15 research outputs found
From Capillary Electrophoresis to Deep Sequencing: An Improved HIV-1 Drug Resistance Assessment Solution Using In Vitro Diagnostic (IVD) Assays and Software
Background: Drug-resistance mutations were mostly detected using capillary electrophoresis sequencing, which does not detect minor variants with a frequency below 20%. Next-Generation Sequencing (NGS) can now detect additional mutations which can be useful for HIV-1 drug resistance interpretation. The objective of this study was to evaluate the performances of CE-IVD assays for HIV-1 drug-resistance assessment both for target-specific and whole-genome sequencing, using standardized end-to-end solution platforms. Methods: A total of 301 clinical samples were prepared, extracted, and amplified for the three HIV-1 genomic targets, Protease (PR), Reverse Transcriptase (RT), and Integrase (INT), using the CE-IVD DeepChek® Assays; and then 19 clinical samples, using the CE-IVD DeepChek® HIV Whole Genome Assay, were sequenced on the NGS iSeq100 and MiSeq (Illumina, San Diego, CA, USA). Sequences were compared to those obtained by capillary electrophoresis. Quality control for Molecular Diagnostics (QCMD) samples was added to validate the clinical accuracy of these in vitro diagnostics (IVDs). Nineteen clinical samples were then tested with the same sample collection, handling, and measurement procedure for evaluating the use of NGS for whole-genome HIV-1. Sequencing analyzer outputs were submitted to a downstream CE-IVD standalone software tailored for HIV-1 analysis and interpretation. Results: The limits of range detection were 1000 to 106 cp/mL for the HIV-1 target-specific sequencing. The median coverage per sample for the three amplicons (PR/RT and INT) was 13,237 reads. High analytical reproducibility and repeatability were evidenced by a positive percent agreement of 100%. Duplicated samples in two distinct NGS runs were 100% homologous. NGS detected all the mutations found by capillary electrophoresis and identified additional resistance variants. A perfect accuracy score with the QCMD panel detection of drug-resistance mutations was obtained. Conclusions: This study is the first evaluation of the DeepChek® Assays for targets specific (PR/RT and INT) and whole genome. A cutoff of 3% allowed for a better characterization of the viral population by identifying additional resistance mutations and improving the HIV-1 drug-resistance interpretation. The use of whole-genome sequencing is an additional and complementary tool to detect mutations in newly infected untreated patients and heavily experienced patients, both with higher HIV-1 viral-load profiles, to offer new insight and treatment strategies, especially using the new HIV-1 capsid/maturation inhibitors and to assess the potential clinical impact of mutations in the HIV-1 genome outside of the usual HIV-1 targets (RT/PR and INT)
Virological and immunological response to HAART in Africans versus Caucasians naĂŻve HIV patients
info:eu-repo/semantics/nonPublishe
Viral Load and CD4 response to PI containing regimen in B versus non-B treatment naĂŻve HIV-1 patients
info:eu-repo/semantics/nonPublishe
Viral load and CD4 cell response to protease inhibitor-containing regimens in subtype B versus non-B treatment-naive HIV-1 patients
SCOPUS: ar.jinfo:eu-repo/semantics/publishe
Resistance testing in HIV-1 infected patients treated with indinavir/ritonavir 800mg/100 mg BID after at least one protease inhibitor-based therapy failure
info:eu-repo/semantics/nonPublishe
Nelfinavir-containing regimen in treatment-naîve HIV-1 patients (pts): comparison of efficacy in B versus non-B subtypes
info:eu-repo/semantics/nonPublishe
Patterns of resistance mutation in B versus (vs) non-B patients (p) with previous PI failure
info:eu-repo/semantics/nonPublishe
Response to boosted-saquinavir (SQV) containing HAART in PI-experienced patients: comparison of B versus non-B subtypes
info:eu-repo/semantics/nonPublishe
Nelfinavir-containing regimen in treatment-naĂŻve HIV-1: comparison of efficacy in B versus non B-subtypes
info:eu-repo/semantics/nonPublishe
Nelfinavir: 12 month safety and efficacy versus boosted Indinavir, each in combination with 2 Nucleoside Reverse Transcriptase Inhibitors, in treatment naĂŻve patients.
info:eu-repo/semantics/nonPublishe