CAES IN THE TIME OF COVID-19
Staff and students within the College of Agriculture, Engineering and Science have been busy during the time of lockdown contributing towards the fight against COVID-19. Read about some of the research being undertaken, initiatives that have been introduced and opinions expressed.
A WORD FROM THE DVC
“Congratulations to the men and women of CAES for standing up to the values and principles of the University of KwaZulu-Natal.”
The culture of linking our research to community engagement is not new in the College of Agriculture, Engineering and Science. When the COVID-19 pandemic forced the university and the nation to join the world to comply with the lockdown regulations of the country, we agreed to continue our good work under protected and safe environments. We agreed to join the efforts of our government as well as national and international organisations. Our staff invested time, existing knowledge and skills to establish new grounds for long-term collaborations with partners in research and social transformation. These efforts will be part of our big plan to turn the challenges of COVID-19 into opportunities. Congratulations to the men and women of CAES for standing up to the values and principles of the University of KwaZulu-Natal.
Professor Albert Modi
DVC and Head of College of AES
Research
CAES academics have been at the forefront of research being conducted in South Africa into the spread of COVID-19 and mitigation strategies to contain the spread of the disease. Read about their findings.
South Africa’s Scientists on the COVID-19 Frontline
Pro-Vice Chancellor for Big Data and Informatics, Professor Francesco Petruccione has partnered with Professor Tulio de Oliveira and KwaZulu Natal’s Research, Innovation and Sequencing Platform (KRISP) to put together a team of more than 20 researchers, including computer scientists, mathematicians, statisticians, bioinformaticians, infectious diseases clinicians, theoretical physicists and quantum computing scientists, to analyze the Covid-19 outbreak in South Africa. The team have produced five of the six Covid-19 viral genomes in the country, which clearly showed how the virus was introduced into South Africa. The data analysis produced by the UKZN CoV Big Data Consortium has been used to advise the Ministerial Advisory Committee on COVID-19. In particular, Dr Maria Schuld and Dr Ilya Sinayskiy, usually working in the field of quantum computing, have shown how successful transdisciplinary research can be.
The scientists have established a fundraising campaign to enable the team of experts to continue their independent analysis of the data and to expand their ability to generate more of this vital information. By supporting the campaign, donors qualify for a Section 18A tax certificate issued by the UKZN Foundation. To support their efforts, click here.
Machine Learning to Detect Evidence of COVID-19 on X-Rays
Professor EB Gueguim Kana, Academic Leader for Research and Higher Degrees in the School of Life Sciences, has collaborated with researchers in South Africa, Nigeria, Cameroon and the UNESCO regional office for Southern Africa to develop a web-based diagnostic tool for COVID-19 that employs machine learning to detect evidence of COVID-19 on chest radiographs (CXR), a method that could provide much-needed decision support for radiologists and clinicians tackling the rapidly expanding pandemic.
Currently the medical interpretation of CXR to draw information about a possible disease takes time and requires substantial medical expertise, leading to delays in obtaining an outcome. In the preliminary report, published on the MedRxiv server, Gueguim Kana and colleagues used machine learning to develop a model that has the capacity to recognise pixels of glass-patterned areas on CXR as distinguishing features of COVID-19 and to differentiate these from other viral- and pneumonia-infected lungs or healthy CXR images.
The model comprises a web interface where medical practitioners can log on and upload chest x-ray images within stipulated specifications. The system analyses the image and generates an outcome, specifying its probability of certainty, within seconds. The system, freely accessible online, is intended to close the gap where there is a lack of available medical expertise and high demand for swift results to determine a diagnosis.
Mapping Durban’s Informal Settlements
SARChI Chair for Land Use Planning and Management, Professor Oni Mutanga and his research team have been involved in an exercise to map informal settlements within the Durban metropolis. This was in response to a request by the Open Cities Lab, a non-governmental organisation (NGO), whose mandate is to assist government and municipalities to build capacity for informed decision-making and evidence based policy and planning, with a focus on areas where this can uplift vulnerable and excluded communities. The request to UKZN was through the Big Data for Science and Society programme, and sought to use satellite and GIS data to map informal settlements in the Durban Metro, in order to facilitate COVID-19 response efforts. This is in line with the UN-Habitat’s COVID-19 Policy and Programme Framework that provides guidance on quantifying the impact of the virus and response to outbreaks in informal settlements and slums.
