title: Detection and quantification of the K103N mutation in HIV reverse transcriptase by pyrosequencing.
abstract: Prolonged treatment of human immunodeficiency virus (HIV)-infected patients with nonnucleoside reverse transcriptase inhibitors (NNRTIs) might result in the selection of resistant mutants, the most frequent being the K103N mutation in reverse transcriptase. Resistance mutations are routinely detected by Sanger sequencing of the whole viral population, which does not detect sequence variants with frequencies below 20%. We have developed a pyrosequencing approach for the analysis of codon 103 of the HIV reverse transcriptase gene in the circulating viral population that detects variants below the limit of conventional sequencing. The method was tested with samples from 5 controls (not exposed to NNRTIs), 6 from patients exposed to NNRTIs and having a K103N mutant virus population detected by conventional sequencing, and 9 from patients previously exposed to NNRTIs that had a wild-type virus population by conventional sequencing. In 7 of 9, samples the mutation could not be detected by either the standard assay or pyrosequencing, while in 2 samples persistence of the mutation could be detected by pyrosequencing. The method might be of practical use in detecting minority variants of HIV in the clinical setting, in epidemiological studies with large numbers of samples, or as a complement to more complex approaches.
authors.affiliation: Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: García-González
authors.forename: Silvia
authors.initials: S
authors.lastname: García-Bujalance
authors.forename: Guillermo
authors.initials: G
authors.lastname: Ruiz-Carrascoso
authors.forename: José Ramón
authors.initials: JR
authors.lastname: Arribas
authors.forename: Juan
authors.initials: J
authors.lastname: González-García
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Bernardino
authors.forename: José Francisco
authors.initials: JF
authors.lastname: Pascual-Pareja
authors.forename: Lorena
authors.initials: L
authors.lastname: Martínez-Prats
authors.forename: Rafael
authors.initials: R
authors.lastname: Delgado
authors.forename: Jesús
authors.initials: J
authors.lastname: Mingorance
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D024882:Drug Resistance, Viral; D005260:Female; D006678:HIV / Q000235:genetics* / Q000302:isolation & purification; D015658:HIV Infections / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests / Q000379:methods; D008875:Middle Aged; D020125:Mutation, Missense; D017422:Sequence Analysis, DNA / Q000379:methods*; D055815:Young Adult
chemical_list: D054303:HIV Reverse Transcriptase