Plasma viral RNA assay in HIV-1 group O infection by real-time PCR

Detection of numerous HIV-1/MO recombinants in France

BACKGROUND

The broad genetic divergence of HIV-1/O relative to HIV-1/M has important implications for diagnosis, monitoring and treatment. Despite this divergence, some HIV-1/M+O dual infections and HIV-1/MO recombinant forms have been reported, mostly in Cameroon, where both groups are prevalent. Here, we describe the characteristics of such infections detected in France in 10 new patients, and discuss their implications for biological and clinical practice, owing to the presence of group O species.

METHODS

The French National Reference Centre for HIV received samples within the framework of mandatory notification of HIV infections, and for expert analysis. A strategy combining serotyping, viral quantification, group-specific molecular amplification and whole-genome sequencing was used for strain characterization and complementary investigations.

RESULTS

We identified one patient with M+O infection, three patients with M+O infection associated with an MO recombinant, and six patients with only an MO recombinant. These atypical infections were detected upon strain characterization (n = 4) or because of anomalies during patient monitoring (n = 6). We identified eight new URF_MO, all but one originating from Cameroon. Interestingly, two distinct recombinant strains were found in two unrelated patients, representing possible precursors of a CRF_MO.

CONCLUSION

Our work highlights the fact that the continuous evolution of HIV can hinder diagnosis and complicate clinical practice. We stress that unexpected results during diagnosis or monitoring necessitate further serological and molecular exploration, these atypical infections influence biological and therapeutic management and necessitate appropriate tools, and specific surveillance is necessary, especially as the frequency of such infections may be underestimated.

HIV-1 non-group M phenotypic susceptibility to integrase strand transfer inhibitors

Objectives

To determine natural phenotypic susceptibility of non-group M HIV-1 to integrase strand transfer inhibitors (INSTIs) in a large panel of 39 clinical strains from groups O, N and P and to identify genotypic polymorphisms according to susceptibility levels.

Methods

Susceptibility to raltegravir, elvitegravir and dolutegravir was evaluated in 36 HIV-1/O, 2 HIV-1/N and 1 HIV-1/P strains plus an HIV-1/M reference strain. IC50 values were determined after 3 days, and fold changes (FCs) were calculated relative to the HIV-1/M strain. Genotypic polymorphism was determined by amplification of codons 19-263 of the integrase; the natural occurrence of resistance-associated mutations was analysed using the main resistance algorithms and the IAS-USA list. VESPA analysis of the strain sequences was used to determine a signature pattern associated with higher FC.

Results

Similar IC50 results were observed for the three drugs. Based on the value for the HIV-1/M reference strain, the data showed FC values <2.5 for raltegravir and dolutegravir, whereas the distribution for elvitegravir was heterogeneous, with FC > 10 for six strains (15%). Analysis of the non-M integrase sequences showed a high level of polymorphism without a major genotypic impact; it also revealed mutations that may be associated with the highest FC values obtained for elvitegravir.

Conclusions

Our phenotypic data showed that non-M strains are globally susceptible to the three currently used INSTIs, but the impact of the high FC values observed for some strains with elvitegravir needs to be explored. Clinical data are now needed to confirm these phenotypic results.

Non-M variants of human immunodeficiency virus type 1

The AIDS pandemic that started in the early 1980s is due to human immunodeficiency virus type 1 (HIV-1) group M (HIV-M), but apart from this major group, many divergent variants have been described (HIV-1 groups N, O, and P and HIV-2). The four HIV-1 groups arose from independent cross-species transmission of the simian immunodeficiency viruses (SIVs) SIVcpz, infecting chimpanzees, and SIVgor, infecting gorillas. This, together with human adaptation, accounts for their genomic, phylogenetic, and virological specificities. Nevertheless, the natural course of non-M HIV infection seems similar to that of HIV-M. The virological monitoring of infected patients is now possible with commercial kits, but their therapeutic management remains complex. All non-M variants were principally described for patients linked to Cameroon, where HIV-O accounts for 1% of all HIV infections; only 15 cases of HIV-N infection and 2 HIV-P infections have been reported. Despite improvements in our knowledge, many fascinating questions remain concerning the origin, genetic evolution, and slow spread of these variants. Other variants may already exist or may arise in the future, calling for close surveillance. This review provides a comprehensive, up-to-date summary of the current knowledge on these pathogens, including the historical background of their discovery; the latest advances in the comprehension of their origin and spread; and clinical, therapeutic, and laboratory aspects that may be useful for the management and the treatment of patients infected with these divergent viruses.

