 86% 71% 96% 89% RNA; 83% 71% DNA: 82% 71% 81% 78%? G2P, FPR 1-20% NR NR Range, 70-94% Pou 2009 (Abs) 3x G2P RNA: 40% 100% RNA: 78% (45) pre- ART DNA: 36% 100% DNA: 77% Abs: abstract; Conc: concordance; ESTA: enhanced sensitivity Trofile assay; G2P: geno2pheno coreceptor system; FPR: false-positive rate (used as cutoff value); NR: not reported; RT-PCR: reverse-transcriptase polymerase chain reaction; Sens: sensitivity; Spec: specificity. Tropism testing by deep sequencing Because of concern that standard V3 sequencing methods used for tropism testing, might miss clinically significant minor HIV variants, so-called deep sequencing, ( ie, V3 sequencing using next generation sequencing methods) has been investigated for tropism testing. While standard sequencing essentially determines a population average V3 loop sequence, deep sequencing allows simultaneous

10 Subject: Laboratory Testing for HIV Tropism Page: 10 of 20 sequencing and quantifying of thousands of individual V3 variants within a viral population. From this, the proportion of non-r5 variants in a given sample can be calculated using bioinformatic interpretation tools similar to those for standard V3 genotyping. Similar to the standard V3 sequencing methods, the FPR for tropism prediction must be prespecified. Retrospective analyses have used G2P and a FPR 3.5% (see Table 3). The proportion of the viral population that can be detected as non-ccr5 for maraviroc treatment to remain effective has been established as 2% or less. (46) Other studies have also reported high concordance between deep sequencing and current tropism assays (32, 47) and between different sequencing platforms (48). Gibson et al reported high concordance between tropism prediction between samples sequenced with deep sequencing and those sequenced with populationbased sequencing: concordance 84%, with kappa=0.37. (49) The sample data in Table 3 suggest that deep sequencing performs similarly to ESTA and the original Trofile assay at predicting response to maraviroc treatment. Moreover, as noted by Swenson et al, the group of patients with 2% to 20% non- CCR5 virus according to deep sequencing had minority non-ccr5 variants that were not reliably detected by the original Trofile assay, but this group of patients had poor response to maraviroc, with 27% of the patients achieving virologic suppression at week 48, similar to the non-ccr5 group as a whole (26%) and to patients with >20% non-r5 virus (25%). (50) Kagan et al re-analyzed samples from the MOTIVATE and A studies to compare ultradeep sequencing either alone or as a reflex test following standard triplicate V3 sequencing to the ESTA test. (51) Both ultradeep sequencing methods demonstrated improved sensitivity in identifying maraviroc responders compared to standard sequencing. These results suggest that detection of minority non-ccr5 variants by deep sequencing may be important for predicting response. Table 3. Performance of HIV V3 Deep Sequencing, Trofile, and ESTA Assays with Reference to Maraviroc Treatment Outcomes Characte ristics Gonzalez- Serna 2011 (37) Swenson 2011 (52) Swenson 2011 (50) Kagan 2012 (51) N Patients RT- PCR Replicates 27 Patients with persistent viral load and on treatment hiatus 859 Drug-naïve patients from MERIT trial 851 Treatmentexperienced patients from MOTIVATE and 1,029 studies 327 Treatmentexperienced patients from MOTIVATE and A studies who received maraviroc 3x 3x 3x 3x Virologic Response Definition <50 copies/ml or reduction 1 log on day 8 <50 copies/ml at week 48 <50 copies/ml at week 48 <50 copies/ml or >2 log decline at week 8 V3 Genotypi ng Algorithm G2P clonal, FPR 3.5 % G2P clonal, FPR 3.5 % PSSMx4/R5 FPR [ 90% conc with G2P] G2P, FPR 5.75% PSSM X4R5, FPR V3 Genotyping vs Virologic Response to MVC Sens=83% Spec=22% Sens=93% Spec=15% Sens=83% Spec=36% PPV a =65% NPV=61% Original Trofile vs Virologic Response to MVC NR NR Sens=93% Spec=17% NR ESTA vs Virologic Response to MVC NR Sens=90% Spec=21% NR PPV=66% NPV=59%

