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Government uses some of the best available minds to help with COVID-19-Models

22 June 2020 | Story Andre Damons | Photo Anja Aucamp

Herklaas_read more — Herkulaas Combrink.

A lot can be said about forecasting and modelling, its accuracy, and how it works. Forecasting and modelling provide any decision-maker with plausible predictions or outcomes to give some kind of estimated consequence. Without this field of science, planning would be difficult, as one would simply make decisions without knowing what might potentially happen to a specific cohort, market, or product. Forecasting as a concept can be seen as a set of mathematical, statistical and/or computational tools applied to a set of assumptions about something.

This is according to Herkulaas Combrink of the Centre for Teaching and Learning at the University of the Free State (UFS) and PhD candidate in Computer Science at the University of Pretoria (UP), following the South African government’s modelling of how many people would contract COVID-19 and die, which has come under fire in recent times – with one expert saying it was “flawed and illogical and made wild assumptions”.

Combrink is of the opinion that South Africa – by using the MASHA Consortium – is using the best minds that the country has to offer. The fact that the leadership took a pragmatic stance and reached out to the scientific community has mitigated a medical disaster in a healthcare system that was not ready a few months ago.

“The government is looking at as many models as they can, but is working very closely with MASHA and the CSIR” says Combrink, who has been involved in clinical surveillance, and also forms part of the modelling team during his secondment to the Free State Department of Health.

Prof Shabhir Madhi, the former head of the SA National Institute for Communicable Diseases (NICD), recently said that the initial modelling and fatality estimates were “back-of-envelope calculations”.

According to a news report, the government’s initial model also predicted that 600 COVID-19 patients would need treatment in intensive care units (ICU) in SA by April 1. But by April 18, the last publicly released figures showed that there were 32 COVID-19 patients in ICU.

Tried-and-tested models

The models currently used are tried-and-tested epidemiological models, mathematical models, and economic forecasting models that have been used in the past. It has now been calibrated to the specifications that we know of this disease, which come from publications. The reason why you would use more than one model is to compare models retrospectively, so that you can see what is going on.

“The government immediately reached out to the best minds in the country, and with the aid of the consortium, took a stance to throw scenarios at the different models and stress test them so that they could know that they are using the best possible models to assist in resource management and decision-making. If government responded in a different way and didn’t reach out, we might not have had a lockdown and subsequently would probably have been in a different position where the country wouldn’t be ready.”

“We can say with a high degree of confidence that the lockdown really helps to ease and flatten the curve in the country. In light of flattening the curve, the right decisions have been made,” says Combrink.

COVID-19 still new

Unfortunately, says Combrink, during the COVID-19 pandemic, there was not enough information related to the disease assumptions and it lacked the rigour and perfection associated with the already existing prediction models. Although it may feel like a lifetime, the first COVID-19 case was only reported in December 2019. Add to this that not all the parameters related to the disease were known in January, it was challenging to determine all the ‘ins and outs’ of this disease.

“Luckily, the mathematics and statistics of an outbreak have been extensively studied, and as a result, we only needed to use the correct parameters to estimate the spread of the disease in some of the outbreak models. The Minister of Health, Dr Zweli Mkhize, and the national modellers led by Dr Harry Moultrie, were transparent with not only their projections, but also how they derived their conclusions and what parameters they used,” says Combrink.

The most important thing in modelling is to calibrate according to what is known about the disease and people, explains Combrink. “It is impossible to predict people and a disease100% accurately, because you don’t always know how a virus will react to every single person’s body and you can’t predict human behaviour.”

“So, there is a certain degree of error and a certain degree of confidence that lies within each model, and that is why you evaluate these models on a regular basis. And this is important. You will never be able to say this is the exact number. Just like the weather. If the weather patterns were predicted to be 12 degrees tomorrow, and it turns out to be 16 degrees, you at least packed a jersey. You knew it was going to be cold. The chances that the weather predicts that it will be 12 and it turns out to be 57 degrees, is virtually zero. It gives you more or less an indication what to prepare for

Models are useful, but can also be wrong

Combrink says if you want to apply any model, you need to understand the assumptions and the limitations of the models. Given a certain set of criteria – what are the assumptions you are making and what are the expected outcomes – you can only act according to that. He says, as time goes by, we can now see that there are some models that yield much better results because we can now compare what was predicted two months ago and what is actually happening.

“Some models are useful. We can get a better understanding of the pandemic’s possible trajectories or gain an understanding of the impact that different interventions have made. Models are used for decision-making. These decision-making strategies can save lives. That is the purpose of models and modelling during these times.”