Single real-time reverse transcription-PCR assay for detection and quantification of genetically diverse HIV-1, SIVcpz, and SIVgor strains

Although antiretroviral treatment availability has improved, the virological monitoring of patients remains largely uneven across regions. In addition, viral quantification tests are suffering from human immunodeficiency virus type 1 (HIV-1) genetic diversity, fueled by the emergence of new recombinants and of lentiviruses from nonhuman primates. We developed a real-time reverse transcription-PCR (RT-PCR) assay that is relatively inexpensive and able to detect and quantify all circulating forms of HIV-1 and its simian immunodeficiency virus (SIV) precursors, SIVcpz and SIVgor. Primers and a probe were designed to detect all variants of the HIV-1/SIVcpz/SIVgor lineage. HIV-1 M plasma (n = 190; 1.68 to 7.78 log(10) copies/ml) representing eight subtypes, nine circulating recombinant forms, and 21 unique recombinant forms were tested. The mean PCR efficiency was 99%, with low coefficients of intra- and interassay variation (<5%) and a limit of quantification of <2.50 log(10) copies/ml, with a 200-μl plasma volume. On the studied range, the specificity and the analytical sensitivity were 100 and 97.4%, respectively. The viral loads were highly correlated (r = 0.95, P < 0.0001) with the reference method (generic HIV assay; Biocentric) and had no systematic difference, irrespective of genotype. Furthermore, 22 HIV-1 O plasmas were screened and were better quantified compared to the gold-standard RealTime HIV-1 assay (Abbott), including four samples that were only quantified by our assay. Finally, we could quantify SIVcpzPtt and SIVcpzPts from chimpanzee plasma (n = 5) and amplify SIVcpz and SIVgor from feces. Thus, the newly developed real-time RT-PCR assay detects and quantifies strains from the HIV-1/SIVcpz/SIVgor lineage, including a wide diversity of group M strains and HIV-1 O. It can therefore be useful in geographical areas of high HIV diversity and at risk for the emergence of new HIV variants.

A new real-time quantitative PCR for diagnosis and monitoring of HIV-1 group O infection

The correct diagnosis and monitoring of HIV-1 group O (HIV-O) infection are essential for appropriate patient management, for the prevention of mother-to-child transmission, and for the detection of dual HIV-M/HIV-O infections. HIV-O RNA quantification is currently possible with two commercial kits (from Abbott and Roche), which quantify HIV-M and HIV-O strains indifferently; therefore, they cannot be used for the specific identification of HIV-O infection. We designed a new real-time quantitative reverse transcription PCR (RT-qPCR assay) (INT-O), which we compared with our previous version, LTR-O, and with the Abbott RealTime HIV-1 kit. Specificity was assessed with 27 HIV-1 group M strains and the prototype strain of group P. Clinical performances were analyzed by using 198 stored plasma samples, representative of HIV-O genetic diversity. Analytical sensitivity, repeatability, and reproducibility were also determined. The detection limit of the INT-O assay was 40 copies/ml, and its specificity was 100%. The repeatability and reproducibility were excellent. Analysis of clinical samples showed a good correlation between the INT-O and LTR-O assays (r = 0.8240), with an improvement of analytical sensitivity. A good correlation was also obtained between the INT-O and Abbott assays (r = 0.8599) but with significantly higher values (0.19 logs) for the INT-O method, due to marked underquantifications for some patients. These results showed that HIV-O genetic diversity still has an impact on RNA quantification. The new assay, INT-O, allows both the specific diagnosis of HIV-O infection and the quantification of diverse HIV-O strains. Its detection limit is equivalent to that of commercial kits. This assay is cheap and suitable for use in areas in which strains of HIV-1 groups M and O cocirculate.

Lack of adaptation to human tetherin in HIV-1 group O and P

Background

HIV-1 viruses are categorized into four distinct groups: M, N, O and P. Despite the same genomic organization, only the group M viruses are responsible for the world-wide pandemic of AIDS, suggesting better adaptation to human hosts. Previously, it has been reported that the group M Vpu protein is capable of both down-modulating CD4 and counteracting BST-2/tetherin restriction, while the group O Vpu cannot antagonize tetherin. This led us to investigate if group O, and the related group P viruses, possess functional anti-tetherin activities in Vpu or another viral protein, and to further map the residues required for group M Vpu to counteract human tetherin.

