Centre for Infectious Disease Epidemiology and Research - CIDER

Current areas of research include:
 

• Cohort studies of HIV treatment, evaluating individual treatment projects, provincial and national programs, and the co-hosting of a regional data centre for collaborative HIV cohort research in Southern Africa (IeDEA-SA), and a global data centre for paediatric HIV treatment cohorts (CIPHER)
   
• Population-level surveillance of infectious disease interventions in the Western Cape Province
   
• Novel service delivery approaches to the prevention of mother-to-child transmission (PMTCT) of HIV, and the identification of gaps in PMTCT services and optimal strategies to minimise these gaps
   
• Health systems research projects including evaluating models of care for HIV service delivery, models of HIV/TB service integration, and issues around task shifting and the use of lay health workers to support infectious diseases services.
   
• Mathematical modeling of HIV, TB, HPV and other infectious diseases and their prevention and treatment
   
• Context-appropriate information systems to monitor HIV, TB and PMTCT service delivery
   
• Collaboration on birth cohort studies

CIDER staff are actively involved in policy processes and advisory groups, provincially, nationally and globally, including:
 

• Staff who are jointly appointed as public health specialists with the Western Cape Department of Health, with service responsibilities in surveillance and impact evaluations
   
• CIDER provides support to the HIV, AIDS, STI and tuberculosis (HAST) directorate in the Provincial Department of Health both through the joint appointees and through a long standing Global Fund grant to support routine HAST information systems
   
• Staff serve on provincial and national HIV guideline committees, and regularly participate in WHO reference groups on HIV treatment, PMTCT, and HIV information systems development
   
• CIDER works closely with a number of civil society organisations including a long standing collaboration with Médecins Sans Frontières, and the South African National AIDS Council
   
• CIDER develop and maintain one of the key information systems used for monitoring HIV and tuberculosis treatment in South Africa (Three Interlinked Electronic Registers – TIER.Net), and provide support to users of the system in ten other countries

The African Health Information Exchange (AHIE) Project

In late 2016 CIDER was awarded a grant from the Bill and Melinda Gates Foundation to establish a reference African Health Information Exchange (AHIE). The aim was to deliver a replicable and context-appropriate implementation of a health information exchange for clinical data, working across national and provincial health departments in South Africa. An important outcome of this would be successful interoperability implementations for key systems that were critical to the HIV and TB response in South Africa. The AHIE project was undertaken by a consortium led by UCT CIDER. Consortium members were the National Department of Health (NDoH), the Council for Scientific and Industrial Research (CSIR), Jembi Health Systems, and the South African National Health Laboratory Service (NHLS).  AHIE Video

The components of AHIE were:
 

HPRS: The scale up of the national health identifier and patient registration system, the Health Patient Registration System (HPRS) led by NDoH. Development of the HPRS was done by a team at the CSIR.  HPRS Video
 

PHDC: The maturation of a set of technologies that could harmonize person-level health data and enable disease cascade reporting from diagnosis through to treatment success to assist patient management at all levels of the health system. The Western Cape Provincial Health Data Centre (PHDC) would serve as the innovation incubator for this component.  PHDC Video

OpenHIM: The consolidation of a standards-based health information exchange (HIE) by adapting and maturing an open interoperability layer, the Open Health Information Mediator (OpenHIM), into a robust standards-based technology stack for widespread adoption.  OpenHIM Video

SPV: The development of a viewing application for clinicians to access consolidated longitudinal clinical data, the single patient viewer (SPV).  SPV Video

TIER.Net: The adaptation of TIER.Net to interoperate with other systems such as the HPRS and the NHLS laboratory information system. TIER.Net is an HIV and TB patient information system developed by CIDER and is used from facility level through to national level in about 4,000 facilities in South Africa.  TIER Video

Exciting outcome of AHIE – The OpenIHP:

As software development work progressed throughout the AHIE project, it became clear that there was a need for an online solution to manage and monitor treatment of patients with HIV and TB. A dynamic data-driven forms engine was added to SPV that enabled the capture of new data to complement and be integrated with existing data in the PHDC, enabling users to view and capture on the same platform, reducing the need to import data from a separate, stand-alone system.

This new converged software platform is called the Open Integrated Health Platform (OpenIHP). Convergence to OpenIHP means that the PHDC, SPV, TIER.Net and enterprise reporting functionality can now be replicated and supported as one consolidated platform. In 2020 the effectiveness and adaptability of OpenIHP was successfully established and the platform has been playing an important role in the Western Cape Province’s response to COVID-19.  OpenIHP Video

Research Officers

Name	Email	Telephone No
Jonathan Euvrard		021 406 6636
Patience Nyakato		021 404 7737
Gem Patten		021 406 6482

Project Managers

Name	Email	Telephone No
Nontobeko Tena-Coki		021 650 2406
Wendy Wiemers

Data Managers

Name	Email	Telephone No
Alexa Heekes
Nicola Maxwell		021 406 6602
Themba Mutemaringa
Mariette Smith		021 406 6482

Software Managers

Name	Email	Telephone No
Meagan Bosland		021 406 6937
Robin Burley		021 406 6937
Prakash Buddiga

Honorary Senior Lecturers

Honorary Research Associate

Centre Manager

Name	Email	Telephone No
Carmelita Sylvester		021 406 6808

Research Administrators

Name	Email	Telephone No
Karin van Wyk		021 650 2316

• Journal articles

• Reports and working papers

2019

• Elise Farley, Hussaina Muhammad Bala, Annick Lenglet, Ushma Mehta, Nura Abubakar, Joseph Samuel, Annette de Jong, Karla Bil, Bukola Oluyide, Adolphe Fotso, Beverley Stringer, Julita Gil Cuesta and Emilie Venables.  I treat it but I don’t know what this disease is’: A qualitative study on noma (cancrum oris) and traditional healing in northwest Nigeria. International Health 2019, 12(1); 28-35.
   
