COVID-19 : Examining wastewater is helping researchers track coronavirus infection trends


Scientists around the world are studying the novel coronavirus (SARS-CoV-2) from many different perspectives in an effort to better understand how it infects the body and spreads from person to person.

The goal is to find therapies for neutralizing and eliminating it. One approach being taken by researchers at EPFL and Eawag – until drug treatments and a vaccine are developed – is to analyze wastewater samples so that health officials can detect the virus before the disease is diagnosed clinically.

“Our study looks at how we can detect the virus in wastewater and measure its concentration before people start developing clinical symptoms – and to determine how much time before,” says Tamar Kohn, head of EPFL’s Environmental Chemistry Laboratory (LCE).

In collaboration with Christoph Ort at Eawag’s Urban Water Management Department and Tim Julian at Eawag’s Environmental Microbiology Department, the researchers pulled off a major feat in showing that the novel coronavirus can be detected and measured in wastewater in a matter of weeks.

The researchers analyzed samples from Lausanne, Zurich and Lugano – including samples from Zurich and Lugano that were collected in late February when the first cases were recorded in Switzerland.

“As a specialist in environmental virology, I was ready to work on the pandemic when it first arrived in Italy,” says Xavier Fernandez Cassi at the LCE. “It was clear to me that the virus would spread to Switzerland. Given how interlinked countries are today, I would’ve been surprised if it didn’t.”

The researchers found traces of the virus in all the samples they collected. While concentrations in the more recent samples were so high that it was fairly easy to measure them, this was not true for the samples from February.

“We were pleasantly surprised to find a signal in wastewater from Lugano – where only one case had been identified at that point – and from Zurich, where only six had been identified,” says Kohn. Working with colleagues at Eawag, they collected samples from nine wastewater treatment plants in Ticino, two in Zurich and one in Lausanne, corresponding to a total of around 800,000 city residents.

Credit: EPFL

The potential ramifications of this study are so important that Cassi and Marie-Hélène Corre, another LCE biologist, received special authorization to work at their EPFL lab during the lockdown.

They were particularly efficient in conducting their experiments since almost nobody else was using the testing equipment, as the campus was nearly deserted. But the researchers had to be extra careful because the novel coronavirus – even though it comes from a known viral family – is nevertheless a zoonotic virus.

“The main characteristic of this virus is that it has envelope – its viral capsid is enveloped in a biological membrane,” says Corre. “The seasonal flu virus and HIV also have envelopes.”

Goal: early warning system

The samples collected since the first cases of COVID-19 were reported in Switzerland are valuable archives. However, the main goal of this study is not to retrace the past but to develop an early warning system.

Ort says: “With samples from 20 large treatment plants distributed across Switzerland, we could monitor wastewater from around 2.5 million people.” If the samples are analyzed rapidly, we could probably detect a resurgence of infections earlier than with diagnostic tests – about a week earlier – especially during the period when the lockdown is being lifted.

Ort has long been concerned with wastewater-based epidemiology, previously focusing on comparisons of drug use across Europe.

“Wastewater doesn’t lie – it reflects what has been excreted by a population within a few hours,” he says. The research team has drawn on their established contacts with local government agencies and wastewater treatment plants.

Tracking infection trends, not absolute case numbers

Since the researchers were able to successfully detect low viral concentrations at the early stage of the COVID-19 outbreak in Switzerland, they should be able to reconstruct the infection curve.

But it will still take a few weeks to analyze the over 300 samples currently in frozen storage at Eawag and EPFL. They won’t be able to calculate the exact number of infections using these data, since there is too much variation in how much of the virus each patient sheds. What will be important to track, however, is the trend.

For example, using samples collected in Lausanne in March and April, the researchers were able to roughly trace the increase in the wastewater concentration of SARS-CoV-2. Kohn estimates that the concentration rose by a factor of between ten and a hundred.

Complex method

Despite the researchers’ initial success, they still need to further improve their method. For example, they don’t yet know what percentage of the wastewater’s viral load is captured when the RNA is extracted after a number of other steps (filtration and centrifugation). There is also much uncertainty in the subsequent selective amplification process for the target sequence. Only when the amount of uncertainty is reduced will they be able to draw robust conclusions about viral concentrations in the original samples.

Coronavirus unlikely to spread via water or wastewater

While genetic material from the novel coronavirus can be detected in wastewater, there is no evidence at present to suggest that the pathogen spreads via water or wastewater. Drinking water in Switzerland is of excellent microbiological quality and remains fit for consumption even during the pandemic.

As of April 2020, some 93% of the global population (about 7.2 billion people) live in countries with some form of movement restrictions in place [1]. A new coronavirus disease, officially named COVID-19 by the World Health Organisation (WHO), has caused a global pandemic with profound changes in many aspects of human life [2].