Results

We found a lack of activity against human tetherin for both the Vpu and Nef proteins from group O and P viruses. Furthermore, we found no evidence of anti-human tetherin activity in a fully infectious group O proviral clone, ruling out the possibility of an alternative anti-tetherin factor in this virus. Interestingly, an activity against primate tetherins was retained in the Nef proteins from both a group O and a group P virus. By making chimeras between a functional group M and non-functional group O Vpu protein, we were able to map the first 18 amino acids of group M Vpu as playing an essential role in the ability of the protein to antagonize human tetherin. We further demonstrated the importance of residue alanine-18 for the group M Vpu activity. This residue lies on a diagonal face of conserved alanines in the TM domain of the protein, and is necessary for specific Vpu-tetherin interactions.

Conclusions

The absence of human specific anti-tetherin activities in HIV-1 group O and P suggests a failure of these viruses to adapt to human hosts, which may have limited their spread.

Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays

The tremendous diversity of human immunodeficiency virus (HIV)-1 strains circulating worldwide has an important impact on almost all aspects of the management of this infection, from the identification of infected persons, through treatment efficacy and monitoring, and prevention strategies such as vaccine design. The areas where HIV-1 genetic diversity is highest are those where the majority of patients in need of treatment and biological monitoring live. With increased access to treatment in these areas, it is expected that the demand for monitoring tools such as viral load assays and resistance tests will also increase, and their reliability will be critical. Regular updates of these assays during the last two decades have aimed at improving their performances in different ways that include their reliability with different HIV-1 strains. We here review to what extent HIV-1 genetic diversity still limits or not the use of currently available viral load and resistance tests.

Biological signature characteristics of primary isolates from human immunodeficiency virus type 1 group O in ex vivo human tonsil histocultures

Human immunodeficiency virus type 1 (HIV-1) group M viruses have achieved a global distribution, while HIV-1 group O viruses are endemic only in particular regions of Africa. Here, we evaluated biological characteristics of group O and group M viruses in ex vivo models of HIV-1 infection. The replicative capacity and ability to induce CD4 T-cell depletion of eight group O and seven group M primary isolates were monitored in cultures of human peripheral blood mononuclear cells and tonsil explants. Comparative and longitudinal infection studies revealed HIV-1 group-specific activity patterns: CCR5-using (R5) viruses from group M varied considerably in their replicative capacity but showed similar levels of cytopathicity. In contrast, R5 isolates from group O were relatively uniform in their replicative fitness but displayed a high and unprecedented variability in their potential to deplete CD4 T cells. Two R5 group O isolates were identified that cause massive depletion of CD4 T cells, to an extent comparable to CXCR4-using viruses and not documented for any R5 isolate from group M. Intergroup comparisons found a five- to eightfold lower replicative fitness of isolates from group O than for isolates from group M yet a similar overall intrinsic pathogenicity in tonsil cultures. This study establishes biological ex vivo characteristics of HIV-1 group O primary isolates. The current findings challenge the belief that a grossly reduced replicative fitness or inherently impaired cytopathicity of viruses from this group underlies their low global prevalence.

Clinical performance of an in-house real-time RT-PCR assay using a fluorogenic LUX™ primer for quantitation of human immunodeficiency virus type-1 (HIV-1)

The South African National Antiretroviral Treatment Guideline recommends the use of HIV viral load assays for routine monitoring of HIV-1 positive patients on Highly Active Antiretroviral Therapy (HAART). Approved commercial HIV-1 viral load assays are expensive for developing countries where a large number of patients are treated in the public sector. The evaluation of an in-house HIV-1 viral load assay (LUX assay) is described using 458 plasma specimens. Good specificity of the LUX assay was demonstrated using 50 seronegative plasma specimens. A group of 142 HIV-1 positive patients was used to assess the agreement between the LUX assay and the COBAS Amplicor assay. An intra class correlation (ICC) coefficient of 0.85 (CI 95%) indicated good agreement between the assays. The Bland-Altman model showed good agreement between the assays for approximately 87% of the results (mean 0.03 [-1.26; 1.32], CI 95%). In a cohort of 55 patients followed-up longitudinally the LUX assay showed similar declines in viral load to the COBAS Amplicor assay in response to therapy. Viral rebound was detected in 5 patients out of 55 by both assays. Thus, the LUX assay compares well to the gold standard and represents an affordable alternative for high volume testing in resource limited settings.

