This project aims to:

  • Quantify losses at each stage of the UTT cascade
  • Assess systemwide retention and transfer in the UTT era
  • Evaluate the impact of UTT on time from clinical presentation to ART uptake, retention, and viral suppression

Project Principal Investigator(s):

Jacob Bor and Dorina Onoya

Project duration:

2014 – present

Funding source:

Evaluating UTT with a National HIV Cohort to Optimise South Africa’s HIV Response (ENCORE), NIH NIAID, R01AI152149 (2020-2025)

Centres for Disease Control and Prevention (CDC)

Analysis of national lab database to evaluate the HIV treatment rollout in South Africa, NIH NIAID (2015-2019)

USAID Cooperative Agreement AID- 674-A-12-0020 (2012-2015)

Meet the

Team

The South African National HIV Pregnancy Cohort project team has benefitted from the skills and expertise of a dynamic and diverse collection of researchers, epidemiologists, clinicians, health economists, public health specialists, data scientists and implementers.

Principal Investigators:

  • Jacob Bor

    HE2RO & Boston University

  • Dorina Onoya

    HE2RO

Collaborators:

  • Mhairi Maskew

    HE2RO

  • Evelyn Lauren

    HE2RO & Boston University

  • Kobus Herbst

    Africa Health Research Institute (AHRI)

  • Dickman Gareta

    Africa Health Research Institute (AHRI)

  • Khumbo Shumba

    HE2RO

  • Cornelius Nattey

    HE2RO

  • Trevor Bell

    National Health Laboratory Service (NHLS)

  • Siya Zondi

    National Health Laboratory Service (NHLS)

  • Sue Candy

    National Health Laboratory Service (NHLS)

  • Koleka Mlisana

    National Health Laboratory Service (NHLS)

  • Adrian Puren

    National Health Laboratory Service (NHLS)

  • Matthew Fox

    HE2RO & Boston University

  • Bill MacLeod

    HE2RO & Boston University

  • Alana Brennan

    HE2RO & Boston University

Project

Objectives

The HIV Cohort was the first cohort created by the NHLS National Lab Cohorts Collaboration. The cohort is currently led by Drs Dorina Onoya and Jacob Bor, supported by the ENCORE R01 (2020-2025).

The following were the project objectives for ENCORE:

Universal Test-and-Treat (UTT) could end the HIV epidemic if enough people start and stay on treatment. In 2016, South Africa eliminated CD4 eligibility criteria for antiretroviral therapy (ART), and in 2017, the country began starting patients on ART on the same day as diagnosis. These policies were designed to increase ART coverage and have been shown to be effective in clinical trials. However, the real-world effectiveness of these UTT policies at scale remains unknown. For this project, the team updated the NHLS National HIV Cohort through the UTT era and linked it with data from South Africa’s facility-based ART monitoring and evaluation system.

ENCORE aimed to:

  1. Quantify losses at each stage of the UTT cascade
  2. Assess systemwide retention and transfer in the UTT era
  3. Evaluate the impact of UTT on time from clinical presentation to ART uptake, retention, and viral suppression

ENCORE was preceded by the ATRACT R01, a project that set out to leverage the existing NHLS data including all CD4, viral load and other lab tests ever conducted within South Africa’s national ART program. Over five years, analyses evaluated the national ART program using these data that are nationally representative and robust to self-transfer across care settings.

Specifically, the project’s aims were to:

  1. Quantify the effect of the national HIV testing campaign on uptake of HIV care and treatment.
  2. Estimate national retention rates in pre-ART care and post-ART initiation.
  3. Establish long run treatment outcomes for a national patient cohort.
  4. Estimate the effects of immediate vs. deferred ART eligibility on retention and clinical outcomes.

