- Only testing people with COVID-19 symptoms underestimates infection rates in a population because many infected people show no or mild symptoms.
- Wastewater can offer a unique way to monitor the health status of an entire community.
- No infectious SARS-CoV-2 has yet been discovered in wastewater, but fragments of viral genetic material have been detected by scientists. Standardised methods continue to be developed to monitor wastewater for COVID-19.
- Viral levels of genetic material can correlate with COVID-19 infections in a population. However, total case numbers in a population cannot yet be inferred directly from the genetic material concentrations in wastewater.
- Wastewater monitoring is most effective when integrated with other public health initiatives, such as clinical testing and contact tracing.
- Wastewater monitoring for COVID-19 can act as an early warning system, can support locations with limited testing capabilities and can monitor the circulation of SARS-CoV-2. The approach could also be applied for other diseases in the future.
- Several countries, including the UK, have now implemented national wastewater monitoring programmes for COVID-19.
The UK infection rate of COVID-19 has been estimated through the testing of symptomatic individuals together with random samples of the population regardless if they have symptoms or not. However, this means that only a small proportion of the population is being tested for current infection with SARS-CoV-2.
Many infected people will not be tested, and their contacts will not be traced because they may have no symptoms yet (pre-symptomatic), might not develop any symptoms at all (asymptomatic) or could experience mild, non-specific symptoms. Scientists have estimated that only testing symptomatic and hospitalised cases may miss up to 80% of SARS-CoV-2 transmissions.
Mass testing (likely using lateral flow tests) is increasingly considered as an additional approach to identify and track COVID-19 infections. This would require testing everyone in a geographic location or venue, whether or not they have symptoms. Lateral flow tests provide results in minutes, but the evidence base about their performance is still incomplete.
Some countries are now also using wastewater monitoring as another way to track and manage COVID-19. Researchers have studied chemicals and microorganisms in wastewater for decades, but its widespread use as a public health monitoring tool is relatively new. Wastewater-based epidemiology is an approach where the wastewater of a community is monitored for chemicals (such as antibiotics, painkillers or illegal drugs) and/or microorganisms (such as disease-causing bacteria or viruses) to understand the community’s behaviour and health status.
Wastewater offers a collective sample from an entire community that is easier to access than samples from individuals. In the past, wastewater monitoring has been used to uncover which drugs people consume in different cities and has helped to trace illegal drug manufacturers. During the global polio eradication programme, countries monitored wastewater for the presence of poliovirus itself and also strains of the virus derived from live vaccines. This was used to assess poliovirus circulation and the immunisation rates within populations.
COVID-19 wastewater monitoring programmes now also exist in the UK with efforts underway in England, Scotland and Wales. Wastewater samples at a range of sewage treatment works are regularly analysed for the presence and concentrations of SARS-CoV-2 genetic material (called RNA). These efforts are part of an early warning system to detect new COVID-19 outbreaks and to support test and trace approaches. This article explains why and how SARS-CoV-2 can be detected in wastewater, how wastewater monitoring may help to manage the COVID-19 pandemic and where wastewater monitoring programmes exist in the UK and worldwide.
Monitoring SARS-CoV-2 levels in wastewater
To successfully apply wastewater monitoring for COVID-19, the following aspects need to be considered:
- Viral fragments (such as RNA) must be present in the faeces and/or urine of an infected person.
- There must be a reliable way to monitor these viral fragments in wastewater.
- There must be a consistent way of collecting wastewater samples.
- There must be a consistent way of estimating from these viral fragments how widespread an infection is in the population being studied.
SARS-CoV-2 in human waste
SARS-CoV-2 predominantly infects the respiratory tract. The virus spreads between people through direct contact and respiratory droplets. An infected person releases virus-containing droplets while breathing, speaking, singing, coughing or sneezing.
It was unclear in the early stages of the pandemic whether fragments of SARS-CoV-2 could also be found in human waste, but it is now clear that many infected people release the virus in their faeces. When analysing samples from infected people, SARS-CoV-2 RNA is mostly detected in respiratory tract samples (70–100% of infected people), sometimes in faeces (30–60%), and rarely in urine (<5%).
SARS-CoV-2 RNA has been detected in the faeces of patients with COVID-19 symptoms, and also in asymptomatic, mildly- and pre-symptomatic people, and those recovering from an infection. SARS-CoV-2 RNA concentrations are highly variable in faeces and urine, but are generally lower than in respiratory droplets.
