It’s long been used to track infectious diseases such as polio, hepatitis A and the norovirus, and for monitoring drugs and chemical contaminants that could affect human health. And now it’s a new low-cost ally in the fight against Covid-19: sewage.
Scientists from the Water Research Commission (WRC), working with the Waterlab at the University of Pretoria and the CSIR, have already detected Covid-19 RNA signals from several wastewater plants in hot spots in Ekurhuleni, Tshwane and KwaZulu-Natal.
Their results from their proof of concept study using wastewater and water quality surveillance to monitor the spread of Covid in communities shows an increase in the viral load in the samples being tested with time.
This “corresponds to the increase in case numbers in hot spots as South Africa enters the peak infection phase”, the WRC said in a science brief this week.
Sars-CoV-2, the virus responsible for Covid-19, is shed at relatively high titres in the stools of some individuals. “Viral gastrointestinal infection, or at least shedding, can remain for some time after clearance of the virus in the respiratory tract.”
However, there are no significantly recorded cases of people shedding the live virus, said Jay Bhagwan, executive manager of water use and waste management at the WRC.
“Basically what they are shedding is the RNA of an ineffective, dead virus, which is not infectious. It’s been broken down and the protein of the virus is the signal that has been left in the waste.”
There is still uncertainty over shedding rates and duration, links between the genetic signal and the infection prevalence and fate within wastewater, and how this changes with wastewater characteristics that may vary with time and seasons, said Dr Nonhlanhla Kalabaila, a research manager at the WRC.
“There are a lot of unknowns and we’re learning by doing.” As infections escalate, and given the challenges associated with individual testing, the surveillance work needs to be scaled-up nationally to complement national interventions, said the science brief.
“This could offer a cost-effective method of understanding the pandemic trends, provide an early warning system, identify hot spots and track the waves of transmission as the pandemic unfolds.”
Wastewater-based epidemiology is an approximate, not accurate, methodology, Bhagwan said. “If I take a sample in the wastewater plant I cannot accurately tell you that there’s are 100 people infected. I can tell you what I’m seeing from the signals is that a significant percentage of your population is showing signs of being infected.
“So, it can show a hot spot and it can show trends and it’s a more low-cost technique that allows you to respond in the areas where we start seeing these trends decreasing and increasing… It will go far in complementing government programmes and provide that early warning, because at the moment it’s difficult to know what is happening in the small rural town or village in SA.”
The science brief describes how the current total picture of Sars-CoV-2 virus circulation in the population is “incomplete”, with the number of Covid-19 patients most likely underestimated “mainly due to the limitations regarding testing and to the likely large number (estimated to be 45%) of asymptomatic individuals”.
Screening in raw sewage water can be a tool to measure the virus circulation in a defined population, such as a city or a small municipality feeding to the same wastewater treatment works.
In communities with poorly functioning wastewater treatment plants, or lacking any formal sewage networks, the likelihood of detecting viral particles, whether infectious or not, is high.
Samples are now being taken for the next phase of the study from raw influenteffluent from eight wastewater treatment works from hot spots around South Africa.
Three package wastewater treatment works will be sampled and hospital wastewater. For surface water analysis, samples will be collected “from at least three rivers with known sewage contamination, two samples of sewage polluted greywater from non-sewered communities will be taken and one groundwater sample from an area serviced by pit latrines”.
Around 10 similar initiatives are under way led by the Water Chamber, City of Cape Town, University of Cape TownUCT, Durban University of Technology, National Institute for Communicable Diseases, Umgeni Water, Aurecon and others.
“Now the big question is: How do we leapfrog this knowledge into a national protocol?” said Bhagwan. When the peak is over, sewage screening will help the early detection of the re-emergence of the virus.
“There’s always going to be a second and third wave coming… This is an early-warning system that keeps checking to see if we’re picking it up or not. Even if we eradicate it, beyond the eradication period we will have to keep checking that it doesn’t resurface.”