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Chohan BH, Ronen K, Khasimwa B, Matemo D, Osborn L, Unger JA, Drake AL, Beck IA, Frenkel LM, Kinuthia J, John-Stewart G. Food insecurity, drug resistance and non-disclosure are associated with virologic non-suppression among HIV pregnant women on antiretroviral treatment. PLoS One 2021; 16:e0256249. [PMID: 34407133 PMCID: PMC8372899 DOI: 10.1371/journal.pone.0256249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/29/2021] [Indexed: 11/25/2022] Open
Abstract
We determined social and behavioral factors associated with virologic non-suppression among pregnant women receiving Option B+ antiretroviral treatment (ART). Baseline data was used from women in Mobile WAChX trial from 6 public maternal child health (MCH) clinics in Kenya. Virologic non-suppression was defined as HIV viral load (VL) ≥1000 copies/ml. Antiretroviral resistance testing was performed using oligonucleotide ligation (OLA) assay. ART adherence information, motivation and behavioral skills were assessed using Lifewindows IMB tool, depression using PHQ-9, and food insecurity with the Household Food Insecurity Access Scale. Correlates of virologic non-suppression were assessed using Poisson regression. Among 470 pregnant women on ART ≥4 months, 57 (12.1%) had virologic non-suppression, of whom 65% had HIV drug resistance mutations. In univariate analyses, risk of virologic non-suppression was associated with moderate-to-severe food insecurity (RR 1.80 [95% CI 1.06–3.05]), and varied significantly by clinic site (range 2%-22%, p <0.001). In contrast, disclosure (RR 0.36 [95% CI 0.17–0.78]) and having higher adherence skills (RR 0.70 [95% CI 0.58–0.85]) were associated with lower risk of virologic non-suppression. In multivariate analysis adjusting for clinic site, disclosure, depression symptoms, adherence behavior skills and food insecurity, disclosure and food insecurity remained associated with virologic non-suppression. Age, side-effects, social support, physical or emotional abuse, and distance were not associated with virologic non-suppression. Prevalence of virologic non-suppression among pregnant women on ART was appreciable and associated with food insecurity, disclosure and frequent drug resistance. HIV VL and resistance monitoring, and tailored counseling addressing food security and disclosure, may improve virologic suppression in pregnancy.
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Affiliation(s)
- Bhavna H Chohan
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Keshet Ronen
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Brian Khasimwa
- Department of Pediatrics, University of Nairobi, Nairobi, Kenya
| | - Daniel Matemo
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Lusi Osborn
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Jennifer A Unger
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Alison L Drake
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A Beck
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington, United States of America.,Department of Medicine, University of Washington, Seattle, Washington, United States of America.,Department of Pediatrics, University of Washington, Seattle, Washington, United States of America.,Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Medicine, University of Washington, Seattle, Washington, United States of America.,Department of Pediatrics, University of Washington, Seattle, Washington, United States of America.,Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
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Application of next generation sequencing in HIV drug resistance studies in Africa, 2005–2019: A systematic review. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Kinuthia J, Ronen K, Unger JA, Jiang W, Matemo D, Perrier T, Osborn L, Chohan BH, Drake AL, Richardson BA, John-Stewart G. SMS messaging to improve retention and viral suppression in prevention of mother-to-child HIV transmission (PMTCT) programs in Kenya: A 3-arm randomized clinical trial. PLoS Med 2021; 18:e1003650. [PMID: 34029338 PMCID: PMC8186790 DOI: 10.1371/journal.pmed.1003650] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/08/2021] [Accepted: 05/09/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Pregnant and postpartum women living with HIV (WLWH) need support for HIV and maternal child health (MCH) care, which could be provided using short message service (SMS). METHODS AND FINDINGS We compared 2-way (interactive) and 1-way SMS messaging to no SMS in a 3-arm randomized trial in 6 MCH clinics in Kenya. Messages were developed using the Health Belief Model and Social Cognitive Theory; HIV messages were integrated into an existing MCH SMS platform. Intervention participants received visit reminders and prespecified weekly SMS on antiretroviral therapy (ART) adherence and MCH, tailored to their characteristics and timing. Two-way participants could message nurses as needed. Clinic attendance, viral load (VL), and infant HIV results were abstracted from program records. Primary outcomes were viral nonsuppression (VL ≥1,000 c/ml), on-time clinic attendance, loss to follow-up from clinical care, and infant HIV-free survival. Among 824 pregnant women randomized between November 2015 and May 2017, median age was 27 years, gestational age was 24.3 weeks, and time since initiation of ART was 1.0 year. During follow-up to 2 years postpartum, 9.8% of 3,150 VL assessments and 19.6% of women were ever nonsuppressed, with no significant difference in 1-way versus control (11.2% versus 9.6%, adjusted risk ratio (aRR) 1.02 [95% confidence interval (CI) 0.67 to 1.54], p = 0.94) or 2-way versus control (8.5% versus 9.6%, aRR 0.80 [95% CI 0.52 to 1.23], p = 0.31). Median ART adherence and incident ART resistance did not significantly differ by arm. Overall, 88.9% (95% CI 76.5 to 95.7) of visits were on time, with no significant differences between arms (88.2% in control versus 88.6% in 1-way and 88.8% in 2-way). Incidence of infant HIV or death was 3.01/100 person-years (py), with no significant difference between arms; risk of infant HIV infection was 0.94%. Time to postpartum contraception was significantly shorter in the 2-way arm than control. Study limitations include limited ability to detect improvement due to high viral suppression and visit attendance and imperfect synchronization of SMS reminders to clinic visits. CONCLUSIONS Integrated HIV/MCH messaging did not improve HIV outcomes but was associated with improved initiation of postpartum contraception. In programs where most women are virally suppressed, targeted SMS informed by VL data may improve effectiveness. Rigorous evaluation remains important to optimize mobile health (mHealth) interventions. TRIAL REGISTRATION ClinicalTrials.gov number NCT02400671.