• Joseph Daniels, Helen Struthers, Kabelo Maleke, Tim Lane, James McIntyre, Tom Coates. ‘My Tablets are on Top of the Fridge’: The Roles of Relationship Desire and Medical Mistrust in ART Adherence for HIV‑Positive MSM and Transgender Women Living in Rural South Africa. Aids and Behaviour 2019, 23; 2849-2858.
   
• Avy Violari, Mark F. Cotton, Louise Kuhn, Diana B. Schramm, Maria Paximadis, Shayne Loubser, Sharon Shalekoff, Bianca Da Costa Dias, Kennedy Otwombe, Afaaf Liberty, James McIntyre, Abdel Babiker, Diana Gibb & Caroline T. Tiemessen. A child with perinatal HIV infection and long-term sustained virological control following antiretroviral treatment cessation. Nature Communications 2019, 10:412.
   
• Victoria Nembaware, Katherine Johnston, Alpha A. Diallo, Maritha J. Kotze, Alice Matimba, Keymanthri Moodley, Godfrey. B. Tangwa, Rispah Torrorey-Sawe and Nicky Tiffin.  A framework for tiered informed consent for health genomic research in Africa.  Nature Genetics 2019, 5; 1566-1571.
   
• Bernard Njau, Christopher Colvin, Esther Lisasi, Damian Damian, Declare Mushi, Andrew Boulle and Catherine Mathews. A systematic review of qualitative evidence on factors enabling and deterring uptake of HIV self-testing in Africa. BMC Public Health 2019, 19, Article 1289.
   
• Zara Shrubber, Nathan Ford. Adherence to HIV post-exposure prophylaxis for children/adolescents who have been sexually assaulted: A systematic review of barriers, enablers, and interventions. Child Abuse and Neglect 2019, Article 104143.
   
• Van Schalkwyk C., Moodley J., Welte A. and Johnson L.F. Are associations between HIV and human papillomavirus transmission due to behavioural confounding or biological effects? Sexually Transmitted Infections 2019, 9(2); 122-128.
   
• Ingrid V. Bassett, Ai Xu, Janet Giddy, Laura M. Bogart, Andrew Boulle, Lucia Millham, Elena Losina and Robert A. Parker. Assessing rates and contextual predictors of 5-year mortality among HIV-infected and HIV-uninfected individuals following HIV testing in Durban, South Africa. BMC Infectious Diseases 2019, 19, Article 751.
   
• Rivka R. Lilian, Kate Rees, Moyahabo Mabitsi, James A. McIntyre, Helen E. Struthers, Remco P.H. Peters. Baseline CD4 and mortality trends in the South African human immunodeficiency virus programme: Analysis of routine data. Southern African Journal of HIV Medicine 2019, 20(1).
   
• Ushma C. Mehta, Cari van Schalkwyk, Prineetha Naidoo, Arthi Ramkissoon, Otty Mhlongo, Niren R. Maharaj, Niree Naidoo, Karen Fieggen, Michael F. Urban, Shaun Krog, Alex Welte, Mukesh Dheda, Yogan Pillay, Neil F. Moran. Birth outcomes following antiretroviral exposure during pregnancy: Initial results from a pregnancy exposure registry in South Africa. Southern African Journal of HIV Medicine 2019, 20(1). 
   
• Hauser A., Kusejko K., Johnson L.F., Wandeler G., Riou J., Goldstein F., Egger M. and Kouyos R. Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. PLoS Computational Biology 2019, 15(6).
   
• Olga Tymejczyk, Ellen Brazier, Constantin T. Yiannoutsos, Michael Vinikoor, Monique van Lettow, Fred Nalugoda, Mark Urassa, Jean d’Amour Sinayobye, Peter F. Rebeiro, Kara Wools-Kaloustian, Mary-Ann Davies, Elizabeth Zaniewski, Nanina Anderegg. Changes in rapid HIV treatment initiation after national “treat all” policy adoption in 6 sub-Saharan African countries: Regression discontinuity analysis. PLoS Medicine 2019, 16(6); 1-16.
   
• Charlotte M. Hoffman, Lise Fritz, Nthabiseng Matlakala, Nontembeko Mbambazela, Jean P. Railton, James A. McIntyre, Jan Henk Dubbink and Remco P. H. Peters. Community-based strategies to identify the unmet need for care of individuals with sexually transmitted infection-associated symptoms in rural South Africa. Tropical Medicine and International Health 2019, 24(8); 987-9931.
   
• Johanna M. E. Venter, Precious M. Mahlangu, Etienne E. Müller, David A. Lewis, Kevin Rebe, Helen Struthers, James McIntyre and Ranmini S. Kularatne. Comparison of an in-house real-time duplex PCR assay with commercial HOLOGIC® APTIMA assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in urine and extra-genital specimens. BMC Infectious Diseases 2019, 19; Article 6.
   
• Lesosky Maia, Raboud Janet, Glass Tracy, Brummel Sean, Ciaranello Andrea, Currier Judith, Essajee Shaffiq, Havlir Diane, Koss Catherine, Ogwu Anthony, Shapiro Roger, Abrams Elaine, Myer Landon. Comparison of guidelines for HIV viral load monitoring among pregnant and breastfeeding women in sub-Saharan Africa. Aidsonline 2019, 34(2); 311-315.
   
• Susan L Norris, Eva A Rehfuess, Helen Smith, Özge Tunçalp, Jeremy M Grimshaw, Nathan P Ford, Anayda Portela. Complex health interventions in complex systems: improving the process and methods for evidence-informed health decisions. BMJ Global Health 2019, 4(Supplement 1).
   
• Marco Vitoria, Ajay Rangaraj, Nathan Ford, and Meg Doherty. Current and future priorities for the development of optimal HIV drugs. Current Opinion in HIV and AIDS 2019, 14(2);143-149.
   