On 11 February 2020, the International Committee on Taxonomy of Viruses announced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the name of the new virus [3].

Unlike all previous pandemics in modern history, COVID-19 is truly a global crisis. Never before have we seen the health care systems of some of the world’s most industrialised nations on the verge of collapse [4].

Unprecedented measures (social distancing, school and workplace closure, and restricted intra- and international movement) have been enforced by governments around the world to stop the spread of COVID-19.

As the world adapts to unprecedented behavioural and societal changes in response to the threat posed by COVID-19, societal operations, including many essential municipal services must also adapt and change.

These essential services such as waste collection and wastewater treatment are routine and indispensable. They play a key role in mitigating infectious disease transmission but are rarely mentioned in public health crises response communications [5, 6, 7].

Under current projections waste and wastewater industries are expected to bear significant financial impacts from COVID-19.

For example, water utilities in the USA are expected to suffer over $27 billion in financial loss due to revenue reduction and expense increase as a direct consequence of COVID-19 [8].

This perspective article aims to examine the role of waste and wastewater management within the global response to COVID-19.

It especially seeks to place lessons from previous epidemics and pandemics in the current context to construct a policy and research road map for the waste and wastewater sectors to join the fight against COVID-19 and future outbreaks of this nature.

Morphology, structure and possible transmission routes of SARS-CoV-2

COVID-19 is an infectious disease caused by a novel coronavirus. The COVID-19 pandemic is the third major zoonotic coronavirus disease outbreak in only two decades, following the SARS (Severe Acute Respiratory Syndrome) outbreak in 2002-2003 and the MERS (Middle East Respiratory Syndrome) outbreak in 2012.

The disease was first reported to the WHO by Chinese Health Officials on 31 December 2019 as atypical pneumonia of unknown cause [9, 10]. The virus is genetically similar to the SARS-CoV coronavirus and is likewise assumed to have crossed the species barrier from animal to human [3, 11]. Although its specific origins are yet to be determined, the likely ancestor is a bat coronavirus [10].

The morphology and structure of SARS-CoV-2 has important implications for waste and wastewater service. Each SARS-CoV-2 virion is a small spherical particle (≈100 nm diameter), consisting of a positive single stranded RNA genome within a fragile lipid envelope [12].

It is a betacoronavirus in the subgenus Sarbecovirus. Although sometimes referred to as “a type of flu”, it is in fact genetically and virologically distinct from influenza viruses as these are negative sense RNA viruses.

SARS-CoV-2 has spike proteins on its surface that bind to host cell proteins and subsequently aid viral entry. Given their small size, SARS-CoV-2 virions can be transmitted via air as part of aerosols [13].

However, due to the delicate nature of the lipid envelope of SARS-CoV-2 virions, the viral particle may become non-viable (i.e. non-infectious) once the envelope is damaged, even though their genetic fragments may still be detected.

A common method for detecting SARS-CoV-2 is nucleic acid testing using real time polymerase chain reaction (RT-PCR) technology. These RT-PCR assays can also be modified and adapted to detect and quantify the virus in environmental samples such as wastewater [5].

The transmission behaviour of SARS-CoV-2 also has important implications for waste and wastewater services. SARS-CoV-2 specifically targets host cells containing ACE2 proteins. ACE2 is an enzyme attached to the outer surface (cell membranes) of cells in the lungs, arteries, heart, kidney, and intestines.

After infecting and exhausting all resources in the host cell to multiply, the viruses leave the cell in a process known as shedding. Data from clinical and virological studies provide evidence that shedding of the SARS-CoV-2 virus is most significant early in the course of the disease, immediately before and within a few days since onset of symptoms [2].

The SARS-CoV-2 virus has namely been detected in blood, sputum, respiratory secretions, and faeces from symptomatic patients [2, 14, 15, 16].

The contribution of viral shedding from asymptomatic and presymptomatic carriers to SARS-CoV-2 transmission remains in question. While it is likely that viral loads in asymptomatic carriers are relatively low, further research is needed [17].

A preliminary report from the WHO indicates that SARS-CoV-2 is transmitted via droplets and contaminated objects during close unprotected contact between an infector and infectee [2].

Data to date suggest that SARS-CoV-2 is highly contagious, with early reports from China indicating that the virus spread rapidly and sustainably throughout some affected communities [18].

Alarming infection incidents among health care workers, cruise-ship and airplane passengers also point to the likelihood of additional transmission mechanisms in confined spaces with dense populations. Several alternative transmission routes are possible but their validity in this context is yet to be determined [19, 20].