11 Section: Medicine Effective Date: July 15, 2015 Subject: Laboratory Testing for HIV Tropism Page: 11 of 20 conc: concordance; ESTA: enhanced sensitivity Trofile assay; G2P: geno2pheno coreceptor system; FPR: false-positive rate (used as cutoff value); MVC: maraviroc; NPV: negative predictive value; NR: not reported; PPV: positive predictive value; RT- PCR: reverse-transcriptase polymerase chain reaction; Sens: sensitivity; Spec: specificity. a PPV (positive predictive value) refers to the proportion of CCR5 subjects who achieved virologic response at 8 weeks. NPV (negative predictive value) refers to the proportion of non-ccr5 subjects who failed to have a virologic response at 8 weeks. Tropism Testing in Patients with Undetectable Viral Load The original studies of genotypic tropism tests, such as those shown in Table 2, were conducted on RNA samples from viremic patients. However, there has been interest in the use of maraviroc as part of a simplification strategy in patients already on antiretroviral therapy with undetectable plasma HIV RNA levels. Another potential indication is as intensification strategy in patients with prolonged suppression of HIV levels but with impaired CD4 gains. A 2012 study by Svicher et al demonstrated the feasibility of determining viral tropism using sequencing of proviral DNA with prediction of tropism with the geno2pheno algorithm in peripheral blood mononuclear cells from 53 subjects with HIV, most of whom had undetectable (94.3%) or low (3.7%) viral loads. 53 Additional studies, outlined in Table 4, have demonstrated high rates of concordance between tropism predicted by proviral DNA or RNA sequencing.

12 Section: Medicine Effective Date: July 15, 2015 Subject: Laboratory Testing for HIV Tropism Page: 12 of 20 Table 4. Performance of HIV Proviral DNA Genotyping Study Study Population Prosperi NR (2010) patients failing antiretroviral treatment Svicher 253 patients with For VL >100 copies (2014) 54 plasma HIV-1 RNA HIV DNA/10 6 PBMCs <50 copies/ml For VL<100 copies Brown 42 patients with (2014) 55 plasma HIV-1 RNA 1000 copies/ml DNA Sequence Success Rate V3 Genotyping Algorithm 93.5% G2P clonal, FPR=5.75% HIV DNA/10 6 PBMCs 60% 97.6% G2P clonal, FPR=10% Comparison Concordance Sens Spec Proviral DNA vs RNA (ref) (n=29) Proviral DNA (whole blood or PBMCs) vs RNA (ref) (n=143) Proviral DNA (whole blood) vs RNA (ref) 87.5% (κ=0.74; 95% CI 0.53 to NR NR 0.95; p<0.001) 96.5% NR NR 93% (κ=0.85) 100% 89% Proviral DNA (PBMCs) vs 95% (κ=0.90) 100% 93% RNA (ref) Proviral DNA (whole blood 98% (κ=0.95) 100% 96% or PBMCs) vs RNA (ref) CI: confidence interval; ESTA: enhanced sensitivity Trofile assay; G2P; geno2pheno; FPR: false positive rate; NR: not reported; PBMC: peripheral blood mononuclear cell; ref: reference group; sens: sensitivity (defined as concordant X4 results between test and reference methods/reference method CCX4); spec: specificity (defined as concordant CCR5 results between test and reference methods/reference method CCR5); VL: viral load