• Boulle A, Heekes A, Tiffin N, Smith M, Mutemaringa T, Zinyakatira N, Phelanyane F, Pienaar C, Buddiga K, Coetzee E, van Rooyen R, Dyers R, Fredericks N, Loff A, Shand L Moodley M, de Vega I and Vallabhjee K. Data Centre Profile: The Provincial Health Data Centre of the Western Cape Province, South Africa.         International Jounrnal of Population Data Science 2019, 4(2).
   
• Bernhard Kerschberger, Michael Schomaker, Alex Telnov, Debrah Vambe, Nicholas Kisyeri, Welile Sikhondze, Lorraine Pasipamire, Siphiwe Mavis Ngwenya, Barbara Rusch, Iza Ciglenecki and Andrew Boulle. Decreased risk of HIV‐associated TB during antiretroviral therapy expansion in rural Eswatini from 2009 to 2016: A cohort and population‐based analysis. Tropical Medicine and International Health 2019, 24(9); 1114-1127.
   
• Kathrin Zurcher, Marie Ballif, Sasisopin Kiertiburanakul, Henri Chenal, Marcel Yotebieng, Beatriz Grinsztejn, Denna Michael, Timothy R Sterling, Kapella M Ngonyani, Anna M Mandalakas, Matthias Egger, April C Pettit, and Lukas Fenner for the International Epidemiology Databases to Evaluate AIDS (IeDEA) consortium. Diagnosis and clinical outcomes of extrapulmonary tuberculosis in antiretroviral therapy programmes in low‐ and middle‐income countries: a multicohort study. Journal of the International AIDS Society 2019, 22(9).
   
• Menard L. Chihana, Helena Huerga, Gilles Van Cutsem, Tom Ellman, Eric Goemaere, Stephen Wanjala, Charlie Masiku, Elisabeth Szumilin, Jean-Francois Etard, David Maman & Mary-Ann Davies. Distribution of advanced HIV disease from three high HIV prevalence settings in Sub-Saharan Africa: A secondary analysis data from three population-based cross-sectional surveys in Eshowe (South Africa), Ndhiwa (Kenya) and Chiradzulu (Malawi). Global Health Action 2019, 12(1).
   
• Sally Hargreaves, Keiran Rustage, Laura B. Nellums, Joshua E. Bardfield, Bruce Agins, Pierre Barker, M. Rashad Massoud, Nathan P. Ford, Meg Doherty Gillian Dougherty and Satvinder Singh. Do Quality Improvement Initiatives Improve Outcomes for Patients in Antiretroviral Programs in Low- and Middle-Income Countries? A Systematic Review. Journal of AIDS 2019, 81(5); 487- 496.
   
• Iyun Victoria, Technau Karl-Gunter, Eley Brian FC, Rabie Helena, Boulle Andrew, Fatti Geoffrey, Egger Matthias, Tanser Frank, Wood Robin, Fairlie Lee, Cotton Mark F., Davies Mary-Ann. Earlier Antiretroviral Therapy Initiation and Decreasing Mortality Among HIV-Infected Infants Initiating Antiretroviral Therapy Within 3 Months of Age in South Africa, 2006–2017. The Pediatric Infectious Disease Journal 2019, 39(2); 127-133.
   
• Leigh F. Johnson, Themba Mutemaringa, Alexa Heekes and Andrew Boulle. Effect of HIV Infection and Antiretroviral Treatment on Pregnancy Rates in the Western Cape Province of South Africa. Journal of Infectious Diseases 2019.
   
• Van Schalkwyk C., Moodley J., Welte A. and Johnson L.F. Estimated impact of human papillomavirus vaccines on infection burden: The effect of structural assumptions. Vaccine 2019, 37(36); 5460-5465. 
   
• Haas A.D., Johnson L.F., Grimsrud A., Ford N., Mugglin C., Fox M.P., Euvrard J., van Lettow, M., Prozesky H., Sikazwe I., Chimbetete C., Hobbins M., Kunzekwenyika C. and Egger M. Extending visit intervals for clinically stable patients on antiretroviral therapy: multicohort analysis of HIV programs in Southern Africa. Journal of Acquired Immune Deficiency Syndromes 2019, 81(4); 439-447.
   
• Bernhard Kerschberger, Kiran Jobanputra, Michael Schomaker, Serge M Kabore, Roger Teck, Edwin Mabhena, Nomthandazo Lukhele, Barbara Rusch, Andrew Boulle and Iza Ciglenecki. Feasibility of antiretroviral therapy initiation under the treat‐all policy under routine conditions: A prospective cohort study from Eswatini. Journal of IAS 2019, 22(10).
   
• Daniel P. O’Brien, Nathan Ford, Amadou G. Djirmay, Alexandra Calmy, Marco Vitoria, Tomas O. Jensen and Vanessa Christinet. Female Genital Schistosomiasis and HIV: Research Urgently Needed to Improve Understanding of the Health Impacts of This Important Coinfection. JAIDS 2019, 80(5); 489-493.   
   
• Johnson Leigh, Anderegg Nanina, Zaniewski Elizabeth, Eaton Jeffrey W, Rebeiro Peter, Carriquiry Gabriela, Nash Denis, Yotebieng Marcel, Ekouevi Didier, Holmes Charles, Choi, Jun, Jiamsakul Awachana, Bakoyannis Giorgos, Althoff Keri, Sohn Annette Yiannoutsos Constantin, Egger, Matthias. Global variations in mortality in adults after initiating antiretroviral treatment- an updated analysis of the International epidemiology Databases to Evaluate AIDS cohort collaboration.  Aidsonline 2019, 33;283-294.
   
• Geneviève A.F.S. van Liere, Marleen M. Kock,Oscar Radebe, Helen E. Struthers, Servaas Morre, James A. McIntyre and Remco P.H. Peters. High Rate of Repeat Sexually Transmitted Diseases Among Men Who Have Sex with Men in South Africa: A Prospective Cohort Study. Sexually Transmitted Disease 2019, 46(11); e105 -107.
   