The UKZN team conducted a desktop based purposive survey approach using satellite images to map numerous visible informal settlements within the Durban Metro. In addition, the centroid geographic location of each individual informal settlement was recorded for easy navigation. The size of each informal settlement was calculated, including an estimate of the number of dwellings using a GIS platform. Names of the informal settlements using secondary data were provided whenever possible, sometimes even using names of the nearest roads.
Waste, Climate Change and COVID-19
Professor Cristina Trois, SARChI Chair for Waste and Climate Change based in UKZN’s School of Engineering, is incorporating the nexus between waste, climate change and human health – from the point of view of the COVID 19 transmission from waste – into research projects emanating from her group. Health risks associated with waste management practices, and the adjustment of these practices accordingly to mitigate/prevent COVID-19 infection as well as mitigate/adapt to climate change are being considered. Just one project being run in the predominantly rural municipality of Ndwedwe in conjunction with the Graduate School of Business, SANEDI and Lotto, focuses on the use of biodigesters from cow-dung and human black-water from toilets for biogas for cooking (household level and in creches) and for heating in rural aquaponic agribusinesses. This research is being expanded to incorporate safe practice for the beneficiaries of these systems with respect to the spreading of the COVID- 19 virus, as well as for the municipalities. Implications on institutional barriers and drivers for the future expansion of these waste-to-energy/biogas systems in light of the current pandemic are being investigated, with particular focus to growing the biogas and renewable energy sector.
Mapping COVID-19 Homesteads via GPS
Professor Trevor Hill and Mr Brice Gijsbertsen from the discipline of Geography, Pietermaritzburg campus, are extending the usefulness of the Cartography Unit to answer difficult questions in collaboration with the Centre for the Aids Programme of Research in South Africa (CAPRISA). They are mapping households in peri-urban and rural areas using GPS. This will allow fieldworkers to navigate to households for COVID-19 community screening, testing and tracking. The project is being piloted in the Vulindlela area outside Pietermaritzburg. Their ultimate goal is to understand the rates and loci of COVID-19 spread, and to enable containment strategies to be accurately planned and precisely implemented.
Online Security in the Time of COVID-19
Senior UKZN lecturer in Computer Science, Dr Brett van Niekerk presented at an international online event, hosted by Cyber in Africa, on the subject of evolving cyber security incidents and threats faced by South Africa, and security cases related to the COVID-19 pandemic and associate lockdown. According to an industry report, the number of cyber-attacks against South Africa has increased tenfold since the lockdown began on 27 March.
SHEFS Hosts Large Virtual Conference During COVID-19 Lockdown
On 30 and 31 March, the Sustainable and Healthy Food Systems (SHEFS) programme hosted its bi-annual meeting via virtual conference, linking 73 participants from partner institutions – including UKZN – based in South Africa, the United Kingdom and India. Although this was the fourth time the broader SHEFS team met to discuss the programme, research plans and outputs, it was the first time the conference was held completely virtually, with all members joining in from their respective homes via the Zoom platform. SHEFS’ foresight helped to reduce its carbon footprint and save global resources that otherwise would have been used through a face-to-face meeting. It also set the stage for its readiness for continued collaboration during the current COVID-19 pandemic. The SHEFS bi-annual virtual conference clearly demonstrated the potential to harness global virtual connectedness to achieve climate and sustainability goals.
Making the Link Between COVID-19 and Obesity
Professor Suna Kassier of the Discipline of Dietetics and Human Nutrition has offered insight into the role obesity plays in the current COVID-19 pandemic, offering advice to everyone in lockdown about how to keep spirits up and weight down. Kassier explained that obesity was associated with an increased risk of developing non-communicable diseases including Type 2 diabetes, coronary heart disease, high blood pressure, a stroke and asthma. Type 2 diabetes and high blood pressure weaken the immune system, and this viral infection could send blood pressure levels soaring, making it fatal in patients with existing hypertension. Contracting a respiratory illness such as COVID-19 would also put the respiratory systems of obese patients under significant strain. Kassier noted that, after Egypt, South Africa was ranked as the second most obese country on the continent with an obesity rate of 28.3%, making it a significant public health concern.
