President Cyril Ramaphosa gave weary and irritable South Africans something to look forward to when, on Sunday evening, he announced that the country will move to Level 3 of the lockdown on 1 June – but, as always, the devil is bound to lurk in the detail.

He has given six addresses to the nation since the state of national disaster was announced on 15 March, and where South Africans were broadly united in their support for the president and his government’s swift action more than two months ago, the national mood has become increasingly frayed as the lockdown began to bite.

Regulations announced by Nkosazana Dlamini-Zuma, the local government minister legally charged with administering the emergency directives, came under fire for the lack of logic and scientific evidence on which it was based, while the machismo of some ministers – notably Police Minister Bheki Cele – rightfully drew flak.

The legality and constitutionality of the National Coronavirus Command Council (NCCC), a newly established body attached to Cabinet but with no apparent statutory standing, has also been challenged as South Africans started to push back and demand answers.

Politics and ideology also came into play in recent weeks as questions were raised over the government’s continued banning of alcohol and tobacco sales, with Ramaphosa seemingly at first supporting the sale of cigarettes, only for Dlamini-Zuma to announce that the ban will remain in place.

And tension between some scientists on the Ministerial Advisory Committee (MAC) – a body of 51 eminent scientists advising the Minister of Health Zweli Mkhize – came to a head over the last seven days, with Professors Glenda Gray, Francois Venter and Shabir Mahdi, among others, criticising the government’s approach to scientific advice. They all broadly agree that advice from the MAC on issues, such as the regulations, aren’t listened to and that the scientists feel sidelined.

Ramaphosa on Sunday night sought to bring a measure of calmness to the fraught environment of recent times. Chief among those was that the economy will by and large be reopened, with retail, construction, manufacturing, financial services and almost every other sector set to return to business on Monday, 1 June.

But restaurants and bars, professional sport and the airline industry – as well as the tobacco industry – will remain closed or constrained in the levels of activity they can undertake.

The implications of the lowering of the risk level from 4 to 3 will be clarified in the coming days – but, as with previous announcements, the minutiae in the detail will determine to what extent South Africans will return to normalcy.

Alcohol sales will be permitted, as will exercise and more freedom of movement. We’re going to have to wait and see what exactly the amendments to the regulations say.

Ramaphosa explained the extent of the public health response and again, like in the past, reiterated the real fear that the full impact of the virus has yet to breach our defences. He said the lockdown has given the public health system time to prepare and authorities space to procure equipment and beds, and to construct field hospitals.  

The president, clearly acutely aware of Mkhize’s strained relationship with key members of the MAC, reached out to them and thanked and acknowledged their contributions, saying their advice was sought before the address.

FULL TEXT | Ramaphosa unveils Covid-19 hotspots, dos and don’ts under level 3 lockdown

“We are extremely grateful for the work they have done and continue to do to ensure that our response is informed by the best scientific evidence. We appreciate the diverse and sometimes challenging views of the scientists and health professionals in our country, which stimulates public debate and enriches our response.”

It has been an almost impossibly difficult and complicated period to navigate – with much of it being the government’s making, it must be said. A broken public health system, a depleted national fiscus, a misfiring public service and a weak economy did not give Ramaphosa the armoury with which to tackle a global pandemic of uncertain scope and impact.

Before the pandemic hit, the country was facing its biggest socioeconomic crisis in decades, with unemployment soaring, economic activity declining and our investment grade tanking. The pandemic, and many of the responses to it, have conspired to only make matters worse.

Our ability to support and sustain livelihoods – either through job creation or social grants – has been severely damaged by the last 10 weeks. And the country’s biggest problems remain as they were two months ago: weak electricity generation, the state of public owned companies, the urgent need for economic reform and the reconstruction of state institutions like the NPA and SARS.

The lockdown could not be sustained, Ramaphosa said. And the spread of the coronavirus is going to get “much worse” before it gets better.