Possibilities include transmission via inanimate/environmental surfaces (fomites), aerosols and the faecal-oral route [17, 21]. All three are likely to be important in specific circumstances [17], highlighting the need to identify critical control points and implement specific measures to mitigate possible COVID-19 transmission during waste and wastewater collection.

Implications for waste services

Fomites are recognised to be key vehicles for the spread of other infectious human viruses (e.g. noroviruses) during outbreaks [22]. Data from SARS-CoV-2 and other coronaviruses suggest that they remain viable in the environment on a range of surfaces for several hours and several days (Figure 1 ).

The survival time of SARS-CoV-2 on hard surfaces and plastic is in the order of days, which suggests that waste materials originating from households and quarantine facilities with positive or suspected COVID-19 patients may contain viable SARS-CoV-2 and could be a source of infection.

In the initial stages of this outbreak, waste collection procedures had not been revised to address the potential threat of COVID-19 in the broader community. Effectively, waste from infectee households and quarantine facilities would meet the definition of clinical waste.

For instance, the Australian Standard AS 3816:2018 defines clinical waste as “any waste that has the potential to cause injury, infection, or offence, arising but not limited to medical, dental, podiatry, health care services and so forth”.

In other words, strict infection control and hygiene standards are required when collecting waste materials from affected households and quarantine facilities.

Figure 1
Figure 1
Lifespan of SARS-CoV-2 in the environment (Refs: [13, 23, 24]).

Home isolation and pop-up quarantine facilities are common practice in countries significantly affected by COVID-19 so that hospitals can be prioritised for severe cases. In many countries, patients with mild symptoms have been directed to self-quarantine at home.

Similarly, hotels and student accommodation are being used by some authorities to quarantine return travellers, including those positive for COVID-19, for at least 14 days.

This unprecedented situation presents new and significant challenges for the provision of waste collection services to these locations and a new challenge to the parties responsible for collecting and handling such waste. In terms of waste management, this widespread outbreak is particularly challenging due to the dispersed nature of cases and infected individuals.

Given the potential role of the environment in the spread of SARS-CoV-2 [25], waste collection from households and quarantine facilities with COVID-19 positive or suspected patients is a critical control point.

Thus, certain steps or locations along the wastewater handling and treatment train, especially those upstream of any pumping stations, can be suitable for implementing monitoring or control measures to prevent the spread of COVID-19.

The importance of using best management practices for waste handling and hygiene (including disinfection of reusable personal protective equipment) should be reemphasised at this time in the context of limiting worker exposure to potentially contaminated waste.

According to the Association of Cities and Regions for Sustainable Resource Management (ACR+), there is a trend among the waste management sector in Europe to protect frontline waste workers by providing separate collection services to COVID-19 infected households and quarantine facilities (Figure 2 ).

A delay in waste collection time of 72 hours (which is the likely life span of COVID-19 in the environment) is also recommended by ACR+. In addition, the collected materials are transported directly to waste incinerators or landfills without any segregation. At the time of this article, it is unclear how many cities or regions within ACR+ have implemented this recommended practice.

Implementation of the revised waste collection protocol in Figure 2 is not simple and requires a high level of coordination with the relevant authorities, especially health departments regarding data sharing and privacy protection.

Due to privacy concerns, there is very limited or no sharing of patient (or suspected patient) data between health authorities and the waste services sector in most countries around the world. Indeed, the authors are not aware of any suitable data sharing mechanisms currently available or in place that can facilitate coordination between health authorities and other sectors whilst preserving privacy.

A data sharing App jointly developed by Apple and Google for contact tracing is a rare example; although this relies on voluntary consent from the patient for identification [26].

Figure 2
Figure 2
Observed trends regarding municipal waste management during the COVID-19 crisis (Modified from

Implications for wastewater services

During the SARS outbreak in 2003, wastewater aerosols were identified as a ‘highly probable’ transmission route affecting residents at the Amoy Gardens complex in Hong Kong.

The outbreak at that location involved over 300 cases and 42 deaths [27]. Follow up investigations confirmed that high concentrations of viral aerosols in building sewer plumbing were drawn into apartment bathrooms through malfunctioning floor drains when bathroom exhaust fans were running [28].

Virus-laden aerosols originating in the bathroom were subsequently extracted via over-sized bathroom exhaust fans into the building’s light well and then spread under prevailing winds to adjacent units up to some 200 m away [29].

Immediately after the investigation, the management committee of the Amoy Gardens complex repaired all defects in the building’s plumbing system [28].

The residual uncertainty around the definitive cause of the Amoy Gardens SARS cluster and the likely role of faulty or improperly functioning plumbing highlight the need to review similar housing complexes where individual apartment units are connected via plumbing air vents so as to prevent disease transmission by aerosols.

