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Pandemic Preparation – the government needs to set up a permanent response initiative urgently

Pandemic Preparation – the government needs to set up a permanent response initiative urgently
Residents are tested for Covid-19. South Africa's world-expert laboratory scientists were able to drive the development of locally relevant Covid-19 tests. (Photo: Dino Lloyd)

A pandemic preparedness strategy should be a high-level, cross-cutting mechanism to coordinate the national components of a robust public health initiative that plans for future pandemics and activates emergency responses when a new pandemic risk develops.

This is an updated version of an early essay on Daily Maverick in April 

The Covid-19 pandemic came as no surprise to infectious disease specialists, as this had been anticipated for decades. Although the spread of a virus from one species to another is, fortunately, a relatively rare event, viruses do have potential to adapt to a new species environment with the potential to spread to become a pandemic. Therefore, it is imperative that countries develop robust strategies for responding to pandemics, supported by clear operational plans at national and subnational levels. This piece argues in favour of a structured, nationally mandated and coordinated, permanent programme to achieve this.

Almost two decades before Covid-19, we were warned of this risk with the spread of two other coronaviruses to humans. There was the “first” Severe Acute Respiratory Syndrome (SARS-CoV-1 virus) in 2002-4, which spread from bats and infected about 8,000 people in China and had a mortality of 8%. Again in 2012, the Middle East Respiratory Syndrome (MERS) virus spread from camels to humans and infected 2,500 people, killing more than 30% of those infected. Pandemics such as HIV/Aids, influenza and Zika are among those that have spread to humans and added to significant human suffering and death. The 2013-16 epidemic of Ebola in West Africa caused 11,323 deaths and had significant human suffering and socioeconomic impact on Africa.

Despite these warnings, the world was still caught unprepared for a pandemic such as Covid-19. As millions succumbed to the various waves across the globe, hospitals became overwhelmed, PPE supplies were in short supply, oxygen was unavailable for severely ill patients, diagnostic tests were unavailable and scale-up took months instead of days/weeks. Surveillance systems were lacking in most parts of the world, and appropriate national intervention teams often did not exist – even in the most resourced countries. Even when effective vaccines were developed in a timely manner, there were limited national plans for acquisition and equitable distribution. Manufacturing capability in LMICs was limited to countries like India. Investing in long-term public health does not garner votes and is just not attractive politically almost anywhere in the world.

The result of this lack of pandemic preparedness was that millions died, the global economy tanked in many regions and, as usual, the poor and marginalised of the world were the worst hit.

We write in support of the South African government setting up a permanent, dedicated “Pandemic Preparedness and Response Initiative for South Africa (PPRISA)” as a matter of urgency. This PPRISA should be a high-level, cross-cutting mechanism set up to coordinate the national components of a robust public health initiative that plans for future pandemics, and then activates emergency responses when a new pandemic risk develops. It needs to be a centrally funded, autonomous body with agency and the national mandate to coordinate, fund and lead the national effort focused on preparing for the next pandemics. The PPRISA strategic plan needs to be a living document, reviewed at regular intervals, and guided by the latest evidence and global guidance, as well as lessons learnt from prior pandemics. The current impetus to vaccine discovery and manufacturing must not wane and our investment must continue beyond this current crisis.

We have learnt a tremendous amount from the Covid-19 pandemic, which we need to translate into action before the next pandemic. It will not be easy. A pandemic preparedness and response strategy should be built on generic preparedness platforms, structures and mechanisms, and should aim to strengthen existing national systems and relationships rather than building new ones. 

There are many elements that need to be included in PPRISA, some of which are shown in the figure below. A selection of these is described below.

The core elements:

A fully functional Public Health Institute

South Africa needs to establish a dedicated national public health institute (NPHI), which will integrate and expand the critical work currently undertaken by the National Institute for Communicable Diseases (NICD) and National Institute for Occupational Health (NIOH) – entities of the National Health Laboratory Service (NHLS). These entities have driven much of the responsibility for the role of a NPHI during Covid-19, but require an injection of resources to build further capacity and infrastructure. They also require sustained, sufficient and predictable funding that is ring-fenced, and the autonomy to respond adequately to future threats. 