• O Radebe, S A Lippman, T Lane, H Gilmore, E Agnew, A Manyuchi and J A McIntyre. HIV self-screening distribution preferences and experiences among men who have sex with men in Mpumalanga Province: Informing policy for South Africa. SAMJ 2019, 109(4); 
   
• Nathan Ford, Catherine Orrell, Zara Shubber, Tsitsi Apollo and Lara Vojnov.  HIV viral resuppression following an elevated viral load: A systematic review and meta-analysis. Journal of IAS 2019, 22(11).
   
• Euvrard, J., Schulz, T., Hilderbrand, K., Bosland, M., Osler, M., Boulle, A. and Davies, M.A. How accurately do routinely reported HIV viral load suppression proportions reflect progress towards the 90-90-90 target in the population on antiretroviral treatment in Khayelitsha, South Africa? South African Medical Journal 2019, 109(3);174-177.
   
• Nicki Tiffin, Asha George, Amnesty Elizabeth LeFevre. How to use relevant data for maximal benefit with minimal risk: Digital health data governance to protect vulnerable populations in low-income and middle-income countries. BMJ Global Health 2019, 4(2).
   
• Kabelo Maleke, Joseph Daniels, Tim Lane, Helen Struthers, James McIntyre and Thomas Coates.  How social stigma sustains the HIV treatment gap for MSM in Mpumalanga, South Africa. Global Health Promotion 2019, 26(4); 6-13). 
   
• lga Tymejczyk, Ellen Brazier, Kara Wools-Kaloustian, Mary-Ann Davies, Madeline Dilorenzo, Andrew Edmonds, Rachel Vreeman, Carolyn Bolton, Christella Twizere, Nicollate Okoko, Sam Phiri, Gertrude. Lelo, Per von Groote, Annette H Sohn and Dennis Nash on behalf of IeDEA Consortium. Impact of Universal Antiretroviral Treatment Eligibility on Rapid Treatment Initiation Among Young Adolescents with Human Immunodeficiency Virus in Sub-Saharan Africa. Journal of Infectious Diseases 2019, jiz547.
   
• Ellen Brazier, Fernanda Maruri, Stephany N Duda, Olga Tymejczyk, C William Wester, Geoffrey Somi, Jeremy Ross, Aimee Freeman, Morna Cornell, Armel Poda, Beverly S Musick, Fujie Zhang, Keri N Althoff, Catrina Mugglin, April D Kimmel, Marcel Yotebieng and Denis Nash for the IeDEA Consortium. Implementation of “Treat‐all” at adult HIV care and treatment sites in the Global IeDEA Consortium: results from the Site Assessment Survey. Journal of IAS 2019, 22(7).
   
• Jennifer Pellowski, Catherine Wedderburn, Jacob A M Stadler, Whitney Barnett, Dan Stein, Landon Myer and Heather J Zar. Implementation of prevention of mother-to-child transmission (PMTCT) in South Africa: outcomes from a population-based birth cohort study in Paarl, Western Cape. BMJ Open 2019, 9(12).
   
• Ying Zhao, Tamaryn Fox, Kathryn Manning, Annemie Stewart, Nicki Tiffin, Ntokozo Khomo, Joshua Leslie, Andrew Boulle, Vanessa Mudaly, Yulene Kock, Graeme Meintjies, Sean Wasserman. Improved Treatment Outcomes with Bedaquiline When Substituted for Second-line Injectable Agents in Multidrug-resistant Tuberculosis: A Retrospective Cohort Study. Clinical Infectious Diseases 2019, 68(9);1522-1529.  
   
• Incidence of switching to second-line antiretroviral therapy and associated factors in children with HIV: an international cohort collaboration. The Collaborative Initiative for Paediatric HIV Education and Research (CIPHER) Global Cohort Collaboration, The Lancet HIV 2019, 6(2);105-115.
   
• Eduard Grebe, Shelley N. Facente, Jeremy Bingham, Christopher D. Pilcher, Andrew Powrie, Jarryd Gerber, Gareth Priede, Trust Chibawara, Michael P. Busch, Gary Murphy, Reshma Kassanjee, Alex Welte and on behalf of the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA). Interpreting HIV diagnostic histories into infection time estimates: analytical framework and online tool. BMC Infectious Diseases 2019, 19; Article 894.
   
• Asha George, Amnesty Elizabeth LeFevre, Tanya Jacobs, Mary Kinney, Kent Buse, Mickey Chopra, Bernadette Daelman, Anie Luis Huicho, Rajat Khosla, Kumanan Rasanathan, David Neha S Singh, Nicki Tiffin, Rajani Ved, Shehla Abbas Zaidi, Helen Schneider. Lenses and levels: the why, what and how of measuring health system drivers of women’s, children’s and adolescents’ health with a governance focus. BMJ Global Health 2019, 4(Supplement 4).
   
• Boltz VF, Shao W, Bale MJ, Halvas EK, Luke B, McIntyre JA, Schooley RT, Lockman S, Currier JS, Sawe F, Hogg E, Hughes MD, Kearney MF, Coffin JM, Mellors JW. Linked dual-class HIV resistance mutations are associated with treatment failure. JCI Insight 2019, 4(19).
   
• Samantha Kaplan, Katleho S. Nteso, Nathan Ford, Andrew Boulle, Graeme Meintjes. Loss to follow-up from antiretroviral therapy clinics: A systematic review and meta-analysis of published studies in South Africa from 2011 to 2015. SA Journal of HIV Medicine 2019, 20(1).
   
• Hoffman RM, Angelidou KN, Brummel SS, Saidi F, Violari A, Dula D, Mave, Fairlie L, Theron G, Kamateeka M, Chipato T, Chi BH, Stranix-Chibanda L, Nematadzira T, Moodley D, Bhattacharya D, Gupta, Coletti A, McIntyre JA, Klingman KL, Chakhtoura N, Shapiro DE, Fowler MG, Currier JS, IMPAACT PROMISE 1077BF/FF team. Maternal health outcomes among HIV-infected breastfeeding women with high CD4 counts: Results of a treatment strategy trial. HIV Clinical Trials, 19(6); 209-224.
   
