Completed Infection & Immunity Public Health & Healthcare

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

Funder Wellcome Charity-funded
Associated organisations Fogarty International Center · National Institute for Communicable Diseases · Stellenbosch University · University of the Witwatersrand Europe PMC affiliations are not treated as award recipients or mapped locations.
Funding £2.0M
Period Jul 2020 — Jun 2022

In plain English

AI plain-English summary

South African researchers are tracking how SARS-CoV-2 spreads through households and communities where one in five adults live with HIV, to see whether co-infection changes who gets severely ill and how the virus transmits. The problem is that nearly all early COVID-19 data came from wealthy countries with low HIV rates. South Africa has high HIV prevalence, widespread tuberculosis, and limited healthcare access—factors that could alter both transmission dynamics and disease severity. Without local data, hospitals cannot predict surges, and public health measures may be misdirected. The team will run household transmission studies, collect sequential blood samples to track antibody responses, and conduct enhanced surveillance at clinics and hospitals in established population sites where they can calculate infection rates. They will also use Google search trends for nowcasting and produce short-term forecasts up to four weeks ahead. If successful, the work will give South Africa’s health system real-time epidemic forecasts tailored to its population, identify which groups—especially people living with HIV—need priority protection, and provide a model for other African countries with similar disease burdens. The digital surveillance component could also become a low-cost early warning tool for future outbreaks.

View original technical description
Factors prevalent in Africa such as malnutrition, HIV, tuberculosis and limited access to healthcare, among others, 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 characterize key transmissibility and clinical features of and the antibody response to SARS-CoV-2 as well as 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 the society in South Africa. Particular emphasis will be given to HIV-infected individuals. The aims will be achieved through the implementation of shedding and household transmission studies, collection of sequential serum samples, enhanced facility-based (hospitals and clinics) surveillance among patients with mild and severerespiratory illness in well-established population-based surveillance sites where incidence can be calculated, and healthcare utilization and serological surveys in selected communities. In addition, digital surveillance (based on Google searches) will be used to complement virological surveillance and nowcasting and short-term forecasting (up to 4 weeks) will be implemented over the duration of the epidemic.

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Researchers

Cecile Viboud (EPMC Awardee)Cheryl Cohen (EPMC Awardee)Jinal Bhiman (EPMC Awardee)Juliet Pulliam (EPMC Awardee)Neil Martinson (EPMC Awardee)

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Original classification

Coronavirus

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