The National Public Health Institute of South Africa (Naphisa) Act, although passed in 2020 in support of the establishment of such an initiative, has not materialised, suggesting inherent challenges that require rethinking such an institute. The experience garnered over the past two and a half years will allow for a fresh look at the proposed structuring of Naphisa, and determine any amendments to that act that may be required to integrate the institute into a broader pandemic preparedness and response body as envisaged herein as “PPRIS”.

We are of the opinion that, even if modifications to the act may be required, such a body must still be accorded a legislatively mandated role if it is to deliver on its mandate. The constituent parts of a Naphisa-like structure are critical public health elements, including laboratory capacity, surveillance, occupational health, epidemiologists and intervention teams.

Making the health system pandemic-prepared

The clinical burden of this pandemic has been particularly hard on healthcare staff and systems. Our health system is not resilient enough, and that led to a regression of services such as programmatic TB, HIV, and NCD treatment platforms, with the added pandemic stress. That translated into untold human suffering and increased mortality, as well as substantial morale injury for an overwhelmed health workforce.  

The health system needs to prepare now for the future, and ensure that the myriad issues are addressed, including staffing numbers, staff training, infrastructure (wards/ICUs/etc), supply chain systems, PPE stores, oxygen supplies, pharmaceutical supplies, laboratory services and IT systems. The health system needs to consider the possibility for temporary hospitals that might be built within short periods to manage acute surges in patients, as well as stocking the country better with essential supplies for those outbreak moments. This requires the health system to have “expandable capacity” that can be available during pandemics. Pandemic preparedness requires that surge capacity plans and business continuity plans are developed for the health and other sectors to ensure sustained capacity during a pandemic. The need for temporary field hospitals around the country during “waves” requires planning, along with a more nimble workforce structure that can expand its capacity to attend to vastly increased numbers of patients.

Residents queue for Covid-19 tests in Alexandra, Johannesburg, on 27 April 2020. (Photo: EPA-EFE / Kim Ludbrook)

The next pandemic may be a respiratory disease like SARS-CoV-2, or something different such as a new gastroenteritis disease, or a meningitis, or other diseases such as those caused by antimicrobial resistance. We need to have well-considered disaster management plans in place to deal with all of these, and a health system prepared to respond.

It is more than ‘health’ – an integrated response from multiple government sectors

While focusing on the health system is important, PPRISA is going to have to be a cross-cutting initiative with a mandate across multiple departments, as infectious disease pandemics cut across all elements of society.

The Covid-19 pandemic, along with lockdowns and associated travel bans, among others, demonstrated the need to ensure that almost all government departments are coordinated. For example, the school and post-school sectors are significantly affected, and both the departments of Basic Education and Higher Education and Training need to be aligned with the health impact. In addition, the economic and social impacts of pandemics are enormous, thus demanding the focusing of all relevant departments. The same applies when there are restrictions on movement relating to lockdowns and/or travel restrictions, and involve the Department of Home Affairs and policing. Treasury is the ultimate funder of interventions, including preparedness activities, and therefore needs to be a central cog in a coordinated PPRISA.  

It is clear that the poor, the marginalised and those discriminated against suffer a disproportionate burden of the pandemic, and women have been exposed to higher levels of marginalisation and domestic violence. It is thus critical that the relevant departments of Social Development and Women Youth and Disabilities play a central role.

Communication and messaging are critical and need to be improved, and thus government communications systems need to be harnessed.

Diagnostic capacity

Laboratories around the globe were unable to perform the volumes of tests required early in the epidemic. New tests needed to be developed rapidly, and these then needed to be bulk-produced by global manufacturers of laboratory test kits. But the major laboratory systems that test samples in bulk are all produced by a limited number of suppliers, and their supply chains are constrained in these situations. It is extremely hard to compete on such testing “platforms”.

South Africa was in some ways fortunate, as the major PCR testing platforms that are used for HIV and TB are the same as those rolled out for SARS-CoV-2 PCR testing. South Africa has the highest HIV numbers in the world and thus had many of these machines. However, it was like many countries in being unable to procure sufficient SARS-CoV-2 PCR test kit volumes that run on those “platforms.” South Africa needs to address this supply chain challenge and develop plans to build the South African diagnostic tools for the next pandemic. When preparing for the next pandemic, it is untenable that a small number of global diagnostics companies have almost complete control of diagnostic platforms, and tight bottlenecks in supply chain systems that mean that countries cannot access nor manufacture the test kits in bulk when required.

