A sensitive phenotypic assay for the determination of human immunodeficiency virus type 1 tropism

Gonzàlez, Núria; Pérez‐Olmeda, Mayte; Mateos, Elena; Cascajero, Almudena; Álvarez, Amparo; Spijkers, Sanne; García-Pérez, Javier; Sánchez-Palomino, Sonsoles; Ruiz‐Mateos, Ezequiel; Leal, Manuel; Alcamí, José

doi:10.1093/jac/dkq379

Cited by 34 publications

(24 citation statements)

References 37 publications

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“…These recombinant viruses were used in a TZM-bl cell line-based HIV neutralization assay. The RV neutralization assay has previously been validated by comparison with the current standardized pseudotype assays, and a good agreement was found (30,32,33). In order to determine whether the RVs in the panel adequately represented the global HIV-1 diversity, we have added the RVs in the panel to the phylogenetic analysis of a large group of 135 reference sequences from the different HIV-1 subtypes taken from the Los Alamos database (http://hiv-web.lanl.gov).…”

Section: Resultsmentioning

confidence: 90%

“…RVs carrying a Renilla luciferase gene in the position of nef were generated by cloning the full-length envelope from HIV-infected patients in the pNL-lacZ/ Env-Ren vector as described previously (33). The envelopes of viral strains NP1525 (E), SF162 (B) QH0692 (B), and MN (B) were amplified from culture supernatants kindly provided by H. Holmes (NIBSC, United Kingdom) through , and 2.9 from HIV-infected patients with an advanced stage of the disease followed in our department.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Broadly Cross-Neutralizing Antibodies in HIV-1 Patients with Undetectable Viremia

Medina-Ramírez

Sánchez-Merino

Sánchez-Palomino

et al. 2011

J Virol

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Several recent studies have identified HIV-infected patients able to produce a broad neutralizing response, and the detailed analyses of their sera have provided valuable information to improve future vaccine design. All these studies have excluded patients on antiretroviral treatment and with undetectable viral loads, who have an improved B cell profile compared to untreated patients. To better understand the induction of neutralizing antibodies in patients on antiretroviral treatment with undetectable viremia, we have screened 508 serum samples from 364 patients (173 treated and 191 untreated) for a broadly neutralizing antibody (bNAb) response using a new strategy based on the use of recombinant viruses. Sera able to neutralize a minipanel of 6 recombinant viruses, including envelopes from 5 different subtypes, were found in both groups. After IgG purification, we were able to confirm the presence of IgG-associated broadly neutralizing activity in 3.7% (7 of 191) of untreated patients with detectable viremia and 1.7% (3 of 174) of aviremic patients receiving antiretroviral treatment. We thus confirm the possibility of induction of a broad IgG-associated neutralizing response in patients on antiretroviral treatment, despite having undetectable viremia. This observation is in stark contrast to the data obtained from long-term nonprogressors, whose little neutralizing activity has been attributed to the low levels of viral replication.

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Section: Resultsmentioning

confidence: 90%

Section: Methodsmentioning

confidence: 99%

Broadly Cross-Neutralizing Antibodies in HIV-1 Patients with Undetectable Viremia

Medina-Ramírez

Sánchez-Merino

Sánchez-Palomino

et al. 2011

J Virol

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“…A tropism test that is easy to use in clinical practice would facilitate the use of CCR5 antagonists for treating CRF01-AE-infected patients. Previous studies have used recombinant phenotypic assays that may be unsuitable for clinical use, particularly in resource-limited countries (19)(20)(21). Genotypic assays have been developed to determine the tropism of HIV-1, but they may be inappropriate for predicting coreceptor usage by the subtype CRF01-AE because of the great variability of the env gene.…”