But, for now, a semblance of normality beckons. Even if we are a diminished country.

Higher Education, Science and Technology Minister Blade Nzimande outlined the government’s plans on Saturday to allow students back on campuses.

Among some of the major announcements were that National Student Financial Aid Scheme (NSFAS) students would receive 10GB free data from June through to August; all students and staff members returning to campuses will be screened upon entry; and one third of students will be allowed back on campuses and in residences under Level 3 of the lockdown. 

Universities

Currently, final-year students in programmes requiring clinical training, particularly in medicine, have been returning since mid-May. All other students have to study through digital and other means until they can return.

Under Level 3, a maximum of 33% of students will be allowed back on campuses and in residences – as long as they can been accommodated in line with health and safety protocols.

President Cyril Ramaphosa previously said most of the country should have reached Level 3 by the end of May.

The students who will be allowed back under Level 3 should be in their final year and must require access to laboratories, technical equipment, data, connectivity and access to residence as well as private accommodation.

Postgraduate students who require laboratory equipment and other technical equipment to undertake their studies may also return.

READ | UCT reveals first group of students who will be allowed back, but no dates confirmed yet

Students in all years of study that require clinical training in their programmes can also go back. Universities can also decide to allow back students to residences who may face “extreme difficulties” in learning at home.

Once Level 3 is announced, students will be given a period of two to three weeks from the announcement date to return back to their campuses. Institutions will issue permits to identified students to allow for their travel. Only a third of students will be allowed back in residences under Level 3.

Students will be screened for Covid-19 symptoms at campus entrances.

Once the country reaches Level 2, two-thirds of the student population will be allowed back. First-year students in all undergraduate programmes will be allowed back as well as students in all years of study who require laboratory and technical equipment to complete the academic year.

Students in all years of study who require practical placements, experiential learning or workplace-based learning to complete the academic year will also be allowed back – provided the workplaces and platforms are open and prepared. Two-thirds of residences may be occupied during Level 2.

Only at Level 1, will all students return.

TVET returns

Technical and Vocational Education and Training (TVET) students will return by specific dates, but if their campuses are in areas that are still on Level 4 during that time – they will remain closed.

These are the return date for engineering students:

N6 & N3: 10 June

N5 & N2: 15 June

N4 & N1: 22 June

For business studies students:

N6: 25 June

N5: 29 June

N4: 06 July

National Certificate (Vocational) Level 4: 13 July

Level 3: 20 July

Level 2: 27 July

All lecturers need to return by 8 June.

CET colleges

Students registered for General Education and Training Certificate, Senior Certificate and National Occupational Certificates at Community Education and Training colleges need to return by 17 June. Exam dates have been postpone to next year to enable them to complete the 2020 academic year.

NSFAS students

Nzimande announced all NSFAS students, including Funza Lushaka teaching bursary students, would receive 10GB daytime and 20GB nighttime data for three months, starting from 1 June until the end of August.

This thanks to a new deal with cellphone service providers which secured “very favourable rates”.

He said these students should register their cellphone numbers with their respective institutions, and they shoud not change their SIM cards during this period.

Nzimande added the government was not in a position to subsidise data to students who fall within the so-called “missing middle” category – those who did not qualify for NSFAS bursaries, but came from households who might have been hit hard by the pandemic.

“We, however, appeal to [cellphone companies] to work with institutions to also offer affordable packages to such students.”

READ | Final year students studying towards degrees in industries at risk of job losses share their fears

He said the government was working towards an affordable higher education loan scheme involving the private sector.

An agreement with the SA Revenue Service has been concluded to provide the NSFAS access to the latest tax data to validate the household income of applicants.

The NSFAS will now also be able to include other income, such as investment and rental, in its applications assessment.

“This will greatly assist towards the finalisation of outstanding appeals,” Nzimande added.

Overall, we estimate that, while 83% to 88% of the population may become infected, most people are expected to have no or mild symptoms

The reports provide projections for the spread of the epidemic at the national and provincial levels.