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Affiliation(s)
- John Kinuthia
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Keshet Ronen
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Jennifer A Unger
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Wenwen Jiang
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Daniel Matemo
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Trevor Perrier
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Lusi Osborn
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Bhavna H Chohan
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Kenya Medical Research Institute, Nairobi, Kenya
| | - Alison L Drake
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Barbra A Richardson
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, Washington, United States of America.,Department of Epidemiology, University of Washington, Seattle, Washington, United States of America.,Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
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Beck IA, Levine M, McGrath CJ, Bii S, Milne RS, Kingoo JM, So I, Andersen N, Dross S, Coombs RW, Kiarie J, Chohan B, Sakr SR, Chung MH, Frenkel LM. Pre-treatment HIV-drug resistance associated with virologic outcome of first-line NNRTI-antiretroviral therapy: A cohort study in Kenya. EClinicalMedicine 2020; 18:100239. [PMID: 31956856 PMCID: PMC6962698 DOI: 10.1016/j.eclinm.2019.100239] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Pre-treatment HIV-drug-resistance (PDR) to WHO-recommended 1st-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral treatment (ART) is increasing in low-resource communities. We evaluated the risk of PDR on treatment failure if detected at single or multiple codons, at minority (2-9%) or higher (≥10%) frequencies during efavirenz- vs. nevirapine-ART. METHODS We conducted a pooled analysis across three cohorts of Kenyans initiating 1st-line NNRTI-ART between 2006 and 2014. Mutations K103N, Y181C, G190A, M184V and K65R were detected by an oligonucleotide ligation assay (OLA) and confirmed by Sanger and next-generation sequencing (NGS). PDR was defined as detection of any mutation by OLA when confirmed by NGS. Treatment failure, defined as plasma HIV RNA ≥400 copies/mL at month-12 of ART, was compared by PDR genotypes. FINDINGS PDR was detected in 59/1231 (4·8%) participants. Compared to wild-type genotypes, PDR in participants prescribed nevirapine-ART was associated with increased treatment failure [PDR 69·2% (27/39) vs. wild-type 10·4% (70/674); p = 0·0001], whether detected as minority [66·7% (4/6)] or higher [69·7% (23/33)] frequencies in an individual's HIV quasispecies (p = 0·002 and p < 0·0001, respectively), or mutations at single [50·0% (12/24)] or multiple [100·0% (15/15)] codons (p < 0·0001). During efavirenz-ART, PDR was also associated with increased virologic failure [PDR 25·0% (5/20) vs. wild-type 5·0% (25/498); p = 0·005], but only if detected at multiple drug-resistant codons [50·0% (3/6); p = 0·003] or high frequencies PDR [33·3% (5/15); p = 0·001]. INTERPRETATION The risk that PDR confers for treatment failure varies by number of mutant codons and their frequency in the quasispecies, with a lower risk for efavirenz- compared to nevirapine-based regimens. PDR detection and management could extend the effective use of efavirenz-ART in low-resource settings. FUNDING NIH, PEPFAR.
