Looking for COVID-19 clues in our sewers

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Friday, January 15, 2021
Juliette O’Keeffe

Managing the COVID-19 pandemic has been a major undertaking for public health agencies, and new tools or innovations that can help with monitoring of the occurrence, spread or resurgence of the virus could help inform and potentially improve public health responses. Wastewater-based epidemiology (WBE) is one tool that has gained widespread interest. Teams across the world are working to assess its potential by understanding how detecting SARS-CoV-2, the virus responsible for COVID-19, in our sewage could be used to tailor public health responses.  

What is wastewater-based epidemiology (WBE)?

WBE assesses the occurrence or quantity of a biological or chemical signal such as a pathogen, a drug, or some other marker of interest in a pooled sample of sewage. It has been used in the past to monitor the rate and timing of illicit drug use in a community, the occurrence of diseases such as polio and measles, as an early warning of hepatitis A and norovirus outbreaks, and even the level of compliance with antiviral use during the H1N1 influenza pandemic in the UK, among other parameters. Wastewater is a useful matrix to study as it provides a pooled sample from a group of people in a specific geographical location at a point in time. It is non-invasive, anonymous, and has the potential to be applied at a range of scales from single facilities to large towns and cities. Viruses such as SARS-CoV-2 do not replicate outside of a host, therefore the quantity detected in wastewater provides an indication of the total quantity being shed by the community at a point in time.

How is SARS-CoV-2 detected in wastewater?

The SARS-CoV-2 virus can be shed in the feces of infected persons, whether they are asymptomatic, symptomatic, or recovering from COVID-19. Viral shedding peaks just before the onset of symptoms and viral RNA can continue to be shed for several weeks, while viable virus rarely persists beyond 7-10 days after symptom onset. There is thus wide between-person variability in viral shedding rate among active and recovering cases. The process to detect SARS-CoV-2 in wastewater usually involves collection of a sample from a wastewater treatment plant, preparation steps to concentrate and extract viral RNA and analysis for genetic markers of SARS-CoV-2 using quantitative, reverse transcription polymerase chain reaction (RT-qPCR). Many labs are still working to refine their methods to improve reliability of results and provide interpretations of viral signal that can inform public health decision making. A Canadian inter-laboratory study organized and analyzed by the Canadian Water Network’s (CWN) COVID-19 WW Coalition, with coordination partnership support from Canada’s National Microbiology Laboratory, and a similar inter-laboratory study between 32 labs in the US coordinated by the Water Research Foundation (WRF), have both identified areas of consensus and areas for further development of methods and controls.

Who is testing for SARS-CoV-2 in wastewater?

Early in the pandemic, researchers in The Netherlands detected SARS-CoV-2 RNA in municipal wastewater before cases had been reported in some communities, and observed a correlation between the increase in the viral RNA signal and reported COVID-19 infections. There have been many other studies since then that have detected SARS-CoV-2 RNA in wastewater. To date, studies have been conducted in over 500 sites in 44 countries, primarily led by university researchers in collaboration with public health agencies and utility operators. Many studies have shown a correlation between the quantity of SARS-CoV-2 viral RNA and the prevalence of reported COVID-19 cases in a population and some have detected presence or the increase in viral RNA in advance of clinical reporting. Retrospective analyses are also being conducted to investigate how the viral signal has changed in wastewater over time, as an indicator of emergence and spread of the virus in different locations (e.g., in Spain).

In Canada, wastewater testing for SARS-CoV-2 is ongoing in over twenty cities, with the framework of the Canadian Coalition on Wastewater-Related COVID-19 Research, coordinated by the CWN helping to foster collaboration among groups of researchers, utility operators and public health units across the country. 

What are the proposed applications of WBE in response to COVID-19?

WBE could potentially enable early detection, help monitor trends, and help to evaluate the impact of public health meaasures. Some may argue that WBE is a solution looking for a problem to solve, with the practical applications to the COVID-19 response still to be demonstrated. The initial analytical groundwork, led by the academic research community, has been essential for demonstrating that SARS-CoV-2 RNA signals can be detected in wastewater. As methods continue to be refined, work is now needed to understand how the data can best be used to complement public health efforts to control COVID-19. Below are examples of potential applications of WBE in the current pandemic.

