HIV Drug Resistance Testing

Updated December, 2009

Robert W. Shafer, M.D. and Jose-Luis Blanco, M.D.

               The evolution of HIV-1 drug resistance within an individual depends on the generation of genetic variation in the virus and on the selection of drug-resistant variants during therapy. HIV-1 genetic variability is a consequence of the high HIV-1 RT error rate of about 1 in 10,000 nucleotides (41). Variability is compounded by the high rate of HIV-1 replication, the accumulation of proviral variants during the course of HIV-1 infection, and the genetic recombination that occurs when viruses with different sequences infect the same cell. As a result, innumerable genetically distinct viruses termed quasispecies evolve in individuals in the months following primary infection (7).

               HIV-1 drug resistance was once the main barrier to successful antiretroviral (ARV) therapy. The virus’s high mutation rate and its extensive genetic variability enable it to develop resistance to any ARV treatment regimen that is not completely suppressive. Tens of thousands of patients treated with the incompletely suppressive ARV regimens available in the pre-HAART era developed virological failure and drug resistance. This early cohort then typically received each of the newly licensed ARVs without sufficiently active accompanying drugs, resulting in the almost inevitable development of extensive multi-drug resistance.

               By 1996, it became apparent that, in previously untreated individuals infected with drug susceptible HIV-1 strains, certain combinations of three drugs from two drug classes led to prolonged virus suppression – defined as a plasma HIV-1 RNA level below the limits of detection of the most recent generation of quantitative assays (e.g. less than 20 to 75 copies/ml) (22). Further studies showed that once virological suppression was maintained for about six months, it would last indefinitely as long as therapy was not interrupted (20, 47). Most patients with virological suppression attain progressive immune reconstitution. However, because ARV therapy does not inhibit proviral HIV-1 DNA, virus eradication is not possible. Recurrent viremia and immunologic decline ensue whenever therapy is discontinued regardless of the duration of previous virological suppression (28, 42, 52).

               The likelihood of sustained virological suppression in patients receiving either initial ARV therapy or ARV therapy following virological failure and drug resistance depends largely on the potency of the new treatment regimen and the number of mutations the virus must acquire to develop drug resistance. When viral replication is uncontrolled, all combinations of two drug-resistance mutations are likely to be produced each day, whereas viruses with three drug-resistance mutations are likely to be uncommon (7). Therefore, the goal of therapy is to attain long-term suppression of virus replication with a regimen that will require multiple drug-resistance mutations before losing its effectiveness. This is what is commonly referred to as a high “genetic barrier” to resistance.

               There are now 24 ARV drugs belonging to six mechanistic classes licensed for treating HIV-1: nine protease inhibitors (PIs), eight nucleoside RT inhibitors (NRTIs), four non-nucleoside RT inhibitors (NNRTI), one integrase inhibitor (INI), one fusion inhibitor, and one CCR5 receptor inhibitor. Nonetheless, HIV-1 drug resistance – although no longer the main barrier to successful therapy – remains a persistent problem. This chapter reviews the clinical scenarios in which HIV-1 drug resistance should be performed, the methods of currently available genotypic and phenotypic resistance testing, and the interpretation of drug resistance test results.

Clinical Scenarios for HIV-1 Drug Resistance Testing

               In high-income countries, drug resistance testing is uniformly recommended in the following clinical scenarios (27, 70): (1) Newly diagnosed ARV-naïve patients, (2) Patients with slow response to ARV therapy or virological rebound following successful therapy, (3) Pregnant women with persistently detectable viremia, and (4) Post-exposure prophylaxis when the source of infection is known. In contrast, in low-income countries, HIV-1 drug resistance testing is recommended primarily for population-level surveillance (5). In middle-income countries drug-resistance testing is usually reserved for patients in whom multiple previous ARV regimens have been unsuccessful.

               The most common method of drug resistance testing is genotypic resistance testing. It is widely available, affordable, and more sensitive to the emergence of early resistance than phenotypic testing. Phenotypic testing is most useful for assessing susceptibility to new ARVs when less is known about the genotypic correlates of resistance or when genotypic resistance tests are difficult to interpret, and for assessing virus co-receptor tropism. In the paragraphs that follow we review the first four scenarios for which HIV-1 drug resistance testing is recommended. We review the recommended methods of determining co-receptor tropism in the section entitled Methods of HIV-1 Drug Resistance Testing.