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Affiliation(s)
- Ingrid A. Beck
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Molly Levine
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Christine J. McGrath
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Steve Bii
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Ross S. Milne
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - James M. Kingoo
- Department of Global Health, University of Washington, Seattle, WA, United States
- Coptic Hope Center for Infectious Diseases, Coptic Hospital, Nairobi, Kenya
| | - Isaac So
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Nina Andersen
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Sandra Dross
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Robert W. Coombs
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - James Kiarie
- Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, WA, United States
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Samah R. Sakr
- Coptic Hope Center for Infectious Diseases, Coptic Hospital, Nairobi, Kenya
| | - Michael H. Chung
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Lisa M. Frenkel
- Center for Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Corresponding author at: Seattle Children's Research Institute, 307 Westlake Ave N, Seattle, WA 98109, United States.
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Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A, Lim J, Ko D, Milne R, Rossouw T, Feucht UD, Chung M, Jourdain G, Ngo-Giang-Huong N, Laomanit L, Soria J, Lai J, Klavins ED, Frenkel LM, Lutz BR. OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories. EBioMedicine 2019; 50:34-44. [PMID: 31767540 PMCID: PMC6921160 DOI: 10.1016/j.ebiom.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
Background HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Nikki Higa
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David McIntyre
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Isaac So
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ruth Kanthula
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
| | - Annie Wong-On-Wing
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jonathan Lim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Daisy Ko
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ross Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
| | - Ute D Feucht
- Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
| | - Michael Chung
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Laddawan Laomanit
- Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Jaime Soria
- Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Eric D Klavins
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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Silverman RA, John-Stewart GC, Beck IA, Milne R, Kiptinness C, McGrath CJ, Richardson BA, Chohan B, Sakr SR, Frenkel LM, Chung MH. Predictors of mortality within the first year of initiating antiretroviral therapy in urban and rural Kenya: A prospective cohort study. PLoS One 2019; 14:e0223411. [PMID: 31584992 PMCID: PMC6777822 DOI: 10.1371/journal.pone.0223411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/21/2019] [Indexed: 12/25/2022] Open
Abstract
Introduction Despite increased treatment availability, HIV-infected individuals continue to start antiretroviral therapy (ART) late in disease progression, increasing early mortality risk. Materials and methods Nested prospective cohort study within a randomized clinical trial of adult patients initiating ART at clinics in urban Nairobi and rural Maseno, Kenya, between 2013–2014. We estimated mortality incidence rates following ART initiation and used Cox proportional hazards regression to identify predictors of mortality within 12 months of ART initiation. Analyses were stratified by clinic site to examine differences in mortality correlates and risk by location. Results Among 811 participants initiated on ART, the mortality incidence rate within a year of initiating ART was 7.44 per 100 person-years (95% CI 5.71, 9.69). Among 207 Maseno and 612 Nairobi participants initiated on ART, the mortality incidence rates (per 100 person-years) were 12.78 (95% CI 8.49, 19.23) and 5.72 (95% CI 4.05, 8.09). Maseno had a 2.20-fold greater risk of mortality than Nairobi (95% CI 1.29, 3.76; P = 0.004). This association remained [adjusted hazard ratio (HR) = 2.09 (95% CI 1.17, 3.74); P = 0.013] when adjusting for age, gender, education, pre-treatment drug resistance (PDR), and CD4 count, but not when adjusting for BMI. In unadjusted analyses, other predictors (P<0.05) of mortality included male gender (HR = 1.74), age (HR = 1.04 for 1-year increase), fewer years of education (HR = 0.92 for 1-year increase), unemployment (HR = 1.89), low body mass index (BMI<18.5 m/kg2; HR = 4.99), CD4 count <100 (HR = 11.67) and 100–199 (HR = 3.40) vs. 200–350 cells/μL, and pre-treatment drug resistance (PDR; HR = 2.49). The increased mortality risk associated with older age, males, and greater education remained when adjusted for location, age, education and PDR, but not when adjusted for BMI and CD4 count. PDR remained associated with increased mortality risk when adjusted for location, age, gender, education, and BMI, but not when adjusted for CD4 count. CD4 and BMI associations with increased mortality risk persisted in multivariable analyses. Despite similar baseline CD4 counts across locations, mortality risk associated with low CD4 count, low BMI, and PDR was greater in Maseno than Nairobi in stratified analyses. Conclusions High short-term post-ART mortality was observed, partially due to low CD4 count and BMI at presentation, especially in the rural setting. Male gender, older age, and markers of lower socioeconomic status were also associated with greater mortality risk. Engaging patients earlier in HIV infection remains critical. PDR may influence short-term mortality and further studies to optimize management will be important in settings with increasing PDR.
