Use of Available Data To Inform The COVID-19 Outbreak in South Africa: A Case Study

Abstract

The coronavirus disease (COVID-19), caused by the SARS-CoV-2 virus, was declared a pandemic by the World Health Organization (WHO) in February 2020. Currently, there are no vaccines or treatments that have been approved after clinical trials. Social distancing measures, including travel bans, school closure, and quarantine applied to countries or regions are being used to limit the spread of the disease, and the demand on the healthcare infrastructure. The seclusion of groups and individuals has led to limited access to accurate information. To update the public, especially in South Africa, announcements are made by the minister of health daily. These announcements narrate the confirmed COVID-19 cases and include the age, gender, and travel history of people who have tested positive for the disease. Additionally, the South African National Institute for Communicable Diseases updates a daily infographic summarising the number of tests performed, confirmed cases, mortality rate, and the regions affected. However, the age of the patient and other nuanced data regarding the transmission is only shared in the daily announcements and not on the updated infographic. To disseminate this information, the Data Science for Social Impact research group at the University of Pretoria, South Africa, has worked on curating and applying publicly available data in a way that is computer readable so that information can be shared to the public-using both a data repository and a dashboard. Through collaborative practices, a variety of challenges related to publicly available data in South Africa came to the fore. These include shortcomings in the accessibility, integrity, and data management practices between governmental departments and the South African public. In this paper, solutions to these problems will be shared by using a publicly available data repository and dashboard as a case study.

A rapid and reproducible picture of open access health facility data in Africa to support the COVID-19 response

“…The lack of such capacity data for South Africa has prompted a group of researchers and volunteers to collate health facility and testing centre data ( Marivate & Combrink, 2020 ). Publicly available data from the Department of Health in South Africa ( NDOH, 2020 ) does not contain information about availability of beds, services or resources.…”

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

“…We analysed daily cases of SARS-CoV-2 in South Africa up to 14 December 2020 from publicly released data provided by the National Department of Health (NDoH) and the National Institute for Communicable Diseases. This was accessible through the repository of the Data Science for Social Impact Research Group at the University of Pretoria (https://github.com/dsfsi/covid19za) 11,12 . The NDoH releases daily updates on the number of confirmed new cases, deaths and recoveries, with a breakdown by province.…”

Bayesian inference of COVID-19 spreading rates in South Africa

“…Due to its further spread and the severity of its associated clinical outcomes, the disease was subsequently declared a pandemic by the World Health Organisation (WHO) on 11 March 2020 [ 1 , 2 ]. In South Africa, by 26 April 2020, 4546 people had been confirmed to have been infected by the coronavirus with 87 fatalities [ 4 ].…”