Household Study of COVID-19, Influenza and RSV Burden, Transmission Dynamics and Viral Interaction in South Africa

The study aims to characterize the community burden (including the clinical features) and transmissibility of SARS-CoV-2 within the context of a functional antibody response. In addition,the study will assess the effect of the interaction of SARS-CoV-2 with influenza virus and RSV on disease severity and transmission dynamics. A household-level prospective cohort study will be conducted in one rural and one urban community located in Mpumalanga Province and North West Province, respectively. The study will be conducted for 12 months of intensive follow up (July 2020 to August 2021) with a post-intensive follow-up continuing for a further 16 months (until December 2022). Two hundred households; 1,000 study participants of all ages; will be randomly selected from a list of 327 hoseholds that participated and successfully completed a 10-months follow-up period in a study similar to that currently proposed, but directed at community burden and transmission dynamics of influenza, respiratory syncytial virus and other respiratory pathogens. Each household and household member will be enumerated and the HIV infection status and the level of immunosuppression of HIV-infected individuals will be assessed. Each household member will be followed twice per week during the intense follow-up period (12 months) of the study. During this period upper respiratory tract samples will be collected irrespective of presence of symptoms and data on key symptoms, healthcare seeking, hospitalization and death will be captured at each follow up visit. Respiratory samples will be tested by reverse transcriptase real-time polymerase chain reaction (rRT-PCR) for SARS-CoV-2, influenza and RSV, and selected samples will be cultured and sequenced. An infection risk questionnaire will be administered to all study participants at enrollment and every month thereafter. Sera will be collected at enrollment and every 2 months during the 12-month intense follow-up period from all participants. In additi