South Africa's COVID-19 response: Surprising outcomes or just poor data management?

South Africa has been committed to improving its health information system and shows that a robust digital has considerable scope to improve healthcare for the entire population. But the COVID-19 pandemic has highlighted that significant gaps remain for the country to achieve its goals.

South Africa is already the worst-affected African country by the COVID-19 pandemic with its official tally of cases inching above 6,65,000 and deaths at 16,206. But, in reality, the actual situation could be far worse. Health Minister Dr. Zweli Mkhize has implied that about 20 percent of the population – 12 million people could have been infected by the virus at some point.

Mkhize implied this while raising questions on immunity to COVID-19 that exists in the South African population but this also raises a question on the accuracy of the official death toll in the country as the actual number of infected people is believed to be almost 20 times more than the official tally of cases.

Shabir Madhi, a professor of vaccinology at Johannesburg’s University of the Witswatersrand has said that roughly 30,000 people could have died from COVID-19 but even that number is significantly lower compared to the death rate in other countries. At the start of the pandemic, it was feared that poverty, crowded townships, inadequate access to clean water, and the prevalence of other deadly diseases like tuberculosis and HIV could mean South Africa’s health system could be quickly overwhelmed by the outbreak. So far, that hasn’t happened, at least according to official statistics and initial estimates.

Getting an idea about the actual picture can be quite tricky in absence of nationwide surveys or an integrated information system that connects all stakeholders and provides all relevant information in one place, including the all-cause mortality data.

Another much-highlighted issue of South Africa’s fight against COVID-19 is the protests by healthcare workers that are demanding wage hikes, better working conditions, and more information on cases among healthcare workers.

In this analysis, we evaluate different aspects of South Africa's COVID-19 response and how better information management could have helped the country better manage this pandemic.

COVID-19 response

South Africa started preparing for COVID-19 weeks before the first confirmed case on March 5. The National Institute for Communicable Diseases (NICD) started testing people for then-unnamed disease on January 28.

The outbreak was declared a Public Health Emergency of International Concern (PHEIC) on January 30 by the World Health Organization and South Africa’s Health Department acted quickly by activating an emergency operations center for the outbreak on the same day. In addition to the operations center, the department also designated 9 hospitals for isolation and treatment of infected people.

Since then, the country has acclaimed that its response is “based on science”, which was a sigh of relief considering South Africa’s history of political leaders doubting that HIV causes AIDS. On March 15, President Cyril Ramaphosa declared a national state of disaster and the country went into lockdown on March 26. On paper, it seemed that the country is doing everything right but that was clearly not the case on the ground.

In mid-April, the narrative was that South Africa’s lockdown was working well and the country was even planning to reopen economic activities. The reality, however, was very different as the country only had a fraction of cases in April than what it has now and testing was lagging behind the country’s own daily targets.

• Not engaging with communities

Within the first few weeks of nationwide lockdown, incidents of violence, looting, and protests were reported from various parts of South Africa as millions of poor people went hungry in absence of daily wage. Poor communities increasingly faced food shortages as a significant portion of South Africans is employed by the informal sector, incomes from which quickly dried up due to strict lockdown measures.

Several violent protests also broke out across the country in April itself over missing and undelivered food parcels promised by the government.

Early on in South Africa’s fight against COVID-19, it was realized that the situation of many residents might have been overlooked and their needs weren’t planned for while implementing restrictions.

South Africa is ranked one of the most unequal countries with 20 percent of the population believed to have inadequate access to food and many live in tough conditions which makes social distancing unfeasible and access to clean water is inadequate.

At various points of time, by various critics, authorities have been blamed for not fully understanding the problems of communities before drafting a response and relying primarily on the elites for consultations.

• Testing lapses

Although South Africa was quick to implement a lockdown, testing lapses could have reduced its effectiveness. During and even before the lockdown, health experts had advised that a lockdown would only help in reducing infection rate if it is complemented by scaling up complementary testing and tracing strategy as well as measures to mitigate the effects of lockdown on the poor.

But that wasn’t done. NHLS boasted of having the capacity to perform 15,000 tests a day on April 9 but the average number of tests per day in the first 10 days of April was below 5,000 and a significant number of even those tests were done by the private sector.

South Africa ultimately managed to increase its testing capacity and is leading the African continent in terms of tests performed. But even the increased capacity was not effective due to backlogs at NHLS.

Initially, the service had maintained that there are no backlogs before finally admitting to about 83,000 unprocessed specimens in the queue for testing as of May 28.

Several accounts of doctors waiting for days or even weeks to receive COVID-19 test results were published in media reports in May which led authorities to come out with the real picture. Delays in getting test results mean patients are already in advanced stages of infection by the time results arrive and, in many cases, are even allowed to further spread the infection.

An automated health information system can help in identifying bottlenecks across the health system and increase accountability by integrating all stakeholders.

