Comparison of Genotypic and Phenotypic HIV Type 1 Tropism Assay: Results from the Screening Samples of Cenicriviroc Study 202, a Randomized Phase II Trial in Treatment-Naive Subjects

KaganRon, M; JohnsonErik, P; SiawMartin, F; BaelenBen, Van; OgdenRichard,; PlattJamie, L; PesanoRick, L; LefebvreEric,

doi:10.1089/aid.2013.0123

Cited by 15 publications

(9 citation statements)

References 55 publications

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“…In the case of subject TV1261, no particular feature of V3 would seem to explain the discordant results between G2P5.75, PSSM X4R5 , and the Trofile assay. Such discordant instances were previously reported in the literature, 39,40 though no clear-cut explanation was provided for these observations. In the present study, at least three separate amplification reactions were performed for each serum sample/ time point.…”

Section: Determination Of Coreceptor Tropismcontrasting

confidence: 53%

“…In the present study, at least three separate amplification reactions were performed for each serum sample/ time point. Such replicate amplification and population sequencing were shown in previous reports to enhance the sensitivity of the genotyping tropism tests, 40,41 thus providing a possible reason for the discordant results obtained for TV1261 when using algorithms versus Trofile.…”

Section: Determination Of Coreceptor Tropismmentioning

confidence: 79%

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Evolution of HIV-1 Coreceptor Usage and Coreceptor Switching During Pregnancy

Ransy

Motorina

Mérindol

et al. 2014

AIDS Research and Human Retroviruses

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Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. To document the evolution of coreceptor tropism during pregnancy, a longitudinal study of envelope gene sequences was performed in a group of pregnant women infected with HIV-1 of clade B (n=10) or non-B (n=9). Polymerase chain reaction (PCR) amplification of the V1-V3 region was performed on plasma viral RNA, followed by cloning and sequencing. Using geno2pheno and PSSMX4R5, the presence of X4 variants was predicted in nine of 19 subjects (X4 subjects) independent of HIV-1 clade. Six of nine X4 subjects exhibited CD4(+) T cell counts <200 cells/mm(3), and the presence of X4-capable virus was confirmed using a recombinant phenotypic assay in four of seven cases where testing was successful. In five of nine X4 subjects, a statistically significant decline in the geno2pheno false-positive rate was observed during the course of pregnancy, invariably accompanied by progressive increases in the PSSMX4R5 score, the net charge of V3, and the relative representation of X4 sequences. Evolution toward X4 tropism was also echoed in the primary structure of V2, as an accumulation of substitutions associated with CXCR4 tropism was seen in X4 subjects. Results from these experiments provide the first evidence of the ongoing evolution of coreceptor utilization from CCR5 to CXCR4 during pregnancy in a significant fraction of HIV-infected women. These results inform changes in host-pathogen interactions that lead to a directional shaping of viral populations and viral tropism during pregnancy, and provide insights into the biology of HIV transmission from mother to child.

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Section: Determination Of Coreceptor Tropismcontrasting

confidence: 53%

Section: Determination Of Coreceptor Tropismmentioning

confidence: 79%

Evolution of HIV-1 Coreceptor Usage and Coreceptor Switching During Pregnancy

Ransy

Motorina

Mérindol

et al. 2014

AIDS Research and Human Retroviruses

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“…The position-specific scoring matrix (PSSM) analyzes the entire V3 sequence and predicts X4 variants based on a scoring of the probability of the amino acid at each position being overrepresented among X4 sequences versus R5 sequences (10). The Geno2Pheno (G2P) algorithm (11) also analyzes the entire V3 sequence and provides a quantitative score (false-positive rate [FPR]) representing the probability of falsely predicting an R5 variant as an X4 variant; the validity of this approach has been assessed in several clinical trials (12)(13)(14)(15)(16). G2P has been widely used in research and clinical settings, but it requires a preset FPR cutoff to call X4 variants.…”

mentioning

confidence: 99%

Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions

Zhou

Bednar

Sturdevant

et al. 2016

J Virol

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HIV-1 requires the CD4 receptor and a coreceptor (CCR5 [R5 phenotype] or CXCR4 [X4 phenotype]) to enter cells. Coreceptor tropism can be assessed by either phenotypic or genotypic analysis, the latter using bioinformatics algorithms to predict tropism based on the env V3 sequence. We used the Primer ID sequencing strategy with the MiSeq sequencing platform to reveal the structure of viral populations in the V1/V2 and C2/V3 regions of the HIV-1 env gene in 30 late-stage and 6 early-stage subjects. We also used endpoint dilution PCR followed by cloning of env genes to create pseudotyped virus to explore the link between genotypic predictions and phenotypic assessment of coreceptor usage. We found out that the most stringently sequence-based calls of X4 variants (Geno2Pheno false-positive rate [FPR] of <2%) formed distinct lineages within the viral population, and these were detected in 24 of 30 late-stage samples (80%), which was significantly higher than what has been seen previously by using other approaches. Non-X4 lineages were not skewed toward lower FPR scores in X4-containing populations. Phenotypic assays showed that variants with an intermediate FPR (2 to 20%) could be either X4/dual-tropic or R5 variants, although the X4 variants made up only about 25% of the lineages with an FPR of <10%, and these variants carried a distinctive sequence change. Phylogenetic analysis of both the V1/V2 and C2/V3 regions showed evidence of recombination within but very little recombination between the X4 and R5 lineages, suggesting that these populations are genetically isolated. IMPORTANCEPrimer ID sequencing provides a novel approach to study genetic structures of viral populations. X4 variants may be more prevalent than previously reported when assessed by using next-generation sequencing (NGS) and with a greater depth of sampling than single-genome amplification (SGA). Phylogenetic analysis to identify lineages of sequences with intermediate FPR values may provide additional information for accurately predicting X4 variants by using V3 sequences. Limited recombination occurs between X4 and R5 lineages, suggesting that X4 and R5 variants are genetically isolated and may be replicating in different cell types or that X4/R5 recombinants have reduced fitness. H uman immunodeficiency virus type 1 (HIV-1) requires the CD4 receptor and a coreceptor to infect host cells. Entry is mediated by the viral envelope protein (Env), which is processed to give two associated subunits, gp120 and gp41, that assemble into a trimeric structure embedded in the viral envelope/membrane. The binding of gp120 to CD4 triggers a structural change that exposes its variable region 3 (V3) loop, which is part of the coreceptor domain (1, 2). The majority of transmitted/founder (T/F) viruses and viruses isolated from the clinically latent stage in HIV-infected subjects use CCR5 as the coreceptor, making the virus CCR5 tropic (or an R5 virus). The virus can evolve to use CXCR4 (CXCR4 tropic [or an X4 virus]), and viruses that have switched core...

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“…On the other hand, as described above, the adoption of genotypic HIV-1 tropism assays in the clinical setting has been hampered by the limited sensitivities of the population-based sequencing assays to detect minor non-R5 variants. Therefore, more sensitive genotypic HIV-1 tropism assays based on deep sequencing have been developed to detect non-R5 variants present at frequencies of Ͻ20% of the population, and these have been shown to correlate well with both phenotypic assays (36,(63)(64)(65)(66)(67) and the virological response to CCR5-receptor antagonists, such as maraviroc (Selzentry/Celsentri, Pfizer, NY) (36,63,66). Nevertheless, a combination of at least two different genotypic assays is still needed to assess the susceptibility of a patient-derived HIV-1 infection to all FDA-approved antiretroviral drugs, including CCR5 antagonists.…”

mentioning

confidence: 99%