Research Group: HIV, Hepatitis and Tuberculosis

Our research group is concerned with the clinical and public health epidemiology of HIV and co-infections with hepatitis B/C and tuberculosis in sub-Saharan Africa. Our main focus is on the epidemiology of HIV and coinfections, long-term outcomes of antiretroviral therapy (ART), the impact of ART on HIV transmission and coinfections, mathematical modelling, and methodological aspects of the analysis of longitudinal data.

We conduct analyses for international organizations such as UNAIDS, the Clinton Health Access Initiative, the World Health Organization (WHO), the Gates Foundation, UNITAID, the World Bank, and other external partners. We also collaborate closely with international partners as well as ISPM’s Cancer research group.


In recent years there have been advances in both policy and technology within the field of HIV treatment. Significant progress has been made toward increasing individual access to potentially life-saving combination antiretroviral therapy (ART), which has led to reductions in HIV-associated morbidity and mortality. These gains, leading toward the goal of universal access to HIV treatment, do not come without challenges in terms of sustainable provision of lifelong ART, drug resistance, loss to follow-up, and underrepresentation of subpopulations in program coverage. Read more


Chronic viral hepatitis B (HBV) infection, the major cause of end-stage liver disease worldwide, is present in 10% of HIV-infected individuals in sub-Saharan Africa. A better understanding of HBV-related clinical and virological outcomes in connection with antiretroviral therapy is urgent, as HIV/HBV-co-infected patients are more likely to die from liver-related complications than HBV-uninfected ones. Read more


Almost half of tuberculosis cases remain undiagnosed. Particularly in lower income countries where HIV prevalence is high, TB accounts for approximately 40% of adult deaths, and drug resistance to first-line drugs is growing and is an emerging public health problem. Read more

Group leader

HIV group members

Hepatitis group members

External collaborators

Hector Jonas (Mozambique)
Hoffmann Christopher (South Africa – USA)
Vinikoor Michael (Zambia – USA)

Tuberculosis group members


  • International epidemiology Databases to Evaluate AIDS (IeDEA) – Southern African regional and multi-regional collaborations
  • IeDEA-SA sites in Lesotho, Malawi, Mozambique, South Africa, Zambia and Zimbabwe
  • Swiss HIV Cohort Study (SHCS)
  • Collaboration of Observational HIV Epidemiological Research Europe (COHERE)
  • London School of Hygiene & Tropical Medicine, London, United Kingdom
  • Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland
  • Institute of Infectious Diseases (IFIK), University of Bern, Switzerland
  • Institute of Medical Microbiology, National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
  • Genomics Unit, FISABIO, University of Valencia, Valencia, Spain
  • University of Cape Town, Cape Town, South Africa
  • Vanderbilt University Medical Center, Nashville, United States
  • Institut de Santé Publique, d’Epidemiologie et de Développement, University of Bordeaux, France
  • Global Hepatitis Program, WHO, Geneva, Switzerland
  • Department of Infectious Diseases, Bern University Hospital, Switzerland

Ongoing projects


We use routinely collected data on HIV-positive patients from large ART databases such as IeDEA Southern Africa, but also conduct dedicated molecular epidemiological studies in the field.

Examples of our research topics include:

  • Continuum of adult HIV and TB care including anti‐retroviral therapy (ART) from diagnosis to outcomes
  • Tracing of patients lost to follow-up
  • Resistances to ART and their transmission
  • Co‐infections and co‐morbidities in HIV‐positive patients
  • Burden and care of cancers in HIV‐positive children and adults
  • Care continuum in HIV‐positive mothers and their children
  • Mental health and mental health care provision in HIV‐positive patients
  • Substance use in adolescents and adults on ART
  • State‐of‐the‐art methods and standards to facilitate multi‐regional analyses of HIV cohort data.



Our main aim is to study the epidemiological, clinical and virological determinants of hepatitis B virus (HBV) infection in HIV+ and HIV- individuals using surveys and clinical cohorts, with additional data collection and analyses of large administrative databases.

Examples of our research include:

  • Study of long-term HBV virological outcomes in a large cohort of HIV/HBV-coinfected individuals in Mozambique and Zambia, and comparison of these outcomes with those of HBV-monoinfected patients
  • Assessment of long-term complications of HBV infection such as liver fibrosis and hepatocellular carcinoma in Zambia
  • Study of hepatitis delta coinfection and its impact on long-term clinical outcomes


We use routinely collected data on HIV-positive patients from large ART databases such as IeDEA Southern Africa, but also conduct dedicated field molecular epidemiological studies. Our research team collaborates with national and international researchers as well as field partners in sub-Saharan Africa.