Subsequent research revealed several in-building fixtures in which pathogen laden aerosols can be generated from wastewater such as vacuum and flushometer toilets [30]. Thus, certain steps or locations along the wastewater handling and treatment train, especially in the upstream collection network may be suitable for implementing monitoring or control measures to prevent the spread of COVID-19.

As SARS-CoV-2 virions are excreted in COVID-19 patients’ faeces, sewage can also be an important point of surveillance for wastewater-based epidemiology. Several groups, notably in Australia, the Netherlands, Sweden, and the USA have already reported detecting traces of SARS-CoV-2 in wastewater [6, 31].

Scientists from the Dutch National Institute for Public Health and the Environment analysed wastewater samples from the Amsterdam Schiphol Airport over several weeks and found that, using RT-PCR, they could detect SARS-CoV-2 within four days of cases being confirmed in the country [2].

Importantly, detection of SARS-CoV-2 RNA in wastewater does not imply that the virus is viable and able to infect humans. Coronavirus in wastewater is relatively short-lived, with 3-log10 reduction in virus titre reportedly occurring within 2–3 days [32].

However, given the genetic similarity of SARS-CoV-2 to the earlier, widely-studied SARS-CoV [33] and the known faecal-oral transmission potential of that virus [15, 34, 35, 36], it is possible that a similar transmission pathway exists for SARS-CoV-2. For example, positive SARS-CoV-2 infection of gastrointestinal glandular epithelial cells has been reported, suggesting that infectious SARS-CoV-2 virions are secreted from virus-infected gastrointestinal cells, establishing the potential for faecal-oral transmission [19].

The same study also indicated that infectious SARS-CoV-2 had been isolated from faecal samples; although at the time of writing, these data remained unpublished [19]. This contrasts with other research that failed to isolate infectious virus from faecal samples (13 samples taken from four patients) [20] so clearly more work is needed to explore the potential for faecal-oral SARS-CoV-2 transmission.

With careful selection of sampling points along a sewer network, wastewater ‘snapshots’ can be used to obtain information pertaining to select populations of varying size, e.g. from a particular quarantine facility, hospital, or local government area, or up to hundreds of thousands of people from a larger catchment area.

In the case of SAR-CoV-2 the monitoring technique is based on analytical genomic approaches similar to those used clinically to diagnose suspected COVID-19 patients. This may also be augmented with additional analytical steps to provide a quantitative measure of the targeted viral RNA concentration [5].

With further development and using well-designed sampling campaigns with suitable spatio-temporal resolution, wastewater monitoring could well become a useful tool to monitor and assess the incidence of COVID-19 disease within populations to inform related public health policy.

True quantitative assessment of community SARS-CoV-2 infection would be extremely challenging due to the large number of factors involved and the unknown variability in these factors (e.g. large variability in SARS-CoV-2 viral shedding rates between people and also within people at different stages of infection, unknown persistence of viral RNA in wastewater, variable flow conditions in sewer systems) [6, 37].

These difficulties, however, do not preclude the usefulness of wastewater monitoring as a semi-quantitative early detection system for SARS-CoV-2 re-emergence (or at worst presence/absence) and potentially also as an ongoing tool for informing jurisdictional policy responses to COVID-19 management.

For example, routine wastewater testing could be used to inform when to relax restrictions on population movement or re-open commerce. Having such information available in real-time to inform policy setting would have substantial economic value given the daily cost of COVID-19-related lockdowns.

For example, the daily cost of strict economy-wide lockdown in the United States has been estimated at some US$11.5 billion [38]. The challenge thus becomes to design a widely-accepted surveillance system to detect the potential community presence of COVID-19 and for various end users – from public health officials to facility operators – to be able to use these insights in their decision-making. This would include an ability to evaluate the effectiveness of different control measures to suppress COVID-19 such as social distancing and city-wide lock down.

Wastewater monitoring has been successfully used to identify illicit drug hotspots [39], and track and provide early warnings of outbreaks of pathogenic viruses such as Hepatitis A and Norovirus [7]. It is highly likely there could be similar potential value in using wastewater-based epidemiology to inform SARS-CoV-2 responses [40].

Experts have clearly warned of the likelihood that novel viruses, in particular RNA viruses, will continue to present a serious threat to global public health and disease control [11, 41]. Although current waste and wastewater management practices such as hospital waste separation and incineration, multi-barrier wastewater treatment and disinfection, and PPE protocols have already been designed to mitigate infectious disease exposure risks for workers and the public, the COVID-19 pandemic has resulted in unprecedented and rapid change.

Most businesses and services were under-prepared for this pandemic. Widespread community infection and quarantining can have major impacts on essential services such as waste and wastewater management, and the potential vulnerabilities in the provision of these services are now more apparent than ever before.



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