Vaccine capacity

South Africa has impressive credentials in some of the areas of vaccine capacity but has been found on the back foot in other aspects. The world powers have dominated the vaccine R&D space, and when vaccines came on the market, these same wealthy countries bought up almost all supplies, and low- and middle-income countries were excluded from accessing sufficient vaccine stocks.

South Africa needs to invest significantly in the continuum of vaccine development at three levels. First, we need to see a return of significant investment in basic research for novel vaccine platforms. This capacity was accelerated with major government funding during the earlier times of HIV vaccine development, but now receives limited support.  Second, manufacturing sites for small volumes of vaccines under development need to be considered for greater investment, so that pilot volumes can be manufactured for clinical trials. Third, investment in capacity for bulk manufacture of vaccines needs to happen over decades, to ensure that we can manufacture the modern types of vaccines now used, such as mRNA-based and “vectored” vaccines.

All three elements of the vaccine continuum listed above take time and much investment in people, policy, governance and infrastructure. South Africa needs to leverage its position as much as possible and choose wisely when investing.  

Therapeutics, including generic medication capacity

South Africa has a growing body of companies that manufacture generic medications. However, this area has massive potential and needs further strategies that harness the current private-sector powers as well as develop new capabilities. For example, South Africa has limited active pharmaceutical ingredient (API) manufacturing capability. As API supply chains are constricted globally, and are substances critical to a finished pharmaceutical vaccine or drug, this needs to be addressed.  South Africa’s human resources in this area also need to be built up over time, with private-sector and higher education institutions collaborating to achieve this.  


A central limitation in manufacturing novel vaccines and medications that work against pandemic infections is the private-sector players in the wealthy countries which limit access to products through aggressive patent protection and not granting non-exclusive licences to others. This age-old profit-driven strategy where poor countries do not access novel drugs and vaccines equitably only serves the wealthy countries, and needs revision of international norms, ethical practices and models of distribution.


This article does not attempt to list all the relevant areas of research that are required. The best way to be prepared for a pandemic is to invest long-term in research projects that prepare data and people to be ready.

We note the importance of governance structures such as the Department of Science and Innovation, working with the Department of Higher Education and Training. These need to be given an expanded mandate to fund pandemic preparedness work, together with the universities, science councils, private research organisations and all other bodies in this area. We note the recent move by the National Research Foundation to fund various new research programmes in this area, and we applaud this. But it is not enough. A PPRISA needs to expand this dramatically.  

It is important to note that we do not propose just more “health research”. There are myriad research areas – from social to economic, business, population, health, policy and other areas too long to list – that are all required for optimal pandemic preparedness.  

Laboratory research capacity

South Africa has been fortunate to have some of the leading laboratory scientific minds pivot from their previous work on HIV, TB and other diseases to SARS-CoV-2. This capacity was built up over decades in fields including virology, genetic diversity, immunology and vaccinology. These world-expert laboratory scientists were able to drive the development of locally relevant Covid-19 tests, as well as detect the newer variants of SARS-CoV-2 and understand the immunology of vaccine protection over time. However, this capacity needs to be strengthened further to ensure greater pandemic preparedness in the future. The importance of long-term surveillance of circulating animal and human viruses cannot be overstated, including dedicated laboratory surveillance teams looking at genetic variation. 

Long-term environmental surveillance of wastewater and other relevant sources has been a critical indicator of new waves of Covid-19, and is an example of the types of environmental surveillance work that should be supported to prepare for future pandemics.

Clinical research capacity

Each new disease requires in-depth clinical research to understand how best to treat patients, and to reduce suffering and death. South Africa is a unique environment, with high levels of other diseases (HIV, TB, non-communicable diseases) in addition to Covid-19, and this needs local research to understand how best to treat optimally.  

Clinical research in South Africa needs to be strengthened further to ensure it maintains its position as a global force in delivering cutting-edge solutions. This does not happen passively. The government needs to lead and work with national and international funding bodies, universities, science councils and clinical teams to build the required skilled staff, review bodies and clinical systems to run major trials and interventions to optimally treat new diseases as fast as possible. This capacity takes many years to build and requires consistent investment to bear fruit.