Early detection of COVID-19 in small communities or facilities

In theory, WBE could be used to detect the presence of viral RNA before cases are reported through clinical testing, allowing for an early and targeted public health response to prevent a larger outbreak, or to inform actions such as increased clinical testing of highlighted locations. Detecting the signal from one or two people shedding SARS-CoV-2 is more likely in a small sample pool, and action can also be targeted more appropriately. This application may be most appropriate on the scale of a COVID-free small community, or similarly in a facility where early detection is important to preventing outbreaks among a resident population, such as in a prison or long-term care facility. WBE may also be helpful where capacity for rapid diagnostic testing and reporting is limited and community awareness and test-seeking behaviour are low. An early warning indicator from wastewater could trigger increases in clinical surveillance in identified hotspots.

At the University of Arizona a team of experts sampled wastewater from dormitories, and detected SARS-CoV-2 RNA in wastewater from one dormitory where no previous cases had been reported. Detection of viral RNA prompted COVID-19 testing of all residents, identifying three students who were positive for COVID-19 and asymptomatic. Further spread throughout the dormitory was prevented by this early detection. This emphasize the potential importance of WBE where prevalence of asymptomatic infection is high. The City of Yellowknife reported a strong SARS-CoV-2 signal in community wastewater that could not be explained by known clinical cases in quarantine, prompting additional testing in the community in December 2020. This may prove be the best Canadian example of the potential to use wastewater monitoring for SARS-CoV-2 to detect emergence of COVID-19 in a community where clinical cases have been rare.  

Some researchers have explored the potential for monitoring directly in the sewer network (sewershed) to detect prevalence of infection on a smaller scale, down to a neighbourhood, street, or facility level.  Sampling in these locations is logistically more difficult and hazardous, compared to a wastewater treatment plant where trained wastewater professionals perform sample collection. To be useful, wastewater must be sampled frequently. For example, to capture a signal with a one-day advance warning, daily sampling would be required. Considering the time required for transport, processing, analysis and reporting, this can be logistically challenging and resource intensive. The US CDC has updated information on the uses and challenges of targeted surveillance. The extent of rollout requires assessment of resource needs, hazards, and the ethical and privacy considerations of sewershed monitoring. Ethical considerations for undertaking WBE research have previously been developed by the Sewage Analysis Core group Europe (SCORE) and more recently by the Canadian Coalition on Wastewater related COVID-19 Research

Monitoring trends in case numbers in larger towns and cities

WBE has been suggested to be a useful leading indicator of trends in COVID-19 case numbers in a larger community. WBE can complement clinical testing by confirming observed trends in case loads or pinpointing hotspots, but it remains to be seen how much advanced warning is possible and how well the viral signal correlates with active case numbers. Currently large fluctuations are observed in wastewater signals, which make it difficult to identify trends. Factors such as testing frequency, the time delay from sample collection to reporting, and characteristics of the sewage system itself, may affect how much advanced warning is possible. There have been some examples of where wastewater signals matched case trends. In Ottawa, researchers observed a significant spike in the viral RNA detected in wastewater in mid-July. This preceded a spike in reported case numbers by approximately three days as shown on the Ottawa COVID-19 Dashboard. Researchers at University of Saskatchewan observed a spike in viral RNA in wastewater in Saskatoon in early November 2020 suggesting that an increase in cases numbers would follow. The reported case data that followed did indicate a large increase in cases over the following weeks but conventional surveillance indicators such as rising positive case numbers, and increasing test positivity rates had also predicted this rise in case numbers. These examples suggest that WBE may be useful in detecting large changes in case numbers or adding confidence in observation of conventional indicators. More research is needed to understand how frequently testing is needed to be useful, how sensitive the viral signal is to smaller changes, and how to account for the wide range of variables such as viral shedding rates and seasonal, weekly and daily changes in wastewater composition.