Combrink uses the weather forecast to explain how modelling works and that models can be wrong. “Yes, models are wrong all the time. Take the concept of weather as an example. How many times has the weather forecast predicted that there is an 80% chance of rain, and then it doesn’t rain? Models can give you a certain degree of confidence in an outcome related to a specific event or scenario, so that you, with some degree of confidence, can go forth and plan accordingly.”

“However, models can’t tell you what exactly will happen tomorrow, or the day after. It is not a crystal ball, and it is not a mirror into the future, but it can give you an indication of what is likely possible related to a specific scenario if you used the right variables. Let us consider that there is an 80% chance of rain in the weather forecast; will you a) go to work without an umbrella or b) with an umbrella? If it doesn’t rain, you are at least prepared for the rain because you took your umbrella. If you didn’t take the umbrella and it does rain, you may run into trouble because you did not appreciate the warning of the weather forecast. I think it is this concept that makes modelling so powerful. You can use it as a tool to prepare for things, in the event that it does happen, with a certain degree of confidence. Just like the previous example, there is also a 20% chance that it might not rain, but wouldn’t you want to be prepared?” explains Combrink.

Models are tools that can be used to base decisions on

No one truly knows how the pandemic will play out, and according to Combrink, it can be said with a high degree of confidence that if nothing is done about the pandemic, we know how it would turn out from a healthcare perspective.

“If you look at some of the global projections they gave months ago (in January and February) and compare it to what they said for March and April, you can see that they predicted, with a fairly good degree of confidence, what actually happened in certain countries. We have a good idea in terms of numbers and how it will play out, but what we will never know is what the impact will be on the socio-economic status of a person, the economy, and the impact on other diseases.”

“We do not know what is going to happen when it comes to mental health and COVID-19, for example. This is why modelling is a multidimensional approach, requiring inputs from various fields. Models can help us in the same way the weather forecast does. It is a tool that we can use to base certain decisions on, to be more prepared, because without it we won’t know to pack an ‘umbrella’ if it is predicted to rain or pack a ‘jersey’ if it is projected to cool down.”

News Archive

During 2011: Achievements at the UFS

2011-12-01

Sarah Shannon

Dr Alex Amtaika, Department of Political Science

During a conference at Khon Kaen University in Thailand, Dr Alexius Amtaika from our Department of Political Science was elected as Executive Director and Convener of the International Committee of Scholars of Local Government. This honour was bestowed upon Dr Alexius during the first International Conference on Local Government at Khon Kaen University.

Sarah Shannon

We all have heard stories about inspirational people, who defy the odds, fight circumstance every day and never give up. Sarah Shannon has cerebral palsy but has never stopped dreaming and achieving them.

Sarah is also a competitive swimmer, and is currently ranked seventh in the world in her class of disabilities.

She is currently completing her postgraduate certificate in Education, Foundation Phrase, through Unisa. She is also studying Sociology at our university.

DW Bester and Sannah Mokone, Rhodes Scholars

Of the four open Rhodes Scholarships available to students from all universities in Southern Africa, two of our students won these prestigious scholarships. DW Bester, B.Sc. Hons. Actuarial Science student, and Sannah Mokone, BPub-cum laude student, joined Oxford University in the United Kingdom in September 2011 to further their studies.

The Rhodes Scholarships, arguably one of the most prestigious scholarships in the world, were founded in 1903 in the will of Cecil John Rhodes and cover the full costs of study at Oxford University.

While academic excellence is a pre-condition for consideration for the Rhodes Scholarship, these scholarships are unique in that Rhodes Scholars are outstanding young students who excel academically, but very importantly, demonstrate leadership, are committed to making a difference in the world, and have the energy to fulfill their ambitions.

Dr Derik Coetzee, Department of Sport and Exercise Sciences

When you suddenly receive a call during a World Cup year and requested to come and assist in leading the Springboks, then you have to know, you have something to offer. This is what happened to Dr Derik Coetzee from our Department of Exercise and Sports Sciences. This year he once again became involved in the Springbok rugby team, after he had been die Bokke’s conditioning trainer from 2004 to 2007.

His primary task as conditioning head was to help in seeing to it that the Springboks reached their best level of play – psychologically, physically an emotionally. Amongst others, his duties included the optimisation of the players’ muscle and explosive power, speed, anaerobic ability and technical skills.

Jefferson J Dirks-Korkee en Mart Kotzé

Jefferson J Dirks-Korkee, from Willowmore in the Eastern Cape, and Mart Kotzé from Bloemfontein, recently made history by being the first students from our Department of Drama and Theatre Arts featuring in an Afrikaans South African film Skoonheid, the first ever to be shown at the Cannes Film Festival.