Newly Diagnosed ARV-Naïve Patients

               In the U.S. and Europe, transmitted HIV-1 drug resistance occurs in about 10% to 15% of previously untreated patients (4, 72). In ARV-naïve patients, drug resistance rates are generally higher in newly infected people than in chronically infected patients in whom wildtype revertants have had more time to replace less-fit transmitted mutant variants (36). Therefore, in regions with high rates of transmitted resistance, drug-resistance testing should be performed at the time of HIV-1 diagnosis whether or not ARV therapy is initiated. Although documented super-infection is uncommon, repeated resistance testing prior to starting therapy should be considered in patients at high risk of superinfection in whom initial therapy was deferred (27).

Slow Virological Response to ARV Therapy or Virological Rebound Following Successful ARV Therapy

               In patients receiving an initial ARV treatment regimen, plasma HIV-1 RNA levels are expected to decrease more than 1 log10 (10-fold) within four weeks and to reach undetectable levels within 16 to 24 weeks. Although the time to complete virological suppression is usually longer in patients with higher pre-therapy plasma HIV-1 RNA levels, virus load should decrease progressively during the initial weeks of therapy. Any confirmed increase greater than 1 log10 during this period should be considered virological failure.

               In patients attaining virological suppression, virological rebound is defined as an increase in plasma HIV-1 RNA to a detectable level that persists despite the redressing of correctable causes of virological failure. Confirmatory virus load testing is required to avoid unnecessary resistance testing and treatment changes resulting from testing errors, transient nonadherence, and other factors such as inter-current infection or vaccination reported to transiently increase virus levels. Persistently detectable viremia, at even low levels, indicates ongoing virus replication associated with a risk of progressive drug resistance and virological rebound (31, 54, 56). To maximize the likelihood that drug resistant variants responsible for virological failure will be identified, resistance testing should be performed while patients are receiving the ARV treatment regimen that appears to be failing. Delays as short as four weeks following treatment discontinuation may be associated with replacement of some mutant virus populations with more-fit wildtype variants (11, 14, 74).

Preventing Mother-to-Child Transmission

               Recommendations for HIV-1 drug resistance testing in ARV-naïve and ARV-experienced pregnant women are essentially the same as those in other HIV-1-infected patients. However, because unsuccessful therapy during the late stages of pregnancy may result in an otherwise avoidable life-long infection of a newborn infant, HIV-1-infected pregnant women should be followed more closely than non-pregnant women and the threshold for drug resistance testing should be lowered. Successful treatment of pregnant women is associated with a less than 1% risk of mother-to-child transmission (9). In contrast, incomplete virus suppression is associated with a significant risk of transmission, often of resistant virus strains (13). Pregnant women may also be at higher risk of incomplete suppression due to unpredictable pharmacokinetic changes that occur during the third trimester (46).

Post-Exposure Prophylaxis

               Post-exposure prophylaxis is recommended for patients with an occupational or sexual exposure considered to be associated with a substantial risk of HIV-1 infection as defined in public health guidelines (33). Post-exposure prophylaxis should be started as soon as possible based on the likely ARV treatment or drug-resistance history of the potential source of infection. Genotypic resistance testing is not helpful in choosing initial prophylaxis, but may guide future modifications to prophylaxis when the results are available.

Methods of HIV-1 Resistance Testing

               HIV-1 drug resistance testing can be genotypically or phenotypically based. Genotypic resistance testing, which is performed with dideoxyterminator Sanger sequencing, is the primary method. There are two FDA-approved kits for sequencing HIV-1 RT and protease: ViroSeq HIV-1 Genotyping System (Abbott Molecular) (17, 48) and TRUGENE HIV-1 Genotyping Kit (Siemens Health Care Diagnostics) (21, 68). Many laboratories have also developed highly reproducible in-house methods of sequencing (63). In contrast, phenotypic susceptibility testing is expensive and not widely available. HIV-1 RT/protease and integrase susceptibility tests are available in two commercial laboratories: Virco Laboratories (Mechelin, Belgium) (24) and Monogram BioSciences (53) (South San Francisco, CA, U.S.). The following sections describe the genotypic basis of antiretroviral drug resistance, methods of genotypic resistance testing and interpretation, methods of phenotypic resistance testing and interpretation, and methods for determining co-receptor tropism.

