Maverick Citizen


Lessons for the future: Here is how South Africa can prepare for the next pandemic

To better prepare for future epidemics, South Africa needs to establish a high-level, independent panel to review the country’s response to Covid-19 and recommend interventions. (Photo: / Wikipedia)

The Covid-19 pandemic did not come as a surprise to infectious disease experts, many of whom had predicted such an event for decades. It might sound premature, but we need to begin preparing for future pandemics now. The next one might occur in a year’s time – or in 20 years’ time. But it’s coming.

The Covid-19 virus has, by February 2021, infected more than 100 million people globally. More than two million have died from the disease. However, it’s likely that this number is far higher. With a global average mortality of about 2%, the tragedy is incalculable. 

But what if the “first” SARS from 2003 emerges again – with its 8% mortality? Or the more limited epidemic of MERS from 2012 – with its 34% mortality? These two viruses are still out there in their respective animal hosts, and there are many millions of other animal viruses with the potential to jump from their host species to humans. 

The planet was woefully underprepared for Covid-19. Even wealthy countries have shown their poor levels of preparedness. However, the differences between the rich and poor – those who are privileged versus those who are vulnerable – have laid bare the challenges of an equitable global response.

To better prepare for future epidemics, South Africa needs to establish a high-level, independent panel to review the country’s response to Covid-19 and recommend interventions. 

The preparedness requirements listed below are by nature long-term. They include systemic and structural elements that need decades to fully establish, and thus require long-term vision and funding. 

The panel should consider the myriad issues that face the nation and the region when confronting a pandemic. The items listed below are not meant to be exhaustive, but are simply some of the long-term interventions that may be required to enable a better response to the next epidemic.

A functional national public health institute

A core feature of a national response should be guided by a national public health institute. The enactment of the National Public Health Institute of South Africa (Naphisa) in August 2020 (which had nothing to do with the Covid-19 epidemic) should be welcomed. 

It allows for a new public health structure to “coordinate, and where appropriate, conduct disease and injury surveillance, provide for specialised public health service, public health interventions, training and research towards the major health challenges affecting the population of the Republic.

This entity is a critical missing element for responses to pandemics. Naphisa should set up the required laboratories, national and provincial surveillance offices, virology and microbiology laboratories, and policies and guidelines, all of which should be in place before the next pandemic so as to advise the government on appropriate interventions. 

South Africa has been fortunate to have excellent data and expert interpretation during the Covid-19 pandemic, and has the good fortune of having the National Institute for Communicable Diseases (NICD) to rely on. 

However, the Naphisa envisaged in the act will have more powers and a broader approach to managing public health issues. Naphisa will also assist nationally with issues such as multi-drug resistant TB, Congo-Crimean hemorrhagic fever, HIV, anthrax, and so on. Naphisa should be fast-tracked, appropriately led and well funded. 

Naphisa should be a public health entity that coordinates the national response. It requires a substantial budget. Public health has always been one of the global “poor cousins”, as it takes decades to get a return on the investment. 

A better prepared laboratory service

Covid-19 has revealed the importance of decades of investment in the disciplines of pathology, such as virology, microbiology, immunology, anatomical pathology and haematology. 

Pathologists have played a critical role in guiding our national response to patient care. Therefore it is critical to invest in the required disciplines and set up the required diagnostic capacity, and have a team of experts trained and ready to respond to such outbreaks. 

The National Health Laboratory Service (NHLS) is a national treasure that provides pathology services to every public hospital and clinic across the country. But it needs to be strengthened as the various disciplines of pathology continue to be under pressure in terms of adequate numbers of expert pathologists, budgets for staff and infrastructure and training programmes for pathologists. 

Given the dominant position of the NHLS in South Africa on account of its reach, infrastructure, personnel, costing structures, and so on, the move towards universal healthcare could be accelerated in the pathology sector – with full integration of public and private sector databases – so that the country has a better national view on pathology and disease profiles across all sectors of society.

The Covid-19 crisis has shown the importance of investing in diverse pathology technology platforms that can test millions of people for a novel pathogen. 

The NHLS was able to repurpose the testing platforms used for HIV and TB for Covid-19 testing better than many other countries. However, the prior investments were inadequate for the surge of testing needed for SARS-CoV-2 in the first wave, and the NHLS (correctly) enlisted the help of private laboratories and universities to cope with the massive workloads. 

