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10 June 2020 | Story Nitha Ramnath | Photo UFS Photo Archive
Prof Anthony Turton.
History was made in South Africa this week when a commercial laboratory became the first to extract COVID-19 RNA from various sewage samples in the country. This was done as a proof of concept, after the Dutch research agency KWR entered into an agreement with the SA Business Water Chamber on 9 April this year.

It was KWR that first demonstrated the potential of wastewater surveillance to identify the total viral load in a defined population in the Netherlands. This technology breakthrough has opened a new chapter in wastewater epidemiology on a global scale.
 
Prof Anthony Turton from the Centre for Environmental Management at the University of the Free State (UFS) says it is now possible to monitor the total viral load in each of the 824 wastewater treatment works in South Africa. Once the population size within the catchment area of the works is known, a calculation of the total viral load is possible, with a reasonable degree of accuracy. This accuracy will improve over time as the technology becomes more robust. 


Rapid deployment of technology
Prof Turton says this proof of concept is significant, because it took just eight weeks after reaching the agreement with KWR to find a laboratory with the necessary capabilities and to conduct the first tests. This is a rapid deployment of technology necessitated by the urgency of the COVID-19 pandemic. The source of funding for this demonstration was the private sector, so no taxpayer money was used. The proof of concept was deliberately designed to achieve two specific objectives. The main objective was to determine whether the Dutch methodology could be replicated in South Africa without major investment into training and procurement of laboratory equipment. The secondary objective was to understand the logistical complexities of sampling at multiple sewage works in one province, and then safely transporting those samples to the laboratory in another province. This emulates what will be needed if this methodology is adopted by government and rolled out across all provinces as required. 

Taking samples
Samples were taken over a 24-hour period using an automatic bulk sampler provided by a service provider at risk. A number of sewage works were sampled to emulate the complexity of a national operation should rapid implementation be required. The first samples were taken on Thursday 4 June. These were prepared according to a precise protocol and were shipped to the laboratory hundreds of kilometres away. The samples were prepared according to the stringent requirements of the protocol, and COVID-19 RNA was successfully extracted on Monday 8 June. Lessons learned in the first trial are being fed back to the team in preparation for the second sampling run that will take place shortly. 

Prof Turton, who serves in a facilitating role and in different capacities with each of the critical components of the overall value chain, is the man in the middle tying this whole process together. This is also a demonstration of the value of a university working in close collaboration with both government and private sector partners towards a common objective.  It is part of the Public Private Growth Initiative (PPGI), where the private sector works closely with the state to deliver core services needed to create employment opportunities as a matter of growing urgency.

Determining if the total viral load is increasing or decreasing
The second sampling run, which is about to be launched, will be a refinement of the first. Lessons learned during the logistical exercise will be applied to streamline the operation and generate an accurate costing of the service. By comparing the data for each sampling sequence, it will be possible to determine with a considerable degree of accuracy whether the total viral load in a given population is increasing or decreasing. When applied to multiple sewage works, it will be possible to identify hotspots for appropriate government intervention. This technical capability will provide robust information to both government and private sector decision-makers as they navigate their way through the complexity of a shutdown and phased re-opening of the national economy. Rapid upskilling of suitably qualified personnel will be needed, and the UFS will be playing a role in that process. 

News Archive

Researchers international leaders in satellite tracking in the wildlife environment
2015-05-29

 

Ground-breaking research has attracted international media attention to Francois Deacon, lecturer and researcher in the Department Animal, Wildlife and Grassland Sciences at the UFS, and Prof Nico Smit, from the same department. They are the first researchers in the world to equip giraffes with GPS collars, and to conduct research on this initiative. Recently, they have been joined by Hennie Butler from the Department of Zoology as well as Free State Nature Conservation to further this research.

“Satellite tracking is proving to be extremely valuable in the wildlife environment. The unit is based on a mobile global two-way communication platform, utilising two-way data satellite communication, complete with GPS systems.

“It allows us to track animals day and night, while we monitor their movements remotely from the computer. These systems make possible the efficient control and monitoring of wildlife in all weather conditions and in near-to-real time. We can even communicate with the animals, calling up their positions or changing the tracking schedules.

“The satellite collar allows us to use the extremely accurate data to conduct research with the best technology available. The volume of data received allows us to publish the data in scientific journals and research-related articles.  

“Scientific institutions and the public sector have both shown great interest in satellite tracking, which opens up new ground for scientific research for this university. Data management can be done, using Africa Wildlife Tracking (AWT) equipment where we can access our data personally, store it, and make visual presentations. The AWT system and software architecture provide the researcher with asset tracking, GPS location reports, geo-fencing, highly-detailed custom mapping, history reports and playback, polling on demand, history plotting on maps, and a range of reporting types and functions,” Francois said.

Data can be analysed to determine home range, dispersal, or habitat preference for any specific species.

Francois has been involved in multiple research projects over the last 12 years on wildlife species and domesticated animals, including the collaring of species such as Black-backed Jackal, Caracal, African Wild Dog, Hyena, Lion, Cheetah, Cattle, Kudu, Giraffe, and Black Rhino: “Giraffe definitely being the most challenging of all,” he said.

In 2010, he started working on his PhD, entitled The spatial ecology, habitat preferences and diet selection of giraffe (Giraffa camelopardalis giraffa) in the Kalahari region of South Africa.

 

Since then, his work has resulted not only in more research work (supervising four Masters students) but also in a number of national and international projects. These include work in the:

  • Kalahari region (e.g. Khamab Nature Reserve and Kgalagadi Transfrontier Park)
  • Kuruman region (Collared 18 cattle to identify spatial patterns in relation to the qualities of vegetation and soil-types available. This project took place in collaboration with Born University in Germany)
  • Woodland Hills Wildlife Estate and Kolomella Iron Ore – ecological monitoring
  • A number of Free State nature reserves (e.g. Distribution of herbivores (kudu and giraffe) and predators (camera traps)

Francois is also involved with species breeding programmes and management (giraffe, buffalo, sable, roan, and rhino) in Korrannaberg, Rustenburg, Hertzogville, Douglas, and Bethlehem as well as animal and ecological monitoring in Kolomella and Beesthoek iron ore.

Besides the collaring of giraffes, Francois and his colleagues are involved in national projects, where they collect milk from lactating giraffes and DNA material, blood samples, and ecto/endo parasites from giraffes in Southern Africa.

With international projects, Francois is working to collect DNA material for the classification of the nine sub-species of giraffe in Africa. He is also involved in projects focusing on the spatial ecology and adaptation of giraffe in Uganda (Murchison Falls), and to save the last 30 giraffe in the DRC- Garamba National Park.

This project has attracted a good deal of international interest. In June 2014, a US film crew (freelancing for Discovery Channel) filmed a documentary on Francois’ research (trailer of documentary). Early in 2015, a second crew, filming for National Geographic, also visited Francois to document his work.

 

More information about Francois’ work is available at the GCF website. 

Read Francois Deacon's PhD abstract

Direct enquiries to news@ufs.ac.za.

 

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