• Joseph Davey D., Bekker L.G., Gomba Y., Coates T., Myer L. and Johnson L.F.Modelling the potential impact of providing pre-exposure prophylaxis (PrEP) to pregnant and breastfeeding women in South Africa. AIDS 2019, 33(8);1391-1395.
   
• Maheu-Giroux, Marsh, Doyle CM, Godin A, Lanièce Delaunay C, Johnson LF, Jahn A, Abo K, Mbofana F, Boily MC, Buckeridge DL, Hankins CA, Eaton JW. National HIV testing and diagnosis coverage in sub-Saharan Africa: A new modeling tool for estimating the 'first 90' from program and survey data. AIDS 2019, 33 (Supplement 3); s255-S269.
   
• Johnson L.F., van Rensburg C., Govathson C. and Meyer-Rath G. Optimal HIV testing strategies for South Africa: a model-based evaluation of population-level impact and cost-effectiveness. Scientific Reports 2019, 9(1).
   
• Lynne M Mofenson, Anton L Pozniak, Jacque Wambui, Elliot Raizes, Andrea Ciaranello, Polly Clayden, Peter Ehrenkranz, Ade Fakoya, Andrew Hill, Saye Khoo, Imelda Mahaka, Surbhi Modi, Cynthia Moore, Andrew Phillips, George Siberry, Kenly Sikwese, Claire Thorne, Heather D Watts, Meg Doherty and Nathan P Ford. Optimizing responses to drug safety signals in pregnancy: The example of dolutegravir and neural tube defects. Journal of IAS 2019, 22(7).
   
• Joseph Sharp, Lynne Wilkinson, Vivian Cox, Carol Cragg, Gilles van Cutsem, Anna Grimsrud. Outcomes of patients enrolled in an antiretroviral adherence club with recent viral suppression after experiencing elevated viral loads.  South African Journal of HIV Medicine 2019, 20(1).
   
• Catherine L. Ward, Inge M. Wessels, Jamie M. Lachman, Judy Hutchings, Lucie D. Cluver, Reshma Kassanjee, Raymond Nhapi, Francesca Little, and Frances Gardner. Parenting for Lifelong Health for young children: A randomized controlled trial of a parenting program in South Africa to prevent harsh parenting and child conduct problems. Journal of Child Psychology and Psychiatry 2019.
   
• Damian Hacking, Zodwa Mgengwana-Mbakaza, Tali Cassidy, Pumeza Runeyi, Laura Trivino Duran, Ruth Henwood Mathys and Andrew Boulle. Peer Mentorship via Mobile Phones for Newly Diagnosed HIV-Positive Youths in Clinic Care in Khayelitsha, South Africa: Mixed Methods Study. JMIR 2019, 21(12).
   
• Lara Vojnov, Miriam Taegtmeyer, Caroline Boeke, Jessica Markby, Lindsay Harris, Meg Doherty, Trevor Peter, Nathan Ford. Performance of non-laboratory staff for diagnostic testing and specimen collection in HIV programs: A systematic review and meta-analysis. PLOS One 2019.
   
• Slogrove A.L., Johnson L.F. and Powis. Population-level mortality associated with HIV exposure in HIV-uninfected infants in Botswana and South Africa: A model-based evaluation. Journal of Tropical Pediatrics 2019, 65(4); 373-379.
   
• Andrew Phillips, Valentina Cambiano, Leigh Johnson, Fumiyo Nakagawa, Rick Homan, Gesine Meyer-Rath, Thomas Rehle, Frank Tanser, Sizulu Moyo, Maryam Shahmanesh, Delivette Castor, Elizabeth Russell, Lise Jamieson, Loveleen Bansi-Matharu, Amir Shroufi, Ruanne Barnabas, Urvi M Parikh, John W Mellors and Paul Revill. Potential impact and cost-effectiveness of condomless-sex-concentrated PrEP in KwaZulu-Natal accounting for drug resistance. Journal of Infectious Diseases 2019.
   
• Nicki Tiffin. Potential risks and solutions for sharing genome summary data from African populations. BMC Medical Genomics 2019, 12( Article 152).
   
• Bernhard Kerschberger, Michael Schomaker, Iza Ciglenecki, Lorraine Pasipamire, Edwin Mabhena, Alex Telnov, Barbara Rusch, Nomthandazo Lukhele, Roger Teck and Andrew Boulle. Programmatic outcomes and impact of rapid public sector antiretroviral therapy expansion in adults prior to introduction of the WHO treat‐all approach in rural Eswatini. Tropical Medicine and International Health 2019, 24(6); 701-714.
   
• Emily A. Kendall, Andrew S. Azman, Gary Maartens, Andrew Boulle, Robert J. Wilkinson, David W. Dowdy and Molebogeng X. Rangaka. Projected population-wide impact of antiretroviral therapy-linked isoniazid preventive therapy in a high-burden setting. AIDS 2019, 33(3); 525-536.
   
• Charlotte M. Hoffman, Nontembeko Mbambazela, Phumzile Sithole, Servaas A. Morré, Jan Henk Dubbink, Jean Railton, James A. McIntyre, Marleen M. Kock, and Remco P.H. Peters. Provision of Sexually Transmitted Infection Services in a Mobile Clinic Reveals High Unmet Need in Remote Areas of South Africa: A Cross-sectional Study. Sexually Transmitted Disease 2019, 46(3); 206-212.
   
• N. Naidoo, N. Matlakala, J. Railton, S. Khosa, G. Marincowitz, J. O. Igumbor, J. A. McIntyre, H. E. Struthers and R. P. H. Peters. Provision of HIV services by community health workers should be strengthened to achieve full programme potential: A cross-sectional analysis in rural South Africa.  Tropical Medicine and International Health 2019, 24(4); 401-408.
   