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Affiliation(s)
- Rachel A. Silverman
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Population Health Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
| | - Grace C. John-Stewart
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ross Milne
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Catherine Kiptinness
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Christine J. McGrath
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | | | - Lisa M. Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Pediatrics, University of Washington, Seattle, Washington, United States of America
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
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Minority and majority pretreatment HIV-1 drug resistance associated with failure of first-line nonnucleoside reverse-transcriptase inhibitor antiretroviral therapy in Kenyan women. AIDS 2019; 33:941-951. [PMID: 30946148 DOI: 10.1097/qad.0000000000002134] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Among women initiating first-line nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based-ART with and without a history of single-dose nevirapine (sdNVP) with or without zidovudine with or without lamivudine (ZDV with and without 3TC) for prevention of mother-to-child HIV transmission (PMTCT), we hypothesized that pre-ART HIV-drug resistance would be associated with virologic failure DESIGN/METHODS:: In a prospectively enrolled study, three genotypic drug-resistance assays [oligonucleotide-ligation-assay (OLA), consensus sequencing, and next-generation sequencing by Illumina] were retrospectively performed to detect pre-ART drug resistance. Minority or majority drug-resistant variants identified in pre-ART RNA and/or DNA, a history of antiretrovirals for PMTCT, and other risk factors were assessed for association with virologic failure. RESULTS Failure occurred in 38/169 (22.5%) women, and was associated with pre-ART drug resistance detected by any assay (OLA of plasma or PBMC, consensus sequencing of PBMC and/or plasma, and next-generation sequencing of PBMC at frequencies of at least 10% and as minority variants; all P < 0.0001). Failure was also associated with PMTCT using sdNVP and ZDV with or without 3TC, but not sdNVP only; however, the longer time-interval between PMTCT and ART initiation observed for sdNVP-only women showed no interaction with failure. Viral loads and OLA of PBMC in longitudinal specimens demonstrated rapid failure and emergence of drug resistance, particularly among sdNVP and ZDV with or without 3TC-experienced women with pre-ART drug-resistant minority variants by next-generation sequencing but without drug resistance by OLA or consensus sequencing. CONCLUSION Pre-ART drug resistance was detected similarly by OLA of PBMC or plasma and by consensus sequencing, and was associated with virologic failure soon after initiation of first-line NVP-based ART. A history of sdNVP and ZDV with or without 3TC for PMTCT or minority variants detected by next-generation sequencing identified additional women with failure. These findings emphasize the value of assessing individual antiretroviral history, particularly nonsuppressive antiretrovirals with at least two drug classes, and testing for pre-ART drug resistance, including minority variants.
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Silverman RA, Beck IA, Kiptinness C, Levine M, Milne R, McGrath CJ, Bii S, Richardson BA, John-Stewart G, Chohan B, Sakr SR, Kiarie JN, Frenkel LM, Chung MH. Prevalence of Pre-antiretroviral-Treatment Drug Resistance by Gender, Age, and Other Factors in HIV-Infected Individuals Initiating Therapy in Kenya, 2013-2014. J Infect Dis 2019; 216:1569-1578. [PMID: 29040633 DOI: 10.1093/infdis/jix544] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/07/2017] [Indexed: 12/27/2022] Open
Abstract
Background Pre-antiretroviral-treatment drug resistance (PDR) is a predictor of human immunodeficiency virus (HIV) treatment failure. We determined PDR prevalence and correlates in a Kenyan cohort. Methods We conducted a cross-sectional analysis of antiretroviral (ARV) treatment-eligible HIV-infected participants. PDR was defined as ≥2% mutant frequency in a participant's HIV quasispecies at pol codons K103N, Y181C, G190A, M184 V, or K65R by oligonucleotide ligation assay and Illumina sequencing. PDR prevalence was calculated by demographics and codon, stratifying by prior ARV experience. Poisson regression was used to estimate prevalence ratios. Results PDR prevalences (95% confidence interval [CI]) in 815 ARV-naive adults, 136 ARV-experienced adults, and 36 predominantly ARV-naive children were 9.4% (7.5%-11.7%), 12.5% (7.5%-19.3%), and 2.8% (0.1%-14.5%), respectively. Median mutant frequency within an individual's HIV quasispecies was 67%. PDR prevalence in ARV-naive women 18-24 years old was 21.9% (9.3%-40.0%). Only age in females associated with PDR: A 5-year age decrease was associated with adjusted PDR prevalence ratio 1.20 (95% CI, 1.06-1.36; P = .004). Conclusions The high PDR prevalence may warrant resistance testing and/or alternative ARVs in high HIV prevalence settings, with attention to young women, likely to have recent infection and higher rates of resistance. Clinical Trials Registration NCT01898754.
