Science vs Coronavirus
The COVID-19 pandemic has reinforced the value of collaborating, sharing data and information. “The fight against this pandemic includes assisting organisations with the establishment of infection prevention and control programmes.”
Knowledge is power, especially when it comes to beating a global pandemic such as COVID-19: from exploring the use of indigenous products, to tracking mobility to better understand the spread of the virus; from producing quality protective wear for use on the frontlines, to supporting small and medium businesses.
The Council for Scientific and Industrial Research (CSIR) is using all the resources at its disposal to save lives and mitigate the effects of COVID-19 on the South African economy, collaborating with multiple experts and top-tier innovation leaders to devise solutions.
These experts are working in tandem with external partnerships forged to equip the country with all the necessary skills, tools and research needed in the fight against the unseen killer.
Tribe Business Magazine approached a few researchers at the CSIR for an inside look into how science and technology is the life support of an entire nation plagued by the pandemic. With their world-class expertise, they explained how the CSIR is helping communities overcome this unprecedented nightmare, and discussed possible solutions to beating the pandemic. Indeed, science is our best chance of overcoming the multiple challenges and surviving the ‘new normal’ in which we will find ourselves long after the virus has dissipated.
“The COVID-19 pandemic is testing our natural behaviour somewhat beyond our imagination, forcing us to work and operate differently.”
The influence of the southern hemisphere winter season on the COVID-19 epidemic in South Africa is unknown. The media is immersed in several speculations, but the only sure thing is that the epidemic will peak here in mid-winter.
Dr Neville Sweijd, director of the Applied Centre for Climate & Earth System Science, a research programme by the CSIR and the National Research Foundation, says that “the months between April and September are usually associated with the influenza season, but the seasonal prevalence of SARS-CoV-2, the organism responsible for the COVID-19 pandemic, is still speculative. This is because it is a novel virus, which has only been circulating for around six months, and the information that is available regarding the environmental influences on the disease comes mostly from countries in the northern hemisphere.”
Sweijd goes on to say there are more than 100 studies that explore the effects of environmental variables on the virus in some way. Learning can also be gleaned from laboratory studies on SARS-CoV-2 and similar viruses that have spread globally in the past, such as those responsible for Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS).There are several other ‘endemic’ human coronaviruses that cause the common cold, which have a seasonal prevalence.
“The COVID-19 Environmental Reference Group (CERG) is investigating how this information translates into the South African experience of the pandemic. Preliminary findings, based on historical average winter conditions, are that as South Africa heads into winter, the portion of the SARS-CoV-2 transmission risk which is attributable to climate will rise due to falling temperatures and humidity in most of the country. In contrast, warmer conditions should result in a marginal decreasing effect on transmission rates in the northern hemisphere as it emerges from winter. With this in mind, it is likely that the late summer onset could have delayed the timing of the peak of the disease,” he concludes.
The e-symposium by the World Meteorological Organization, titled “Climatological, Meteorological and Environmental factors in the COVID-19 pandemic”, was held at the beginning of August to evaluate the possibility of COVID-19 manifesting over the next few years, at least until an effective vaccine or treatment is widely available. It also discussed the likelihood of whether or not SARS-CoV-2 and its variants would become one of the family of common viruses with a seasonal prevalence, and the likelihood of a ‘second wave’ in the winter of 2021. The CERG has participated in other global discussions with colleagues in both the northern and southern hemispheres, who are considering these scenarios.
The virtual international symposium would assess what has been learnt and what is understood, and what can be reliably predicted about the role of environmental variables’ influence on the trajectory of the COVID-19 epidemic from a global, hemispheric, regional and local perspective, Sweijd explained. The outcome of the conference will include a synthesis of the information presented and recommendations for further research and operational responses at global to local scales.
Keeping a watchful eye on our water
Since the start of the COVID-19 pandemic, the CSIR Microbiology and Parasitology Laboratory has screened many water samples for the presence of SARS-CoV-2 and other infectious viruses. Water samples were received from many of the country’s leading water utilities, as well as utilities from some neighbouring countries. Researchers have not detected any infective viruses in any of the drinking water samples that have been analysed to date.
According to CSIR microbiologist and senior researcher Wouter le Roux, who has worked in the field of water-related microbiology for 15 years, “Scientists do not consider SARS-CoV-2 to be a water-borne pathogen because these respiratory viruses lack the characteristics that typically provide environmental durability. Robust water-borne pathogens usually survive environmental stresses well because they have attributes like DNA genomes and resistant cell walls; the COVID-19 viruses lack these features.”
The laboratory can test raw (source) and final (treated) drinking water samples for the presence of certain viruses. The test screens water samples for viruses that infect human-like cells, and the COVID-19 virus can be detected using this approach.
“According to the World Health Organization, there have been no reports of viable SARS-CoV-2 viruses in treated drinking water. It is important to mention that the test does not identify the specific viral agents; instead, it warns us of the presence of certain viruses that can cause human disease upon consumption,” Le Roux adds.
The laboratory will continue to provide the service to the water sector, ensuring the safety checks remain in place—not just for COVID-19 but also for other waterborne diseases that will continue to pose health risks to vulnerable communities.
Innovation leader Siemens has been a long-standing partner of the CSIR in South Africa and has co-operated in various fields of research, including manufacturing and mining.
