title: Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba.
abstract: As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.
authors: Virology Department, Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Yoan
authors: Y
authors: Alemán
authors: Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
authors: Lore
authors: L
authors: Vinken
authors: Virology Department, Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Vivian
authors: V
authors: Kourí
authors: Virology Department, Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Lissette
authors: L
authors: Pérez
authors: Virology Department, Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Alina
authors: A
authors: Álvarez
authors: Hospital at Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Yeissel
authors: Y
authors: Abrahantes
authors: Hospital at Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Carlos
authors: C
authors: Fonseca
authors: Hospital at Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Jorge
authors: J
authors: Pérez
authors: Virology Department, Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Consuelo
authors: C
authors: Correa
authors: Virology Department, Institute of Tropical Medicine "Pedro Kourí", Havana City, Cuba.
authors: Yudira
authors: Y
authors: Soto
authors: Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
authors: Yoeri
authors: Y
authors: Schrooten
authors: Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium; Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universida de Nova de Lisboa, Lisboa, Portugal.
authors: Anne-Mieke
authors: AM
authors: Vandamme
authors: Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
authors: Kristel
authors: K
authors: Van Laethem
mesh_terms: D003462:Cuba; D024882:Drug Resistance, Viral / Q000235:genetics*; D060005:Genotyping Techniques; D017320:HIV Protease Inhibitors / Q000494:pharmacology; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D015203:Reproducibility of Results; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology
chemical_list: D017320:HIV Protease Inhibitors; D018894:Reverse Transcriptase Inhibitors