Implementation of a point mutation assay for HIV drug resistance testing in Kenya

Horacio A. Duarte, Ingrid A. Beck, Molly Levine, Catherine Kiptinness, James M. Kingoo, Bhavna Chohan, Samah R. Sakr, Michael H. Chung, Lisa M. Frenkel

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Objectives: An increasing prevalence of HIV pretreatment drug resistance (PDR) has been observed in Africa, which could decrease the effectiveness of antiretroviral therapy (ART) programs. We describe our experiences, the costs and challenges of implementing an oligonucleotide ligation assay (OLA) for management of PDR in Nairobi, Kenya. Design: An observational report of the implementation of OLA in a Kenyan laboratory for a randomized clinical trial evaluating whether onsite use of OLA in individuals initiating ART would decrease rates of virologic failure. Methods: Compared detection of mutations and proportion of mutants in participants viral quasispecies by OLA in Kenya vs. Seattle. Reviewed records of laboratory workflow and performance of OLA. Calculated the costs of laboratory set-up and of performing the OLA based on equipment purchase receipts and supplies and labor utilization, respectively. Results: OLA was performed on 492 trial participants. Weekly batch-Testing of median of seven (range: 2-13) specimens provided test results to Kenyan clinicians within 10-14 days of sample collection at a cost of US$ 42 per person tested. Cost of laboratory setup was US 32 594. Challenges included an unreliable local supply chain for reagents and the need for an experienced molecular biologist to supervise OLA performance. Conclusion: OLA was successfully implemented in a Kenyan research laboratory. Cost was twice that projected because of fewer than predicted specimens per batch because of slow enrollment. OLA is a potential simple, low-cost method for PDR testing in resource-limited settings (RLS). Ongoing work to develop a simplified kit could improve future implementation of OLA in RLS.

Original languageEnglish (US)
Pages (from-to)2301-2308
Number of pages8
Issue number16
StatePublished - 2018
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health through the following grants: R01 AI100037 (L.M.F.), R01 AI110375 (L.M.F.), the UW CFAR P30 AI027757 (K.K.H.), the Pediatric Scientist Development Program K12 HD000850 (H.A.D.), and T32 AI07140 (H.A.D.). The Coptic Hope Center for Infectious Diseases is supported by the PEPFAR through a cooperative agreement (U62/CCU024512-04) from the Centers for Disease Control and Prevention (CDC).

Publisher Copyright:
© 2018 Lippincott Williams and Wilkins. All rights reserved.


  • HIV
  • drug resistance
  • efavirenz
  • nevirapine
  • oligonucleotide ligation assay
  • point mutation assay
  • preantiretroviral therapy resistance
  • virologic failure


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