• Mark N. Lurie, Kipruto Kirwa, Julia Callaway, Morna Cornell, Andrew Boulle, Angela M. Bengtson, Mariette Smith, Natalie Leon and Christopher Colvin. Quantifying the HIV treatment cascade in a South African health sub‐district by gender: Retrospective cohort study. Tropical Medicine and International Health 2019.
   
• Sarah Jane Steele, Hartini Sugianto, Quentin Baglione, Sandra Sedlimaier, Aline Aurore Niyibizi, Kristal Duncan, Julia Hill, Jesper Brix, Mit Philips, Gilles Van Cutsem and Amir Shroufi. Removal of user fees and system strengthening improves access to maternity care, reducing neonatal mortality in a district hospital in Lesotho. Tropical Medicine and International Health 2019, 24(1); 2-10.
   
• Bock P, Nel K, Fatti G, Sloot R, Jennings K, Voget J, Gunst C, Farmer N, Cloete R, Grobbelaar N, Louis F, Floyd S, Hayes R, Ayles H, Beyers N, Fidler S on behalf of the HPTN 071 (PopART) team. Renal dysfunction by baseline CD4 cell count in a cohort of adults starting antiretroviral treatment regardless of CD4 count in the HIV Prevention Trials Network 071 [HPTN 071; Population Effect of Antiretroviral Therapy to Reduce HIV Transmission (PopART)] study in South Africa. HIV Med 2019, 20(6).
   
• Marcel Yotebieng, Ellen Brazier, Diane Addison, April D Kimmel, Morna Cornell, Olivia Keiser, Angela M Parcesepe, Amobi Onovo, Kathryn E Lancaster, Barbara Castelnuovo, Pamela M Murnane, Craig R Cohen, Rachel C Vreeman, Mary-Ann Davies, Stephany N Duda, Constantin T Yiannoutsos, Rose S Bono, Robert Agler, Charlotte Bernard, Jennifer L Syvertsen, Jean d’Amour Sinayobye, Radhika Wikramanayake, Annette H Sohn, Per M von Groote, Gilles Wandeler, Valeriane Leroy, Carolyn F Williams, Kara Wools-Kaloustian, Denis Nash and for the IeDEA Treat All in sub-Saharan Africa Consensus Statement Working Group. Research priorities to inform “Treat All” policy implementation for people living with HIV in sub‐Saharan Africa: a consensus statement from the International epidemiology Databases to Evaluate AIDS (IeDEA). Journal of IAS 2019, 22(1); 1-16.
   
• Peter Bock, Colette Gunst, Leonard Maschilla, Rory Holtman, Nelis Grobbelaar, Dillon Wademan, Rory Dunbar, Geoffrey Fatti, James Kruger, Nathan Ford, Graeme Hoddinott and Sue-Ann Meehan. Retention in care and factors critical for effectively implementing antiretroviral adherence clubs in a rural district in South Africa. Journal of IAS 2019, 22(10).
   
• Sabin Nsanzimana, Muhammed Semakula, Vedaste Ndahindwa, Eric Remera, Dieudonne Sebuhoro, Jean Paul Uwizihiwe, Nathan Ford, Marcel Tanner, Steve Kanters, Edward J. Mills and Heiner C. Bucher. Retention in care and virological failure among adult HIV+ patients on second-line ART in Rwanda: a national representative study. BMC Infectious Diseases 2019, 19(Article 312).
   
• Dorothy Sebikari, Mona Farhad, Terry Fenton, Maxensia Owor, Jeffrey S. A. Stringer, Min Qin, Nahida Chakhtoura, Benjamin H. Chi, Friday Saidi, Neetal Nevrekar, Avy Violari, Tsungai Chipato, James A. McIntyre, Dhayendre Moodley,Taha E. Taha, Gerhard Theron and Mary Glenn Fowler. Risk Factors for Adverse Birth Outcomes in the PROMISE 1077BF/1077FF Trial. JAIDS 2019, 81(5); 521-532.
   
• Joseph Daniels, Helen Struthers, Kabelo Maleke, Christina Catabay, Tim Lane, James McIntyre & Tom Coates. Rural school experiences of South African gay and transgender youth. Journal of LGBT Youth 2019, 16(4); 355-379.
   
• Catriona Waitt, Catherine Orrell, Stephen Walimbwa, Yashna Singh, Kenneth Kintu, Bryony Simmons, Julian Kaboggoza, Mary Sihlangu, JulieAnne Coombs, Thoko Malaba, Josaphat Byamugisha, Alieu Amara, Joshua Gini, Laura Else, Christie Heiburg, Eva Maria Hodel, Helen Reynolds, Ushma Mehta, Pauline Byakika-Kibwika, Andrew Hill, Landon Myer, Mohammed Lamorde, Saye Khoo. Safety and pharmacokinetics of dolutegravir in pregnant mothers with HIV infection and their neonates: A randomised trial (DolPHIN-1 study). PLoS Medicine 2019, 16(9).
   
• P. Govender, Graeme Meintjes, Phetho Mangena, Jeremy Nel, Samantha Potgieter, Denasha Reddy, Helena Rabie, Douglas Wilson, John Black, David Boulware, Tom Boyles, Tom Chiller, Halima Dawood, Sipho Dlamini, Thomas S. Harrison, Prudence Ive, Joseph Jarvis, Alan Karstaedt, Matamela C. Madua, Colin Menezes, Mahomed-Yunus S. Moosa, Zaaheera Motlekar, Amir Shroufi, Sarah Lynn Stacey, Merika Tsitsi, Gilles van Cutsem, Ebrahim Variava, Michelle Venter, Rachel Wake. Southern African HIV Clinicians Society guideline for the prevention, diagnosis and management of cryptococcal disease among HIV-infected persons: 2019 update. South African Journal of HIV Medicine 2019, 20(1).
   
