When trying to assess the infection rate of Covid-19 in any given population, the number of recorded confirmed cases is far from a perfect metric. In the UK, while citizens are encouraged to undergo bi-weekly asymptomatic lateral flow testing, the published daily number of confirmed cases is exclusively derived from laboratory-confirmed positive tests carried out by people with Covid-19 symptoms. This metric will tend to underestimate the infection rate, as asymptomatic or very mild cases are unlikely to be recorded.

As such, the UK infection rate has instead been estimated through the testing of symptomatic individuals, alongside random samples of the population who are tested regardless of whether or not they have symptoms. However, this method also has its shortcomings.

“It’s really expensive and actually extremely biased trying to get people to agree to be sampled,” says UK Centre for Ecology & Hydrology senior scientist Dr Andrew Singer, who is leading the country’s National Wastewater Epidemiology Surveillance Programme (N-WESP).

“Random testing is imperfect because people have to consent and they don’t do so uniformly,” he adds. “The alternative to that is wastewater.”

Wastewater monitoring offers a unique way to assess the health status of select communities and consequently entire nations. Fragments of viral genetic material from Covid-19, which are shed in human waste, can be detected in sewage through polymerase chain reaction (PCR) tests and give some indication of the scale of disease spread. Wastewater has been monitored in the UK since early 2020 for traces of Covid-19.

Why monitor wastewater for Covid-19?

Wastewater monitoring offers a way to take a collective sample from an entire population, something that is easier to obtain and arguably more informative than samples from randomly selected individuals. Researchers have studied the microorganisms in wastewater for decades, and wastewater epidemiology been successfully used to detect polioviruses and inform eradication efforts since the 1980s.

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Singer says: “We’ve been capturing wastewater from outside of buildings and from sewage works, which is taken back to the lab.”

While SARS-CoV-2 is a virus that predominantly infects the respiratory tract, released by infected people through breathing, speaking, singing, coughing and sneezing, 30 – 60% of them also release viral RNA in their faeces too. This faecal shedding has been found in patients of all disease severities, including asymptomatic and pre-symptomatic people, as well as those recovering from an infection.

While many highly infectious diseases out there can transmit through wastewater, fortunately Covid-19 is not one of them. But even though the traces of SARS-CoV-2 found in wastewater aren’t infectious, they can still tell public health researchers a lot about the spread of the disease.

Wastewater analysis can’t pinpoint how many individuals are infected with Covid-19 at any given time, but it can help researchers understand where the disease is circulating and get an early warning for potential spikes in infection should these levels peak. If levels peak in a certain town or city, for example, this can be followed up with additional testing and public health messaging. Samples can also be taken from sewers in specific areas within the infection zone, to try and find the source of the outbreak.

“John Snow was probably one of the first wastewater epidemiologists,” says Singer. “In 1854 he found a hotspot of people infected with cholera, and the connection to all of them was an infected water pump. When they closed the pump the problem went away. It’s not exactly the same thing but it’s very close to the same concept.”

How does wastewater monitoring for Covid-19 work?

Wastewater contains several different chemical and biological substances, some of which could potentially interfere with the measurement of Covid-19 RNA. The levels of RNA are also much lower than they would be in the nose or throat swabs used to diagnose the disease in infected individuals.

While traditional PCR only provides information about whether or not a genetic material is present, quantitative PCR (qPCR) can measure the concentration of genetic material. To measure SARS-CoV-2 in wastewater, scientists often use reverse transcriptase quantitative PCR (RT-qPCR). An enzyme is used to translate the traces of viral RNA in the water into complementary DNA, which this then replicated and measured with qPCR.

Still, the results from wastewater epidemiology aren’t foolproof. Now that the UK is no longer under lockdown, people are moving across the country a lot more freely, potentially skewing the results.

Singer says: “If people are pooing in locations where they aren’t residing, then you will have this disconnect between cases in an area and amounts of viral RNA in sewage. Commuting is a really important factor.”

Using anonymised data from cellular signals can allow public health bodies monitoring local wastewater to see where daily commuting routes are and assess how many people are moving in what direction on a daily basis. This information can help to feed into their disease modelling and give them better estimates of how many people in the local area are infected and which other areas they might be spreading disease to.

The future of wastewater monitoring

As well as monitoring the spread of Covid-19 and acting as an early warning system for local outbreaks, wastewater monitoring can also help detect the spread of variants of concern.

“We will probably be doing wastewater surveillance for Covid-19 forever, and one of the highest priorities is to look for new variants,” says Singer. “We’re sequencing quite a number of samples at present.”

The technology could also be useful in parts of the world where access to Covid-19 testing is limited. Testing wastewater for Covid-19 traces is far less resource-intensive than testing individual people, and could help to provide a picture of population health in territories where laboratory capacity is lower.

Going forward, Singer has confidence in the UK’s wastewater surveillance, noting that about 70% of the population is already having their wastewater surveyed for Covid-19. This winter, he expects N-WESP to start looking for flu, norovirus and RSV in wastewater too, due to concerns about winter waves of seasonal viruses following their effective eradication over the past two years.