Examples of our research include:

  • Impact of HIV infection on the population genomics of drug-resistant Mycobacterium tuberculosis: insights from macro-evolutionary analyses
  • Extrapulmonary tuberculosis in antiretroviral therapy programs in low- and middle-income countries: diagnosis and clinical outcomes in adults and children
  • Analysis of tuberculosis seasonality in Southern Africa
  • Opportunistic infections in the era of combination ART: collaborative analysis of European HIV Cohort Studies (COHERE), with an emphasis on HIV and tuberculosis
  • Population genomics of Mycobacterium tuberculosis in HIV-infected and HIV-negative patients in Switzerland: the nationwide molecular-epidemiological tuberculosis study
  • Bacterial sputum microbiota and functional bacterial diversity in tuberculosis patients versus controls from Switzerland and sub-Saharan Africa: impact on clinical presentation and outcomes


Completed projects


(Selection, 2015 onward. Also see ‘Publications’ tab)

  • Low implementation of Xpert MTB/RIF among HIV/TB co-infected adults: A 19 low/middle income country survey from the IeDEA Consortium
  • The effect of initiating tenofovir on HIV treatment outcomes in adults in Southern Africa: a regression discontinuity analysis
  • Prevalence and clinical correlates of alcohol use disorders among HIV-infected adults in urban Zambia
  • Prediction of second-line needs: a mathematical model
  • First-line antiretroviral drug discontinuations due to toxicity in children at two antiretroviral treatment centres in South Africa.
  • Assessing the effects of initiating tenofovir on HIV treatment outcomes in adults in Southern Africa using the 2010 WHO ART guideline change as a natural experiment: a regression discontinuity analysis
  • Age and mortality in ART programs in South Africa
  • Growth of Southern African HIV-exposed uninfected infants in the first 6 months of life
  • Growth & mortality outcomes for different ART criteria in children aged 1-5 years: a causal modelling analysis from West and Southern Africa
  • Characteristics and outcomes of perinatally HIV-infected adolescents
  • Decision rules to guide targeted HIV-1 viral load monitoring of ART: development and validation in resource-limited settings
  • Virologic Outcomes of HIV-Infected Children Undergoing a Single-Class Drug Substitution from Lopinavir/Ritonavir- to Efavirenz-Based Antiretroviral Treatment: A retrospective cohort study.
  • CD4 count at antiretroviral therapy initiation and the risk of loss to follow-up: Results from a multicentre cohort study
  • Immunodeficiency at the start of ART: a global view
  • Can CD4 monitoring in virologically suppressed children be reduced or stopped?
  • When to start ART in African children aged 1-5 years
  • Clinical correlates of alcohol use disorders among HIV-infected adults in Zambia.
  • Outcomes in HIV-positive children on lamivudine monotherapy as a holding regimen
  • HIV viral loads as an independent risk factor for TB in South Africa
  • Reconciling IeDEA mortality estimates and national mortality statistics in South Africa
  • Trends in ART discontinuation by age in Malawi, 2004-2014
  • Virological failure in South African children and adolescents: baseline characteristics and management strategies
  • Outcomes in HIV-positive children on lamivudine monotherapy as a holding regimen in the IeDEA Southern African cohorts
  • What does adolescent transition mean in sub-Saharan Africa?  Predictors of transfer in Southern African perinatally HIV-infected adolescents.
  • 10-year mortality in South African ART programmes
  • Incidence of antiretroviral drug discontinuations due to toxicity in children
  • Changes in eGFR over time in patients on tenofovir
  • Adherence to antiretroviral therapy during and after pregnancy in the Malawi "Option B+" programme.
  • Retention and diagnosis among HIV-exposed children enrolled in Malawi's national HIV program


  • Trends in hepatitis B virus testing practices and management in HIV clinics across sub-Saharan Africa
  • Impact of antiretroviral therapy on liver fibrosis among HIV-infected adults with and without HBV coinfection in Zambia.
  • Hepatitis B infection, viral load and resistance in HIV-infected patients in Mozambique and Zambia
  • Absence of active hepatitis C virus infection in human immunodeficiency virus clinics in Zambia and Mozambique
  • Liver fibrosis in treatment-naïve HIV-infected and HIV/HBV co-infected patients: Zambia and Switzerland compared
  • Association between hepatitis B co-infection and elevated liver stiffness among HIV-infected adults in Lusaka, Zambia
  • Hepatitis B viral load in dried blood spots: A validation study in Zambia


  • Tuberculosis in HIV treatment programmes in low-income countries within the global IeDEA network: a survey on integration of services, diagnostic, screening, preventive and treatment practices
  • Collection of key tuberculosis variables in ART programs within the IeDEA consortium: diagnostics, treatment and risk factors for incident tuberculosis
  • Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing
  • HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis (Swiss HIV Cohort and Molecular Epidemiology of Tuberculosis Study Groups,
  • Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low incidence country (Swiss HIV Cohort and Molecular Epidemiology of Tuberculosis Study Groups,
  • Tuberculosis mortality and living conditions in Bern, Switzerland, 1856-1950
  • Influenza pandemics and tuberculosis mortality in 1889 and 1918: analysis of historical data from Switzerland
  • HIV viral load as an independent risk factor for tuberculosis in South Africa