Genotypic Resistance Testing

               Genotypic resistance testing has become the standard method for HIV-1 drug resistance testing because of its relatively low cost, widespread availability, documented reproducibility, and validation in clinical trials. Genotypic resistance testing usually involves the direct (i.e. without cloning) dideoxyterminator (Sanger) sequencing of complementary DNA generated from RNA extracted from patient plasma samples. Although genotypic resistance tests are more difficult to interpret than typical antimicrobial in vitro susceptibility tests, HIV-1 genotypic testing is usually more sensitive than phenotypic tests at detecting reductions in drug susceptibility. Genotypic tests detect mutations present as mixtures, even when the mutation is present at a level too low to affect drug susceptibility in a phenotypic assay. In addition, genotypic tests often identify transitional mutations or antagonistic mutations that are often not associated with reduced susceptibility in a phenotypic assay but which indicate the potential for the rapid emergence of resistance during selective drug pressure (61).

               Genotypic resistance testing involves sequencing the entire protease gene (encompassing at least codons 10 to 90) and adjacent 5’ polymerase-coding region of the RT gene (encompassing at least codons 41 to 238). Gag cleavage site mutations have been shown to influence PI susceptibility and may raise or lower the genetic barrier to resistance to particular PIs. However, most of these mutations are compensatory and it is not clear how knowledge of these mutations should influence therapy selection. Likewise, RT mutations beyond position 238 have been shown to influence NRTI and NNRTI susceptibility. However, most of these mutations are also compensatory and, as above, it is not known how their presence should guide therapy decisions. Integrase and gp41 sequencing assays for detecting raltegravir and enfuvirtide resistance, respectively, are also available from several reference laboratories.

               Standard direct PCR Sanger sequencing is able to detect more than one variant at the same nucleotide position, provided the variant is present at a level of about 20% of the total virus population in a sample. These “minority” variants appear as electrophoretic mixtures on a sequencing chromatogram. Several other genotypic testing approaches have been developed to detect minority variants present at lower levels. These include point mutation assays designed to detect individual mutations, clonal sequencing methods, and ultra-deep pyrosequencing (454 Life Sciences, a Roche company). However, none of these other methods have been validated for clinical use. Point mutation assays (e.g. INNO-LiPa, OLA (16), and allele-specific real-time PCR (29, 50) must be optimized for each mutation they are designed to detect and are at risk for false-negative and false-positive results caused by sequence variability surrounding drug-resistance mutations (32). The main disadvantage of clonal sequencing is that it is expensive and labor-intensive — 50 to 100 clones must be sequenced in order to detect variants present in about 1% to 2% of the virus population. Ultra-deep pyrosequencing is currently too complicated for most clinical laboratories. Moreover, the clinical significance of variants present at very low levels requires further study (62).

Phenotypic Susceptibility Testing

               There are two commercially available in vitro HIV-1 susceptibility tests: PhenoSense, performed by Monogram BioScience (53), and Antivirogram, performed by Virco Laboratories (24). The PhenoSense and Antivirogram each use PCR to amplify from patient plasma, the genes encoding the targets of therapy. Both assays amplify the 3’ part of the gag gene, the entire protease, and the 5’ polymerase coding region of RT (positions 1 to 311 for PhenoSense and 1 to 400 for the Antivirogram). The amplified material is incorporated into a recombinant virus lacking the target of therapy by either ligation (PhenoSense) or homologous recombination (Antivirogram). A standardized virus inoculum is then used to infect cell lines that support HIV-1 replication. In the PhenoSense assay, virus replication at a range of drug concentrations is monitored by a luciferase gene cassette that emits light in proportion to the number of virions after one round of replication. The Antivirogram assay measures the intensity of a tetrazolium dye that, when reduced by cellular mitochondrial enzymes, produces color in proportion to the number of viable cells present after several cycles of HIV-1 replication.

               The PhenoSense assay is used more commonly in clinical settings than the Antivirogram assay. It is more sensitive than the Antivirogram assay at detecting NRTI resistance (75) and its susceptibility results for ARVs belonging to other classes are likely to be more reproducible. However, it is not yet known whether the differences between the two assays for these other ARV classes are clinically relevant. Both assays have established biological and clinical cut-offs: (i) a biological cut-off defined as the greatest fold-decrease in susceptibility typically observed in wildtype clinical isolates, (ii) a lower clinical cut-off defined as the fold decrease in susceptibility at which the virological response to an ARV is less than expected compared with wildtype, and (iii) an upper clinical cut-off defined as the fold decrease in susceptibility at which the virological response to an ARV may no longer be present. Clinical cut-offs are a useful guide to interpreting phenotypic susceptibility results. However, it should be recognized that response to therapy occurs along a continuum of drug susceptibility.