Measuring the effect of public health interventions

Alongside observation of trends in case numbers, WBE has also been proposed as a tool for observing and assessing the impacts of public health measures such as mask mandates, curtailing of certain activities, lockdown measures or travel restrictions. In locations with poor COVID-19 testing capacity in the community, low levels of diagnostic test-seeking, or slow reporting of clinical results, changing viral RNA signals in wastewater may indicate, broadly, if public health measures are having an effect. There may be lessons to be learned from retrospective analysis of viral RNA in wastewater combined with data on adherence to public health measures that may inform the management of future waves or future pandemics. If combined with retrospective genomic analysis, insights may also be gained on how the virus spread within and between communities. There has been interest in whether WBE could detect the emergence of new genetic variants of the virus. While this is possible, challenges remain in trying to detect identifiers of true variants among the mixture of RNA fragments present in a pooled sewage sample. Work is ongoing to improve sensitivity so that concerning genetic variants can be detected before they become widespread.

What are some of the challenges still to be overcome?

Many challenges remain around the areas of analytical methods, sampling methods (raw wastewater vs. primary sludge; composite sampling vs. passive sampling), establishing meaningful monitoring programmes, and translating data on viral-RNA in wastewater into meaningful indicators. Some of the key issues that remain to be addressed include:

Analytical issues

  • Refining analytical methods and quality controls, identifying suitable reference materials, accounting for inhibition in analysis, defining conditions of storage, and sampling to analysis time interval.
  • Improving understanding of the influence of variables in the sewer network on viral signal (seasonal or weekly changes in rainfall, stormflow, temperature, travel time, and the size and diversity of catchment area) and identifying how to normalize data to fluctuations in sewage composition.
  • Understanding the relationship between viral shedding among active and recovering cases and how to account for between-person variability in interpreting the viral RNA signal in wastewater during an uptrend or a downtrend in cases, especially in a small community with one or a few active cases.

Establishing a monitoring programme

  • Determining responsibility and human resource capacity for sample collection and analysis and defining the monitoring strategies that fit the intended purposes.
  • Assessing logistical and health and safety concerns for sample collection, analysis, and reporting, especially outside of municipal wastewater treatment plants or sewer networks.
  • Assessing capacity for timely laboratory analysis (e.g., availability of sample processing and RT-qPCR test capacity) and reporting.
  • Assessing the potential to integrate WBE into existing surveillance systems.
  • Estimating the costs of scaling up and determining who will pay (local, provincial, national), weighed against the potential benefits of using WBE in various applications.

Translating research into practical tools to assist public health decision making

  • Determining how to communicate timely and meaningful data to decision makers, with a clear understanding of what can and cannot be indicated by WBE results.
  • Determining how to transition from a research-led undertaking to one driven by the needs of public health, that is integrated with epidemiological and clinical information, and can ensure data quality.
  • Determining the level or change in signal of viral RNA that should trigger a response, and the type of response that should be taken (e.g., increased clinical testing, changes to public health orders etc.).

Key messages and future outlook

WBE cannot, and should not, be considered as a candidate to replace the gold standard of clinical diagnostic testing, which will still be needed to confirm whether a symptomatic or exposed person is COVID-19 positive. Whether it provides better indicators of disease prevalence than other tools such as antigen prevalence surveys remains to be seen. WBE will likely be able to complement or supplement, rather than replace, other conventional sources of evidence to guide essential public health actions. Work is needed to refine methods, improve reliability and consistency of data and to both customize and demonstrate the most cost effective and meaningful applications of WBE to the COVID-19 response.

The most promising uses of WBE may be as an early warning signal for small communities or facilities, or in regions with poor clinical diagnostic capacity and reporting or low test-seeking behaviour among the population. It may also be useful in detecting the emergence of new variants of a disease if methods can be refined to detect variants at a low enough frequency to provide an early warning. To be meaningful on a larger scale, WBE testing should be conducted at a frequency that provides an advantage over existing clinical testing. Integration of WBE into existing surveillance systems may help to overcome some logistical challenges that would accompany a new monitoring programme, but assigning responsibilities, assessing laboratory capacity, and evaluating additional costs will be needed.

WBE may also provide a useful tool for future research, informing understanding and actions as vaccination levels increase in the population, with retrospective data analysis providing insights into the progression of the pandemic and the impacts of various public health interventions. Continued post-COVID surveillance could also help to identify emerging pathogens before they become widespread in a community.