Zoonotic disease capacity

Pandemics in humans occur when a microbe of another animal species “jumps” to humans. This has been true for SARS-CoV-2, MERS, SARS-1, Ebola, Zika and HIV, etc. Thus, the importance of addressing zoonotic diseases cannot be underestimated. The “OneHealth” approach to pandemics looks at the entire microbe ecosystem of humans and animals, and looks to safeguard both over time and understand how to reduce the risk to transmission between species.  

The OneHealth approach needs considerable investment, ensuring that those addressing human infections and those studying animal diseases are optimally linked and funded to reduce the future risks.

Regulatory body capacity

South Africa is fortunate to have had a longstanding history of a regulatory body that governs the clinical trials of new medicines and vaccines, as well as being the agency that licenses those which are shown to be effective and safe. The South African Health Products Regulatory Authority (Sahpra) – analogous to the US FDA – is a critical cog in the pandemic preparedness system, which should be strengthened further.  

In a “post-truth” age where there are systematic attacks on whether novel vaccines and drugs should be used widely, the importance of a science-driven regulatory body with sufficient autonomy and capacity to independently review clinical trial applications, as well finally license vaccines and drugs, is critical. Their mandate to safeguard the population of South Africa through their detailed data review and oversight of each application should be expanded.

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There is a need to strengthen Sahpra within the regional and global context as well. The move to have a pan-African regulatory authority is positive, and Sahpra should be a driver of that. The WHO and other bodies are also trying to align national regulatory bodies across the globe, and South Africa has plenty to contribute to, and gain from, these efforts.

Where should it be?

If the proposed PPRISA is to work, it will need to be an entity with agency, empowered with an adequate coordinating mandate, together with financing, autonomy and ability to influence a wide range of sectors and institutions. PPRISA will need to have the people and mandate that crosses all government departments, state-owned enterprises (SAMRC, NHLS, CSIR, NRF, etc), universities, private research entities, the private sector, NGOs and other relevant bodies.  

Clinical associate Oupa Mofokeng helps a patient with a mobile oxygen unit to the bathroom during the Covid-19 pandemic. (Photo: Chris Collingridge)

The placing of this entity must ensure that it is empowered to create the future pandemic preparedness in a way that balances current needs with future requirements.

This may need a completely new entity, or an appropriate alignment within government that will allow for all these functions to develop. This needs to be an inclusive body, but government-led. This article supports the concept of a thorough due diligence to ensure that the entity is placed, structured, governed and financed appropriately.

Who should fund it?

The funding of this PPRISA needs to reflect the components described above. There is an obvious need for greater investment directly from Treasury, and from within the public and private components of the health sector, the science and research sectors, the animal health sectors, economic sectors, as well as the groups responsible for safe working and learning environments, etc. It is important that this is a fully fledged public-private-partnership, since pandemics affect all.

Thus, the body proposed should be an overarching coordinating body that receives funding and support through a mechanism “higher” than a single government department. It should also attract funding from the private sector and international donors. Having a node of pandemic preparedness excellence in South Africa will be an extremely attractive vehicle to fund by the international community, which will see this as part of securing their own safety.


Future pandemics will occur. The next one may emerge soon or in a few decades. But it will happen!

We need to be prepared. South Africa should develop a permanent, well-funded Pandemic Preparedness and Response Initiative of SA (PPRISA) so that we are all better capacitated to respond to future outbreaks. DM

Adjunct Associate Professor Tim Tucker, CEO of SEAD Consulting and Adjunct Associate Professor at the School of Public Health and Family Medicine, University of Cape Town

Professor Glenda Gray, President and CEO of the SA Medical Research Council

Professor Ntobeko Ntusi, Chair and Head of the Department of Medicine, University of Cape Town and Groote Schuur Hospital

Professor Koleka Mlisana, Executive Director, National Health Laboratory Service.  Co-Chair COVID-19 Ministerial Advisory Committee

Precious Matsoso, Department of Pharmacy and Pharmacology, and Director of the Health Regulatory Science Platform, University of the Witwatersrand.

The writers were panellists at The Gathering event on 24 November, 2022.


"Information pertaining to Covid-19, vaccines, how to control the spread of the virus and potential treatments is ever-changing. Under the South African Disaster Management Act Regulation 11(5)(c) it is prohibited to publish information through any medium with the intention to deceive people on government measures to address COVID-19. We are therefore disabling the comment section on this article in order to protect both the commenting member and ourselves from potential liability. Should you have additional information that you think we should know, please email [email protected]"

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