HIV-1 Tropism

               At the time of initial HIV-1 infection, 80-90% of patients have viruses that use CCR5 exclusively as their coreceptor (R5 tropic). During the course of infection, about 50% of patients with subtype B infections are eventually found to harbor viruses that use the CXCR4 receptor (X4 tropic). The emergence of X4 tropism usually occurs in later disease stages and, in the absence of ARV therapy, is followed by accelerated CD4 cell depletion. When X4-tropic viruses emerge, they usually co-circulate with R5-tropic viruses as minor variants. The main determinants for coreceptor tropism are in the V3 loop of HIV-1 env. However, changes outside of the V3 loop also influence coreceptor tropism either in combination or independently of V3 changes (23).

               The number and type of mutations by which an R5-tropic virus becomes X4 tropic is complex and depends on the sequence of the initially circulating R5-tropic virus. In subtype B viruses, the presence of positively charged amino acids at positions 11 or 25 in the V3 loop has a 70% sensitivity and 90% specificity for predicting X4 tropism. However, the sensitivity and specificity for predicting X4 tropism appears to be different in other subtypes. Moreover, the sensitivity for detecting X4 tropism in clinical isolates is below 70% because X4 tropism is often present at levels that cannot be detected by standard sequencing (20%) but that will emerge once an R5 inhibitor is begun (38).

               A phenotypic assay has been developed to assess the tropism of complete env genes (gp120 plus gp41) amplified from patient samples – Enhanced Sensitivity Tropism Assay (ESTA, formerly Trofile, Monogram BioSciences). Amplified env genes are ligated into env expression test vectors that, following co-transfection with env-deleted genomic vectors, are used to create a population of pseudovirions. CD4+ cells expressing CCR5 or CXCR4 are inoculated with these pseudovirions and infection of each cell type is measured with a luciferase-based reporter system (73). Given sufficiently high plasma HIV-1 RNA levels, this assay can reliably detect X4-tropic variants present at levels as low as 1% and it is the only assay that has been validated in clinical trials (67). However, its limited availability and expense continue to spur efforts to develop a genotypic counterpart test for tropism either using newer sequencing technologies like ultradeep pyrosequencing (2, 69) or by combining standard genotypic tests with clinical data (67).

Interpretation of HIV-1 Resistance

               Testing HIV-1 drug resistance is mediated by mutations in the molecular targets of ARV therapy. Data linking HIV-1 mutations with drug resistance fall into three main groups: (i) in vitro and in vivo selection data, (ii) in vitro phenotypic susceptibility data, and (iii) clinical outcome data (61). Mutations that emerge during in vitro selection experiments and in vivo in patients developing virological failure while receiving a specific ARV agent provide Darwinian evidence for the role of specific mutations in either reducing ARV susceptibility or compensating for the decreased fitness associated with other drug-resistance mutations. Correlations between genotypic data and the in vitro susceptibility of viruses containing specific mutations or combinations of mutations provide direct functional evidence linking mutations to drug resistance (59).

               More than 50 clinical trials and retrospective studies have published correlations between genotypic resistance data and clinical outcome data. However, the near impossibility of controlling for the large number of confounding factors influencing virological outcome means that most of these studies were underpowered. In addition to exhibiting diverse patterns of drug-resistance mutations prior to the start of therapy, the patients in these studies usually had heterogeneous pre-therapy CD4 counts, plasma HIV-1 RNA levels, previous treatment histories, and levels of adherence to ARV therapy. However, licensing studies for a new ARV, which are typically large and have fewer confounding factors, have often led to clinically useful heuristics (also called “genotypic susceptibility scores”). A summary of published studies linking pre-therapy drug-resistance mutations with subsequent responses to a new salvage therapy ARV can be found at http://hivdb.stanford.edu/pages/genotype-clinical.html.

