Testing for infectious diseases in wastewater

Waterlab in South Africa has developed a cost-effective and non-invasive method of tracking and predicting the spread of COVID-19, hepatitis E, norovirus and other infectious diseases through the microbiological analysis of wastewater.

By her own admission, Dr. Gina Pocock, Specialist Consultant at Waterlab, never had any great burning ambition to pioneer a potentially life-saving diagnostic methodology, but she possesses an obvious energy and optimism that drove the South African company’s success.

A beginning in wastewater-based epidemiology to predict the spread of diseases

Pocock describes having "no interest whatsoever" in the water industry until, during her PhD studies in microbiology she recalls developing a new fascination with the biological properties of algae. An early career in environmental and engineering consulting soon led to Pocock acquiring a role at Waterlab, an already well-established company based in Pretoria offering water quality analysis and regulatory and compliance services to the South African water sector. At the time, Waterlab had no molecular laboratory, but that changed quickly.

R&D projects refine wastewater-based epidemiology

“Waterlab and the KWR Water Research Institute in the Netherlands were perfect partners and we certainly couldn't have achieved what we did without Eureka support." - Pocock

A society's wastewater holds many secrets about how we live. It can be used to track the prevalence of drug abuse in a community, for example, and although wastewater’s role in epidemiology is not new, the rapid emergence of COVID-19 led to a renewed interest in its potential to mitigate the effects of global pandemics.

The process of studying a wastewater sample is relatively simple: skimmed milk is added and pathogens are spun out of the mix in a centrifuge and subjected to nucleic acid extraction to release the RNA and DNA fragments, followed by polymerase chain reaction (PCR) testing, where consistency in the timing and the temperature of the sampling is vital. At the height of the COVID-19 pandemic, Waterlab's experience in the country’s wastewater treatment sector also proved to be invaluable.

Wastewater-based epidemiology is non-invasive, and because one set of RNA samples can reveal as much data as a thousand patient test results, it is highly cost-effective. However, the process does require investment in expensive laboratory equipment, like centrifuges, and access to a ready supply of PCR tests.

While most of the research and development work on wastewater-based epidemiology was initially taking place in Europe, Pocock and her colleagues were quick to see its potential (and the benefit Waterlab could bring) in the very different conditions that South Africa faced during the COVID-19 pandemic.

Pocock succeeded in securing enough funding from the South African Water Research Commission to conduct an initial proof of concept in collaboration with the University of Pretoria early in 2020 within weeks of taking up her new job at Waterlab. She then secured funding later that year from Eureka’s call for COVID-19 solutions.

By the end of 2020, a full-scale project was underway in both South Africa and the Netherlands. Waterlab and the University of Pretoria worked in collaboration with the KWR Water Research Institute and Royal Haskoning DHV in the Netherlands.

Collaboration across the (waste)water

"When my colleagues and I weren't up to our ankles in slime and pondweed we were up to our elbows in sewage in the lab" - Pocock

That the collaboration was with organisations some 13,000 kilometres away in the Netherlands is far from surprising: it was in the Netherlands, after all, that water technologies were first pioneered over seven hundred years ago. That the Waterlab team was led by women is perhaps more surprising, especially in a country where less than 13% of women study STEM disciplines.

The challenges the team faced in South Africa were also very different to those in the Netherlands. Unlike in Northern Europe, water treatment infrastructure in many parts of South Africa have suffered from decades of underinvestment and poor maintenance. Add to that the fact that 40% of the South African population are not connected to a sewer system and it becomes clear there is a stark contrast between the work of Waterlab, who sampled both sewered and unsewered communities and KWR where most if not all sewage reaches a wastewater treatment works.

There were even more difficulties carrying out their project: as the months passed during the prolonged global lockdowns of 2020 and 2021, no planes landed at Johannesburg’s airport and no ships sailed into Cape Town. Basic laboratory glassware was hard to come by, let alone new centrifuges and extraction kits, and the few PCR tests there were mostly prioritised for clinical use.

Despite these seemingly insurmountable challenges, the project succeeded in proving that wastewater-based epidemiology is a vital tool not only in corroborating other evidence of the spread of COVID-19 among some of the most marginalised and vulnerable populations in the developing world but also in predicting its spread and providing public health authorities with timely data to mitigate the effects. The same methodology could also be applied to other infectious diseases.

Not just a new market, but a whole new business

"It's no exaggeration to say that our involvement with Eureka has resulted in a whole new business stream for Waterlab." - Pocock

Following the success of their project, Waterlab has continued its pioneering work in wastewater-based epidemiology in both sewered and unsewered communities in South Africa whilst also investing in building the necessary future capacity to continuing doing so; its bespoke molecular laboratory, built with the help of the South African Department of Science and Innovation through Eureka’s programmes, was completed in December 2021, and Waterlab continues to support the growth of the women in its team.

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Posted 20 February 24