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 10 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).
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http://dx.doi.org/10.3390/v15020571 | DOI Listing |
Anal Chim Acta
January 2025
School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China. Electronic address:
Background: Capillary electrophoresis (CE) is a highly versatile separation technique widely used in analytical chemistry. Traditionally, CE can be categorized as either aqueous or non-aqueous systems based on the buffer solvents employed. For decades, non-aqueous CE has been predominantly associated with the use of organic solvents, a perception deeply ingrained in the scientific community.
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March 2025
Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China. Electronic address:
The major hurdle of xenotransplantation is the immune response triggered by human natural antibodies interacting with carbohydrate antigens on the transplanted animal organ. Specifically, terminal glycoprotein motifs such as galactose-α1,3-galactose (α-Gal) and N-glycolylneuraminic acid (Neu5Gc) are significant obstacles. Little is known about the abundance and compositions of asparagine-linked complex carbohydrates (N-glycans) carrying these motifs in mammalian organs.
View Article and Find Full Text PDFAnal Biochem
January 2025
Advanced Electrophoresis Solutions Ltd., 380 Jamieson Parkway, Unit 7 and 8, ON, N3C 4N4, Canada; AES Biotech Jiaxing Ltd., No. 501 South Changsheng Road, Economic and Technological Development Zone, Jiaxing City, Zhejiang Province, PR China. Electronic address:
Characterizing major bovine milk proteins, including whey and casein, is of significant interest in the dairy industry. The diverse array of protein proteoforms can be different in terms of genetic variation, breed ways, lactation stage, and animal nutritional status. Current routine methods for bovine milk protein profiling are typically based on immunological techniques, infrared spectroscopy, slab gel isoelectric focusing, capillary electrophoresis, and high-performance liquid chromatography.
View Article and Find Full Text PDFElectrophoresis
January 2025
Department of Medical Chemistry and Clinical Biochemistry, Second Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic.
Hemoglobinopathies, hereditary disorders affecting the structure or production of hemoglobin, were detected by routine HbA measurements by capillary electrophoresis (CE) at the University Hospital Motol, Prague. The potential of ultraviolet-visible (UV-Vis) and Fourier-transform infrared (FTIR) spectroscopy for the detection and characterization of hemoglobinopathies was investigated. FTIR spectra were recorded with a very high resolution (0.
View Article and Find Full Text PDFBlood
January 2025
Massachusetts General Hospital, Boston, Massachusetts, United States.
BMT CTN 1506 ("MORPHO"; NCT02997202) was a randomized phase 3 study of gilteritinib compared to placebo as maintenance therapy after hematopoietic stem cell transplantation (HCT) for patients with FLT3-ITD-mutated acute myeloid leukemia (AML). A key secondary endpoint was to determine the impact on survival of pre- and/or post-HCT measurable residual disease (MRD), as determined using a highly sensitive assay for FLT3-ITD mutations. Generally, gilteritinib maintenance therapy was associated with improved relapse-free survival (RFS) for participants with detectable peri-HCT MRD, whereas no benefit was evident for those lacking detectable MRD.
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