               Interpreting the results of HIV-1 genotypic drug-resistance tests is one of the most difficult challenges facing clinicians who care for HIV-1-infected patients. First, there are many mutations associated with drug resistance (64). Second, there are synergistic and antagonistic interactions among these drug-resistance mutations (35). Third, some mutations may not reduce susceptibility by themselves but may compensate for the effect of other mutations or may be sentinel indicators of emerging drug resistance (55). As a result, several systems for interpreting genotypic resistance test results have been developed (37, 57). A recent analysis suggests that these interpretation systems, though far from perfect, are strongly significant predictors of response or lack of response to a new treatment regimen when evaluated in a model that also considers previous treatment history and baseline plasma HIV-1 RNA levels and CD4 counts (57). Moreover, although many systems differ from one another in their precise rules, they are highly concordant and perform equally well (57).

               However, despite the availability of online interpretation systems, it is still useful for physicians to have some knowledge about the most common and clinically relevant ARV-resistance mutations. The handout summarizes the mutations associated with NRTI, NNRTI, PI, and INI resistance. The following sections attempt to place the data from the handout into a meaningful context for the clinician.

NRTIs

               M184V is the most commonly occurring NRTI resistance mutation. Although M184V causes more than 200-fold decreased susceptibility to 3TC and FTC, several lines of evidence have suggested that these NRTIs may still provide continued benefit in the presence of M184V. This may be because M184V is also associated with decreased HIV-1 fitness and increased susceptibility to AZT, d4T, and TDF. M184V also moderately decreases phenotypic susceptibility to ABC and ddI.

               Thymidine analog mutations (TAMs) are caused almost exclusively by AZT and d4T. The presence of multiple Type I TAMs (M41L, L210W, and T215Y) is associated with high-level resistance to AZT and d4T and intermediate cross-resistance to ABC, ddI, and TDF (34, 44). The presence of multiple Type II TAMs (K67N, K70R, and K219Q/E) is associated with intermediate resistance to AZT and d4T and potential low-level resistance to ABC, ddI, and TDF. Although TAMs were once the most commonly occurring mutations, they now occur less frequently in high-income countries, where AZT and, in particular, d4T are used less commonly.

               In patients receiving regimens without thymidine analogs, K65R and L74V have replaced the TAMs as the mutations that occur most commonly in combination with M184V (12, 49). K65R confers low-level resistance to d4T, intermediate resistance to 3TC and FTC, and high-level resistance to ddI, ABC, and TDF (51, 59). AZT is the only nucleoside active against K65R; in fact it is more active against viruses with K65R than against wildtype viruses (15, 19). L74V causes intermediate resistance to ABC and high-level resistance to ddI (59).

               T69SSS, and Q151M are multi-NRTI resistance mutations. T69SSS nearly always occurs in combination with multiple TAMs (Rhee et al. 2007). Q151M usually occurs in combination with several otherwise uncommon mutations (A62V, V75I, F77L, and F116Y) (58).

NNRTIs Cross-Resistance Among the NNRTIs is Common

               IThe most frequently occurring NNRTI-resistance mutations are associated with resistance to multiple NNRTIs and the low genetic barrier to NNRTI resistance allows multiple drug-resistant viruses to emerge in patients with virological failure on an NNRTI-containing regimen (1, 30). The most common NNRTI-resistance mutation, K103N, confers high-level resistance to NVP and EFV but retains susceptibility to ETR. The second-most common mutation, Y181C, confers high-level resistance to NVP (about 50-fold) and low-level resistance to ETR (about 5-fold) and EFV (about 2-fold) (59, 71). However, ETR is likely to be more active than EFV in patients with Y181C alone because of its higher potency and higher genetic barrier to resistance. L100I, K101P, V179F, G190E, and M230L are associated with high-level resistance to ETR when they occur in combination with Y181C/I/V (71). Nearly all of these mutations (except possibly V179F) are also associated with high-level resistance to NVP and EFV, particularly when they occur with other NNRTIs.

               V106M, Y188L, and G190S confer high-level resistance to NVP and EFV but have minimal effect on ETR (71). V106A, Y188C/H, and G190A confer high-level NVP resistance and intermediate phenotypic EFV resistance; however, EFV has generally not proven clinically useful in patients with these mutations who are failing NVP (59). A98G, K101E, V108I, and V179D are each associated with low-level resistance to multiple NNRTIs (59). However, these mutations may have the greatest clinical impact on NVP because of its lower potency and lower genetic barrier to resistance relative to EFV and ETR (3).