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Affiliation(s)
- Rachel A Silverman
- Department of Epidemiology, University of Washington, Seattle.,Department of Global Health, University of Washington, Seattle
| | | | | | - Molly Levine
- Seattle Children's Research Institute, Washington
| | - Ross Milne
- Seattle Children's Research Institute, Washington
| | | | - Steve Bii
- Seattle Children's Research Institute, Washington
| | - Barbra A Richardson
- Department of Global Health, University of Washington, Seattle.,Department of Biostatistics, University of Washington, Seattle
| | - Grace John-Stewart
- Department of Epidemiology, University of Washington, Seattle.,Department of Global Health, University of Washington, Seattle.,Department of Medicine, University of Washington, Seattle.,Department of Pediatrics, University of Washington, Seattle
| | - Bhavna Chohan
- Department of Global Health, University of Washington, Seattle
| | | | - James N Kiarie
- Department of Obstetrics and Gynaecology, University of Nairobi, Kenya
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle.,Seattle Children's Research Institute, Washington.,Department of Medicine, University of Washington, Seattle.,Department of Pediatrics, University of Washington, Seattle.,Department of Laboratory Medicine, University of Washington, Seattle
| | - Michael H Chung
- Department of Epidemiology, University of Washington, Seattle.,Department of Global Health, University of Washington, Seattle.,Department of Medicine, University of Washington, Seattle
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9
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Soria J, Mugruza R, Levine M, León SR, Arévalo J, Ticona E, Beck IA, Frenkel LM. Pretreatment HIV Drug Resistance and Virologic Outcomes to First-Line Antiretroviral Therapy in Peru. AIDS Res Hum Retroviruses 2019; 35:150-154. [PMID: 30560685 DOI: 10.1089/aid.2018.0239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Access to nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) first-line antiretroviral therapy (ART) for HIV has been increasing in Peru since a national ART program was initiated in 2004. Between 2007 and 2009, we found a 1% prevalence of pre-ART HIV drug resistance (PDR) among antiretroviral (ARV)-naive Peruvians. Given that PDR has been associated with virologic failure (VF) of ART, in 2014-2015 we enrolled a follow-up cohort at the same institution to determine whether the rate of transmitted resistance had increased and compared virologic outcomes of those with and without PDR. Blood specimens from ARV-naive individuals were assessed for PDR to NNRTI-based ART by an oligonucleotide ligation assay (OLA) sensitive to 2% mutant within an individual's HIV quasispecies at reverse transcriptase codons M41L, K65R, K103N, Y181C, M184V, and G190A, and by Sanger consensus sequencing (CS). Rates of VF (plasma HIV RNA >200 copies/mL) were compared between those with and without PDR. Among 122 ARV-naive adults, PDR was detected by OLA in 17 (13.9%) adults. Compared with the 2007-2009 cohort, the proportion with PDR at OLA codons was significantly increased (p < .001). A total of 11 of 19 OLA mutations conferring high-level drug resistance were also detected by CS, and 8 additional participants had mutations encoding low-level resistance detected by CS for a total of 25 participants (20.5%). VF at month 6 of NNRTI-ART appeared greater in participants with versus without PDR [4/18 (22.2%) vs. 3/71 (4.2%); p = .03]. An increasing prevalence of PDR was detected among ARV-naive Peruvians. Studies are needed to determine risks of specific PDR mutations.
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Affiliation(s)
- Jaime Soria
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
- Northern Pacific Global Health Research Fellows Training Consortium, University of Washington, Seattle, Washington
| | - Raquel Mugruza
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
| | - Molly Levine
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Jorge Arévalo
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
| | - Eduardo Ticona
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
- Faculty of Medicine. Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ingrid A. Beck
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington
| | - Lisa M. Frenkel
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington
- Department of Pediatric, University of Washington, Seattle, Washington
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
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10
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Natoli ME, Rohrman BA, De Santiago C, van Zyl GU, Richards-Kortum RR. Paper-based detection of HIV-1 drug resistance using isothermal amplification and an oligonucleotide ligation assay. Anal Biochem 2018; 544:64-71. [PMID: 29229373 PMCID: PMC5854266 DOI: 10.1016/j.ab.2017.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 01/17/2023]
Abstract
Regular HIV-1 viral load monitoring is the standard of care to assess antiretroviral therapy effectiveness in resource-rich settings. Persistently elevated viral loads indicate virologic failure (VF), which warrants HIV drug resistance testing (HIVDRT) to allow individualized regimen switches. However, in settings lacking access to HIVDRT, clinical decisions are often made based on symptoms, leading to unnecessary therapy switches and increased costs of care. This work presents a proof-of-concept assay to detect M184V, the most common drug resistance mutation after first-line antiretroviral therapy failure, in a paper format. The first step isothermally amplifies a section of HIV-1 reverse transcriptase containing M184V using a recombinase polymerase amplification (RPA) assay. Then, an oligonucleotide ligation assay (OLA) is used to selectively label the mutant and wild type amplified sequences. Finally, a lateral flow enzyme-linked immunosorbent assay (ELISA) differentiates between OLA-labeled products with or without M184V. Our method shows 100% specificity and 100% sensitivity when tested with samples that contained 200 copies of mutant DNA and 800 copies of wild type DNA prior to amplification. When integrated with sample preparation, this method may detect HIV-1 drug resistance at a low cost and at a rural hospital laboratory.
