‘We’re the poo crew’: sleuths test for Covid by reading signs in sewage

They call themselves the “poo crew” – a team of health detectives who are tracking down and heading off Covid outbreaks by reading the signs in our sewage. And they are expanding. Earlier this month, the Environmental Monitoring for Health Protection Programme opened a purpose-built laboratory on the fringes of Exeter, its sterile interior in stark contrast to the unsanitary subject of its investigations.

The opening of the laboratory marks a dramatic expansion of what was, until less than a year ago, just a soil pipe dream: testing sewage for coronavirus to understand where it is circulating and get an early warning of future potential spikes in infection. In the future, this network could be expanded to monitor other infectious diseases including flu.

“Right now, what it means is we can identify and contain the spread of Covid. But moving beyond that, arguably what the NHS would like to know is what do we need to be prepared for in any given area? Through this programme we might be able to provide information to hospitals and local commissioning groups about what the health of the community looks like and what the demands might be, that could allow for the optimisation of resources and the saving of money,” said Dr Andrew Engeli of the Joint Biosecurity Centre, which is leading the project in collaboration with Defra, the Environment Agency and other partners including the devolved governments of Wales, Scotland and Northern Ireland.

The idea was conceived during the early months of the pandemic, after reports that coronavirus was being shed in the faeces of some infected individuals. The immediate concern was that this might render public toilets and swimming pools potent sources of infection, although further studies have suggested that the risk of contracting Covid-19 from sewage is minimal.

However, scientists at the Environment Agency’s Starcross laboratory near Exeter also saw such observations as an opportunity. “We were on standby to offer clinical Covid testing for the NHS, but then a Dutch group published a paper saying that they had found coronavirus in wastewater about five days before they saw a change in clinical cases,” said Dr Jonathan Porter, a microbiologist who has been involved in the wastewater programme from the outset. “When it turned out that our services weren’t going to be useful to the NHS, we decided we should pick this up and give it a go.”

Last July, they began processing samples from 44 wastewater treatment plants, accounting for the combined excretions of 23% of England’s population. The detection of a sudden spike in coronavirus RNA in sewage from a plant near Trowbridge, Wiltshire, provided a crucial first test. “There was no coronavirus really in Trowbridge at that time, but we saw a small spike in the data which lined up with four or five cases that were detected through testing,” said Glenn Watts, deputy director of science at the Environment Agency.

Since then, the programme has been expanded to include hundreds of sites, covering around two-thirds of the population of England. Similar programmes are being developed in Scotland, Wales and Northern Ireland, as well as in about 28 other countries around the world – although the English and Scottish programmes are among the most advanced. “I don’t think anyone else is operating at this scale,” Watts said.

The samples arrive by courier at 6am each morning, having been harvested from sewage pipes as they spew their contents into wastewater treatment plants across England before processing. Teeming with bacteria, viruses, and the mushy remnants of our meals, these 500ml plastic bottles of cloudy grey fluid are an epidemiological treasure trove of information about our collective health just waiting to be mined.

The individually barcoded bottles, which look a lot like fizzy drinks containers, are logged on to the system and then wheeled up to the processing lab on silver trolleys, where scientists load samples of fluid into centrifuge tubes, and spin them to separate the liquid components from the solids. It’s dirty work, but done for the public good inside carefully enclosed cabinets designed to both prevent contamination of the sewage samples from outside sources, and to protect the laboratory staff from the multitude of disease-causing microbes they contain.

Chemicals are added to the liquid portion of the samples to extract and purify the genetic material from numerous viruses that it contains, until all that remains from the original 500ml sample is a couple of raindrops-worth of viral RNA. Finally, this is loaded into PCR (Polymerase chain reaction) machines that detect and quantify the amount of RNA from Sars-CoV-2.

Using this data to make sense of how much virus is circulating in England’s cities and towns is by no means straightforward. The amount of poo carried by sewers varies according to the time of day, and the surge in solids may come later in university towns – where students get up later – compared with more rural locations. It can also be diluted by large amounts of rainwater, so all of this must be carefully factored into the scientists’ calculations.

Wastewater analysis is not accurate enough to tell us how many individuals are infected with Covid in any given area at any given time. However, it can provide an early warning of escalating cases in specific geographical areas that can be followed up with additional community testing and messaging, or the sewage equivalent of surge testing – where manhole covers are lifted up and samples taken from sewers in specific areas of a city, say, to try to narrow down the source of the outbreak.

Sewage from individual households or tower blocks is not monitored – although separate research is investigating whether sewage from school wastepipes could be used as an early warning system of outbreaks among pupils, many of whom may be asymptomatic.

“It is like taking a stool sample from a collective bowel,” said James Trout, who oversees the laboratory.

Efforts are also under way to develop methods of using wastewater to trace variants of concern. As proof of concept, during January and February, the team used sewage collected from Bristol to identify 118 separate coronavirus mutations, including those associated with the B117 variant, and the so-called “Bristol variant” – a version of B117 with an additional E484K mutation – in samples from 11 sub-catchments of the city, each containing about 27,000 people. The variant was detected in eight of these areas, including one where no confirmed or suspected cases had been detected through other means. This information was relayed to local and national response teams, to help track and contain its spread.

Related: UK scientists find evidence of human-to-cat Covid transmission

Sars-CoV-2 is not the only virus that is excreted in our poo. Indeed, labs around the world have previously used wastewater to monitor the success of polio vaccination programmes. In Wales, wastewater monitoring is being expanded to keep tabs on other viruses of public health concern, such as influenza, norovirus, and hepatitis A and E. Once such infrastructure has been developed, it could also theoretically be piggybacked to detect viruses in air filters from hospitals or workspaces, say.

It is hardly the most glamorous job, but these sewage sleuths are committed to their cause. “We’re the poo crew. We know a ridiculous amount about poo, but still not as much as we’d like to know,” Engeli said. “It’s way more complicated than we thought.”