               PIs PIs are usually administered with low-levels of ritonavir (indicated by “/r” following the PI name) in order to increase PI levels by interfering with the CYP4503A metabolic pathway (26). Lopinavir is coformulated with ritonavir. Tipranvir, darunavir, and saquinavir are licensed for use only in combination with ritonavir. Atazanavir and fosamprenavir are licensed for use with and without ritonavir, but ritonavir-boosting is recommended in most circumstances to increase the genetic barrier to resistance. Many experts recommend avoiding nelfinavir, which is not boosted by ritonavir, because it is associated with an unacceptable risk of virological failure and drug resistance. Indinavir is rarely recommended because ritonavir-boosting is associated with a high risk of nephrolithiasis and because unboosted indinavir must be taken three times daily apart from meals.

               Although multiple protease mutations are usually necessary for HIV-1 to develop clinically significant levels of resistance to a ritonavir-boosted PI, some mutations can single-handedly confer reduced susceptibility to one or more PIs. Their presence indicates that a particular PI – even when boosted – may not be effective. These mutations are underlined in bold red in the PI Resistance Mutations Table.

               When administered with two NRTIs, atazanavir/r, fosamprenavir/r, saquinavir/r, lopinavir/r, and darunavir/r are considered equally effective for first-line therapy (70). When virological failure does occur it is usually in the absence of PI-resistance mutations. The frequent ability to re-suppress these patients with the same PI-containing regimen suggests that many of these virological failures are associated with nonadherence. Lopinavir/r, tipranavir/r, and darunavir/r are the mainstays of salvage therapy in patients with either transmitted or acquired PI resistance. Darunavir/r is uniformly more active than lopinavir/r, both phenotypically and clinically (10, 40). However, darunavir/r is not as widely available in low-income countries and, in contrast to lopinavir/r, it requires separate doses of darunavir and ritonavir. Tipranavir/r is rarely active against viruses with high-level darunavir/r resistance and it should probably be reserved for treating patients with darunavir failure (who often have viruses containing mutations such as I50V, I54L, and L76V that increase tipranavir/r susceptibility) (25, 60).

INIs

               INI genotyping is indicated in patients who have failed an INI-containing regimen. Three common mutational pathways associated with raltegravir resistance have been reported in such patients: G140S + Q148HKR, N155H  E92Q (and/or other less-potent accessory mutations), and Y143CHR (usually in combination with T97A and other accessory mutations) (8, 18). Each of these patterns are associated with a more than 100-fold decrease in raltegravir susceptibility. The least-common pattern of mutations – characterized by Y143CHR – appears to retain phenotypic susceptibility to elvitegravir (65), another INI in advanced clinical development. Viruses with many other common patterns or raltegravir-resistance mutations retain susceptibility to S/GSK1349572, an investigational INI in phase II clinical trials (45).

Enfuvirtide

               Although enfuvirtide is one of the most potent ARVs, resistance may develop rapidly in patients receiving it for salvage therapy without a sufficient number of additional active drugs. Indeed, the emergence of resistance strains followed by virological rebound has been observed in some patients within two to four weeks (6, 39). Enfuvirtide resistance is confined to a 10-amino-acid region of gp41 (codons 36 to 45). One mutation is usually associated with about 10-fold decreased enfuvirtide susceptibility, whereas two mutations are usually associated with about 100-fold decreased susceptibility (43, 66). However, enfuvirtide susceptibility testing is rarely performed because most patients with virological failure are found to have high-level resistance and because there are no other fusion inhibitors licensed or in clinical development.

CCR5 Inhibitors

               Approximately 80% of patients who experience virological failure while receiving a CCR5 inhibitor will have had low levels of X4-tropic viruses prior to therapy. The remaining 20% typically have CCR5-resistant viruses that retain R5 tropism. As noted in the Methods, there are many efforts underway to develop genotypic tests with comparable sensitivity and specificity to the ESTT for detecting X4-tropic variants. However, genotypic testing for resistant viruses that retain R5 tropism is not yet feasible. Although the genetic determinants for this type of R5-tropic resistance have been identified in several viruses, the patterns of mutations identified so far have been too diverse to be reliably be identified by genotypic testing.

FIGURES

Table 1: Protease Inhibitor (PI) Resistance Mutations [Download PDF]

Figure 1: NRTIs

Figure 2: NNRTIs

Figure 3: PIs

Figure 4: INIs

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