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• W2564837112 endingPage "e0166902" @default.
• W2564837112 startingPage "e0166902" @default.
• W2564837112 abstract "The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5–10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice." @default.
• W2564837112 created "2017-01-06" @default.
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• W2564837112 date "2016-12-13" @default.
• W2564837112 modified "2023-10-14" @default.
• W2564837112 title "An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies" @default.
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• W2564837112 doi "https://doi.org/10.1371/journal.pone.0166902" @default.
• W2564837112 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5154500" @default.
• W2564837112 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/27959928" @default.
• W2564837112 hasPublicationYear "2016" @default.
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