2024-03-28T20:06:33Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1505532020-01-14T08:15:42Zcom_10261_79com_10261_1col_10261_332
2017-05-29T08:56:08Z
urn:hdl:10261/150553
An efficient microarray-based genotyping platform for the identification of drug-resistance mutations in majority and minority subpopulations of HIV-1 quasispecies
Martín, Verónica
Perales, Celia
Dos Santos, Helena G.
Abia, David
Domingo, Esteban
Comunidad de Madrid
Ministerio de Ciencia e Innovación (España)
Ministerio de Economía y Competitividad (España)
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.
2017-05-29T08:56:08Z
2017-05-29T08:56:08Z
2016-12-13
2017-05-29T08:56:11Z
artículo
PLoS ONE 11 (2016)
http://hdl.handle.net/10261/150553
10.1371/journal.pone.0166902
http://dx.doi.org/10.13039/501100003329
http://dx.doi.org/10.13039/501100004837
http://dx.doi.org/10.13039/100012818
27959928
eng
Publisher's version
Sí
https://creativecommons.org/licenses/by/4.0/
openAccess
Public Library of Science