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Affiliation(s)
- Mary E Natoli
- Department of Bioengineering, Rice University, 6100 Main St MS-142, Houston, TX 77005, USA
| | | | - Carolina De Santiago
- Department of Bioengineering, Rice University, 6100 Main St MS-142, Houston, TX 77005, USA
| | - Gert U van Zyl
- National Health Laboratory Service, Tygerberg Business Unit, Coastal Branch, South Africa; Division of Medical Virology, Stellenbosch University, Parow, South Africa
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11
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Kanthula R, Rossouw TM, Feucht UD, van Dyk G, Beck IA, Silverman R, Olson S, Salyer C, Cassol S, Frenkel LM. Persistence of HIV drug resistance among South African children given nevirapine to prevent mother-to-child-transmission. AIDS 2017; 31:1143-1148. [PMID: 28301421 PMCID: PMC5884446 DOI: 10.1097/qad.0000000000001446] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES We set out to examine the prevalence and persistence of mutations conferring high-level nonnucleoside reverse transcriptase (NNRTI)-resistance in a cohort of HIV-infected children who had failed prophylaxis to prevent mother-to-child-transmission (PMTCT). DESIGN A prospective observational cohort study at the Pediatric HIV Clinic at Kalafong Provincial Tertiary Hospital in Pretoria, South Africa. METHODS Children referred for initiation of antiretroviral therapy (ART) were enrolled from July 2010 through February 2013. HIV drug resistance testing was performed using the oligonucleotide ligation assay (OLA) on dried blood spots (DBS) collected at enrolment and monthly follow-up visits for 2 years. RESULTS South African children who failed HIV-prophylaxis had a high prevalence of NNRTI-resistant HIV (46/88; 52%). Among children with NNRTI-resistance, the frequency of the predominant resistant variant in each child's HIV-quasispecies was high (median 96%) at study entry (median age 7.5 months), and in 26 out of 27 followed a median of 13 months persisted at a high frequency (median 89%). CONCLUSION Our finding that infants who fail HIV-prophylaxis frequently have long-lived NNRTI-resistant HIV suggests that resistance will likely persist through 36 months of age, when children qualify for NNRTI-based ART. These children may benefit from HIV drug resistance testing to guide selection of their treatment.
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Affiliation(s)
- Ruth Kanthula
- University of Washington, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | | | | | | | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | | | - Scott Olson
- University of Washington, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Christen Salyer
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | | | - Lisa M. Frenkel
- University of Washington, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
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12
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Drake AL, Unger JA, Ronen K, Matemo D, Perrier T, DeRenzi B, Richardson BA, Kinuthia J, John-Stewart G. Evaluation of mHealth strategies to optimize adherence and efficacy of Option B+ prevention of mother-to-child HIV transmission: Rationale, design and methods of a 3-armed randomized controlled trial. Contemp Clin Trials 2017; 57:44-50. [PMID: 28315480 DOI: 10.1016/j.cct.2017.03.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/01/2017] [Accepted: 03/13/2017] [Indexed: 01/12/2023]
Abstract
BACKGROUND Lifelong antiretroviral therapy (ART) (Option B+) is recommended for all HIV-infected pregnant/postpartum women, but high adherence is required to maximize HIV prevention potential and maintain maternal health. Mobile health (mHealth) interventions may provide treatment adherence support for women during, and beyond, the pregnancy and postpartum periods. METHODS AND DESIGN We are conducting an unblinded, triple-arm randomized clinical trial (Mobile WACh X) of one-way short message service (SMS) vs. two-way SMS vs. control (no SMS) to improve maternal ART adherence and retention in care by 2years postpartum. We will enroll 825 women from Nairobi and Western Kenya. Women in the intervention arms receive weekly, semi-automated motivational and educational SMS and visit reminders via an interactive, human-computer hybrid communication system. Participants in the two-way SMS arm are also asked to respond to a question related to the message. SMS are based in behavioral theory, are tailored to participant characteristics through SMS tracks, and are timed along the pregnancy/postpartum continuum. After enrollment, follow-up visits are scheduled at 6weeks; 6, 12, 18, and 24months postpartum. The primary outcomes, virological failure (HIV viral load ≥1000copies/mL), maternal retention in care, and infant HIV infection or death, will be compared in an intent to treat analysis. We will also measure ART adherence and drug resistance. DISCUSSION Personalized and tailored SMS to support HIV-infected women during and after pregnancy may be an effective strategy to motivate women to adhere to ART and remain in care and improve maternal and infant outcomes.