Like all models, the National Covid-19 Epi Model, which generates the projections, comprises a set of formal assumptions about how the world might work. This article is intended to shed light on some of those assumptions, as well as explain major sources of uncertainty and discuss some limitations and next steps.     

Developing a mathematical model to simulate the spread of a disease in the context of public health is a multidisciplinary and collaborative process.

It would be incorrect to assume that a disease model applied to different settings or countries would result in the same findings.

Though the biological assumptions on disease transmission may be the similar across settings, there are vast differences to be accounted for in health infrastructure, national health management policy, methods of prevention, operational challenges, population behaviour and access to care.

It is therefore important to work with disease and public health specialists to collate available information for the model before transforming this data into equations, algorithms and computer code.

And as no two countries, health systems and populations are the same, so too, will each disease model be unique and have its own challenges. 

Current estimates 

Let’s review the numbers.

The current version of the model estimates that South Africa can expect a total of 12 million to 13 million symptomatic cases of Covid-19 to have accumulated by early November.

The epidemic may peak, with around 1 million active cases, between mid-July and late August.

Overall, we estimate that, while 83% to 88% of the population may become infected, most people are expected to have no or mild symptoms.

Only about 1% of the population is expected to develop severe symptoms; however, we expect that this 1% will be sick enough to need hospitalisation.

As a result, the projections suggest that hospital capacity is likely to be overwhelmed, with all ICU beds, in the public and private sector, filled by mid-July, or earlier.

There are, however, many factors that could cause deviations from these projections, including individual behavior change and tighter (or looser) restrictions than we currently assume. 

The modelling approach 

The projections are generated using a type of model that represents the population as a number of mutually exclusive groups, commonly known as “compartments”.

These groups represent different infection and disease states.

In the National Covid-19 Epi Model, there are compartments representing susceptible people, those who have been infected but are not yet able to transmit the virus, those who are infectious but not ill (either asymptomatic or presymptomatic), multiple groups of ill individuals (e.g., those with mild or severe illness, those in hospital, and those in ICU), recovered people, and those who have died.

Each of the compartments is tracked through time, and the number of new infections depends on the interaction between the numbers of susceptible and infectious people.

The model also keeps track of how and when people in different compartments get tested, which allows us to project the number of cases that will be detected by particular dates.  

In order to run the model, we have to set values for the rates and probabilities of people transitioning between the various compartments.

Deciding on which values to use has been an important role of the broader South African Covid-19 Modelling Consortium.

The Consortium is a group of researchers from academic, non-profit, and government institutions across South Africa who work to provide, assess, and validate model projections for government planning purposes.

The group includes not just modellers, but also epidemiologists, virologists, actuaries, intensivists and other clinicians, and demographers.

These experts from diverse fields have given extensive input based on their own experience and on their knowledge of the global literature to inform the values used in the models.  

Nevertheless, there are some values that can’t be estimated directly from data or based on existing expertise.

For example, the model allows us to modify the transmission rate by adjusting the rate of contact between individuals in the population through time, but it is particularly difficult to determine values for the transmission rate in relation to the efficacy of intervention measures.

For this reason, we have considered two different scenarios when looking at the long-term projections.

Under the optimistic scenario, we assume that the Level 5 lockdown reduced the contact rate by 60%, the Level 4 lockdown reduced the contact rate by 35%, and measures in place after 31 May will reduce the contact rate by 20%, relative to pre-lockdown levels (what we used to know as “normal life”).

Under the pessimistic scenario, we assume that the Level 5 lockdown reduced the contact rate by only 40%, Level 4 reduces the contact rate by 25%, and measures in place after 31 May will reduce the contact rate by 10%.

The projections vary under the two scenarios. 

Key assumptions 

No country knows the true number of people infected with Covid-19. The number of laboratory-confirmed cases depend on the testing criteria and testing capacity of the country.

