Characterisation of SARS-CoV-2 transmission dynamics, clinical features and disease impact in South Africa: a setting with high HIV prevalence


  • Prof Cheryl Cohen

    National Institute for Communicable Diseases, South Africa

  • Dr Cecile Viboud

    Fogarty International Center, USA

  • Dr Jinal Bhiman

    National Institute for Communicable Diseases, South Africa

  • Prof Juliet Pulliam

    Stellenbosch University, South Africa

  • Prof Neil Martinson

    University of the Witwatersrand, South Africa

Project summary

Factors prevalent in Africa such as malnutrition, HIV, tuberculosis and limited access to healthcare may impact both transmission dynamics and disease progression associated with SARS-CoV-2 infection, as well as the burden on the healthcare system and society.

We aim to characterise the key transmissibility and clinical features of, and the antibody response to, SARS-CoV-2. We also aim to enhance surveillance for COVID-19, identify groups at increased risk of severe illness, estimate the disease burden of medically- and non-medically attended mild, severe-non-fatal and fatal illness, and forecast the impact of the outbreak on the healthcare system and society in South Africa. 

Particular emphasis will be given to HIV-infected individuals. We will achieve the aims by implementing shedding and household transmission studies, collecting sequential serum samples, enhancing facility-based (hospitals and clinics) surveillance among patients with mild and severe respiratory illness in well-established population-based surveillance sites where incidence can be calculated, and carrying out healthcare utilisation and serological surveys in selected communities. 

In addition, digital surveillance based on Google searches will be used to complement virological surveillance. Nowcasting and short-term forecasting (up to four weeks) will be implemented over the duration of the epidemic.