Some studies have reported SARS-CoV-2 infections of the gut. Scientists think that virus present in sputum (mucous coughed up from the lungs) and saliva may be swallowed and infect the gut. However, evidence suggests that faeces and urine mostly contain only virus fragments (such as RNA) and little to no infectious virus. In this, SARS-CoV-2 is different to other viruses such as norovirus or poliovirus.
These are highly infectious waterborne diseases, mostly infecting people through contact with human waste. Infectious SARS-CoV-2 from wastewater is difficult to recover, despite several attempts. In July 2020, the World Health Organization stated that no infectious SARS-CoV-2 had yet been detected from untreated or treated wastewater. It is also not known how much viral RNA is released in human waste at different stages of COVID-19 infection.
Detecting SARS-CoV-2 in wastewater
While similar molecular methods are used to quantify SARS-CoV-2 RNA in wastewater and clinical samples, many other analyses steps differ. For example, unlike a clinical sample (such as a nose or throat swab), wastewater contains many different chemical and biological substances, some of which can inhibit measurement of RNA. Scientists have adapted existing wastewater virus monitoring methods (such as those used for norovirus or viruses causing hepatitis) for SARS-CoV-2, but standard protocols are still being developed.
Levels of SARS-CoV-2 RNA are generally much lower in wastewater than in nose or throat swabs. Virus detection in wastewater typically requires concentrating the viral genetic material into a smaller volume to improve detection. This can mean filtering the wastewater to retain virus fragments or through adding certain chemicals to bind the fragments.
Most concentration methods are inexpensive and easy to set-up. However, they may be time-consuming and difficult to perform when handling many samples, which can require careful logistics. Another disadvantage is that concentration methods not only concentrate the virus, but also other compounds present in wastewater.
Some of these compounds can later interfere with the molecular analysis. Viral RNA concentrations are typically measured with molecular methods based on polymerase chain reaction (PCR). PCR mimics the way living organisms replicate their genetic material (DNA) using special equipment to increase the amount of genetic material from a sample so that it can be detected.
Traditional PCR only provides information on whether genetic material is present or not, while quantitative PCR (qPCR) measures the concentration of genetic material. To measure SARS-CoV-2 RNA concentrations in wastewater, scientists often use qPCR with a reverse transcriptase step (RT-qPCR). Here, an enzyme first translates the viral RNA into complementary DNA which is then replicated and measured with qPCR. In the national UK monitoring programmes, all laboratories measure the gene copies of SARS-CoV-2 RNA per litre of wastewater sample collected with RT-qPCR.
Scientists recommend including process controls when measuring SARS-CoV-2 in wastewater to correct for viral losses during the concentration step and molecular analysis. For example, murine hepatitis virus (MHV, a mouse coronavirus with a similar structure to SARS-CoV-2) can be added to the original wastewater sample at a known concentration.
After the concentration step, SARS-CoV-2 and MHV are both measured with PCR-based methods. The calculated loss in MHV during this process is used to correct the measured SARS-CoV-2 concentration.
In the UK, most peoples’ houses are connected to the sewer system. This means that wastewater from toilets, sinks, showers or baths is collected per building and then travels through pipes to a wastewater treatment plant.
Wastewater samples for virus detection can be taken at different locations within this sewer system. Samples taken at the inlet of the wastewater treatment plant allows for virus monitoring of the whole population connected to this plant. Depending on the size of the plant, one wastewater sample can screen for COVID-19 infections in several thousand people.
It is estimated that current wastewater monitoring can detect at least 1 infected person in 1000, but this depends on the sewer network and variable release of SARS-CoV-2 RNA from infected individuals. SARS-CoV-2 RNA concentrations in faeces and urine can vary greatly between patients.
In general, wastewater monitoring is easier to apply in large urban communities (populations over 10,000) than in dispersed rural communities, which may have hundreds of small treatment plants.
However, analysing samples at the inlet of the wastewater treatment plant does not provide precise information on where a COVID-19 outbreak is happening in the population. To monitor fewer people at a local community level, samples can be taken instead in sewage drains serving buildings or neighbourhoods.
This approach is called ‘near-source tracking’. It can be applied to focus wastewater monitoring on more vulnerable or higher risk groups, for example in hospitals, care homes, schools, prisons or factories.
Wastewater sampling is typically performed by one of two methods: grab sampling or composite sampling. For ‘grab sampling’, the wastewater is collected at one time point (for example on Monday at 9 am).
