{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T14:02:30Z","timestamp":1773583350217,"version":"3.50.1"},"reference-count":31,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2020,7,29]],"date-time":"2020-07-29T00:00:00Z","timestamp":1595980800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    HIV drug resistance (HIVDR) threatens progress achieved in response to the HIV epidemic. Understanding the costs of implementing HIVDR testing programs for patient management and surveillance in resource-limited settings is critical in optimizing resource allocation. Here, we estimate the unit cost of HIVDR testing and identify major cost drivers while documenting challenges and lessons learnt in implementation of HIVDR testing at a tertiary level hospital in Kenya.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    We employed a mixed costing approach to estimate the costs associated with performing a HIVDR test from the provider\u2019s perspective. Data collection involved a time and motion study of laboratory procedures and interviewing laboratory personnel and the management personnel. Cost analysis was based on estimated 1000 HIVDR tests per year. Data entry and analysis were done using Microsoft Excel and costs converted to US dollars (2019).\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    The estimated unit cost for a HIVDR test was $271.78 per test. The main cost drivers included capital ($102.42, 37.68%) and reagents (101.50, 37.35%). Other costs included: personnel ($46.81, 17.22%), utilities ($14.69, 5.41%), equipment maintenance costs ($2.37, 0.87%) and quality assurance program ($4, 1.47%). Costs in relation to specific laboratory processes were as follows: sample collection ($2.41, 0.89%), RNA extraction ($22.79, 8.38%), amplification ($56.14, 20.66%), gel electrophoresis ($10.34, 3.80%), sequencing ($160.94, 59.22%), and sequence analysis ($19.16, 7.05%). A user-initiated modification of halving reagent volumes for some laboratory processes (amplification and sequencing) reduced the unit cost for a HIVDR test to $233.81 (13.97%) reduction.\u00a0\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions:<\/ns4:bold>\n                    Capital expenditure and reagents remain the most expensive components of HIVDR testing. This cost is bound to change as the sequencing platform is utilized towards maximum capacity or leveraged for use with other tests. Cost saving in offering HIVDR testing services is also possible through reagent volume reduction without compromising on the quality of test results.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.23379.1","type":"journal-article","created":{"date-parts":[[2020,7,29]],"date-time":"2020-07-29T10:55:09Z","timestamp":1596020109000},"page":"793","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Cost analysis of implementing HIV drug resistance testing in Kenya: a case study of a service delivery site at a tertiary level hospital in Kenya"],"prefix":"10.12688","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7921-6351","authenticated-orcid":false,"given":"Rachael W.","family":"Gachogo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel N.","family":"Mwai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1195-8762","authenticated-orcid":false,"given":"Frank G.","family":"Onyambu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2020,7,29]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"875-886","DOI":"10.1309\/AJCPELMG6GX6RQSM","article-title":"Building laboratory infrastructure to support scale-up of HIV\/AIDS treatment, care, and prevention: In-country experience.","volume":"131","author":"A Abimiku","year":"2009","journal-title":"Am J Clin Pathol."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"e105790","DOI":"10.1371\/journal.pone.0105790","article-title":"Development, Validation and Clinical Evaluation of a Low Cost In-House HIV-1 Drug Resistance Genotyping Assay for Indian Patients.","volume":"9","author":"A Acharya","year":"2014","journal-title":"PLoS One."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"e0117176","DOI":"10.1371\/journal.pone.0117176","article-title":"Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba .","volume":"10","author":"Y Alem\u00e1n","year":"2015","journal-title":"PLoS One."},{"key":"ref-4","article-title":"Costs of Hiv Viral Load and Early Infant Diagnosis Testing in Kenya","author":"C Cintron","year":"2017"},{"key":"ref-15","doi-asserted-by":"publisher","first-page":"S63-9","DOI":"10.1093\/infdis\/jit109","article-title":"Antiretroviral Treatment Sequencing Strategies to Overcome HIV Type 1 Drug Resistance in Adolescents and Adults in Low-Middle-Income Countries.","volume":"207","author":"A De Luca","year":"2013","journal-title":"J Infect Dis."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"251-257","DOI":"10.1097\/COH.0b013e32834732e8","article-title":"Genotypic resistance testing in routine clinical care.","volume":"6","author":"D Dunn","year":"2011","journal-title":"Curr Opin HIV AIDS."},{"key":"ref-6","article-title":"Cost analysis of implementing HIV drug resistance testing in Kenya: a case study of a service delivery site at a tertiary level hospital in Kenya.","author":"R Gachogo","year":"2020a","journal-title":"figshare."},{"key":"ref-7","article-title":"Cost analysis of implementing HIV drug resistance testing in Kenya: a case study of a service delivery site at a tertiary level hospital in Kenya.","author":"R Gachogo","year":"2020b","journal-title":"figshare."