Whispers of Viruses and Bacteria in Wastewater

Professor Marlene Wolfe, one of the leaders of the US Sewer Coronavirus Alert Network (SCAN) team, said in an interview with the British Medical Journal: We can take that sample, which is less than a gram of wastewater solids, from communities all across the country: that small sample can represent up to 4 million people in some cases.”.

The whisper of SARS-CoV-2 was loud in less than a gram of wastewater sample. At the end of 2022, more than 3,800 monitoring stations in at least 70 countries around the world are watching the wind and listening to the whisper of SARS-CoV-2 in the water.

Figure 1: History of Wastewater Science Terminology

History of Wastewater Science Terminology

The origin of the detected wastewater can be traced back to the Broad Street cholera outbreak in Soho, London in 1854. At that time, in a public well and cesspool near a house where many people died of cholera, feces were found to leak bacteria and contaminate the water supply system of the pump, causing an epidemic. 

  • In the mid-1950s, "Wastewater Tracing or Tracking" appeared successively after the research on the wastewater infected by snail schistosomiasis in South Africa. 
  • Around 1970s, "wastewater monitoring" and "wastewater surveillance, "WWS)" or "Wastewater-Based Surveillance (WBS)" are commonly used in industrial wastewater detection research.
  • In the 2000s, issues such as tracking heroin and other illicit drugs emerged as "sewage epidemiology" and "wastewater-based epidemiology (WBE)". The mixed use of subject terms mainly describes the scientific based on the premise that the substances excreted by humans in wastewater can be used to calculate the initial concentration.

However, by 2014, the term "wastewater epidemiology" gradually replaced the term "sewage epidemiology". Although the terms sewage and wastewater are still commonly used interchangeably, the recent official documents of the World Health Organization (WHO) mainly use the term "wastewater surveillance". Scholars also suggested the standardization of related science and technology, and supported the use of "wastewater surveillance (WWS)" and "wastewater epidemiology (WBE)" as common terms.

If we examine the differences in definitions, we can distinguish them from the perspective of public health (Figure 1):

  • wastewater tracing or tracking is mainly to identify the source of pathogens or toxins;
  • wastewater monitoring is an action to ensure that waste water discharge does not cause public health risks ;
  • wastewater surveillance emphasizes systematic, continuous testing of wastewater for the benefit of public health and may be relevant for public health policy;
  • wastewater epidemiology (WBE) is the scientific field that links pathogens and chemicals found in wastewater to population health.

Which infectious human pathogens were studied in wastewater before COVID-19?

Wastewater surveillance (WWS) has been used to assess waterborne and fecal-oral pathogens that cause diarrhea-related diseases. The well-studied pathogens of human infectious diseases include picornaviridae, caliciviridae and reoviridae, etc. (indicated by * in Fig. 2). Epidemics of international concern such as coronavirus, Ebola virus, Zika fever, and polio/poliomyelitis virus (indicated by *** in Figure 2) have provided information on public health actions or policies, but influenza is rare founded in WWS literature.

Figure 2: Wastewater Surveillance (WWS) of known infectious diseases before the COVID-19 pandemic: virus classification by family/genus












If the coronavirus is the subject, the early coronavirus wastewater monitoring is in view of the emergence of new viruses with high epidemic potential, which usually involves complex dynamic effects on animals, humans and the environment. Therefore, since the 1970s, environmental monitoring has been implemented by monitoring surface water, mud and biosolids to understand the status of such viruses in the water cycle, ex. human coronavirus (HCoV), human coronavirus 229E (CoV-229E), HKU1 and severe acute respiratory syndrome coronavirus (SARS-CoV); zoonotic coronaviruses such as Middle East respiratory syndrome coronavirus (MERS-CoV) and animal coronaviruses: such as bovine coronavirus (BCoV), mouse hepatitis virus (MHV), etc. This stage focuses on coronavirus, the survival status of viruses in wastewater and the efficiency of virus recovery, etc., but the overall knowledge is still very scarce and fragmented.

After the COVID-19 pandemic

Figure 3: Overview of Wastewater Surveillance (WWS) after COVID-19

The COVID-19 pandemic has seen extensive adaptation of global wastewater surveillance (WWS), and wastewater can also be an effective potential application for surveillance of respiratory-transmitted pathogens. Technologies for detecting SARS-CoV-2 and new variants through wastewater are becoming more sophisticated. 

Figure 3 generally illustrates the current WWS in addition to early development of chemicals such as drugs, cleaning agents, industrial pollutants or pathogens like antibiotic-resistant bacteria, etc., as well as human infectious disease pathogens (described in Figure 2).

After COVID-19, in addition to the new monitoring of SARS-CoV-2, monkeypox and influenza RSV have recently become emergencies of international concern, and such pathogens have also become the focus of WWS, especially when most people cannot receive RSV clinical test, wastewater data can fill the gaps. 

