Open AccessGenotyping performance evaluation of commercially available HIV-1 drug resistance test
Author(s) -
Rosemary Audu,
Chika Onwuamah,
Jonathan Okpokwu,
Godwin Imade,
Georgi. Odaibo,
Azuka Okwuraiwe,
Musa Adesola Zaidat,
Philippe Chebu,
OC Ezechi,
Agbaji Oche,
Olaleye Olufemi David,
Jay Osi Samuel,
Ibrahim Dalhatu,
Ahmed Mukhtar,
Joshua DeVos,
Chunfu Yang,
Elliot Raizes,
Beth Chaplin,
Phyllis J. Kanki,
Idigbe Emmanuel
Publication year - 2018
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0198246
Subject(s) - genotyping , hiv drug resistance , drug resistance , viral load , human immunodeficiency virus (hiv) , genotype , virology , medicine , biology , microbiology and biotechnology , genetics , gene , antiretroviral therapy
Background ATCC HIV-1 drug resistance test kit was designed to detect HIV-1 drug resistance (HIVDR) mutations in the protease and reverse transcriptase genes for all HIV-1 group M subtypes and circulating recombinant forms. The test has been validated for both plasma and dried blood spot specimen types with viral load (VL) of ≥1000 copies/ml. We performed an in-country assessment on the kit to determine the genotyping sensitivity and its accuracy in detecting HIVDR mutations using plasma samples stored under suboptimal conditions. Methods Among 572 samples with VL ≥1000 copies/ml that had been genotyped by ViroSeq assay, 183 were randomly selected, including 85 successful genotyped and 98 unsuccessful genotyped samples. They were tested with ATCC kits following the manufacturer’s instructions. Sequence identity and HIVDR patterns were analysed with Stanford University HIV Drug Resistance HIVdb program. Results Of the 183 samples, 127 (69.4%) were successfully genotyped by either method. While ViroSeq system genotyped 85/183 (46.5%) with median VL of 32,971 (IQR: 11,150–96,506) copies/ml, ATCC genotyped 115/183 (62.8%) samples with median VL of 23,068 (IQR: 7,397–86,086) copies/ml. Of the 98 unsuccessful genotyped samples with ViroSeq assay, 42 (42.9%) samples with lower median VL of 13,906 (IQR: 6,122–72,329) copies/ml were successfully genotyped using ATCC. Sequence identity analysis revealed that the sequences generated by both methods were >98% identical and yielded similar HIVDR profiles at individual patient level. Conclusion This study confirms that ATCC kit showed greater sensitivity in genotyping plasma samples stored in suboptimal conditions experiencing frequent and prolonged power outage. Thus, it is more sensitive particularly for subtypes A and A/G HIV-1 in resource-limited settings.