Key Findings

And Impacts

The ENCORE project has generated substantial evidence on South Africa’s HIV treatment program through updated linkage of the NHLS National HIV Cohort and integration of the NHLS Cohort with TIER.net data in five provinces. Key findings include:

Advanced record linkage and novel validation methods:

From 2004 to 2023, the NHLS National HIV Cohort was successfully updated and a record linkage algorithm was integrated into routine NHLS/NICD data systems. Novel methods were developed to validate record linkage using non-representative gold standard data and to assess the impacts of linkage error on epidemiological analyses. Additionally, a privacy-preserving linkage was conducted between the NHLS cohort and the TIER.net without using patient identifiers. Finally, the AHRI Unified Data Platform (AUDP) was created, linking HIV treatment and population-based surveillance records in rural South Africa.

The documentation of treatment cascade insights:

Evolving trends in early ART initiation under South Africa’s UTT policy were documented. Between 2015 and 2020, patterns of patient losses from HIV care across HIV treatment guideline periods were identified. The durability of viral suppression on treatment was tracked and patient retention and treatment outcomes were assessed to provide a comprehensive overview of HIV care during the UTT era.

Monitoring & testing trends:

Tracking trends in CD4 count testing volumes provided insights for monitoring disease advancement. Both the fall and rise in hospital-based care for HIV patients was documented from 2004 to 2017. The following patient mobility and engagement patterns were noted:

  • Mobility and clinic switching patterns among patients initiating antiretroviral therapy from 2010 to 2016.
  • Adherence to treatment during the first two years after ART initiation.
  • Care pathways and patterns of re-engagement among patients who temporarily left treatment.

Policy changes, impacts and documentation:

Policy changes in South Africa were examined for their impact on HIV care. Additionally, the impact of privacy-preserving strategies on patient outcome assessments within the national program was also assessed. And lastly, from 2004 to 2017 the fall and rise in hospital-based care for people with HIV was documented.

Resources

Published papers

  • Lauren, Evelyn, Khumbo Shumba, Matthew P. Fox, William MacLeod, Wendy Stevens, Koleka Mlisana, Jacob Bor, and Dorina Onoya. “The fall—and rise—in hospital-based care for people with HIV in South Africa: 2004–2017.” PLOS Global Public Health 4, no. 9 (2024): e0002127.

  • Onoya, Dorina, Khumbo Shumba, Caroline Mudara, Cornelius Nattey, Dickman Gareta, Evelyn Lauren, William Macleod, Matthew P. Fox, Koleka Mlisana, and Jacob Bor. “Timing of ART initiation with treatment policy changes in South Africa: a cohort study.” JAIDS Journal of Acquired Immune Deficiency Syndromes (2022): 10-1097. https://journals.lww.com/jaids/abstract/9900/timing_of_art_initiation_with_treatment_policy.748.aspx

  • Shumba, Khumbo, Jacob Bor, Cornelius Nattey, Dickman Gareta, Evelyn Lauren, William Macleod, Matthew P. Fox, Adrian Puren, Koleka Mlisana, and Dorina Onoya. “Record linkage without patient identifiers: proof of concept using data from South Africa’s national HIV program.” PLOS Global Public Health 5, no. 7 (2025): e0004835. https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0004835

  • Nattey, Cornelius, Dorina Onoya, Khumbo Shumba, Dickman Gareta, William Macleod, Matthew P. Fox, Adrian Puren, Koleka Mlisana, and Jacob Bor. “Monitoring for advanced disease in the universal test and treat era: trends in CD4 count testing in South Africa.” BMC Global and Public Health 3, no. 1 (2025): 2.https://link.springer.com/article/10.1186/s44263-024-00118-6

  • Dzomba, Armstrong, Khumbo Shumba, Cornelius Nattey, Evelyn Lauren, Alana Brennan, William McLoed, Matthew P. Fox, Jacob Bor, and Dorina Onoya. “HIV patient treatment adherence trajectories in first 24-months post-ART initiation among adults: an electronic health records cohort from South Africa.” JAIDS Journal of Acquired Immune Deficiency Syndromes (2022): 10-1097. https://journals.lww.com/jaids/fulltext/2025/12010/hiv_patient_treatment_adherence_trajectories_in.4.aspx

  • Maskew M, Bor J, MacLeod W, Carmona S, Sherman GG, Fox MP. Adolescent HIV treatment in South Africa’s national HIV programme: a retrospective cohort study. Lancet HIV. 2019 Oct;6(11):E760-E768. DOI: https://doi.org/10.1016/S2352-3018(19)30234-6.