Testing can only help in containing COVID-19 if results are received timely enough to trace contacts of infected people. Backlogs pending up to days and even weeks mean that testing and tracing cannot be effective no matter how many tests are conducted.

• Data problems

Although Ministry of Health’s spokesperson Dr Lwazi Manzi sent out daily updates on the number of tests, cases, recoveries, and deaths, critics have complained that some key information was held back including the actual testing capacity, how much of it is utilized, and tests as well as cases with a breakdown by age and gender. This information is critical for making effective decisions.

The government has also admitted to holding back modeling data from the public being “mindful of the stigma of the virus”. That data was being used to make key decisions including extensions of lockdown.

There were problems in data collection as well. Medical professionals and experts have raised concerns over old infrastructure as well as decentralized reporting systems that hinder the effectiveness of COVID-19 reporting mechanisms.

South African Medical Association’s (SAMA) chairperson Dr Angelique Coetzee has said that “the provinces are still on a paper system. We are in the fourth industrial revolution, but our healthcare system is still in the first industrial revolution.”

Paper-based data collection and reporting not only delays the process but also significantly increases the burden of staff. An automated health information system, on the other hand, can help strike the right balance between reporting and operational work of healthcare workers along with enabling the generation of a variety of information, including patient diagnosis, admissions, comorbidities, and deaths.

The National Institute for Communicable Diseases (NICD) has established a sentinel hospital surveillance system, DATCOV, to monitors and describe trends related to COVID-19. Interim director of the NICD Professor Lynn Morris has said that patient demographics get collected at the time of sample collection, however, the completeness of the data varies depending on labs. She also acknowledged that there are some delays in reporting, however, "most hospitals reporting through the DATCOV system do so consistently."

• Corruption

In a report about how various South African government departments spent the COVID-19 relief package, Auditor-general Kimi Makwetu revealed that there are “clear signs” of overpricing, potential fraud, and sidestepping of supply chain management legislation.

He also noted that there is a lack of validation, integration, and sharing of data across government platforms that results in erratic disbursements of government aid. Poor management of data is a problem also shared by the health system of South Africa.

The report uncovered “frightening findings” that included personal protective equipment (PPE) like masks, gloves, and kits being bought for as much as five times more than the price advised by the national treasury.

Further investigations will also be done at the municipal level on the spending of the funds that were meant to assist vulnerable households with food parcels, unemployment grants, support small business, farmers.

President Ramaphosa has also reacted to the public fury regarding the COVID-19 corruption, which he says has ‘infected’ South Africa. He has also penned an open letter to all members of his party asking them to stand against those who have exploited the funds meant to tackle the pandemic.

• Health workers’ protests

South African healthcare workers have protested against poor working conditions, wages, inadequate information about the screening of health workers, and urged the government to end corruption in the purchase of COVID-19 personal protective equipment.

Among other demands, they have also asked for better dissemination of information about COVID-19 cases among health workers. “When our workers ask for information about infections, they are charged by their managers, yet the minister releases statistics every day,” said National Education, Health and Allied Workers' Union (NEHAWU) leader Zola Saphetha.

In another report on the state of the public healthcare system, the union raised concerns about the accuracy of government COVID-19 statistics, particularly on the rate of infection and deaths per district. "Almost in all institutions, it was commonly held that there was a deliberate under-counting, especially with regard to the recorded and reported incident and causes of deaths," the report said. An effective health information system can connect all stakeholders and simplify the cumbersome process of getting access to reliable data.

The report also raised concerns about the system of data collection across institutions saying that “(the challenges faced by) DATCOV Surveillance System in gathering data validates this view in that there seems to be no uniform or standardized method of recording across the institutions.”

• Low death rate, or is it?

Although South Africa has some of the best data collection mechanisms in Africa, the current situation has shown that there’s still a huge scope for improvement.

According to official statistics, South Africa’s death rate is 2.4 percent compared to 9.9 percent in the United Kingdom, 6.1 percent in Canada, and 11.7 percent in Italy.

But as mentioned earlier, experts have said that deaths and cases could be far higher than the official statistics. One report by the South African Medical Research Council (SAMRC) had said that excess natural deaths in the country rose by 17,000, a 59 percent increase compared to past years. This report was released at a time when the country had only recorded about 6,000 deaths and the official toll has now crossed 16,000.

In absence of reliable all-cause mortality data and an integrated health information system, it's still far too early, and difficult to estimate real numbers.

South Africa’s health information system

The South African government’s commitment to a robust health information system has been longstanding and articulated by a series of investments and various policy documents. Hence, it’s clear that there is an enabling policy environment for the development of a health information system to measure quality.

Over the past many years, South Africa has taken several initiatives to improve its health information system. With the District Health Information System, the country took the first step in 1996. The system has since been embedded in health facilities across all provinces and has even transitioned to WebDHIS being used for routine data collection, analysis, and utilization for decision making.

