>>COVID-19 Response

In late 2019, a cluster of cases of severe pneumonia were identified in China, now known to be caused by a newly identified virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This cluster of cases quickly spread worldwide, causing severe disease and a high mortality rate in the elderly, those with chronic co-morbidities, and the immunosuppressed. The South African National Institute for Communicable Diseases (NICD) reported its first cases on the 5th of March 2020, and by 18 May 2020 had reported 15 515 cases with 264 deaths. Critical to effective prevention, control, and response to the Coronavirus Disease 2019 (COVID-19) epidemic will be a nationally coordinated system of disease surveillance, to enable both rapid detection of transmission geography and allocation of scarce prevention and intervention resources to areas of highest need. The South African Population Research Infrastructure Network (SAPRIN) is a well-positioned partner to take on this surveillance exercise. It is a Department of Science and Innovation (DSI)-funded national network of health and demographic surveillance research infrastructures, hosted by the SA Medical Research Council. SAPRIN has three nodes (in Mpumalanga, Limpopo and KwaZulu-Natal) running a longitudinal whole population platform, and are able to rapidly leverage their ongoing household health and socio-demographic surveillance to assist with the COVID-19 pandemic monitoring and response, through the provision of accurate information about outbreak knowledge, spread, and impacts should COVID-19 penetrate the rural communities where SAPRIN operates.

In the MRC/Wits-Agincourt Unit, which runs the Mpumalanga node, we added a COVID-19 specific questionnaire to our telephonic surveillance with a proxy in each household (~20 000 households), starting from May 2020, as well as a more indepth fortnightly surveillance of 750 households for 2 years.

Call centre agents at work in the MRC/Wits-Agincourt Unit state of the art call centre

We are glad to report that the Agincourt HDSS is proving its adaptability to respond to this crisis. In March, South Africa had no data on the possible rural impact of COVID-19. The MRC/Wits-Agincourt Research Unit responded to this worrying gap by working with the Human Sciences Research Council (HSRC) and the South African Population Research Infrastructure Network (SAPRIN). Taking advantage of our existing infrastructure and experience in telephonic surveillance, a study was completed with over 1300 participants randomly selected from our existing HDSS database, and sought to investigate awareness of COVID-19 symptoms and preventive measures, as well as the impact of South Africa’s national lockdown. The data contributed to a national study.

100 key stakeholders such as health care workers, home based carers, participants in a project focused on public involvement in health care decision making, educators and community leaders are currently being interviewed about their experiences since South Africa’s lock down, and this will form the basis of a report highlighting rural voices, to be used to guide further health service planning and research.

We knew that we had to urgently help the Mpumalanga Province’s COVID-19 response by intensifying public engagement activities, appointing a full time medical doctor to lead the Bushbuckridge sub-district COVID-19 Response in Research & Development Strategy, and seconding another doctor, the Head of Public Engagement and other staff to augment this effort. We are working with local authorities and community groups; the three hospitals and 40 clinics in the sub-district and the community screening teams. It has been interesting to note the speed at which this team was established to strengthen the health system in the sub-district. Data from the HDSS and the existing clinic link project is being leveraged to assist service providers with making decisions about the health and social response to the pandemic. Currently, we are making headway in assisting the sub-district develop and analyse data from screening, testing, and future admissions of COVID-19 cases – as we write, on day 60 of lockdown, three cases have been confirmed in the sub-district.

Collaborators: MRC/Wits-Agincourt Unit; National Institute of Communicable Diseases, South Africa; Usher Institute, School of Molecular, Genetic and Population Health Sciences, University of Edinburgh; and Social Work, School of Political and Social Sciences, University of Edinburgh
Building on our partnership with the National Institute for Communicable Diseases (NICD), we have embarked on data collection from individuals from the Agincourt health and socio-demographic surveillance system (HDSS) who seek care from the hospitals serving the subdistrict, namely, Matikwane, Mapulaneng and Tintswalo. Our current focus is on those presenting with respiratory conditions and any other chronic disease. This is an extension of our ongoing population-clinic link project, where we have been collecting data since 2014 from patient records of all those seeking care in the eight public sector clinics within the Agincourt HDSS. Working with an NICD team led by Prof Cheryl Cohen, we will augment data collected through the population-clinic link system with more focus on data collection of pneumonia and influenza-like illnesses in these eight clinics and the three hospitals. This will allow the well-functioning population-clinic link system to comprehensively assess the burden of illness including respiratory conditions and co-morbidities. Given COVID-19 and the potential rising burden on secondary and tertiary care, this will allow fuller understanding of patient linkage-to-care from community-to-clinic-to-hospital, their health outcomes, and the effects of interventions. The collection of data in the hospitals is initially funded for 3 months (May-July 2020) by a grant from the University of Edinburgh.

As the COVID-19 epidemic continues to grow in South Africa, the MRC/Wits-Agincourt Unit, working closely with the National Institute of Communicable Diseases (NICD), has begun implementing the second round of the PHIRST study, with additional work on SARS-CoV-2, so the study name is now PHIRST-C. PHIRST-C stands for “A Prospective Household study of SARS-CoV-2, Influenza, and Respiratory Syncytial virus community burden, Transmission dynamics and viral interaction in South Africa. It aims to characterize the community burden (including the clinical features) and transmissibility of SARS-CoV-2 within the context of a functional antibody response through frequent testing of study participants. In addition, it will assess the effect of the interaction of SARS-CoV-2 with influenza and respiratory syncytial viruses on disease severity and transmission dynamics. We will conduct a household-level prospective cohort study from an early stage of the epidemic in the Agincourt health and socio-demographic surveillance site in rural Mpumalanga and in urban Klerksdorp in the North West. The study will be conducted for 6 months from July-December 2020 with post-study follow-up continuing for a further 12 months.

This study will provide essential information on the natural history of the virus that will impact decisions on optimal strategies for the containment and mitigation of the current and potential future epidemics of SARS-CoV-2 locally, regionally and globally.

PHIRST C fieldwork training in the MRC/Wits Agincourt field offices

Members of the MRC/Wits-Agincourt Unit staff have already undergone rigorous training in COVID-19 safety and prevention and are excited to get into the field. We look forward as a Unit to adding meaningful contributions to the global COVID-19 response.