• Bella Hwang, Amir Shroufi, Tinne Gils , Sarah Jane Steele, Anna Grimsrud, Andrew Boulle, Anele Yawa, Sasha Stevenson, Lauren Jankelowitz, Marije Versteeg Mojanaga, Indira Govender, John Stephens, Julia Hill, Kristal Duncan, Gilles van Cutsem. Stock-outs of antiretroviral and tuberculosis medicines in South Africa: A national cross-sectional survey. PLOS One 2019, 14(3).
   
• Rebe Kevin, Hoosen Nikhat, McIntyre James A. Strategies to improve access for MSM in low-income and middle-income countries.  Current Opinion in HIV and AIDS 2019, 14(5); 387-392.
   
• Julie Jesson, Michael Schomaker, Karen Malasteste, Dewi K Wati, Azar Kariminia, Mariam Sylla, Kouakou Kouadio, Shobna Sawry, Mwangelwa Mubiana-Mbewe, Samuel Ayaya, Rachel Vreeman, Catherine C McGowan, Marcel Yotebieng, Valeriane Leroy and Mary-Ann Davies on behalf of the IeDEA global cohort consortium. Stunting and growth velocity of adolescents with perinatally acquired HIV: differential evolution for males and females. A multiregional analysis from the IeDEA global paediatric collaboration. Journal of IAS 2019, 22(11).
   
• Kelsey K. Case, Leigh F. Johnson, Mary Mahy, Kimberly Marsh, Virginie Supervie and Jeffrey W. Eaton. Summarizing the results and methods of the 2019 Joint United Nations Programme on HIV/AIDS HIV estimates. AIDSonline 2019, 33; 197-201.
   
• Geoffrey Jobson, Moyahabo Mabitsi, Jean Railton, Cornelis J. Grobbelaar, James A. McIntyre, Helen E. Struthers, Remco P.H. Peters. Targeted mentoring for human immunodeficiency virus programme support in South Africa. Southern African Journal of HIV Medicine 2019, 20(1).
   
• David C. Boettiger, Matthew G. Law, Annette H. Sohn, Mary-Ann Davies, Kara Wools-Kaloustian, Valeriane Leroy, Marcel Yotebieng, Michael Vinikoor, Rachel Vreeman, Madeleine Amorissani-Folquet, Andrew Edmonds, Geoffrey Fatti, James Batte, Lorna Renner, Aebola Adedimeji, and Azar Kariminia on behalf of the International Epidemiology Databases to Evaluate AIDS. Temporal Trends in Co-trimoxazole Use Among Children on Antiretroviral Therapy and the Impact of Co-trimoxazole on Mortality Rates in Children Without Severe Immunodeficiency. Journal of Paediatric Infectious Diseases Soceity 2019, 8(5); 450-460.
   
• Rice B, Boulle A, Schwarcz S, Shroufi A, Rutherford G, Hargreaves J. The Continuing Value of CD4 Cell Count Monitoring for Differential HIV Care and Surveillance. JMIR Public Health 2019, 5(1).
   
• Sabine Hermans; Morna Cornell; Keren Middelkoop and Robin Wood. The differential impact of HIV and antiretroviral therapy on gender‐specific tuberculosis rates. Tropical Medicine and International Health 2019, 24(4); 454-462.
   
• Johnson L.F., Mutemaringa T., Heekes A. and Boulle A. The effect of HIV infection and antiretroviral treatment on pregnancy rates in the Western Cape province of South Africa. Journal of Infectious Diseases 2019, jiz362.
   
• Nicola Wearne, Charles R. Swanepoel, Maureen S. Duffield, Bianca J. Davidson, Kathryn Manning, Nicki Tiffin, Andrew Boulle, Brian L. Rayner, Priyanka Naidu and Ikechi G. Okpechi. The effects of add-on corticosteroids on renal outcomes in patients with biopsy proven HIV associated nephropathy: a single centre study from South Africa. BMC Nephrology 2019, 20 (Article 44).
   
• Sarah Jane Steele, Naeemah Abrahams, Kristal Duncan, Nataly Woollett, Bella Hwang, Lucy O’Connell, Gilles van Cutsem, Amir Shroufi. The epidemiology of rape and sexual violence in the platinum mining district of Rustenburg, South Africa: Prevalence, and factors associated with sexual violence. PLOS ONE 2019, 14(7).
   
• A Myburgh, R Kassanjee, PR Pretorius. The influence of delayed sample processing time on PO2 values in critically ill patients with sepsis-induced leucocytosis. Southern African Journal of Anaesthesia and Analgesia 2019, 25(6); 21-25.  
                   
• Makhakhe N, Meyer-Weitz A, Struthers H, McIntyre J. The role of health and advocacy organisations in assisting female sex workers to gain access to health care in South Africa. BMC Health Services Research 2019, 19 (Article 746).
   
• Porgo T.V., Norris S.L., Salanti G., Johnson L.F., Simpson J.A., Low N., Egger M. and Althaus C.L.The use of mathematical modelling studies for evidence synthesis and guideline development: a glossary. Research Synthesis Methods 2019, 10(1); 125-133.
   
• Catherine Le, Paula Britto, Sean Brummel, Risa Hoffman, Jonathan Li, Patricia Flynn, Taha Taha, Anne Coletti, Mary Fowler, Ronald Bosch, Rajesh Gandhi, Karin Klingman, James McIntyre, Judith Currier. Time to viral rebound and safety after antiretroviral treatment interruption in postpartum women compared with men.  AIDS 2019, 33(14); 2149-2156.
   
• Malango T. Msukwa, Olivia Keiser, Andreas Jahn, Joep J. van Oosterhout, Andrew Edmonds, Nozgechi Phiri, Ronald Manjomo, Mary-Ann Davies and Janne Estill. Timing of combination antiretroviral therapy (cART) initiation is not associated with stillbirth among HIV‐infected pregnant women in Malawi. Tropical Medicine and International Health 2019, 24(6);727-735.
   