However, the partial electronic stage of South Africa’s health information systems causes problems like that of interoperability, unavailability of patient-level data, and issues in reporting aggregated data across public and private health sectors, or across levels of care pathways.

Experts have also raised concerns about the number of health indicators included for reporting purposes saying that there is no clear delineation to the health outcomes that some of them support.

Interoperability remains an issue as numerous health measurement platforms exist that provide information on health system inputs, processes, service delivery, outcomes, and impacts. Despite these platforms, data quality remains a significant barrier to assessing health-system performance on quality of care, as acknowledged in a report by the South African Lancet National Commission.

Health Patient Registration System (HPRS): Prepared for the National Health Insurance (NHI), this system is considered as the most reliable and vast source of patient demographic data in South Africa. This system allows identity verification when patients interact with the health system and have already registered more than 44 million people in an electronic system.

HPRS is often touted as a pre-requisite for the development of a nationwide patient electronic health record (EHR). The country is already working to achieve that and the eHealth Strategy 2019-24 says that “the diagnostic, treatment and billing modules needed for an EHR in the context of NHI are yet to be developed.”

Yet, several reports have quoted healthcare workers as saying that health records remain a mess, especially in the public sector. As pointed out earlier, some places still keep paper-based records and interoperability remains a major issue as other databases like that of laboratories and TB haven’t been linked to this system.

DATCOV Surveillance System: This hospital surveillance system was established by NICD to monitor and report COVID-19 hospitalization trends across South Africa. This system was aimed at supporting the country’s COVID-19 response by providing critical information needed for effective decision-making.

DATCOV system was explained to the public and private hospitals of all nine provinces and they were invited to register as users and share information. Through the system, hospitals can share the following data elements on COVID-19 admissions: demographic data; clinical information including comorbidities; clinical care including intensive care unit admission, ventilation, and drugs received; and outcomes such as death, discharge, transfer, or admissions.

The NICD, which assists the government in collecting COVID-19 data, is reportedly gathering the data from about 75 percent of hospitals across the country. But according to the interim director of the NICD, Professor Lynn Morris, there are some delays in reporting, however, "most hospitals reporting through the DATCOV system do so consistently." She has also said that the completeness of COVID-19 data varies between different labs.

Several other problems persist with the health information system of South Africa:

• Paper-based recording

While electronic systems have been implemented in a few areas, the significant number of public health centers in South Africa still make use of a paper-based record system.

Primary health care (PHC) is mainly provided by nurses at community health centers (CHCs) and clinics in the public health sector, which is under-resourced and there is insufficient expertise to support electronic data collection methods. Information required for monitoring and evaluation purposes by the Department of Health is often handwritten by nurses within each clinic and then aggregated for data capturers to be entered in electronic HIS. This process is associated with poor data quality and a high work burden for health workers.

• Capacity problems

Lack of infrastructure including computer equipment as well as reliable internet connectivity is also often highlighted as a further challenge to implementing HIS systems. This has been a particular difficulty in remote areas and such systems need more equitable access to high-quality telecoms infrastructure. Yet another challenge is the lack of technical know-how for data collection and analysis.

These gaps have resulted in differing levels of advancements within and across provinces with non-interoperable HIS being deployed, which leads to duplication of effort and discrepancies in reporting.

Insufficient expertise and training of healthcare workers in electronic systems also lead to the suboptimal collection, utilization, and reporting of data.

• Interoperability issues

South Africa eHealth Strategy 2019-24 has also acknowledged that “fragmented and poorly coordinated systems” remain one of the strategic challenges in the country’s eHealth journey.

Referencing to information systems assessments by CSIR, the strategy adds, “several individual systems had been developed to address various aspects of the health system, but there needs to be a further development of architecture and an integrated platform to make them interoperable.”

A plethora of electronic systems has flooded the South African health system in recent years due to which little or no communication is possible between different systems which makes it difficult for institutions to work together. There has since been a greater focus on the need to synchronize systems.

Conclusion and agenda for discussion

Interoperability and lack of training of ground-level workers seem to be the biggest problems faced by South Africa's health information system. But the country has set up a good base for national-level EHR by enrolling the majority of the population in HPRS. The next stage should be making different systems interoperable and integrating all stakeholders into the system after taking appropriate security measures.

South Africa has been committed to improving its health information system and shows that a robust digital has considerable scope to improve healthcare for the entire population. But the COVID-19 pandemic has highlighted that significant gaps remain for the country to achieve its goals.

VisionRI's Centre of Excellence on Emerging Development Perspectives (COE-EDP) aims to keep track of the transition trajectory of global development and works towards conceptualization, development, and mainstreaming of innovative developmental approaches, frameworks, and practices.