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"177-187","DOI":"10.1093\/cid\/ciy463","article-title":"Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society - USA Panel.","volume":"68","author":"H G\u00fcnthard","year":"2019","journal-title":"Clin Infect Dis."},{"key":"ref-25","doi-asserted-by":"publisher","first-page":"190","DOI":"10.4102\/ajlm.v4i1.190","article-title":"Building laboratory capacity to support HIV care in Nigeria: Harvard \/ APIN PEPFAR, 2004\u20132012.","volume":"4","author":"D Hamel","year":"2015","journal-title":"Afr J Lab Med."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"e0210559","DOI":"10.1371\/journal.pone.0210559","article-title":"Presence, persistence and effects of pre-treatment HIV-1 drug resistance variants detected using next generation sequencing: A Retrospective longitudinal study from rural coastal Kenya.","volume":"14","author":"A Hassan","year":"2019","journal-title":"PLoS One."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"529-539","DOI":"10.1128\/JCM.02347-12","article-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.","volume":"51","author":"S Inzaule","year":"2013","journal-title":"J Clin Microbiol."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"2485-2496","DOI":"10.1097\/QAD.0000000000001964","article-title":"HIV-1 second-line failure and drug resistance at high-level and low-level viremia in Western Kenya.","volume":"32","author":"R Kantor","year":"2018","journal-title":"AIDS."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"508","DOI":"10.4102\/ajlm.v5i3.508","article-title":"Pre-Ebola virus disease laboratory system and related challenges in Liberia.","volume":"5","author":"S Kennedy","year":"2016","journal-title":"Afr J Lab Med."},{"key":"ref-14","first-page":"221-229","article-title":"Implementing HIV-1 Genotypic Resistance Testing in Antiretroviral Therapy Programs in Africa: Needs, Opportunities, and Challenges.","volume":"15","author":"R Lessells","year":"2013","journal-title":"AIDS Rev."},{"key":"ref-16","doi-asserted-by":"publisher","first-page":"15181","DOI":"10.12688\/f1000research.20083.1","article-title":"Performance characteristics of a modified HIV-1 drug resistance genotyping method for use in resource-limited settings [version 1; peer review: 2 approved].","volume":"8","author":"E Magomere","year":"2019","journal-title":"F1000Res."},{"key":"ref-17","doi-asserted-by":"publisher","first-page":"941-951","DOI":"10.1097\/QAD.0000000000002134","article-title":"Minority and majority pretreatment HIV-1 drug resistance associated with failure of first-line nonnucleoside reverse-transcriptase inhibitor antiretroviral therapy in Kenyan women.","volume":"33","author":"R Milne","year":"2019","journal-title":"AIDS."},{"key":"ref-18","article-title":"Kenya Nationl health accounts 2012\/2013","year":"2015"},{"key":"ref-19","doi-asserted-by":"publisher","DOI":"10.13140\/RG.2.2.20647.65448","article-title":"Kenya National Health Accounts FY 2015\/16 Republic of Kenya Ministry of Health","author":"D Mwai","year":"2017"},{"key":"ref-20","doi-asserted-by":"publisher","first-page":"1-6","DOI":"10.1016\/S1473-3099(18)30120-8","article-title":"Personal View Laboratory medicine in Africa since 2008\u202f: then , now , and the future.","volume":"3099","author":"J Nkengasong","year":"2018","journal-title":"Lancet Infect Dis."},{"key":"ref-21","doi-asserted-by":"publisher","first-page":"2581-2593","DOI":"10.1128\/JCM.00756-15","article-title":"Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering.","volume":"53","author":"V Novitsky","year":"2015","journal-title":"J Clin Microbiol."},{"key":"ref-22","doi-asserted-by":"publisher","first-page":"57-60","DOI":"10.1016\/j.puhe.2019.02.016","article-title":"Revisiting aid dependency for HIV programs in Sub-Saharan Africa.","volume":"170","author":"B Olakunde","year":"2019","journal-title":"Public Health."},{"key":"ref-23","doi-asserted-by":"publisher","first-page":"377-382","DOI":"10.1086\/499363","article-title":"Laboratory Medicine in Africa: A Barrier to Effective Health Care.","volume":"42","author":"C Petti","year":"2006","journal-title":"Clin Infect Dis."},{"key":"ref-24","doi-asserted-by":"publisher","first-page":"e146-e154","DOI":"10.1016\/S2352-3018(17)30190-X","article-title":"Cost-effectiveness of public-health policy options in the presence of pretreatment NNRTI drug resistance in sub-Saharan Africa: a modelling study.","volume":"5","author":"A Phillips","year":"2018","journal-title":"Lancet HIV."},{"key":"ref-26","doi-asserted-by":"publisher","first-page":"1475-1479","DOI":"10.1097\/QAD.0000000000001081","article-title":"Tracking development assistance for HIV\/AIDS: the international response to a global epidemic.","volume":"30","author":"M Schneider","year":"2016","journal-title":"AIDs."},{"key":"ref-27","article-title":"UNAIDS DATA 2019","year":"2019"},{"key":"ref-10","article-title":"Recommended Methods for Validation of an In-House Genotyping Assay for Surveillance of HIV Drug Resistance","year":"2018"},{"key":"ref-28","article-title":"Technical and Operational Considerations for Implementing HIV Viral Load Testing","year":"2014"},{"key":"ref-29","article-title":"WHO\/HIV RESNET HIV drug resistance laboratory strategy","year":"2010"},{"key":"ref-30","article-title":"Hiv drug resistance report 2019","year":"2019"},{"key":"ref-31","doi-asserted-by":"publisher","first-page":"e28184","DOI":"10.1371\/journal.pone.0028184","article-title":"Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.","volume":"6","author":"Z Zhou","year":"2011","journal-title":"PLoS 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this work","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}