• Vincent Wong, Erin Jenkins, Nathan Ford and Heather Ingold. To thine own test be true: HIV self-testing and the global reach for the undiagnosed. JIAS 2019, 22( S1).
   
• K Anderson, R Muloiwa, M-A Davies. Treatment outcomes in perinatally infected HIV-positive adolescents and young adults after ≥10 years on antiretroviral therapy. South African Medical Journal 2019, 109(1); 27-34.
   
• Damian J. Damian, Bernard Njau, Ester Lisasi, Sia E. Msuya and Andrew Boulle. Trends in maternal and neonatal mortality in South Africa: A systematic review. Systematic Reviews 2019, 8 (Article 76).
   
• Stover John, Glaubius Robert, Morenson Lynne, Dugdale Caitlin M, Davies Mary-Ann, Patten Gabriela, Yiannoutsos Constantin. Updates to the Spectrum/AIM model for estimating key HIV indicators at national and subnational levels. Aidsonline 2019, 33; 227-234.
   
• Diwakar Mohan, Jean Juste Harrisson Bashinwa, Pierre Dane, Sara Chamberlain, Nicki Tiffin, Amnesty Lefevre. Use of Big Data and Machine Learning Methods in the Monitoring and Evaluation of Digital Health Programs in India: An Exploratory Protocol. JMIR 2019, 8(5).
   
• M. Schomaker, M.A. Luque-Fernandez, V. Leroy and M.A. Davies. Using longitudinal targeted maximum likelihood estimation in complex settings with dynamic interventions. Statistics in Medicine 2019, 38(24); 4888-4911.
   
• Gabriela Patten, Michael Schomaker,  Mary-Ann Davies, Helena Rabie, Gert van Zyl, Karl Technau, Brian Eley, Andrew Boulle, Russell B. Van Dyke, Kunjal Patel, Nosisa Sipambo, Robin Wood, Frank Tanser, Janet Giddy, Mark Cotton, James Nuttall, Gadija Essack, Brad Karalius, George Seage, Shobna Sawry, Matthias Egger and Lee Fairlie for IeDEA Southern Africa. What Should We Do When HIV-positive Children Fail First-line Combination Antiretroviral Therapy? A Comparison of 4 ART Management Strategies. Pediatric Infectious Disease Journal 2019, 38(4); 400-405.
   
• Mehta Ushma, Kalk Emma, Fairlie Lee, Boulle Andrew, Rees Helen. Why South Africa urgently needs to support the development of pregnancy exposure registries. South African Medical Journal 2019, 109(5); 294-295.

2014

• Leigh F. Johnson. THEMBISA Version 1.0: A model for evaluating the impact of HIV/AIDS in South Africa. Centre for Infectious Disease Epidemiology and Research working paper February 2014.

2011

• Leigh F. Johnson, Katharina Kranzer, Keren Middelkoop, Robin Wood. A model of the impact of HIV/AIDS and antiretroviral treatment in the Masiphumelele community. Centre for Infectious Disease Epidemiology and Research working paper June 2011.
   
• Khayelitsha 2001 - 2011 Summary Activity Report: 10 Years of HIV/TB Care At Primary Health Care Level. Médecins Sans Frontières, Western Cape Province Department of Health, City of Cape Town Department of Health, University of Cape Town, Centre for Infectious Disease Epidemiology and Research.
   
• Khayelitsha 2001 - 2011 Activity Report: 10 Years of HIV/TB Care At Primary Health Care Level. Médecins Sans Frontières, Western Cape Province Department of Health, City of Cape Town Department of Health, University of Cape Town, Centre for Infectious Disease Epidemiology and Research.
   
• Leigh F. Johnson & Andrew Boulle. Technical appendix to “How should access to antiretroviral treatment be measured?“ Published in the Bulletin of the World Health Organization. Centre for Infectious Disease Epidemiology and Research January 2011.

2010

• Osler, M., Boulle, A. Three Interlinked Electronic Registers (TIER.Net) Project: A working paper September 2010. Cape Town, University of Cape Town.
   
• Leigh Johnson. A model of paediatric HIV in South Africa. Centre for Infectious Disease Epidemiology and Research working paper December 2010.

2008

• Roundtable discussion on progress in the Western Cape Province in addressing HIV treatment needs: What does our data tell us? Minutes from meeting held on 15 April 2008.
   
• Schneider, H., van Rensburg, D. & Coetzee, D. Health systems and antiretroviral access: Key findings and policy recommendations. (2008), Bloemfontein, University of the Free State.
   
• Stinson, K., Myer, L. & Boulle, A. An evaluation of approaches to the initiation of antiretroviral therapy during pregnancy among HIV-infected women in Cape Town. (2008), Cape Town, University of Cape Town.
   
• Schneider, H., Boulle, A., Coetzee, D., Engelbrecht.M., Goudge, E., van Rensburg-Bonthuyzen, J., Pienaar, D. Models of care for antiretroviral service delivery in three provinces: Western Cape, Free State and Gauteng. (2008), Cape Town, University of Cape Town.

2006

• Pienaar D., Myer L., Cleary S., Coetzee D., Michaels D., Cloete K., Schneider H. & Boulle A. Models of Care for Antiretroviral Service Delivery. (2006). Cape Town, University of Cape Town.
   
• Osler, M., Bock, P., White, C., Cloete, K., Smuts, B., Slingers, N., Zweigenthal, V., Naidoo, P., Van Niekerk, L., Channing, L., Cragg, C., Kredo, T., Mehta, U., Naledi, T. & Boulle, A. The Western Cape Antiretroviral Programme: Monitoring Report. (2006), Cape Town, Provincial Government of the Western Cape.Bloemfontein, University of the Free State.