A RealTime HIV-1 viral load assay for automated quantitation of HIV-1 RNA in genetically diverse group M subtypes A–H, group O and group N samples

The Abbott RealTime HIV-1 assay is an automated test for monitoring HIV-1 viral load in plasma samples. The assay uses reverse transcription polymerase chain reaction (RT-PCR) technology with homogeneous real-time fluorescent detection. Automated sample preparation is performed on the m2000sp instrument where RNA is isolated using magnetic microparticle technology and dispensed to a PCR tray together with the amplification reagents. The PCR tray is then transferred to the Abbott m2000rt instrument for amplification and real-time detection. The assay utilizes two distinct sets of primers and probes for HIV-1 and for internal control (IC). The IC is processed along with each sample to control for sample recovery and inhibition. The HIV-1 primer and probe sequences are targeted to the integrase (IN) region of the polymerase (pol) gene. Due to the selection of a highly conserved target region and a novel, mismatch tolerant probe design, the assay can quantitate HIV-1 group M subtypes A-H, group O, and group N isolates. The assay provides high reproducibility and a wide dynamic range, allowing quantitation from 40 copies to 10 million copies of HIV-1 RNA per milliliter of plasma. HIV-1 RNA concentrations detected with 95% probability were 25copies/mL with 1.0mL of plasma, 39copies/mL with 0.6mL of plasma, 65copies/mL with 0.5mL of plasma, and 119copies/mL with 0.2mL of plasma.

Impact of HIV-1 genetic diversity on plasma HIV-1 RNA Quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test

The high genetic diversity of HIV-1 has a major impact on the quantification of plasma HIV-1 RNA, representing an increasingly difficult challenge. A total of 898 plasma specimens positive for HIV-1 RNA by commercial assays (Amplicor v1.5; Roche Diagnostic Systems, Alameda, CA or Versant v3.0; Bayer Diagnostics, Emeryville, CA) were tested using the Agence Nationale de Recherches sur le SIDA second-generation (G2) real-time reverse transcriptase polymerase chain reaction (RT-PCR) test: 518 samples containing HIV-1 of known subtype, including 88 from 2 subtype panels and 430 harboring B (n = 266) and non-B (n = 164) group M HIV-1 subtypes from patients followed up in 2002 through 2005 at Necker Hospital (Paris, France), and 380 samples from 10 different countries (Argentina, Cambodia, Cameroon, Central African Republic, France, Ivory Coast, Madagascar, Morocco, Thailand, and Zimbabwe). HIV-1 RNA values obtained by G2 real-time PCR were highly correlated with those obtained by the Amplicor v1.5 for B and non-B subtypes (R = 0.892 and 0.892, respectively) and for samples from diverse countries (R = 0.867 and 0.893 for real-time PCR vs. Amplicor v1.5 and real-time PCR vs. Versant v3.0, respectively). Approximately 30% of specimens harboring non-B subtypes were underquantified by at least -0.51 log10 in Amplicor v1.5 versus 5% underquantified in G2 real-time PCR. Discrepant results were also obtained with subtype B samples (14% underquantified by Amplicor v1.5 vs. 7% by G2 real-time PCR). Similar percentages were observed when comparing results obtained with the G2 real-time PCR assay with those obtained using the Versant assay. Addressing HIV-1 diversity, continual monitoring of HIV-1 RNA assays, together with molecular epidemiology studies, is required to improve the accuracy of all HIV RNA assays.

Evaluation of the Roche Cobas TaqMan and Abbott RealTime extraction-quantification systems for HIV-1 subtypes

OBJECTIVES

We conducted a comparison of the Abbott Molecular RealTime (Rungis, France) and Roche Diagnostics Cobas Taqman (Meylan, France) automated nucleic acid extraction and real-time polymerase chain reaction (PCR) amplification systems for their capacity to quantify HIV RNA of various subtypes. The systems were tested on culture supernatants belonging to HIV-1 group M (n = 29), HIV-1 group O (n = 8), and HIV-2 (n = 7). We also tested 88 plasma samples from patients infected with HIV-1 group M (B-D [n = 7], A-CRF01 [n = 16], CRF02 [n = 49], and other strains [n = 16]).