As has been the experience of many countries around the world, the majority of Covid-19 infections will show no or only mild symptoms, with only a fraction of those seeking care at outpatient or hospital facilities or Covid-19 testing.

Therefore, the true total number of people infected with Covid-19 (which is what our total infection projections show) is much higher than the number of cases reported.

We focus on these numbers however, as we will believe that severe cases will present for hospitalisation and require care regardless of whether or not they have been tested and identified as Covid-19 positive.           

Important uncertainties 

Disease models help us understand and unpack the key drivers of infection, the many uncertainties and the likely impact of interventions.   

As Covid-19 is a new infectious disease, there are still many things that are unknown.

Some of these unknowns are about the disease generally (e.g. how many people who are infected never develop symptoms, how long does immunity last after infection) and some are specific to South Africa (e.g. how does South Africa’s disease and age profile influence the severity of Covid-19 infections?).

We don’t know whether people living with HIV and/or TB are more susceptible to infection, or whether they experience more severe disease. There is also very little evidence on the role of children in transmission.  

There is considerable uncertainty regarding the proportion of infected individuals who remain asymptomatic, and the relative infectiousness and the duration of infectiousness of these asymptomatic individuals.

This has important implications for the transmission dynamics in the model and the projected number of hospitalisations and deaths. One way that scientists explore the impacts of uncertainty is to conduct what’s known as a “sensitivity analysis” – essentially asking the question of how sensitive key results are to the assumptions that are made in areas of uncertainty.

Our national long-term report contains an example of a sensitivity analysis focused on understanding the importance of the assumptions made about asymptomatic infections.  

We run multiple scenarios to help us understand how the epidemic may progress under different assumptions and uncertainties.

This enables us to explore which of the unknowns will have a big impact on the trajectory of the epidemic. Our projections show a probable range of values rather than a single estimate, which capture some of this uncertainty. 

What are the next steps? 

We are continuously updating our model as new data become available. This includes re-calibrating the model to match observed trends of detected cases and deaths in South Africa.

We also keep abreast of the global scientific literature and adjust our underlying assumptions when new information becomes available.

For example, earlier versions of the model assumed that most infections would cause symptomatic cases; however, new data and analyses suggest that the asymptomatic proportion of infections is higher, so we have adjusted the corresponding value in the model.

We are also in the process of adapting the model to better represent the patterns of hospitalisation times and outcomes to reflect data from South Africa.  

The model also changes when new questions get asked. Currently, we’re developing new versions of the model that will account for the excess mortality expected once the country’s health care capacity is breached, and that will allow us to more flexibly investigate a range of interventions, particularly ones that focus on reducing contact for specific age groups.

We also continually improve our model based on ongoing peer-review. This makes the model projections more reliable over time. 

In conclusion 

As we said at the beginning, models are tools that can help us think about the future. They do not tell us what the future will hold. The projections we have made are based on a simplified, and fairly pessimistic, set of assumptions about people’s behaviour.

The true outcome of the epidemic will depend on many factors, and one of the most important factors will be individuals’ behaviour.

We can each of us help continue to flatten the curve by reducing our contacts, observing physical distancing, washing our hands well and often, wearing non-medical masks, isolating ourselves when we are sick, and quarantining ourselves when we know we’ve been in contact with someone who was infected.

Changing the course of the epidemic is our shared responsibility. 

About the authors: 

Prof. Juliet Pulliam is the Director of the South African Centre for Epidemiological Modelling and Analysis (SACEMA), which is a national DSI-NRF Centre of Excellence hosted by Stellenbosch University. She is also a Professor of Applied Mathematics at Stellenbosch University. Prior to moving to SACEMA in July 2016, she spent five years as a faculty member in the Department of Biology and the Emerging Pathogens Institute (EPI) at the University of Florida. Juliet received a PhD in Ecology and Evolutionary Biology from Princeton University in 2007 and spent three years as a Research and Policy for Infectious Disease Dynamics (RAPIDD) Program Fellow at the US National Institute of Health’s Fogarty International Center. Her research focuses on applications of mathematical modelling to applied questions in infectious disease epidemiology, with a particular focus on emerging, zoonotic, and vector-borne pathogens.  