CEO of Siemens for Southern and Eastern Africa, Sabine Dall’Omo, says that in March this year, when Europe said it did not have enough ventilators, Siemens decided to partner with the CSIR to develop a locally engineered version. Dall’Omo explains that Siemens designed and supplied the software, so it would have two outlets. “One is our software and team centre out of our Product Lifecycle Management software that enables us to stimulate digital twins so that you don’t have to go into prototype production and, ultimately, optimise. This is because you don’t want to have a product that’s ISO-certified and can’t be used post-pandemic in the supply. It should be used whenever it’s needed and not just as a crisis solution. If the correct paperwork is not done and the standards are not adhered to, it might not be supplied later into the market—and these are really innovative ideas.” Throughout this process, Siemens has created innovative solutions that should stay on the market long after the COVID-19 pandemic has passed.
In July, the CSIR produced (or has started production on) the ventilators with a team of suppliers. It has funding for 10 000 ventilators in South Africa. From the value, engineering and software side, Siemens is contributing about R8 million to that project to make sure things are moving forward.
Dall’Omo adds, “We’re currently also working with the Department of Health in the Eastern Cape and Gauteng to identify how we can participate in alleviating the health crisis specifically in the hospital environment. We’re proud to have been the technology partner on this project with the CSIR to provide the Product Lifecycle Management software support.”
Expert insight for modelling of COVID-19
Professor Pravesh Debba, manager of Spatial Planning and Systems at the CSIR, is leading a group of digital modellers and collaborators who aim to share critical information, knowledge and data with the national Department of Health, the National Institute for Communicable Diseases (NICD) and other government departments, in responding effectively to the challenges brought about by the COVID-19 pandemic.
Data science as well as statistical and mathematical modelling are at the forefront of understanding the spread of the outbreak and being able to forecast the number of deaths; test different strategies and interventions; determine the number of those who are critically ill at a specific point in time at a particular location; as well as determine if there are adequate intensive-care unit beds, ventilators and other critical resources within our healthcare system.
“One of the greatest challenges in adequately responding to such disasters lies in the weakness of our systems when it comes to collecting quality, timely and disaggregated spatial data. The lack of interoperability, standards and sharing of data between different levels—local, regional, national, and internationally—limits the extent to which we can effectively respond to the COVID-19 situation. The ownership of this information and data ranges across various government, academic, public and private sectors, as well as science councils,” says Prof. Debba.
“The COVID-19 pandemic is testing our natural behaviour somewhat beyond our imagination, forcing us to work and operate differently. Modelling of COVID-19 has the ability to understand the effect of the different levels of lockdown, both socially (social distancing) and economically. This helps the government make decisions based on science.”
Through collaboration with the South African Medical Research Council, the Human Sciences Research Council, and the universities of KwaZulu-Natal, Pretoria, Witwatersrand and Hasselt in Belgium, as well as the NICD, the modelling group focuses on three different modelling approaches:
The first is a data-driven modelling approach, performed to determine reliable forecasting of the number of cases, recoveries and deaths at national and provincial levels. This nonlinear epidemiological growth model is crucial to being able to effectively manage the rising case load and allocate resources over the short term, as well as develop continuous updates of the final size of the outbreak, turning point and duration. The model is also compared to the compartmentalised Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological models used by the National Coronavirus Command Council through the NICD.
The second approach is to use ward-level case data to support and improve the understanding of area-level variation of the COVID-19 epidemic in South Africa and its drivers for targeted interventions. The objective was to assess the spatial epidemic dynamics of COVID-19 in South Africa to determine local clusters of infection and hotspot detection. By complementing this derived spatial database with socio-economic data and environmental data (and hopefully in future also adding burden of diseases), spatial statistical methods were used to perform spatial regression and interpolation. This approach also helped to assess spatial dependence at both global and local levels to identify locations of high COVID-19 rates and predict where additional clusters of infection will occur.
The third modelling approach was to assist the NICD in developing a spatial SEIR model that would be able to respond to different lockdown scenarios in different municipalities, based on the forecast of the pandemic at a local level, while taking into account differences in transmission rates, population density, demographics and other factors at a localised level.
For Prof. Debba, the COVID-19 pandemic has reinforced the value of collaborating, sharing data and information, performing quality data checks, and exercising good analytical modelling and data science to contribute to the scientific fraternity—enhancing decision making for the country. This approach can illuminate the difficult, but critical, choices that are constantly being made.
Scientific studies into a traditional medicine that may help improve the body’s ability to fight off and recover from infection may be helpful in the fight against COVID-19. The Prijap Biolife traditional medicine has been in the market for 10 years and has been used to treat patients who have been infected by the human immunodeficiency virus.
With expertise in advanced agriculture, food science and health, the CSIR collaborated with the University of Pretoria—combining their research and development capabilities to conduct in-vitro studies on a liquid extract of the product in 2019. Researchers from the CSIR and the University of the Free State are proposing further studies to ensure the product is scientifically and clinically certified, and are preparing funding proposals.
This South African patented product, with its unique preparation method, offers potent activities that could potentially be effective in treating symptoms that are associated with coronavirus infection. These include immune-building, anti-inflammatory, detoxifying, appetite-increasing and energy-boosting activities. These aspects have proven to be key elements that contribute to improving the body’s ability to fight off and recover from infections. However, further scientific and clinical studies are required to ensure the validity of some of the product claims.
While the CSIR continues to endeavour using its research and development capabilities on indigenous knowledge systems and the agro-processing sector to support the government in the fight against COVID-19, it equally aims to support a competitive bio-innovation industry through the valorisation of plant-genetic resources and indigenous knowledge to develop new products and processes.
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