The movie won the Queer Palm Award at the 2011 Cannes International Film Festival, where Robert de Niro was the chairperson of the panel of judges.

Prof. Muriel Meiring, Department of Haematology and Cell Biology

Prof. Muriel Meiring, Specialist Scientist in our Department of Haematology and Cell Biology, is responsible for establishing the Specialised Haemostasis Laboratory at our university and the Universitas Hospital’s National Health Laboratory Service. She established this centre as a reference centre for Von Willebrand disease, a genetic bleeding disorder, in South Africa. This laboratory is internationally recognised for their research and as a reference laboratory.

Prof. Meiring develops and tests antithrombotic (anti-clotting) agents and her long list of publications, research awards and congress presentations has earned her a nomination for the Department of Science and Technology’s Distinguished Woman Scientist Award. She was one of two scientists of the National Health Laboratory Services (NHLS) to receive the award – Prof. Meiring being the only woman from our university.

Medical facilities from all over the country make use of her and her team’s expertise when testing for blood disorders and she hopes to expand the centre even further.

Melinda Jonker

Melinda Jonker, one of our third-year financial economic students, won the overall national competition of the prestigious Traders Trophy competition at the Johannesburg Stock Exchange (JSE).

The competition, sponsored by Nedbank Capital and Oxyor in Amsterdam, requires participants to trade actual JSE-listed shares against one another on a simulated platform. The winner is determined not only by the highest profit, but also by the technique used throughout the trading session.

Christopher Diab, also a student from our Department of Economics, won the regional UFS competition.

ASSAf members

Seven of our academic colleagues have been elected as members of the Academy for Science of South Africa (ASSAf). They are Proff. Hendrik Swart, Physics; André Roodt, Chemistry; Zakkie Pretorius, Plant Sciences; Max Finkelstein, Mathematics; James du Preez, Microbial, Biochemical and Food Biotechnology; Maryke Labuschagne, Plant Breeding; and Neil Roos from our Postgraduate School.

Due main objective of the Academy is to promote and apply scientific thought in the service of the society, in order to determine the quality and scope of the role that the Academy can plays in the country’s life and progress, and eventually apply it

Other colleagues who are currently members of ASSAf include Proff. Jonathan Jansen, Vice-Chancellor and Rector; Johan Henning, Dean: Faculty of Law; and Frans Swanepoel, Senior Director: Research Development.

Samantha Renda-Dollman

Samantha Renda-Dollman, a BSc (Zoology) student on our Qwaqwa Campus, has obtained 19 distinctions out of the 22 modules she has written since 2009.

Her hard work earned Samantha the prestigious Dux Student award of our 2011 Annual Student Affairs Excellence Awards, held at our Qwaqwa Campus. This makes her the best overall academic performer of the entire student body on this campus.

Jaco Griessel

Jaco Griessel, an Honours student at our Odeion School for Music, received a prestigious Mandela Rhodes bursary for 2012 to study towards his Master’s degree next year.

Jaco, who is currently busy with his BMus Honours degree, is a performer par excellence, with many achievements to his name. In 2010, he received the Fanie Beetge Prize for the best undergraduate student in Systematic Music Studies. A year before, he received the same prize as best undergraduate student in Historic Music Studies. He shall continue his Master’s degree with Music Composition as field of specialisation at our university in 2012.

Prof. Helena van Zyl, UFS School of Management

Prof. Helena van Zyl, Director of the UFS Business School, was elected as President of the South African Association of Business Schools (SABSA). Since the beginning of 2010 she has been acting as president. Prof. Van Zyl is the first woman to occupy this position and also the first woman who is currently heading a business school in South Africa. She will serve SABSA as the president for the next two years.

Prof. Zakkie Pretorius, Department of Plant Sciences

Research by Prof. Zakkie Pretorius from our Department of Plant Sciences, has become part of Phase II of a mayor global project to combat deadly strains of a wheat pathogen that poses a threat to global food security.

Prof. Pretorius focuses on the identification of resistance in wheat to the stem rust disease and will assist breeders and geneticists in the accurate phenotyping of international breeding lines and mapping populations. In addition, Prof. Pretorius will support scientists from Africa with critical skills development through training programmes.

The Ug99 strain was discovered in Kenya in 1998, but are now also threatening major wheat-growing areas of Southern and Eastern Africa, the Central Asian Republics, the Caucasus, the Indian subcontinent, South America, Australia and North America.