Meanwhile, the progress in wastewater genome monitoring technology has solved the problem of multiple virus strains in wastewater. As shown in Figure 3, according to the WHO classification of coronavirus variant strains, new variants can be found in wastewater samples 14 days in advance, and clinical monitoring can be determined instances of virus transmission that cannot be captured, for high-risk groups such as student dormitories, airports, hospitals, nursing homes and other long-term care facilities. In addition to providing early warnings, it can also help contain and mitigate virus outbreaks. In the long run, WWS is more an important tool for tracking the dynamics of viral lineages in combination with dominance.

Further analysis from the perspective of wastewater epidemiology (WBE), in resource-rich countries is mainly assessed in sewers and sewage systems, but in resource-poor environments, most residents are not connected to centralized wastewater treatment plants, using pit toilets, septic or open defecation, so the WWS process varies depending on the wastewater system.

Overall, as shown in Figure 4, WBE includes the process of sampling, sampling methods, virus concentration and concentration techniques, use of control viruses in the control process, virus isolation, RNA extraction, virus detection and quantitative sequencing, and finally completes epidemiological modeling to analyze epidemic trends.

However, WBE still faces many challenges, such as sampling control: daily changes in water flow, differences in wastewater systems, weather factors, temperature, sedimentation rate, and virus shedding and other factors. In terms of virus recovery and concentration: concentration method efficiency, RNA extraction, purification efficiency and storage of RNA, etc. Plus virus detection and/or quantification. Challenges such as RNA quality, RNA quantity, PCR inhibitors, and normalization of data will all affect COVID-19 wastewater surveillance, which faces shortcomings such as low recovery rate and long processing time.

Figure 4: Analysis Process of COVID-19 Wastewater Epidemiology (WBE)

WWS is intended to complement, not replace clinical tests

SARS-CoV-2 wastewater surveillance differs from clinical diagnostic testing in the design and interpretation of community-scale sampling programs, as well as in the different assays which attempted to concentrate and extract RNA from wastewater and environmental water samples.

Because viral RNA can be discharged into wastewater before symptoms and diagnostic testing, SARS-CoV-2 wastewater surveillance can help document trends in high-prevalence cases of COVID-19, and in cases of low prevalence or lack of clinical testing evidence.

Early warning can be provided, while wastewater viral load can be used to monitor the impact of public health social measures, including increased or relaxed restrictions, as well as enhanced risk communication, warning the community about the (re)emergence of the virus, and advising the community about testing, quarantine, isolation, as well as suggest actions such as vaccinations and seeking health care.

In sum, WWS advantages include providing objective metrics that are less susceptible to biases inherent in clinical testings, such as 

  • health-seeking behaviour, 
  • disease severity (including symptomatic and asymptomatic), 
  • healthcare and testing accessibility, 
  • physician and individual response to testing propensity, 
  • cost and reporting constraints, etc.

We take the interactive COVID-19 WWS of the New Zealand Institute of Environmental Research and Science as an example (Figure 5). This dashboard has been launched in July 2022 to allow the public to track the footprints of SARS-CoV-2 and view national and regional epidemics, etc. latest trends.

It provides a spatial-temporal visual map; it presents wastewater statistics and provides functions such as regional options, search, and comparison of trends in different periods. 

  • From Figure 5(a), we can observe that Wellington shows that the wastewater data and the corresponding spikes of confirmed cases are different in three time periods (green dotted circles): during the peak period of the epidemic, due to sufficient clinical testing, the confirmed cases and wastewater data are about the same.
  • In the low epidemic period, the peak of wastewater data far exceeds the confirmed status due to factors such as people feeling tired (or thinking it is unnecessary) to rub their noses, the overall detection capacity slows down, or the willingness to report decreases. 
  • The public can also check the latest SARS-CoV-2 variant virus. Figure 5 (b) and (c) show the ratio and trend information respectively.

In general, the wastewater data not only supplements clinical monitoring, but also provides background information on the public’s epidemic prevention environment base. The dashboard shows that wastewater data covers 73% of the population in New Zealand. A small sample of less than one gram only needs a few expensive PCRs.

Compared with the costs of tests and costs for clinical PCR, yes, using WWS to listen to the muttering sounds from all directions in the wastewater is cheaper and wider. Plus, virus and bacteria of various kinds can be identified, warned and tracked broadly. It can also assist the public in preventing and managing risks by them selves, easily in their daily life and sustainably for the whole country health.

Figure 5:SARS-CoV-2 wastewater monitoring network of the Institute of Environmental Science and Research (ESR) in New Zealand
COVID-19 Wastewater Surveillance Dashboard: https://esr-cri.shinyapps.io/wastewater


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