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Keeping track of a coronavirus outbreak is a slippery task. The only way to accurately track the number of cases in an area is very widespread testing. Countries such as Australia, Denmark and South Korea perform hundreds or even thousands of tests for every single confirmed case of Covid-19 they uncover.
But the UK government is now reaching for a way to track new outbreaks that doesn’t rely solely on swabs and individual testing. Instead, researchers are trawling through sewage to find traces of Sars-Cov-2 – the virus that causes Covid-19 – in our faeces.
Water companies and several universities – including, Bangor, Bath, Edinburgh and Newcastle – are currently collecting sewage samples from wastewater treatment plants across the UK to track the rise and fall in viral concentrations against the official numbers of daily new infections. “The sewage is sort of like an asymptomatic carrier because it’s got virus particles in it, but they’re not causing disease,” says David Graham, professor of ecosystems engineering at Newcastle University, who is collecting weekly samples in County Durham.
The tests are being coordinated as part of a national trial by the Department for Environment, Food and Rural Affairs and the Environment Agency. Data gathered from the projects will eventually feed into the Covid-19 Alert System created by the Joint Biosecurity Centre, an independent body made up of civil servants that monitors the spread of coronavirus across the country and advises the chief medical officers of England, Scotland, Wales and Northern Ireland on how to deal with regional spikes in infection.
We already know that people infected with Sars-CoV-2 can shed traces of the virus within three days of being infected. This is potentially much quicker than it takes for people exposed to the virus to develop symptoms, which usually happens between five and six days but can take up to two weeks. And since many people show no symptoms at all, or only mild symptoms and so never put themselves forward for a swab test, the hope is that wastewater analysis could give us a more complete picture of how the virus is spreading.
Scientists can use a method called polymerase chain reaction (PCR) to find traces of Sars-Cov-2 in untreated wastewater and capture data on large populations in a way that is much cheaper and less invasive than continuously testing them for the virus. This could provide a real-time indication of how coronavirus spreads in a particular area and provide an early warning of outbreaks. But can it tell us exactly how many people have coronavirus?
After collecting samples of untreated sewage in wastewater treatment plants, researchers extract very small fragments of the virus’s genetic material, known as RNA, in the lab. Although detectable in faeces, Sars-Cov-2 degrades quickly once it is excreted from the body and mixed with water so the fragments found in sewage are no longer infectious.
Higher viral concentrations in a region’s wastewater indicate there is a higher number of infected people contributing to the sewage system. Any emerging clusters could then prompt clinical testing or quarantine in that region until track and trace is completed, which could be particularly useful in countries where individual tests are in short supply.
Researchers Australia, France, the Netherlands and the United States have been testing untreated wastewater for Sars-Cov-2 since March and have generally observed that the rise and fall of virus concentration mirrors the officially reported rates of infection. A two-month-long survey in Paris even noticed there was a sharp rise in viral concentrations in sewage a few days before hospital cases surged while Italian scientists found traces of coronavirus in wastewater from 18 December 2019, six weeks before two Chinese tourists in Rome tested positive for the virus.
Looking for the presence of a virus in untreated wastewater is not new and has been done for years to track polio and gastroenteritis outbreaks. Sewage testing has also been used to uncover what illegal drugs people consume in different cities, and even helped Chinese police track down and arrest illegal drug manufacturers.
In addition to testing people who report symptoms of disease, frequent wastewater sampling could be used as a tool to warn against incipient outbreaks. “A daily sample from wastewater is ideal, but if the resources are limited, every alternate day is fine too,” says Warish Ahmed of the Australian public research agency CSIRO, which carried out a pilot study at two wastewater treatment plants in Brisbane, Australia in March and April. Sewage monitoring has since been rolled out across the entire state of Queensland. “Both clinical tests and sewage monitoring will aid in identifying the second wave. Sewage monitoring is not going to replace clinical testing but provides additional information on the prevalence of Covid-19 in a community,” says Ahmed.
Wastewater testing could also provide a picture of how the disease spreads across cities. If samples can be collected before the wastewater enters a treatment plant, for example in the drains of a particular borough, scientists could monitor the presence of Sars-Cov-2 in the population living in that borough. It takes between half a day and three days for the sewage to move from toilets to the treatment plants so frequent sampling could quickly pick up on changes in viral concentrations and detect new clusters of infections.
As people are slowly returning to work, one would expect to see a rise in viral concentrations in the wastewater of areas that are predominantly places of work, such as the borough of Westminster. “Naturally, in places where there is an even mix of work and home you have a much more difficult time assessing whether the shedding is occurring at work or at home,” says Andrew Singer, a senior scientist at the NERC Centre for Ecology and Hydrology, who is supporting the sewage testing trials in the UK. Breaking large cities up into pockets defined by the sewage system would allow for a more targeted approach in dealing with outbreaks, he says.
But sewage testing is nowhere near as precise as individual swab tests. Using computer models that take account of how many viral particles individuals shed and how they become diluted in sewage, scientists can translate viral concentrations into infection trends in a catchment area. However, making inferences about the exact number of people who may be infected is not that simple. Laurent Moulin, a microbiologist at the public water authority Eau De Paris and one of the authors of the Parisian study, points out that viral shedding varies among individuals and over the course of their infection. “This disease is quite strange because some people shed a lot of virus, others shed very low amounts of virus so there is a huge range of concentrations between patients,” he says.
Since PCR is designed to work on double-stranded DNA, scientists first need to convert the genetic material of coronavirus, RNA, using an enzyme. They will then perform repeated chemical reactions to make enough copies of the so-called complementary DNA until they become detectable in the wastewater sample. But because the Sars-Cov-2 particles are highly fragile, they are easily damaged in the process. This means scientists may not be measuring the exact concentrations that were present in the original sewage sample. “When people first started measuring the virus, they were basically using methods off the shelf that had been used to measure other types of virus. The problem, from a perfectionist perspective, is that coronavirus is really weird because of its strange chemistry,” says Graham.
His team at Newcastle University has been exploring a way to keep track of how many viral particles may be lost in the PCR process. By adding another human coronavirus, which acts as a surrogate for Sars-Cov-2, to the original sample, they can compare the concentrations of this surrogate before and after processing the sample. This tells them how effective PCR may be at recovering the genetic material and allows them to account for any traces of Sars-Cov-2 that may have been lost in the process.
Wastewater surveillance could be used as an early-warning system to alert authorities of an emerging outbreak, days before people develop symptoms and report to doctors and hospitals. It could inform the need for localised lockdowns and tell us when the disease is disappearing so that lockdown measures can be eased again. But the method is no substitute for a rigorous test, track and trace regime. “Nothing that you’re going to do related to this environmental sampling is going to provide you something as precise as what you get through a test in a clinical lab,” says Graham.
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