The NHLS was unable to process the required volumes of SARS-CoV-2 PCR in part because they were unable to procure the required kits/reagents that are used by the abovementioned machines. Many countries had the same problem. 

South Africa needs to look at building increased human and technological capacity to expand testing capabilities, and to become more self-sufficient in the production of testing systems that can be used immediately at the onset of an outbreak. 

The NHLS needs to develop a comprehensive pandemic preparedness strategic plan that is updated every year and which guides a strategy for laboratory testing. 

Better epidemiology data

The age of “precision public health” is here.

The existing data systems of the public health system are inadequate for epidemic interventions. They were not designed for that. The ministerial advisory committee would have been in a better position to advise the government if there had been improved data to work with. 

The government should fast-track a national electronic health record system that captures everyone in South Africa and their health-seeking behaviours and diagnoses. 

The important “single patient identifier system” that has failed to materialise over many years would have been exceptionally useful within the Covid-19 epidemic response. 

Such systems allow for a greater ability to know who is being infected, where they are and how best to allocate human and infrastructure resources. They would also allow for a better view on treatment interventions, and determining which work better than others. 

Some provinces had improved GIS-based outbreak responses where they were able to track hotspots and communities with increased transmission. This allowed for more focused interventions once superspreader events were picked up in near real time. This needs to be expanded to all provinces. 

Government data systems should embrace precision public health, including incorporating more modern developments of mapping diseases through, for example, tracking on GIS systems in real time, integrating laboratory diagnosis with disease presentation and severity, integrating unique patient numbers with numbers of staff to assist them, migration of people, and so on. 

The data systems should integrate the clinical features with the basic science so that the clinical results can be integrated with data sets from the molecular surveillance teams. This is the future of epidemic control – having real-time and integrated data systems.

Covid-19 has shown that viruses spread very quickly across borders. Therefore, data systems need to be trans-national and shared with all to diminish spread and improve patient outcomes across the region. 


The role of diagnostic and molecular surveillance cannot be underestimated and is linked to the above data and Naphisa discussions. 

The next pandemic may again develop in a far-off country – or right here in South Africa. Nobody knows where or when it could happen. 

Irrespective, the role of fully funded surveillance under Naphisa and the academic community is critical to detect both minor and major disease outbreaks and assist with guiding interventions. This requires a full training system for budding surveillance officers and a leadership skilled in epidemiology, infectious diseases and measuring interventions. 

Molecular surveillance of diseases is a critical arm, as it allows us – as with SARS-CoV-2 – to understand transmission routes, transmissibility, virulence and so on, and to be able to understand whether vaccines will work or not. SA’s current excellence in this area needs to be strengthened further.

The description of the SARS-CoV-2 variants by South African scientists allowed the country to map where these variants emerged, where they were spreading to, and importantly, whether they were more transmissible. 

It has also given guidance on whether certain vaccines will work. This molecular surveillance capacity is a specialist one that takes decades to be fully established and capacitated. There is a body of leading molecular epidemiologists in SA who need further support. 

Vaccine R&D and manufacture

The country needs to finally decide if it wants to be a full value-chain vaccine manufacturer or not. It is not a credible vaccine manufacturer in 2021 and is certainly not able to manufacture any vaccines from scratch for pandemic response when short timelines are critical. 

Developing vaccine manufacturing capacity properly takes decades and massive investment. 

Biovac and others have particular skills in their respective corporate environments. For example, Biovac is mainly in the business of buying general vaccines and providing them to the state. They are not manufacturers of vaccines. 

South African companies have negotiated agreements to purchase Covid-19 vaccines in bulk and formulate and divide them into smaller vials of 5-10 doses, before putting labels on them. But if a bulk vaccine is not available to import from international manufacturers, then there is nothing to formulate and fill the vials with. 

This requires considerable thought about what the country wants in the future. If SA wants to be a capacitated vaccine manufacturing country, it needs to invest fully in such capacity in advance of the next pandemic. 

It needs a whole cadre of people to be capacitated over decades, in addition to building the infrastructure and regulatory compliance.

Developing new vaccines is another important long-term capacity that can be strengthened. South Africa has excellent vaccine scientists. However, the translation into manufacturing commercial vaccines across the full value chain has not materialised to any great degree because the required investment in that sector has not been sufficient. 

South Africa now has the opportunity to do what India and others did decades ago – invest in a fully capacitated vaccine R&D sector that is linked to human and animal vaccine manufacture.

