title: Field evaluation of a broadly sensitive HIV-1 in-house genotyping assay for use with both plasma and dried blood spot specimens in a resource-limited country.
abstract: HIV-1 drug resistance (HIVDR) assays are important tools in clinical management of HIV-infected patients on antiretroviral therapy (ART) and surveillance of drug-resistant variants at population levels. The high cost associated with commercial assays hinders their use in resource-limited settings. We adopted and validated a low-cost in-house assay using 68 matched plasma and dried blood spot (DBS) samples with a median viral load (VL) of 58,187 copies/ml, ranging from 253 to 3,264,850 against the commercial assay ViroSeq. Results indicated that the in-house assay not only had a higher plasma genotyping rate than did ViroSeq (94% versus 78%) but also was able to genotype 89.5% (51/57) of the matched DBS samples with VLs of ≥ 1,000 copies/ml. The sensitivity in detecting DR mutations by the in-house assay was 98.29% (95% confidence interval [CI], 97.86 to 98.72) on plasma and 96.54 (95% CI, 95.93 to 97.15) on DBS, and the specificity was 99.97% (95% CI, 99.91 to 100.00) for both sample types compared to ViroSeq. The minor DR mutation differences detected by the in-house assay against ViroSeq did not result in clinical significance. In addition, cost analysis showed that the in-house assay could reduce the genotyping cost by about 60% for both plasma and DBS compared to ViroSeq. This field condition evaluation highlights the potential utility of a cost-effective, subtype-independent, in-house genotyping assay using both plasma and DBS specimens for HIVDR clinical monitoring and population-based surveillance in resource-limited settings.
authors.affiliation: Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya.
authors.forename: Seth
authors.initials: S
authors.lastname: Inzaule
authors.forename: Chunfu
authors.initials: C
authors.lastname: Yang
authors.forename: Alex
authors.initials: A
authors.lastname: Kasembeli
authors.forename: Lillian
authors.initials: L
authors.lastname: Nafisa
authors.forename: Jully
authors.initials: J
authors.lastname: Okonji
authors.forename: Boaz
authors.initials: B
authors.lastname: Oyaro
authors.forename: Richard
authors.initials: R
authors.lastname: Lando
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Mills
authors.forename: Kayla
authors.initials: K
authors.lastname: Laserson
authors.forename: Timothy
authors.initials: T
authors.lastname: Thomas
authors.forename: John
authors.initials: J
authors.lastname: Nkengasong
authors.forename: Clement
authors.initials: C
authors.lastname: Zeh
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology* / Q000627:therapeutic use; D024882:Drug Resistance, Viral / Q000235:genetics; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000175:diagnosis / Q000188:drug therapy; D015497:HIV-1 / Q000145:classification / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000191:economics / Q000379:methods; D009154:Mutation; D010641:Phenotype; D011533:Proviruses / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D019562:Viral Load; D014779:Virus Replication
chemical_list: D019380:Anti-HIV Agents