Dr Sheetal Silal is the Director of the Modelling and Simulation Hub, Africa (MASHA) and senior lecturer in the Department of Statistical Sciences at the University of Cape Town (UCT). She is an Honorary Visiting Research Fellow in Tropical Disease Modelling at the Nuffield Department of Medicine at Oxford University. She received a PhD in Mathematical Modelling of Infectious Diseases in 2014 from UCT. Her primary research area is the development and application of mathematical models to malaria, pertussis, and other infectious diseases in South Africa, sub-Saharan Africa and globally, with a focus  on using mathematical models to predict the dynamics and control of diseases to evaluate the potential impact of control programmes in reducing morbidity and mortality, and supporting policy development. 

Gesine Meyer-Rath, MD, PhD, is a medical doctor and health economist working on the economics of infectious disease interventions in low- and middle-income settings. She is an Associate Professor at the Center for Global Health and Development, Boston University, US, and lives in Johannesburg where she works at the Health Economics and Epidemiology Research Office (HE2RO), a collaboration between Boston University and the University of the Witwatersrand. Her focus lies on modeling methods for economic evaluation and translating research into recommendations for public policy. 

Dr Harry Moultrie is a medical doctor and epidemiologist at the NICD’s Centre for Tuberculosis. His current research focus is the geospatial distribution of TB in South Africa. He has worked on a number of peer-reviewed journal articles on, among others, antiretroviral therapy and HIV/AIDS. 

The sale of alcohol, physical sittings of Parliament, resumption of domestic travel and opening of churches were just some of the issues leaders of opposition parties raised with President Cyril Ramaphosa on Wednesday.

They sought to sway Ramaphosa on numerous issues they want to be taken into consideration ahead of the country moving to Level 3 of the nationwide lockdown.

The president remained tight-lipped on what the plans were and gave no indication of any concessions to be made under in the imminent phase of the lockdown, insiders said.

News24 was reliably told in the virtual meeting, which kicked off at 07:00 on Wednesday, party leaders were given ample time to share their views on how the country should be navigating the coronavirus pandemic and the related lockdown to curb the spread of infection.

The country has been under lockdown since March when the government adopted a five-alert level that allows for the staggered reopening of the economy.

Ramaphosa was joined at the meeting by several members of Cabinet including Health Minister Zweli Mkhize and Cooperative Governance Minister Nkosazana Dlamini-Zuma whose department has been responsible for promulgating the regulations adopted by the government during the crisis.

Some of the suggestions made to the president included increased liquor prices and sin tax in the hope that many would not flock to outlets or even panic buy booze.

“We were really happy that Mkhize and Dr Dlamini-Zuma were present today, often the president skirts over issues or just doesn’t answer some of our questions because it seems he doesn’t have in-depth knowledge, today they stepped in to assist and clarify some issues,” said the ATM’s leader, Vuyo Zungula, to News24.

Alcohol and tobacco

He added while some in the room had been for and against the sale of alcohol, which is set to come into effect during Level 3 but under strict conditions, party leaders were also concerned with how the reintroduction of alcohol needed to take shape.

“The sense is that South Africa needs to avoid the India experience where the resumption of liquor results in safety regulations being discarded,” said Zungula.

OPINION | Where there are illegal smokes, there’s a fire

Ramaphosa is also said to not have provided answers to concerns over whether Police Minister Bheki Cele had the capacity to deal with the increased sales of tobacco and alcohol on the black market.

Dlamini-Zuma used the meeting to once again raise issues against the sale of tobacco, telling opposition leaders that world health regulations have been explicit about the role of the product in the battle against the virus which attacks the respiratory system.