  • Matthew P Fox, Jacob Bor, Alana T Brennan, William B. MacLeod, Mhairi Maskew, Wendy Susan Stevens, Sergio Carmona. How much is retention in HIV care underestimated due to patient transfers? Estimating system-wide retention using a national laboratory database in South Africa. PLoS Medicine 2018; 15(6):e1002589

  • Carmona, J. Bor, C. Nattey, B. MaughanBrown, M. Maskew, M.P. Fox, D.K. Glencross, N. Ford, W. MacLeod. Persistent high burden of advanced HIV disease in South Africa: data from a nationwide laboratory cohort. Clin Infect Dis. 2018 Mar 4;66(suppl_2):S111-S117.

  • Johnson LF, Patrick M, Stephen C, Patten G, Dorrington RE, Maskew M, Jamieson L, Davies MA. Steep Declines in Pediatric AIDS Mortality in South Africa, Despite Poor Progress Toward Pediatric Diagnosis and Treatment Targets. Pediatr Infect Dis J. 2020 Sep;39(9):843-848. doi: https://doi.org/10.1097/INF.0000000000002680.

  • Fox MP, Brennan AT, Nattey C, Macleod WB, Harlow A, Mlisana K, Maskew M, Carmona S, Bor J. Delays in repeat HIV viral load testing for those with elevated viral loads: A national perspective from South Africa. JIAS. 2020 July;23(7):e25542. DOI: https://doi.org/10.1002/jia2.25542

  • Jacob Bor, William MacLeod, Katia Oleinik, James Potter, Alana Brennan, Sue Candy, Mhairi Maskew, Matthew P Fox, Ian Sanne, Wendy S Stevens, Sergio Carmona. Building a National HIV Cohort from Routine Laboratory Data: Probabilistic Record-Linkage with Graphs. Published in bioRxiv 2018, doi: https://doi.org/10.1101/450304

  • Harlow AF, Bor J, Brennan AT, Maskew M, MacLeod W, Carmona S, Mlisana K, Fox MP. Impact of Viral Load Monitoring on Retention and Viral Suppression: A Regression Discontinuity Analysis of South Africa’s National Laboratory Cohort. American Journal of Epidemiology. 2020 July. https://doi.org/10.1093/aje/kwaa140.

  • Bor J, Gage A, Onoya D, Maskew M, Tripodis Y, Fox MP, et al. (2021) Variation in HIV care and treatment outcomes by facility in South Africa, 2011–2015: A cohort study. PLoS Med 18(3): e1003479. https://doi.org/10.1371/journal.pmed.1003479

  • Maskew M, Bor J, Hendrickson C, MacLeod W, Bärnighausen T, Pillay D, Sanne I, Carmona S, Stevens W, Fox MP. Imputing HIV treatment start dates from routine laboratory data in South Africa: a validation study. BMC health services research. 2017 January 17;17(1):41. PubMed PMID: 28095905; PubMed Central PMCID: PMC5240407

  • Clouse K, Vermund SH, Maskew M, Lurie MN, MacLeod W, Malete G, Carmona S, Sherman G, Fox MP. Mobility and Clinic Switching Among Postpartum Women Considered Lost to HIV Care in South Africa. Journal of acquired immune deficiency syndromes. 2017 April 1;74(4):383-389. PubMed PMID: 28225717; PubMed Central PMCID: PMC5324708

  • Bor J, Fox MP, Rosen S, Venkataramani A, Tanser F, Pillay D, et al. (2017) Treatment eligibility and retention in clinical HIV care: A regression discontinuity study in South Africa. PLoS Med 14(11): e1002463. https://doi.org/10.1371/journal.pmed.1002463

