Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study

Fehr, Jan; Glass, Tracy R.; Louvel, Séverine; Hamy, François; Hirsch, Hans H.; Wyl, Viktor von; Böni, Jürg; Yerly, Sabine; Bürgisser, Philippe; Cavassini, Matthias; Fux, Christoph A; Hirschel, Bernard; Vernazza, Pietro; Martinetti, Gladys; Bernasconi, Enos; Günthard, Huldrych F.; Battegay, Manuel; Bucher, Heiner C.; Klimkait, Thomas

doi:10.1186/1479-5876-9-14

Cited by 10 publications

(9 citation statements)

References 36 publications

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“…This test, termed PhenXR, permits up to four rounds of virus replication in the presence of inhibitor. Details have been described elsewhere, and the test has been validated for diagnostic drug resistance testing (27). For all above-mentioned env variants, a replicative fitness of Ͼ70% compared to that of the wild-type NL4-3 was noted.…”

Section: Resultsmentioning

confidence: 99%

“…In order to address this possibility further, we employed a replicative phenotyping system (deCIPhR), which uses patient-derived full-envelope sequences for recombinantly reconstituting a fully infectious virus, similar to the format described earlier (27). This test allows for the expansion of virus during four replication cycles in the presence of inhibitors, and the virus carries envelopes from clinical specimens.…”

Section: Resultsmentioning

confidence: 99%

“…Principles and details of the replicative phenotyping protocol have been described elsewhere (27,28) with the following adaptations for tropism analysis. Amplification of the HIV-1 Env gene isolated from clinical samples was successfully performed when virus loads were greater than 500 copies/ml (29).…”

Section: Methodsmentioning

confidence: 99%

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A Diagnostic HIV-1 Tropism System Based on Sequence Relatedness

et al. 2015

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dKey clinical studies for HIV coreceptor antagonists have used the phenotyping-based Trofile test. Meanwhile various simplerto-do genotypic tests have become available that are compatible with standard laboratory equipment and Web-based interpretation tools. However, these systems typically analyze only the most prominent virus sequence in a specimen. We present a new diagnostic HIV tropism test not needing DNA sequencing. The system, XTrack, uses physical properties of DNA duplexes after hybridization of single-stranded HIV-1 env V3 loop probes to the clinical specimen. Resulting "heteroduplexes" possess unique properties driven by sequence relatedness to the reference and resulting in a discrete electrophoretic mobility. A detailed optimization process identified diagnostic probe candidates relating best to a large number of HIV-1 sequences with known tropism. From over 500 V3 sequences representing all main HIV-1 subtypes (Los Alamos database), we obtained a small set of probes to determine the tropism in clinical samples. We found a high concordance with the commercial TrofileES test (84.9%) and the Web-based tool Geno2Pheno (83.0%). Moreover, the new system reveals mixed virus populations, and it was successful on specimens with low virus loads or on provirus from leukocytes. A replicative phenotyping system was used for validation. Our data show that the XTrack test is favorably suitable for routine diagnostics. It detects and dissects mixed virus populations and viral minorities; samples with viral loads (VL) of <200 copies/ml are successfully analyzed. We further expect that the principles of the platform can be adapted also to other sequence-divergent pathogens, such as hepatitis B and C viruses. The predominant virus variant in early stages of the clinical manifestation of disease, CCR5-tropic HIV, is found in approximately 80% of treatment-naive patients (1, 2). Although this number can vary for the different virus subtypes, the percentage of CXCR4-tropic HIV isolates is generally low and tends to rise with disease progression (3-6). Nevertheless, the fraction of CCR5-tropic viruses in clinical specimens continues to stay at Ͼ50% throughout the course of infection (7,8). As such, the molecular interactions between the viral envelope and the cellular chemokine receptor CCR5 were recognized as potentially attractive targets for drug development and have yielded compounds and drugs able to specifically block CCR5-tropic HIV (9-11). It is this selectivity of the inhibition of one (CCR5) and not the other (CXCR4) viral coreceptor that necessitates tropism testing prior to prescribing drugs of this particular class. Although the chemokine receptor binding site in the HIV envelope is constituted mainly by the V3 loop, the V1/V2 regions, and the C4 conserved region in the HIV protein gp120, coreceptor tropism is dictated predominantly by amino acid sequences of the V3 region (12, 13). But also sequences of other variable env regions can contribute as secondary sites to the viral tropism (14-17).Initially, all...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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A Diagnostic HIV-1 Tropism System Based on Sequence Relatedness

et al. 2015

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“…In the first European Quality Assessment panel [9,10], the Swiss system was found to match well with the expected outcome (fig. 3).…”

Section: Test Performancementioning

confidence: 96%

The XTrack System: Application and Advantage

Klimkait

2012

Intervirology

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“…For reasons of cost, accessibility, and turnaround time, genotypic testing is generally favoured over phenotypic testing, although the latter may provide additional useful information in the case of complex mutational patterns which are difficult to interpret [4]. Following an earlier review in the journal [3], recent developments in the clinical use of genotypic testing are described.…”

Section: Introductionmentioning

confidence: 97%