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Affiliation(s)
- Alison L Drake
- Department of Global Health, University of Washington, Box 359909, Seattle, WA 98195-7236, USA.
| | - Jennifer A Unger
- Departments of Global Health and Obstetrics and Gynecology, University of Washington, Box 359909, Seattle, WA 98195-7236, USA.
| | - Keshet Ronen
- Departments of Global Health and Epidemiology, University of Washington, Box 359909, Seattle, WA 98195-7236, USA.
| | - Daniel Matemo
- Department of Research and Programs, Kenyatta National Hospital, PO Box 20723-00202, Nairobi, Kenya.
| | - Trevor Perrier
- Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195-7236, USA.
| | - Brian DeRenzi
- Department of Computer Science, University of Cape Town, Room 306, Computer Science Building, Cape Town, South Africa.
| | - Barbra A Richardson
- Department of Biostatistics, University of Washington, Box 359909, Seattle, WA 98195-7236, USA.
| | - John Kinuthia
- Department of Research and Programs, Kenyatta National Hospital, PO Box 20723-00202, Nairobi, Kenya.
| | - Grace John-Stewart
- Departments of Global Health, Medicine, Epidemiology, and Pediatrics, University of Washington, Box 359909, Seattle, WA 98195-7236, USA.
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13
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Beck IA, Payant R, Ngo-Giang-Huong N, Khamduang W, Laomanit L, Jourdain G, Frenkel LM. Development and validation of an oligonucleotide ligation assay to detect lamivudine resistance in hepatitis B virus. J Virol Methods 2016; 233:51-5. [PMID: 27025356 DOI: 10.1016/j.jviromet.2016.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/26/2016] [Indexed: 12/26/2022]
Abstract
Treatment of chronic hepatitis B virus (HBV) infection with lamivudine-monotherapy rapidly selects mutant variants in a high proportion of individuals. Monitoring lamivudine resistance by consensus sequencing is costly and insensitive for detection of minority variants. An oligonucleotide ligation assay (OLA) for HBV lamivudine-resistance was developed and compared to consensus sequencing. Both assays detected drug resistance mutations in 35/64 (54.7%) specimens evaluated, and OLA detected minority mutants in an additional six (9.4%). OLA may offer a sensitive and inexpensive alternative to consensus sequencing for detection of HBV drug resistance in resource-limited settings.
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Affiliation(s)
- Ingrid A Beck
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Rachel Payant
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Nicole Ngo-Giang-Huong
- Unité Mixte Internationale 174, Institut de Recherche pour le Développement (IRD)-Programs for HIV Prevention and Treatment (PHPT), Chiang Mai, Thailand; Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Woottichai Khamduang
- Unité Mixte Internationale 174, Institut de Recherche pour le Développement (IRD)-Programs for HIV Prevention and Treatment (PHPT), Chiang Mai, Thailand; Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Laddawan Laomanit
- Unité Mixte Internationale 174, Institut de Recherche pour le Développement (IRD)-Programs for HIV Prevention and Treatment (PHPT), Chiang Mai, Thailand
| | - Gonzague Jourdain
- Unité Mixte Internationale 174, Institut de Recherche pour le Développement (IRD)-Programs for HIV Prevention and Treatment (PHPT), Chiang Mai, Thailand; Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Lisa M Frenkel
- Seattle Children's Research Institute, Seattle, WA, USA; University of Washington, Seattle, WA, USA.