Resources

Conference presentations

  • Gareta, Dickman, Dorina Onoya, Kobus Herbst, and Jacob Bor. “Piloting and validating the linkage of routine ART and laboratory records in an HIV endemic setting.” International Journal of Population Data Science 7, no. 3 (2022): 2004. https://pmc.ncbi.nlm.nih.gov/articles/PMC9645014/

  • Lauren, Evelyn, Dickman Gareta, Khumbo Shumba, Dorina Onoya, and Jacob Bor. “Enhancing integration of administrative databases in South Africa’s HIV program: Validation of record linkage using non-representative gold standard.” International Journal of Population Data Science 9, no. 5 (2024). https://ijpds.org/article/view/2899

  • Gareta, Dickman, Evelyn Lauren, Khumbo Shumba, Kobus Herbst, Dorina Onoya, and Jacob Bor. “Developing an integrated HIV clinical and population database in rural south Africa.” International Journal of Population Data Science 9, no. 5 (2024). https://ijpds.org/article/view/2830

  • Bor J, Fox MP, Maskew M, Onoya D, Brennan AT, Haber NA, Barnighausen T, Carmona S, Stevens W, Puren AJ, MacLeod WB. Impact of UTT on viral suppression in South Africa: a national cohort study. Poster presentation, CROI, Boston, 2020.

  • Bor J, Fox MP, Nattey C, Maughan-Brown B, Maskew M, Onoya D, Brennan AT, Barnighausen T, Yapa HM, Carmona S, Stevens W, Puren AJ, MacLeod WB. Late presentation persists under UTT in South Africa: a national cohort study. Accepted for poster presentation, CROI, Boston, 2020.

  • Age at HIV diagnosis within South Africa’s Early Infant Diagnosis program, 2010-2015. (Poster). Ahmad Haeri Mazanderani, William B. MacLeod, Jacob Bor, Gayle G. Sherman. CROI 2018, March 2018, Boston, MA.

  • Time to repeat viral load testing for patients with a first elevated viral load after ART initiation: A national perspective from South Africa. MP Fox, AT Brennan, M Maskew, J Bor, W MacLeod, S Carmona. Presented at the International Workshop on HIV and Observational Databases (IWHOD 2018), Malaga, Spain March 22-24, 2018.

  • Persistent high burden of advanced HIV disease in South African children and adolescents at entry into care: data from a longitudinal nationwide laboratory cohort. S. Carmona, M. Maskew, G. Sherman, J. Bor, M. Penazzato, M. Fox, N. Ford, W. Macleod. Presented at the 22nd International AIDS Conference (AIDS 2018), Amsterdam 23-27 July 2018.

  • Jacob Bor, William MacLeod, Katia Oleinik, Sue Candy, Mhairi Maskew, Matthew Fox, Cornellius Nattey, Brendan Maughan-Brown, James Potter, Wendy Stevens, Ian Sanne, Sergio Carmona: Record linkage of national laboratory data in South Africa: a novel platform for HIV policy evaluation. Presented at the International Health Economics Association 2017 World Congress, July 9, 2017, Boston MA.

  • Clouse K, Vermund SH, Maskew M, Malete G, Fox MP. Continuity of Care Among Pregnant Women Lost to Follow-up After Initiating ART. Themed Discussion. Conference on Retroviruses and Opportunistic Infections – Boston, MA (February 2016)

  • MacLeod W, Bor J, Fraser N, Gorgens M, Sanne I, Stevens W, Phokojoe M, Pillay Y, Carmona S. Measuring Viral Load Suppression in South Africa Using a Novel, National Database. Poster Conference on Retroviruses and Opportunistic Infections – Boston, MA (February 2016)

  • Maskew M, Bor J, Hendrickson C, MacLeod W, Barnighausen T, Pillay D, Sanne I, Carmona S, Stevens W, Fox M. Imputing Clinical Records from Routine Laboratory Data: Date of ART Initiation. Poster Conference on Retroviruses and Opportunistic Infections – Boston, MA (February 2016)