INITIATIVES
A number of initiatives have been put in place by College staff and students to help the university community cope with the unusual circumstances brought about by the COVID-19 pandemic. Read about their interventions here.
UKZN Pro Vice-Chancellor for Big Data and Informatics, Professor Francesco Petruccione, has turned to the online world so as to continue with his monthly data@breakfast seminar series during the national COVID-19 lockdown. With the use of the online “Zoom” webinar tool, participants can tune in at 07h30 sharp to listen to top specialists from the comfort of their own homes. To date expert sessions have been presented by COVID-19 war room members Dr Richard Lessells, Professor Tulio de Oliviera, Professor Salim Abdool Karim and Professor Mosa Moshabela. Topics have covered local and global responses to the pandemic; the science behind South Africa’s particular response; COVID-19 genomics and epidemiology; and the national debate on smoking and COVID-19. Cybersecurity issues have also been covered by Dr Brett van Niekerk. To watch these presentations visit the Data@Breakfast page or YouTube channel.
The CAES Student Support Services team has been hard at work and have developed a video and resources for UKZN students and staff on mental health issues during the lockdown. The video examines various overwhelming feelings which students and staff may feel during this time of uncertainty and fear. It focuses in particular on anger, grief, depression and anxiety. The team did not have access to sophisticated studios and editing equipment as they did this from home, but have done a great job in spite of limited resources. The video unpacks each of the four commonly-experienced emotions and provides viewers with a range of possible coping strategies and skills. Visit their Coronavirus support page or view their informative infographic.
UKZN’s Employee Wellness Programme for staff members and their immediate families is operational during the national COVID-19 #lockdown period. The service includes 24-hour telephonic counselling with a qualified counsellor; guidance on legal, financial, and family care matters; and trauma and manager support. The service is available 24/7/365 to staff and their immediate families living in the same household by dialing 0800-254-255 (toll-free). Download the ICAS On-the-Go app from the Google Play Store or the App Store. After installing this free app, open it to register. Your company code is UKZ001.
Dr Tanja Reinhardt, Coordinator of UKZN’s Science and Technology Education Centre (STEC@UKZN) has used the time of lockdown to come up with some innovative online materials and workshops for little (and big) people stuck at home and needing some scientific stimulation. Apart from a weekly newsletter with mathematical and science teasers and experiments aimed at young learners (find them here), Reinhardt is also offering weekly online workshops via zoom, where children can experiment with scientific principles using common household items and ingredients. Email stec@ukzn.ac.za to find out more.
With staff and student access to campus restricted by COVID-19 and online learning being the modus operandi at UKZN for the foreseeable future, the College Dean for Teaching and Learning (T&L), Professor Naven Chetty, has created a useful Teaching and Learning website to act as a point of reference and repository for relevant information. Training materials for staff and students as well as for general communication regarding Teaching and Learning in the College can be accessed here. Staff are encouraged to routinely visit the T&L webpage to view the available resources.
SARChI Chair in Waste and Climate Change, Professor Cristina Trois has been tasked by UKZN Vice-Chancellor Professor Nana Poku to lead a ‘GreenUKZN-COVID-19 Free’ task team post lockdown. Their aim will be to plan and implement clean projects, waste awareness campaigns and health and safety guidelines for the safe disposal of waste on campus, when normal University activities resume. The team will also develop guidelines to avoid the future spread of the virus in laboratories when research activities recommence. The team’s brief is to ensure best practice waste management in times of COVID 19 on a multi-campus environment.