Churches

The ACDP, which shares the views of the ATM on churches, seemed to believe the meeting gave a glimmer of hope regarding the resumption of church gatherings, its leader, Kenneth Meshoe who has tested positive for Covid-19, told News24, saying he believed this was a matter currently being looked into.

“I think the good thing about the meeting is that we weren’t given three minutes to make a point but beyond that the president didn’t give away anything, he seemed to hear us and spoke of more consultations,” said Meshoe.

The ACDP leader said Ramaphosa gave diplomatic responses when asked about parliamentarians being able to physically meet as well as the request to consider further relaxing domestic travel in the country.

OPINION | Covid-19 and the disruption of the Church

The president is said to not want to impose his views on Parliament, leaving it to the speaker to make that decision.

“We find it difficult to operate via Zoom and to keep executive accountable as they don’t respond to letters or answer questions,” said Zungula.

No indication

The FF Plus’ Pieter Groenewald is another leader who attended the meeting. He said it had left him uncertain on the way forward as the president gave nothing away.

“The one time he was shaking his head as if to agree with me on the economy being reopened, especially the sole proprietor business and the small businesses but in the end Dr Nkosazana Dlamini-Zuma came and responded. They were just sticking to their position that these are their levels,” added Groenewald.

He said there was no true indication of whether the country was moving to Level 3 on a national level, nor did he share details of when he would address the nation.

Groenewald, however, said Ramaphosa gave some explanation regarding the decision to declare a national state of disaster as opposed to a state of emergency.

He added the president had told opposition leaders he received advice from lawyers that a state of emergency would require Parliament’s approval after 21 days and for it to also approve the regulations, which Ramaphosa could not see happening then.

“But that’s not an excuse, that’s not a good excuse as Parliament is holding virtual meetings, portfolio committees are functioning,” he said.

While Ramaphosa is expected to continue with his consultations, it is likely he might address the nation before the end of the week.

Reopening of schools

The IFP’s Velenkosini Hlabisa said he found the discussions with Ramaphosa fruitful.

He told News24 the government’s approach was a lot in line with his party’s wishes, however, it had concerns over the reopening of schools.

Hlabisa said he had called on the government to exercise maximum caution in this regard and ensure the agreements reached between the Department of Basic Education and unions were adhered to.

READ | Back to school: Will pupils be forced to return? Education dept answers questions

“If regulations are ignored it would be like testing deep waters and playing with the lives of children and teachers.”

Referring to a debate on whether moving the country down a level when the World Health Organisation felt it was not ready, Hlabisa said he agreed with the president’s view that it was time for South Africa to move on from Level 4.

“What consoles us are that the numbers of recoveries are also high, a sign that we are managing the virus.”

The Gauteng Department of Social Development has outlined strict guidelines for the donation and distribution of food parcels in the province during lockdown.

Head of department Thembeni Mhlongo urged donors to deliver donations to the provincial food bank, situated at 30 Mandy Road, Reuven, Booysens.

Companies and organisations will be expected to present their addresses, registration numbers and donation contents.

Mhlongo said those who wish to distribute directly to communities must first obtain authorisation from the department.

“All applications to distribute donations should be submitted to the department no less than 48 hours before the envisaged distribution date. Upon receipt of the authorisation letter from the department, the organisation must inform a local police station prior to the delivery of food supplies,” said Mhlongo.

She said food relief must preferably be delivered to individual households and, if more than 50 beneficiaries are targeted, police must be informed 24 hours before the distribution date.

“A distribution plan must be drawn in consultation with the SAPS, metro police, SANDF and the department to ensure public order policing availability. Social distancing and sanitisation must be enforced.

“Distribution must be done in collaboration with the department or social development unit within a municipality. Expiry dates of food must be confirmed by government officials, and consumables without expiry dates must not be allowed for distribution,” Mhlongo said.