Prof. Danie Strauss, research fellow in the Faculty of Humanities

Prof. Danie Strauss, a research fellow in our Faculty of the Humanities, won the Dooyeweerd Prize from the Board of the Association for Reformational Philosophies in Amsterdam. Prof. Strauss, former Dean of our Faculty of the Humanities and head of our Department of Philosophy, won the prize for his book Philosophy: Discipline of the Disciplines. The prize is awarded for work in the field of systematic philosophy.

Nida Jooste and Ryan Lamb, Abe Bailey Travel Bursary holders

Nida Jooste and Ryan Lamb are two of the proud recipients of Abe Bailey Travel Bursaries. Both students are academic achievers, but also excel in other fields. This is what set them apart from the rest of the applicants for the bursaries.

Ryan (23), a Medical Physics Honours student at our Faculty of Health Sciences, received the Senate’s Medal for the best Bachelor’s Degree student at the UFS. He was one of 100 students at the Brightest Young Minds Summit this year and was one of the 2008 delegates to the World Youth Forum, hosted by the International Association for Poetry and Solidarity in Italy.

Nida (21) is a very familiar face on our Bloemfontein Campus, as she served as the Deputy Chairperson of our Interim Student Council in 2011.

Loerie Award for Tarran Jacobs, Elizabeth Forson and Mafohlela Mahlatsi

The creativity of a group of students from our university was rewarded with a bronze Loerie Award after they won an internal competition. Tarran Jacobs, Elizabeth Forson and Mafohlela Mahlatsi, all third-year Marketing Communication students, won the award for an advertisement they designed for Cansa.

Each year, the third-year Marketing Communication students of our Department of Communication Science have the opportunity to flex their creative muscles in the Copy-writing class. The challenge is to design two advertisements for any charity organisation by applying the knowledge they gained from the subject in a practical way. The top three groups are then entered for the Loerie and Pendoring awards – two of the most prestigious awards in the South African advertising industry.

The top three groups designed advertisements for Cansa, the South African Blood Service and Crime Line.

Hendrik Kruger and Anke Malan walk away with awards at Pfizer UKZN Young Health Scientists Research Symposium

Two students in our Faculty of Health Sciences won awards at a Pfizer UKZN Young Health Scientists Research Symposium.

Hendrik Kruger, a medical student, represented his group, which won the clinical category with the paper “Injury patterns of occupants surviving motor vehicle accidents in the Free State”. This presentation was based on a study which is the first of its kind in South Africa.

The group with Anke Malan from our Department of Nutrition and Dietetics as presenter received the prize in the community-based category with the presentation ’Knowledge, practices and perceptions of undergraduate students at the UFS regarding the risk factors of osteoporoses’. Anke’s team was also nominated as the overall winner of the symposium. Presentations were delivered in three categories, namely clinical, community-based and laboratory research.

Prof. Louis Scott, Department of Plant Sciences

Prof. Louis Scott from our Department of Plant Sciences was formally rewarded the Fellowship of Royal Society of South Africa (RSSA).

Prof. Scott is an internationally recognised Palinologist at our university and a B-rated scientist.

Fellows of the RSSA are considered to be part of a very elite group of South African scientists who have achieved international acknowledgment.

Prof. Aldo Stroebel, International Academic Programmes in the Office of the Vice-Chancellor

Prof. Aldo Stroebel has been elected as a Founding Member of the South African Young Academy of Science (SAYAS).

He is Associate Professor in our Centre for Sustainable Agriculture, Rural Development and Extension, as well as the Director of International Academic Programmes in the Office of the Vice-Chancellor.

The Young Academy has as its objectives to represent young scientists in advising the government on science and technology policy and human resource development. In addition, they will prepare the SAYAS to join the Global Young Academy (GYA) to engage with high-level international bodies, including the World Economic Forum.

Prof. Lodewyk Kock, Department of Microbial, Biochemical and Food Biotechnology

Prof. Lodewyk Kock was a sought-after keynote speaker at various conferences and seminars around the globe on our nanotechnology breakthrough research.

He delivered keynote lectures at international conferences of repute in the USA, China and Greece. In the USA he delivered a the keynote address at the Conference & Exhibition on Pharmaceutical Regulatory Affairs (Pharma-2011), held in Baltimore, and was a keynote speaker at the 2nd World Congress on Biotechnology in Philadelphia. He was also invited to present various lectures abroad.

He posted two video lectures in e-conference format on his research on the web page of the journal Translational Biomedicine. He was also invited by the International Society of Translational Medicine (ISTM) to head their “Molecular Imaging” Division.

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