SAEES staff member Dr Alfred Odindo has been working closely with Vulindlela community members to co-design safe, cost-effective and socially acceptable waste management and sanitation innovations to establish a circular economy. The project, RUNRES: ‘The rural-urban nexus: Establishing a nutrient loop to improve city region food system resilience’ is working in Vulindlela to implement sanitation innovations to recover waste in order to strengthen the resilience of smallholder agriculture in the community. Several community workshops and focus group discussions have been conducted with the support of traditional leadership and ward councillors to define challenges and provide solutions. However, the project has had to adapt with changing times precipitated by the COVID-19 pandemic and is using ICT tools to reach out to the community. This has proved to be immensely successful with the farmers who are able to connect seamlessly and join meetings using Zoom and WhatsApp.
A student in the School of Mathematics, Statistics and Computer Science (SMSCS), Mr Sibonelo Mhlongo, is working with his mother’s small clothing manufacturing business to arrange for the manufacture and provision of fabric masks to the University when staff and students return to campus. Mhlongo, who is a third year student studying applied mathematics and statistics, is originally from Mtubatuba near St Lucia in northern KwaZulu-Natal. When UKZN issued a challenge to students to contribute ideas for the facilitation of continued teaching and learning under pandemic conditions, Mhlongo and his family decided to propose the manufacture of masks for UKZN, in the UKZN colours. This initiative will not only provide much needed employment to ladies in Mtubatuba but also contributes practically to the welfare of the UKZN community.
Opinionista
Leading College academics have contributed to the COVID-19 debate in the press. Read about their opinions here.
 | Professor Brij Maharaj from the discipline of Geography on the Howard College campus appeared in the Cape Times, Mercury and Daily Maverick on 21 April with an opinion piece arguing that COVID-19 gives us a chance to plot a new global path – and to give planet Earth a breath. Read his piece here. |
 | A group of researchers linked to UKZN’s Centre for Transformative Agricultural and Food Systems (CTAFS) and the uMngeni Resilience Project (URP) and led by Dr Tafadzwa Mabhaudhi have pointed to the fact that as the COVID-19 pandemic takes hold in South Africa a crisis within a crisis is looming. Years of apartheid have left behind a very dualistic system that serves very distinct social groups. The spread of the virus is likely to devastate further these marginalised groups who already face challenges such as poor health, low food and nutritional security, and limited access to resources and services to mitigate risk. A big part of efforts must also be focused on stemming the spread of COVID-19 itself. Crucial preventative measures will be essential to slowing the impacts of the virus, including informal food systems and smallholder producers. |
 | Professor Suna Kassier from Dietetics and Human Nutrition at UKZN has provided some advice to maintain healthy consumption habits while dealing with added stress under the COVID-19 lockdown. Kassier explains that the uncertainty of this global pandemic can exponentially increase the daily stress most people experience. She encouraged people to be mindful about their stress coping mechanisms, which on its own, she said, is a positive step in the right direction. She advised against dipping into alcohol stockpiles and drinking more than one would under normal circumstances, saying that alcohol contributes to weight gain and a depressed mood. Kassier also advised against killing extra time by snacking absent-mindedly but rather suggested various cost-effective, healthy snack options, as well as regular meals, even small ones, to avoid the headaches, anxiety and nervousness that can result from fluctuating blood sugar levels. In a separate opinion piece, Kassier recommended the value of laughter to lessen stress levels in the current time of uncertainty, saying that laughter was one contagion that added value to one’s life! |
 | Postdoctoral researcher in the School of Life Sciences, Dr Yvette Ehlers Smith, presented her views in a Mail and Guardian opinion piece on how protecting nature can protect us in a time of COVID-19. Ehlers Smith argues that as South Africa grapples with the tragic effect of the coronavirus on people, the economy and society it’s increasingly clear that our status as a megadiverse country is a blessing, but that our reliance on nature tourism is a risk. If South Africa were to establish a nature conservation philosophy that is less dependent on tourism and benefits public health, people and the economy, the advantages would be enormous in the long run. That is why it is imperative that we do everything we can now, before it’s too late, to ensure our biodiversity doesn’t become a casualty of the pandemic. |
COVID-19 Resources
Take a look at the resources below which can assist you during the lockdown period and inform you on the developments of COVID-19.