Vaccine distribution

The distribution of Covid-19 vaccines to the entire population is one of the largest logistics exercises ever attempted. The difficulties of getting the vaccines to those who need them are significant, particularly when certain vaccines require up to -70°C storage. 

It is unclear if the country even has sufficient storage capacity for a -70°C vaccine in major metropolitan areas, let alone in the remote clinics around the country that will administer such vaccines.

South Africa’s track record with inoculating babies with routine vaccines, and more recently pre-adolescents for HPV, has shown to be lacking. And now we need to vaccinate the majority of the population to achieve herd immunity. 

This requires a comprehensive rethink of our primary healthcare vaccine systems and processes, and redesign them for both this Covid-19 vaccine effort and future pandemics.

Health system issues

It is sometimes said that the health system in South Africa is broken. However, this does not tell the whole story. 

Millions of people receive their clinical care, laboratory results, X-rays, medication and so forth at thousands of clinics across SA. This poorly functioning system needs to be developed further so that pharmaceutical and vaccine supplies are available more consistently, and that the various aspects of “health systems strengthening” are addressed.

The system needs to be ready to handle the next pandemic. This is not something that happens passively – it is an active public health program of capacitating healthcare workers across the spectrum in advance of the next pandemic, and ensuring that they are ready for it. The system needs to be able to care for, and vaccinate, millions in need during an epidemic and have the infrastructure and skilled staff to do that. 

Coordinating major sectors better

It is often said that public and private sectors should work together. That’s true, but pandemic responses need to be more empowered and there needs to be a review of the levels of coordination that have occurred, even within government. 

It is notable that even government departments operating under the same leadership system varied significantly in their responses. 

There are major groupings in society which span the public and private sectors that need to be looked at as opportunities for better interventions. Sectors such as schooling, the more diverse post-schooling education and training institutions, the military, police, unions and industry should be regulated to work together during pandemics, with common protocols and common interventions. 

The civilian health system is often very removed from the military health system. But in an emergency of this scale, there should be improved coordination when it comes to clinical care and vaccinations.

Military service communities are experts in setting up temporary clinics and support services at short notice. Their capacities should be used more creatively within a humanistic and medical framework rather than looking to them only as an adjunct to the policing function when lockdowns are contemplated.

Global equity

The Covid-19 pandemic has demonstrated deep inequities globally, with wealthy countries mopping up supplies of essential materials such as PPE, ventilators, oxygen, and more recently, vaccines.

South Africa has the opportunity to work even more actively with other countries to ensure a more equitable distribution of essential medical support. 

SA needs to plan ahead of time to ensure that disaster responses are adequately capacitated. The emergency stores of PPE and other hospital products need to be reviewed for appropriateness and quantities. 

In addition, serious discussions need to be held around the restrictive use of patents covering vaccines and therapeutic drugs. 

The global poor are disproportionately affected by pandemics, and well resourced countries need to ensure that there is a more equitable distribution of novel interventions, and that patents do not prevent the poor from getting access.

Regional solidarity

This epidemic has demonstrated the porous nature of national boundaries. Viruses have no respect for such artificial lines on maps, and there are major transmission modes both within and between countries. 

This offers opportunities for regional cooperation on both biological interventions and humanitarian needs. Vaccine nationalism is highly destructive, and even well-meaning initiatives such as the Covax mechanism have their limitations as wealthy countries will inevitably vacuum up early supplies using commercial pressures. 

Africa has the opportunity to put in place alliances across the region for pandemic control and vaccine procurement. These can be improved for the regional purchasing of treatments, too, as they become available. 

Final thoughts

The world has seen spectacular levels of responsiveness to Covid-19, and incredibly fast development of interventions such as vaccines. These scientists are the modern-day superheroes of the world, bringing vaccines to the world – well, parts of it – within 12 months of virus discovery.

But, as we begin to emerge from this pandemic, we need to recognise that we are underprepared as a nation and as a world for future epidemics.

It is proposed that the country learn from this pandemic as soon as possible and put in place a formal review mechanism – perhaps a high-level presidential panel – to define a long-term pandemic strategy to better prepare us for the future. 

We should reflect honestly on both our successes and our failures and address the various opportunities to introduce systemic changes to ensure that the next pandemic is less able to leave this wake of destruction. DM/MC

Tim Tucker is a clinical virologist and CEO of the public health organisation, SEAD Consulting. He is also adjunct Associate Professor at University of Cape Town School of Public Health and Family Medicine.

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]


"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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