13 Section: Medicine Effective Date: July 15, 2015 Subject: Laboratory Testing for HIV Tropism Page: 13 of 20 Garcia et al reported in abstract form the results of the PROTEST study, which evaluated the initiation of maraviroc plus 2 nucleoside reverse-transcriptase inhibitors in aviremic subjects based on genotypic tropism testing of proviral DNA, rather than viral RNA. (56) The study included 74 maraviroc naïve HIV- 1 patients with viral load less than 50/mL on stable antiretroviral therapy, requiring medication change due to toxicity, and CCR5 HIV by proviral DNA genotypic tropism testing. Of the included subjects, 62 (84%) maintained a viral load less than 50/mL through 48 weeks of therapy. A remaining 12 (16%) discontinued treatment: 2 (3%) withdrew informed consent; 2 (3%) died to non-study-related causes; 5 (7%) developed protocol-defined virologic failure; and 1 each (1% each) had a shift to CCX4 between the screening and baseline visits, was lost to follow up), or developed an antiretroviral therapy-related adverse event. Practice Guidelines and Position Statements The HIV Medicine Association of the Infectious Disease Society of North America released updated guidelines on the on the management of persons infected with HIV in 2013.(57) These guidelines state that tropism testing should be performed if the use of a CCR5 antagonist is being considered (strong recommendation, high quality evidence). The guidelines also state that routine tropism testing is not recommended prior to initiation of other regimens because of cost and lack of demonstrated benefit. The guidelines do not specify the preferred method of tropism testing. The European Consensus Group on clinical management of tropism testing states that tropism testing is indicated for patients who fail treatment or have unacceptable toxicity and a CCR5 inhibitor is being considered. (34) In the absence of adequate data, the group provides no guidance regarding the question of testing for newly diagnosed patients whose immediate treatment plan does not include a CCR5 inhibitor. In the absence of evidence, the group provides no guidance regarding tropism testing for newly diagnosed patients whose immediate treatment plan does not include a CCR5 inhibitor. In the absence of adequate data, the group could provide no guidance regarding the question of testing treatment-naïve patients prior to the start of a regimen not including a CCR5 inhibitor, in anticipation of need for a fast change to a CCR5 inhibitor due to the toxicity of the initial treatment regimen. For patients with a plasma HIV RNA load >1,000 copies/ml, tropism testing can be done by Trofile ESTA or by population genotypic analysis of the V3 loop, indicating for both a moderate level of evidence based on well-designed, nonrandomized trials or cohort studies with long-term clinical outcomes. For patients with a plasma HIV RNA load <1,000 copies/ml, genotyping is the preferred method. The Health and Human Services Panel on Antiretroviral Guidelines for Adults and Adolescents published federally approved HIV/AIDS medical practice guidelines in 2014, which make the following recommendations on coreceptor tropism assays: (58) Recommendations with A (strong) rating: A coreceptor tropism assay should be performed whenever the use of a CCR5 coreceptor antagonist is being considered (level of evidence: I [data from randomized controlled trials]). A phenotypic tropism assay is preferred to determine HIV-1 coreceptor usage (level of evidence: I).

14 Subject: Laboratory Testing for HIV Tropism Page: 14 of 20 Recommendations with B (moderate) rating: Coreceptor tropism testing is also recommended for patients who exhibit virologic failure on a CCR5 antagonist (level of evidence: III [expert opinion]). A genotypic tropism assay should be considered as an alternative to predict HIV-1 coreceptor usage (level of evidence: II [data from well-designed nonrandomized trials or observational studies with long-term clinical outcomes]). U.S. Preventive Services Task Force Recommendations Not applicable Summary Based on the evidence from the clinical studies used for FDA approval, and the labeled requirement for tropism testing immediately prior to initiating a course of maraviroc, HIV tropism testing using the enhanced sensitivity version of the phenotypic Trofile assay is considered medically necessary for both treatment-experienced and treatment-naïve patients who are being considered for immediate treatment with maraviroc. The evidence comparing HIV V3 population genotyping to original Trofile and enhanced sensitivity Trofile assay (ESTA), using maraviroc response as the reference for all assays, strongly suggests that genotyping is equivalent to Trofile assays in selecting patients likely to respond to maraviroc, the outcomes of interest. Studies evaluating genotyping and using paired ESTA results for reference suggest that genotyping may be somewhat less sensitive for detecting CXCR4-tropic samples, but these studies were smaller, and most did not test in triplicate. V3 ultra-deep sequencing methods appear to have greater sensitivity in identifying CXCR-4 tropic viruses, and therefore are likely to identify additional patients with HIV tropism who are negative on standard sequencing. Based largely on the maraviroc response results, HIV V3 population genotyping is considered medically necessary for patients considering immediate maraviroc treatment. Either phenotyping or genotyping may be used to determine tropism when considering maraviroc treatment; both are not required. Currently, patient management decisions are based on monitoring of CD4 cell counts and HIV plasma viral load. Studies would be needed to support improved outcomes with additional tropism monitoring during treatment. Pending such studies, tropism testing during treatment with co-receptor antagonists is investigational. In addition, data are not available to support the use of phenotypic tropism testing to predict prognosis, or to determine tropism in advance of a possible need for a regimen change to a coreceptor antagonist at a later date; accordingly, these indications are also investigational. Medicare National Coverage There is no national coverage determination.

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