For ‘composite sampling’, individual samples are taken at regular intervals over a period of time, usually 24 hours (for example on Mondays, samples are taken hourly throughout the day). Composite samples offer a more representative measure of the population under surveillance, but the approach requires more expensive and specialised equipment than grab sampling.
Estimating infection rates
Some studies have shown SARS-CoV-2 RNA concentrations to correlate with COVID-19 cases. However, exact infection rates cannot yet be calculated from SARS-CoV-2 wastewater monitoring. This is because calculating exact infection rates from a sample relies on knowing how much virus is released from faeces and/or urine during different infection stages and how long it can persist in different sewer networks. Researchers do not know this yet for SARS-CoV-2.
Instead, scientists are starting to estimate viral RNA concentrations per inhabitant based on wastewater monitoring. For this, scientists need to know how many people are contributing to a wastewater sample and if rain and/or industrial wastewater diluted the sample. This is important so that monitoring results can be compared over time and across different regions.
Population census data can be used to estimate the virus concentration per inhabitant. However, this does not capture population fluctuations due to commuter activities, tourism or other movements.
While these fluctuations may have negligible impacts in large populations (over 100,000 people), they might contribute to higher uncertainties in smaller populations. ‘Biomarkers’ can also be used to estimate populations and account for wastewater dilutions.
A biomarker is a substance (such as cholesterol or nicotine), genetic fragment (such as human mitochondrial DNA or RNA) or other microorganism (such as CrAssphage) that are released at more predictable levels by humans.
Current COVID-19 wastewater monitoring approaches mostly focus on analysing trends rather than predicting underlying infection numbers. For example, if the observed viral concentrations are significantly high in relation to the estimated population, this could indicate a viral outbreak in the underlaying population. Many experts think that wastewater monitoring is most effective when integrated into other public health initiatives such as clinical testing and contact tracing.
Reasons for wastewater monitoring
Wastewater monitoring for COVID-19 can be used for various reasons, as discussed in a scientific brief by the World Health Organization. Some of these reasons include:
- As an early warning system. Studies in several countries, including in the Netherlands and United States, have found a correlation between SARS-CoV-2 RNA levels in wastewater and COVID-19 clinical case reports. In the Netherlands, viral RNA could be measured days before the first clinical cases were reported in the country. To act as an early warning system, wastewater monitoring needs to be closely linked to a plan for immediate action in the event of a positive signal or significant rise in RNA concentration. It is not clear yet which viral RNA thresholds in wastewater should trigger what action. Using wastewater monitoring as an early warning system requires frequent sampling at many locations to provide enough data. This is expensive and can be logistically tricky.
- Detecting SARS-CoV-2 in locations with limited population testing. Testing wastewater samples could help to optimise the use of limited testing resources. For example, if viral RNA levels in wastewater exceed a certain threshold for a population, targeted mass testing could be implemented to find and isolate infected people. This approach could also help to reinforce public health measures in selected areas to limit transmissions such as mask wearing and physical distancing. Wastewater monitoring for COVID-19 could also help to monitor the circulation of SARS-CoV-2 within communities with high levels of hesitance to testing and/or low levels of adherence to self-isolation.
- Monitoring circulation of SARS-CoV-2. Current individual testing is unlikely to identify infected people with no or mild COVID-19 symptoms. Wastewater monitoring could help to understand whether COVID-19 is decreasing in an area. It could also support decision-making on whether public health and social measures need adjusting. However, it is currently not clear how useful wastewater monitoring is as evidence of non-circulation of SARS-CoV-2. This is because little is currently known about how long the viral RNA can persist in sewer networks.
The infrastructure to monitor COVID-19 through wastewater could also be used to monitor other viruses of public health concern such as influenza.
Use of wastewater monitoring in the COVID-19 outbreak
The Netherlands was the first country to implement a national COVID-19 wastewater monitoring programme. Their government publishes the SARS-CoV-2 RNA concentrations in wastewater per 100,000 inhabitants regularly on a public COVID-19 dashboard.
Many other countries, including the UK, Australia, Germany, Italy and Finland have also started or are planning to implement national wastewater monitoring programmes to complement public health metrics. In addition to national efforts, many universities, such as the University of Arizona, have also set up their own wastewater monitoring programmes. The University of California Merced summarises global SARS-CoV-2 wastewater monitoring efforts online.
In the UK, government-led projects for England, Wales and Scotland were first announced in June 2020 to detect SARS-CoV-2 RNA in wastewater. The English project is coordinated by Defra, the Environment Agency and the Joint Biosecurity Centre (JBC); bringing together researchers, water companies and devolved governments in Scotland and Wales, who each have their own monitoring programmes.
