Twice a week, a team of scientists from South Africa’s National Institute for Communicable Diseases (NICD) traverses the country’s metropolitan areas, visiting up to 50 wastewater treatment sites to fill bottles with effluent.
The bottles are sealed and disinfected, then transported to a network of laboratories across the country where their contents will be tested for the presence of SARS-CoV-2, the virus that causes COVID-19.
This kind of wastewater surveillance has been used for decades to detect and monitor the spread of viruses and pathogens including cholera, poliovirus, noroviruses and influenza.
Now the emergence of COVID-19 has reiterated its role as a cost-effective tool for disease monitoring and the early detection of community infection.
In this instance, it relies on the fact that an infected person can shed the virus through faeces and urine, even when asymptomatic.
As such sequencing faecal matter can establish the burden of community infection in a specific location and help health authorities to target their response efforts accordingly.
“It is difficult to test everyone who has COVID-19, but it is easy to take a single wastewater test and you will have effectively tested everyone who lives in a particular area,” explains Dr Kerrigan McCarthy, a specialist pathologist at NICD.
Based on the data collected from such samples in South Africa, Dr McCarthy says COVID-19 levels in wastewater have correlated closely with reported cases and variants circulating at the time.
“At the height of the pandemic, we gained some confidence in wastewater results because we picked up an increase of SARS-CoV-2 levels before we started seeing increases in clinical testing.
We were also able to sequence the genome in wastewater and that helps us tell which variant is moving around and what the genetic changes are,” she adds.
In line with World Health Organization (WHO) recommendations, in addition to COVID-19, this type of environmental surveillance also continues to be used to monitor polio in several countries across the African Region.
“If you sample wastewater for polio, it can tell you if people living in a specific area have the virus circulating among them. This is helpful because only one in 100 people with polio has symptoms,” says Dr McCarthy.
“So, testing wastewater has been a good way to understand the spread of the virus and contribute to polio eradication efforts.”
Zambia started sampling wastewater for polio in 2018. The method has continued to serve as a vital early detection tool in a context where neighbouring Democratic Republic of Congo and Malawi have reported cases of circulating vaccine-derived poliovirus and wild poliovirus respectively this year.
“With this kind of surveillance, you are getting samples from whoever is using the sewer system, so should there be any viruses in the effluent or wastewater, they will be picked up by the laboratory,” says Belem Matapo, a disease surveillance officer at the WHO Zambia country office.
“The cost is also very low compared to taking individual samples from suspected cases.”
In the instance of Ghana, the country used existing infrastructure developed for polio to pilot wastewater monitoring for COVID-19 between November 2020 and May 2021, with the help of a grant from the Bill and Melinda Gates Foundation.
“Ghana already had the structures for environmental surveillance in place, so when COVID-19 happened, we decided to build on the existing expertise to support the preparedness response,” says Habib Yakubu, an associate director for research projects at Emory University, who led the pilot project.
With just 10% of Ghana’s population connected to the national sewer network, Yakubu’s team also relied on communal toilet facilities to get a better understanding of what was happening within communities.
“We were able to show a corresponding relationship between the SARS-CoV-2 signal in the environment and clinical cases that were coming to hospitals in both urban and rural areas. This was critical in informing public health decisions and putting in place all the protocols to prevent exposure,” Yakubu says.
However, despite such benefits, few other African countries have adopted water surveillance as part of their wider COVID-19 response.
In addition to South Africa and Ghana, COVIDPoops19, a dashboard that documents global SARS-CoV-2 wastewater monitoring efforts, lists Nigeria, Uganda, Kenya and Malawi as the other African countries with ongoing COVID-19 wastewater surveillance initiatives.
This is in part due to a lack of requisite laboratory infrastructure in many countries on the continent. “Most African countries must rely on a central laboratory in the capital city for results.
“In the case of Ghana, samples collected from outside the capital are often batched, packed in coolers, and shipped back to Accra once a week. With this type of work, time is important. If you delay testing the sample, it might no longer be meaningful.” Yakubu explains.
With the right systems in place, however, Dr McCarthy reaffirms that wastewater surveillance can make a significant difference in communities with high population density, low socioeconomic status and a dearth of health services, particularly access to COVID-19 testing.
As African countries transition away from the acute stage of the pandemic, testing rates have simultaneously declined across the board. As of 3 November, 90% of countries in the WHO African Region did not achieve the recommended testing target of 10 tests per 10,000 people per week.
For Dr McCarthy, this reiterates the role that wastewater surveillance can still play going forward.
“Now that we are testing fewer cases, wastewater monitoring becomes increasingly important because we can tell where any increase in cases is occurring and what variants are circulating,” she says. “This can help us to identify any possible resurgence as early as possible.”