Section: Discussionmentioning

confidence: 99%

Genotypic Prediction of HIV-1 CRF01-AE Tropism

et al. 2013

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f HIV-1 subtype CRF01-AE predominates in south Asia and has spread throughout the world. The virus tropism must be determined before using CCR5 antagonists. Genotypic methods could be used, but the prediction algorithms may be inaccurate for non-B subtypes like CRF01-AE and the correlation with the phenotypic approach has not been assessed. We analyzed 61 CRF01-AE V3 clonal sequences of known phenotype from the GenBank database. The sensitivity of the Geno2pheno10 genotypic algorithm was 91%, but its specificity was poor (54%). In contrast, the combined 11/25 and net charge rule was highly specific (98%) but rather insensitive (64%). We thus identified subtype CRF01-AE determinants in the V3 region that are associated with CXCR4 use and developed a new simple rule for optimizing the genotypic prediction of CRF01-AE tropism. The concordance between the predicted CRF01-AE genotype and the phenotype was 95% for the clonal data set. We then validated this algorithm by analyzing the data from 44 patients infected with subtype CRF01-AE, whose tropism was determined using a recombinant phenotypic entry assay and V3-loop bulk sequencing. The CRF01-AE genotypic tool was 70% sensitive and 96% specific for predicting CXCR4 use, and the concordance between genotype and phenotype was 84%, approaching the concordance obtained for predicting the tropism of HIV-1 subtype B. Genotypic predictions that use a subtype CRF01-AE-specific algorithm appear to be preferable for characterizing coreceptor usage both in pathophysiological studies and for ensuring the appropriate use of CCR5 antagonists.

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“…Human DCs were generated from peripheral blood monocytes by treatment with granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-4 (IL-4) as described previously (77). Peripheral blood mononuclear cells were isolated from buffy coat preparations from healthy donors (Transfusions Centre, Madrid, Spain) by Ficoll-Hypaque centrifugation, followed by plastic adherence to enrich monocytes.…”

Section: Methodsmentioning

confidence: 99%

“…The pIRES-Vpx plasmid (Clontech) containing cDNA encoding the Vpx viral protein was kindly provided by Mario Stevenson (University of Miami) (39). The pJR-Ren plasmid was generated by cloning gp160 from the JR-FL clone (R5 tropism) in place of the NL4-3 env gene in pNL4-3Ren (77). pROD10 (78) is an infectious molecular clone of HIV-2 rod, provided by Beatrice Labrosse (Diderot University, Paris, France).…”

Section: Methodsmentioning

confidence: 99%

Different Expression of Interferon-Stimulated Genes in Response to HIV-1 Infection in Dendritic Cells Based on Their Maturation State

Calonge

Bermejo

Díez-Fuertes

et al. 2017

J Virol

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Dendritic cells (DCs) are professional antigen-presenting cells whose functions are dependent on their degree of differentiation. In their immature state, DCs capture pathogens and migrate to the lymph nodes. During this process, DCs become resident mature cells specialized in antigen presentation. DCs are characterized by a highly limiting environment for human immunodeficiency virus type 1 (HIV-1) replication due to the expression of restriction factors such as SAMHD1 and APOBEC3G. However, uninfected DCs capture and transfer viral particles to CD4 lymphocytes through a trans-enhancement mechanism in which chemokines are involved. We analyzed changes in gene expression with whole-genome microarrays when immature DCs (IDCs) or mature DCs (MDCs) were productively infected using Vpx-loaded HIV-1 particles. Whereas productive HIV infection of IDCs induced expression of interferon-stimulated genes (ISGs), such induction was not produced in MDCs, in which a sharp decrease in ISG-and CXCR3-binding chemokines was observed, lessening trans-infection of CD4 lymphocytes. Similar patterns of gene expression were found when DCs were infected with HIV-2 that naturally expresses Vpx. Differences were also observed under conditions of restrictive HIV-1 infection, in the absence of Vpx. ISG expression was not modified in IDCs, whereas an increase of ISG-and CXCR3-binding chemokines was observed in MDCs. Overall these results suggest that sensing and restriction of HIV-1 infection are different in IDCs and MDCs. We propose that restrictive infection results in increased virulence through different mechanisms. In IDCs avoidance of sensing and induction of ISGs, whereas in MDCs increased production of CXCR3-binding chemokines, would result in lymphocyte attraction and enhanced infection at the immune synapse.

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A sensitive phenotypic assay for the determination of human immunodeficiency virus type 1 tropism

Abstract: We describe a system to assess co-receptor tropism based on the generation of chimeric replication-competent viruses with high sensitivity in the detection of minor populations. A good correlation of our results with Trofile™ assays was found.

Cited by 34 publications

References 37 publications

Broadly Cross-Neutralizing Antibodies in HIV-1 Patients with Undetectable Viremia

Broadly Cross-Neutralizing Antibodies in HIV-1 Patients with Undetectable Viremia

Genotypic Prediction of HIV-1 CRF01-AE Tropism

Different Expression of Interferon-Stimulated Genes in Response to HIV-1 Infection in Dendritic Cells Based on Their Maturation State

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