Wastewater samples are collected between one to several times a week by water companies and analysed at selected laboratories. During a pilot, the approach was successfully tested in an area in the South West of England where wastewater data showed a spike in SARS-CoV-2 RNA despite relatively low numbers of people seeking tests.
This information was passed on to NHS Test and Trace and the local council, who were able to alert local health professionals to the increased risk and contact people in the area to warn of the increase in cases.
In October 2020, testing of wastewater for SARS-CoV-2 was performed across more than 90 wastewater treatment plants in the UK.
- In England, Defra, the Environment Agency and JBC are collaborating with support from the Office for National Statistics (ONS). The testing is being led by the Environment Agency’s Starcross laboratory in Exeter and Bangor University. As of October, 44 wastewater treatment plants are monitored, covering 22% of the English population, with sampling across the sewer networks in several towns and cities, and plans to expand the monitoring programme to cover 80% of the population. Wastewater monitoring is planned to support mass testing programmes across eight core cities in England (including Greater London), after scaling work started in Liverpool.
- In Scotland, the Scottish Environment Protection Agency (with support from the Scottish Government and Public Health Scotland) collaborates with Scottish Water, the Scottish Government’s Centre of Expertise for Waters and academic partners from the University of Edinburgh’s Roslin Institute and Heriot-Watt University. As of November, 28 wastewater treatment plants are monitored, covering 40–50% of the Scottish population. The Scottish data for SARS-CoV-2 RNA levels in wastewater can be accessed through a dashboard.
- In Wales, Public Health Wales (with support from the Welsh Government), Bangor University, Cardiff University and Welsh Water are collaborating. As of October, 20 wastewater treatment plants are monitored, covering 80% of the Welsh population. Wastewater monitoring is also used to support mass testing on where and when to test (such as in Merthyr Tydfil). The Welsh programme is being expanded to also include monitoring for other viruses of public health concern such as influenza A/B, norovirus, and hepatitis A/E.
- In Northern Ireland, as of November, routine monitoring of wastewater samples is not yet taking place. However, discussions are ongoing to implement such a programme.
To better understand the relationship between SARS-CoV-2 RNA concentrations in wastewater and clinical COVID-19 cases in the population, all programmes also collect complementary data such as the area served by the wastewater treatment plant, water flows in the sewer network and chemical concentrations in wastewater (ammonia and orthophosphate).
As well as national wastewater monitoring programmes, there are also several other, local government- and/or research-led projects taking place to monitor COVID-19 in wastewater. For example, the JBC is conducting pilots to see how COVID-19 sources can be better identified using wastewater.
Bangor University monitors viral RNA concentrations in the wastewater leaving their halls of residence. This allowed the detection of COVID-19 cases in the student population before cases were formally confirmed. Newcastle University and Northumbrian Water perform regional wastewater monitoring for COVID-19 in County Durham
The N-WESP project brings together scientists and collaborators from 23 organisations across the UK to better understand the presence and infectivity of COVID-19 in wastewater. The project led by the UK Centre for Ecology and Hydrology is developing wastewater monitoring methods to provide advances in sampling, processing and analysis used within the national programmes of wastewater surveillance.
Middlesex University is leading the TERM project, applying the ‘near-source tracking’ approach to determine if wastewater monitoring can act as an early indicator of outbreaks in schools.
Defra and JBC have published a summary paper on 4 December 2020 for the Scientific Advisory Group on Emergencies (SAGE) on monitoring wastewater in the UK. It provides a technical overview of wastewater-based epidemiology and its application for COVID-19, a summary of the UK wastewater programmes and presents some results for the English programme.
This article is based on a literature review and interviews with a range of stakeholders. POST would like to thank interviewees and peer reviewers for kindly giving up their time during preparation of this article, including:
Dr Mariachiara Di Cesare, Middlesex University London*
Prof Lian Lundy, Middlesex University London*
Prof Davey Jones, Bangor University
Dr Andrew Singer, UK Centre for Ecology & Hydrology*
Dr Josh Bunce, Department for Environment, Food and Rural Affairs*
Dr Jasmine Grimsley, Joint Biosecurity Centre, Department of Health and Social Care*
Christopher Spence, Joint Biosecurity Centre, Department of Health and Social Care
Dr Alwyn Hart, Environment Agency*
Prof David Graham, Newcastle University*
Dr Marcos Quintela-Baluja, Newcastle University*
* denotates people and organisations who acted as external reviewers of the article
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