  • Bor J, Brennan A, Fox MP, Maskew M, Stevens W, Carmona S, MacLeod W. District prevalence of unsuppressed HIV in South African Women: Monitoring Programme Performance and Progress Towards 90-90-90. (Oral) 21st International AIDS Conference – Durban, South Africa (July 2016)

  • Fox MP, Bor J, MacLeod W, Maskew M, Brennan A, Stevens W, Carmona S. Is retention on ART underestimated due to patient transfers? Estimating system-wide rentention using a national labs database in South Africa. (Oral) 21st International AIDS Conference – Durban, South Africa (July 2016)

  • MacLeod WB, Fraser N, Bor J, Shubber Z, Carmona S, Pillay Y, Gorgens M. Analysis of age-and sex-specific HIV care cascades in South Africa suggests unequal progress towards UNAIDS 90-90-90 treatment targets. (Poster) 21st International AIDS Conference – Durban, South Africa (July 2016)

  • Maskew M, Bor J, MacLeod W, Carmona S, Sherman G, Fox MP. The youth treatment bulge in South Africa: increasing numbers, inferior outcomes among adolescents on ART. (Oral) 21st International AIDS Conference – Durban, South Africa (July 2016)

  • Maskew M, Hendrickson C, MacLeod W, Sanne I, Carmona S, Stevens W, Fox MP, Bor J. Utilizing laboratory data to impute ART start dates and monitor cohort treatment outcomes. (Poster) 21st International AIDS Conference – Durban, South Africa (July 2016)

  • Nattey C, Maughan-Brown B, MacLeod W, Maskew M, Carmona S, Fox MP, Bor J. Rising CD4 counts at clinical presentation: evidence from a novel national database in South Africa.  (Poster) 21st International AIDS Conference – Durban, South Africa (July 2016)

Policy

Briefs

  • Fox MP, Nattey C, Maskew M, Murphy J, Mlisana K, MacLleod W, Sergio C, Brennan AT, Bor J. Impact of South Africa’s National HIV testing Campaign on Numbers Enrolling in Care. HE²RO Policy Brief Number 35, Health Economics and Epidemiology Research Office, 2020.

  • Fox MP, Brennan AT, Nattey C, Macleod WB, Harlow A, Mlisana K, Maskew M, Carmona S, Bor J. Delays in repeat HIV viral load testing for those with elevated viral loads: A national perspective from South Africa. Johannesburg: HE²RO Policy Brief Number 36, Health Economics and Epidemiology Research Office, June 2020.

Manuscripts in Progress /

Under Review

  • Updated National NHLS HIV cohort paper – Target Journal: TBI – Lead: Jacob Bor/Evelyn Lauren

  • Durability of HIV viral suppression in a South African national cohort – Target Journal: The Lancet HIV – Lead: Evelyn Lauren

  • Assessing Patient Retention and Treatment Outcomes in South Africa’s UTT Era – Target Journal: TBI – Lead: Dorina Onoya/Khumbo Shumba – Status: Pending (Findings need to be updated with more recent data)

  • The impact of privacy-preserving record linkage strategies on assessing patient outcomes in South Africa’s HIV program – Target Journal: BMC Medical Research Methodology – Lead: Khumbo Shumba

  • Linkage of HIV treatment and population-based surveillance records in rural South Africa: the AHRI Unified Data Platform (AUDP) – Target Journal: Archives of Public Health – Lead: Dickman Gareta

  • Mobility and clinic switching among patients initiating antiretroviral therapy in South Africa from 2010-2016 – Target Journal: AIDS care – Lead: Cornelius Nattey

  • Characterising care trajectories and re-engagement in care among ART Patients in South Africa – Target Journal: TBI – Lead: Khumbo Shumba

  • Understanding the care cascade in the UTT era – Target Journal: TBI – Lead: Bill MacLeod/Dorina Onoya

  • HIV mortality in the era of universal test and treat – using Africa Health Research Institute’s Unified Data Platform (AUDP) – Target Journal: TBI – Lead: Dickman Gareta