International interest in SA team led by UFS professor who isolated Covid-19 in sewage

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Since a South African team associated with the University of the Free State (UFS) became the first to isolate the SARS-CoV-2 virus from wastewater and developed a viable virus risk forensic service, there has been interest in this technology from a range of role players in North America, Africa, the Middle East, and Southeast Asia, to the South African government.

Prof Anthony Turton from the Centre for Environmental Management at the UFS says contact has been made with two separate scientific teams working in South Africa – one in the Western Cape associated with the Department of Health, and one coordinated by the Water Research Commission reporting to the Department of Water and Sanitation (DWS) – both of which are developing next-generation science. 

Prof Turton says the team has also presented a formal report to the DWS to show that first-generation science is quite capable of generating accurate data that is of great value to planners by feeding into national decision-making bodies.  


A proud achievement 

“As the person who conceptualised this service, I am very proud to be a South African citizen. My background is in national security, so it was that skill set which I applied to the problem when I asked the question – how can we provide the best available information in the shortest possible time, in the face of high risk and growing uncertainty, using the best available technology? This is only possible when one is trained in the intelligence sciences. Intelligence is about converting raw data, often from contested sources, into actionable bits of information with a defined level of certainty.” 

“However, the truly remarkable portion is the team that we rapidly assembled. By hand-picking the right kind of people for the team, we could unlock the power of synergy where 1 + 1 becomes 3. We, as South Africans, have developed a world first, and this is something we can collectively be deeply proud of. This is a proudly South African achievement, not an individual achievement. The benefits belong to society, because even when I was at the CSIR, I championed the notion of ‘science in the service of society’, and here we have another example,” says Prof Turton.


Using available technology

With the 824 wastewater treatment works (WWTW) in the country, the DWS can rapidly deploy this technology to any existing area of concern if they see value in it.  “At present, government is waiting for second-generation science to become available, but that is probably 24 months away at best. In the interim, a crisis is unfolding in the present, and first-generation science is clearly capable of providing sufficiently accurate information to assist in decision-making around the deployment of increasingly scarce resources.”

“DWS used similar technology in the cholera crisis a while back, so they are aware of the benefits. From a society perspective, the question is whether government must wait for the second-generation science to emerge before using the technology, even though first-generation technology can provide an important part of the missing data as explained above. This is what the foreign entities have grasped.”

According to Prof Turton, the interest shown in this technology is from both government and the private sector in North America, Africa, the Middle East, and Southeast Asia. A number of key decision-makers see the value of this technology in mitigating both financial and political risk. 

“They recognise that this pandemic is here to stay for a while, so they intend to get ahead of the curve, which is what the forensics service allows. An example is a condominium where a few hundred people live, but who are unable to use the facilities that they pay levies for. This service will enable all residents in a specific condominium to rebuild trust that they live in a ‘safe space’.” 

“For government, they recognise that this technology can feed data into their mapping systems. They refer to a ‘heat map’ that shows areas of viral activity and areas of relative safety. In one case, the focus is on monitoring each building in a city to identify which building is safe and which is a hot spot,” says Prof Turton.  


Next-generation science 

He explains that next-generation science refers to the algorithms used to extrapolate viral-load data to a larger cohort of people. The first-generation science was about the detection of the virus as a binary measurement: “Is the virus present, yes or no?”

“The current science can do this without a problem. Second-generation science is about how much virus is present? Is this more, or less, than we saw last week? If so, how much bigger or smaller is the signal? If so, can we mathematically calculate from a defined quantum of signal an accurate probability of the total viral load in the population being sampled?” 

“From this, can we say that 15% of the population is shedding virus (a number currently only possible from sewage surveillance) but personal testing shows us that only 5% of the population is positive? If so, we can then say that 10% of the population is both positive and asymptomatic. This has major implications for decision-makers, business owners, tourism operators, and governments who are losing revenue because of failing economies.” 

More importantly, says Prof Turton, is that this missing piece of data will become vital in testing for herd immunity, or the efficacy of a vaccine once available. 


The cost of the service 

By presenting a formal report to DWS, the team was able to get an accurate costing of the service. The cost of a single sewage sample, which can accurately monitor a geographically defined cohort (let’s say 100 000 people for the sake of illustration), is equivalent to 15–20 individual samples (nasal swabs, for example). “We can sample 100 000 people at the same cost as 15 can be sampled individually. More importantly, it is highly unlikely that any government in the world will ever reach anything more than 10% sampling at individual level. This tells us that while individual sampling might be very useful, it is logistically complex, and has a political risk when it cannot be rolled out across a large enough portion of society,” says Prof Turton.  

“The virus-risk forensic service that we have been developing can identify specific hot-spot areas, and those can be targeted for higher saturation coverage of individual testing. For example, in the DWS PoC, we identified one specific WWTW that is a definite hot spot, but another that has no viral signal at all. This means that those people living in the area with no viral signal are safe and do not need to be individually tested, but those in the hot spot need to be isolated and targeted for individual testing. More importantly, we can now say that the hot-spot area is likely to result in demand for medical services in a specific area, so planning can be done before the wave hits the hospital,” explains Prof Turton.   

With the submission of the formal report to government, the Business Water Chamber, and the Public Private Growth Initiative (PPGI), we can now announce a team to offer this virus-risk forensic service to any party with a need for this support in both the public and private sectors. 

The team is:

• Prof Anthony Turton – Centre for Environmental Management at the UFS, responsible for the conceptual design of the virus-risk forensic service. 
• Dr Mpafane Deyi – a graduate from the UFS and CEO of Amanzi-4-All, responsible for implementation of the service to both private and public sector partners.
• Dr Leon Geustyn – Director of Amanzi-4-All, responsible for the mathematical and technical aspects of the risk-based diagnostic service. 
• Dr Shaun Groenink – Director of GreenHill Laboratories, responsible for the laboratory support required.
• Dr Cara-Lesley Bartlett – Senior Scientist at GreenHill Laboratories.
• Mr Neil Madgwick – Director of Praecautio, responsible for the coordination of laboratories as the service grows across the African continent.
• Mr Kevin Lindsay – Director of Instru-Serve, responsible for the refinement of bulk sampling techniques and the supply chain from point of collection to the laboratories.