RESULTS

The Abbott RealTime system quantified all 29 HIV-1 group M supernatants. One of these samples was not detected by the Roche Cobas TaqMan system. The Abbott RealTime system quantified 7 HIV-1 group O strains. Neither technique cross-reacted with HIV-2. The 79% intraclass correlation coefficient for the 88 plasma samples was barely acceptable, but 4 plasma samples were underestimated by more than 1 log by the Roche Cobas TaqMan system. Similar values were obtained for subtype B and D strains with the tests, indicating that the primers and probes are suitable for these strains. In contrast, the large differences observed with other subtypes, particularly CRF02, show the importance of primer and probe selection.

CONCLUSION

The limitation of real-time PCR to span the entire diversity of HIV must be taken into account during treatment monitoring, resistance studies, and clinical trials.

Circulating (cell-free) nucleic acids - A promising, non-invasive tool for early detection of several human diseases

Circulating nucleic acids (CNA) are present in small amounts in the plasma of healthy individuals. However, increased levels of plasma CNA have been reported in a number of clinical disorders like cancer, stroke, trauma, myocardial infarction, autoimmune disorders, and pregnancy-associated complications. CNA has received special attention because of its potential application as a non-invasive, rapid and sensitive tool for molecular diagnosis and monitoring of acute pathologies and the prenatal diagnosis of fetal genetic diseases. This review throws light on the current status of blood CNA as a diagnostic marker and its potential as a powerful tool in the future.

HIV-1 viral load assays for resource-limited settings

The authors discuss studies on the low-cost viral load assays that are currently available and their potential for use in resource-limited settings.

Pediatric HIV infection: diagnostic laboratory methods

The diagnosis of HIV-1 infection in infants and children continues to present challenges. Currently available virologic assays are sensitive and specific and allow early detection of perinatally acquired HIV infection. Identification soon after birth allows for the rapid initiation of antiretroviral therapy and preservation of the infant's immune system. Serologic diagnostic methods, including HIV-ELISA, Western blot, and immunofluorescence Assay can be used to make the diagnosis of HIV infection in infants older than 18 months of age, children, and adolescents. Recently developed rapid tests allow for testing outside clinical sites, provide results in a short period of time, and allow for prompt initiation of effective prophylaxis in cases of exposure particularly maternal to child transmission. We discuss here the diagnostic management of HIV-exposed infants and HIV-infected children.

Fluorogenic LUX primer for quantitation of HIV-1 by real-time RT-PCR

Measurement of HIV-1 viral load in plasma is an important marker of disease progression and efficacy of antiretroviral therapy. Real-time polymerase chain reaction (PCR) offers an opportunity to develop more affordable alternative viral load assays. This article reports on the development of a novel real-time reverse-transcriptase (RT)-PCR assay for quantitation of HIV-1 RNA copies. This assay utilizes the LightCycler (version 2) real-time PCR platform and light upon extension (LUX) primer for specific detection of amplicons. An external standard (ES) for quantitation of viral RNA represents an in vitro transcribed RNA. The LUX assay shows a wide linear (R2 = 0.99) dynamic range from 4 x 10(6) to 4 x 10(2) copies/mL. Analytical sensitivity of the assay is 4 x 10(2) copies/mL of ES RNA. Intra- and inter-assay variability of the LUX assay was less than 0.5log(10) copies of ES RNA (i.e., no clinically significant variability was found). Virology quality assurance (VQA) HIV-1 RNA copy controls were used to validate ES and preliminarily evaluate the assay performance. This feasibility study demonstrated that the LUX assay is sensitive, reproducible, and compares well to the Roche Amplicor tests used for characterization of the RNA copy controls. These results suggest further evaluation of the LUX assay using a large cohort of well-characterized samples from HIV-1 positive individuals.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Diagnostic developments involving cell-free (circulating) nucleic acids

BACKGROUND

The detection of circulating nucleic acids has long been explored for the non-invasive diagnosis of a variety of clinical conditions. In earlier studies, detection of circulating DNA has been investigated for the detection of various forms of cancer. Metastasis and recurrence in certain cancer types have been associated with the presence of high levels of tumor-derived DNA in the circulation. In the case of pregnancies, detection of fetal DNA in maternal plasma is a useful tool for detecting and monitoring certain fetal diseases and pregnancy-associated complications. Similarly, levels of circulating DNA have been reported to be elevated in acute medical emergencies, including trauma and stroke, and have been explored as indicators of clinical severity. Apart from circulating DNA, much attention and effort have been put into the study of circulating RNA over the last few years. This area started from the detection of tumor-derived RNA in the plasma of cancer patients. Soon after that, detection of circulating fetal RNA in maternal plasma was described. Plasma RNA detection appears to be a promising approach for the development of gender- and polymorphism-independent fetal markers for prenatal diagnosis and monitoring. This development also opens up the possibility of non-invasive prenatal gene expression profiling by maternal blood analysis. Besides circulating DNA and RNA in plasma and serum, cell-free DNA in other body fluids, such as urine, has been detected in patients with different clinical conditions. Regardless of the sources of cell-free DNA for clinical use, the amount is frequently scarce.