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14
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Panpradist N, Beck IA, Chung MH, Kiarie JN, Frenkel LM, Lutz BR. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation. PLoS One 2016; 11:e0145962. [PMID: 26751207 PMCID: PMC4713472 DOI: 10.1371/journal.pone.0145962] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Internal Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - James N. Kiarie
- Departments of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Lisa M. Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Departments of Pediatrics and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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15
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Budambula V, Musumba FO, Webale MK, Kahiga TM, Ongecha-Owuor F, Kiarie JN, Sowayi GA, Ahmed AA, Ouma C, Were T. HIV-1 protease inhibitor drug resistance in Kenyan antiretroviral treatment-naive and -experienced injection drug users and non-drug users. AIDS Res Ther 2015; 12:27. [PMID: 26279669 PMCID: PMC4537595 DOI: 10.1186/s12981-015-0070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/07/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Although injection drug use drives antiretroviral drug resistance, the prevalence of protease inhibitor (PI) resistance among Kenyan IDUs remains undetermined. We, therefore, explored PI resistance mutations and their association with viral load and CD4+ T cell counts in HIV-1 infected IDUs (ART-naive, n = 32; and -experienced, n = 47) and non-drug users (ART-naive, n = 21; and -experienced, n = 32) naive for PI treatment from coastal Kenya. RESULTS Only IDUs harboured major PI resistance mutations consisting of L90M, M46I and D30 N among 3 (6.4 %) ART-experienced and 1 (3.1 %) -naive individuals. Minor PI mutations including A71T, G48E, G48R, I13V, K20I, K20R, L10I, L10V, L33F, L63P, T74S, V11I, and V32L were detected among the ART-experienced (36.2 vs. 46.9 %) and -naive (43.8 vs. 66.7 %) IDUs and non-drug users, respectively. All the four IDUs possessing major mutations had high viral load while three presented with CD4+ T cell counts of <500 cells/ml. Among the ART-naive non-drug users, CD4+ T cell counts were significantly lower in carriers of minor mutations compared to non-carriers (P < 0.05). CONCLUSION Transmitted drug resistance may occur in IDUs underscoring the need for genotyping resistance before initiating PI treatment.
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Affiliation(s)
- Valentine Budambula
- />Department of Environment and Health Sciences, Technical University of Mombasa, Mombasa, Kenya
| | - Francis O. Musumba
- />Department of Biomedical Science and Technology, Maseno University, Maseno, Kenya
- />Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Mark K. Webale
- />Department of Biomedical Science and Technology, Maseno University, Maseno, Kenya
| | - Titus M. Kahiga
- />Department of Pharmacy and Complementary Medicine, Kenyatta University, Nairobi, Kenya
| | - Francisca Ongecha-Owuor
- />Department of Medicine, Therapeutics, Dermatology and Psychiatry, Kenyatta University, Nairobi, Kenya
| | - James N. Kiarie
- />Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - George A. Sowayi
- />Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | | | - Collins Ouma
- />Department of Biomedical Science and Technology, Maseno University, Maseno, Kenya
- />Health Challenges and Systems Program, African Population and Health Research Centre, Nairobi, Kenya
| | - Tom Were
- />Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, P. O. Box 190, Kakamega, 50100 Kenya
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16
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Oligonucleotide ligation assay detects HIV drug resistance associated with virologic failure among antiretroviral-naive adults in Kenya. J Acquir Immune Defic Syndr 2014; 67:246-53. [PMID: 25140907 DOI: 10.1097/qai.0000000000000312] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Transmitted drug resistance (TDR) is increasing in some areas of Africa. Detection of TDR may predict virologic failure of first-line nonnucleoside reverse transcriptase inhibitor (NNRTI)-based antiretroviral therapy (ART). We evaluated the utility of a relatively inexpensive oligonucleotide ligation assay (OLA) to detect clinically relevant TDR at the time of ART initiation. METHODS Pre-ART plasmas from ART-naive Kenyans initiating an NNRTI-based fixed-dose combination ART in a randomized adherence trial conducted in 2006 were retrospectively analyzed by OLA for mutations conferring resistance to NNRTI (K103N, Y181C, and G190A) and lamivudine (M184V). Post-ART plasmas were analyzed for virologic failure (≥1000 copies/mL) at 6-month intervals over 18-month follow-up. Pre-ART plasmas of those with virologic failure were evaluated for drug resistance by consensus and 454-pyrosequencing. RESULTS Among 386 participants, TDR was detected by OLA in 3.89% (95% confidence interval: 2.19 to 6.33) and was associated with a 10-fold higher rate of virologic failure (hazard ratio: 10.39; 95% confidence interval: 3.23 to 32.41; P < 0.001) compared with those without TDR. OLA detected 24 TDR mutations (K103N: n = 13; Y181C: n = 5; G190A: n = 3; M184V: n = 3) in 15 subjects (NNRTI: n = 15; 3TC: n = 3). Among 51 participants who developed virologic failure, consensus sequencing did not detect additional TDR mutations conferring high-level resistance, and pyrosequencing only detected additional mutations at frequencies <2%. Mutant frequencies <2% at ART initiation were significantly less likely to be found at the time of virologic failure compared with frequencies ≥2% (22% vs. 63%; P < 0.001). CONCLUSIONS Detection of TDR by a point mutation assay may prevent the use of suboptimal ART.
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