METHODS

Technical advancements in detecting free DNA have been made over the years.

CONCLUSIONS

It is likely that further developments in the field of circulating nucleic acids will provide us with new diagnostic and monitoring possibilities over the next few years.

Transfer and evaluation of an automated, low-cost real-time reverse transcription-PCR test for diagnosis and monitoring of human immunodeficiency virus type 1 infection in a West African resource-limited setting

There is an urgent need for low-cost human immunodeficiency virus type 1 (HIV-1) viral load (VL) monitoring technologies in resource-limited settings. An automated TaqMan real-time reverse transcription-PCR (RT-PCR) assay was transferred to the laboratory of the Centre de Diagnostic et de Recherches sur le SIDA, Abidjan, Côte d'Ivoire, and assessed for HIV-1 RNA VL testing in 806 plasma samples collected within four ANRS research programs. The detection threshold and reproducibility of the assay were first determined. The quantitative results obtained with this assay were compared with two commercial HIV-1 RNA kits (the Versant version 3.0 and Monitor version 1.5 assays) in specimens harboring mainly the circulating recombinant form 02 strain (CRF02). The clinical evaluation of this test was done in different situations including the early diagnosis of pediatric infection and the monitoring of antiretroviral-treated patients. The quantification limit of our method was 300 copies/ml. The HIV-1 RNA values obtained by real-time PCR assay were highly correlated with those obtained by the Versant kit (r = 0.901; P < 0.001) and the Monitor test (r = 0.856; P < 0.001) and homogeneously distributed according to HIV-1 genotypes. For the early diagnosis of pediatric HIV-1 infection, the sensitivity and specificity of the real-time PCR assay were both 100% (95% confidence intervals of 93.7 to 100.0 and 98.3 to 100.0, respectively), compared to the Versant results. Following initiation of antiretroviral treatment, the kinetics of HIV-1 RNA levels were very comparable, with a similar proportion of adults and children below the detection limit during follow-up with our technique and the Versant assay. The TaqMan real-time PCR (12 dollars per test) is now routinely used to monitor HIV-1 infection in our laboratory. This technology should be further evaluated in limited-resource countries where strains other than CRF02 are prevalent.

Phenotypic Susceptibility to Nonnucleoside Inhibitors of Virion-Associated Reverse Transcriptase From Different HIV Types and Groups

OBJECTIVES

To evaluate a phenotype assay based on plasma reverse transcriptase (RT) to assess HIV susceptibility to nonnucleoside RT inhibitors (NNRTIs). To compare RT-based phenotype with recombinant virus assay (RVA) phenotype- and genotype-based analysis. To assess group O and HIV-2 susceptibility to NNRTIs in correlation with genotype polymorphisms.

METHODS

RT activity was quantified and its susceptibility to efavirenz, nevirapine, and delavirdine measured as drug concentration resulting in 50% inhibition. RT phenotype was compared with genotype analysis. Eighteen plasma samples from 14 group M- and culture supernatants from 4 group M-, 9 group O-, and 7 HIV-2-infected patients were investigated. RT-based and RVA-based phenotypes were compared for identical plasma from 9 group M-infected patients.

RESULTS

RT-based and RVA-based phenotypes were in complete agreement. RT-based phenotype- and genotype-predicted susceptibility were concordant for all but 1 group M samples. One plasma showed susceptibility to 3 NNRTIs by phenotypes, despite the presence of 101E and 106I/V residues. The HIV-2 RTs were totally resistant to the NNRTIs tested. Among HIV-1 group O, 6 were totally resistant to NNRTIs independently of the presence of the 181C mutation and 3 were susceptible to some NNRTIs.

CONCLUSION

Plasma RT-based phenotype could be useful as a simple alternative for monitoring resistance to NNRTIs. This assay is suitable for highly divergent strains. It would be particularly useful for large epidemiologic survey of the natural HIV polymorphism and the potential impact in emergence of drug resistance, particularly to nevirapine, widely used to prevent mother-to-child transmission.