Detection of Covid-19 in wastewater is a disease monitoring technique that has recently risen to prominence. Based on experience gained from evaluating a third-party wastewater Covid-19 monitoring programme implemented for a client, we discuss some of the advantages and limitations of wastewater monitoring, and some of the challenges that can be encountered in implementation.

What is Covid-19 wastewater detection?

Monitoring Covid-19 infection rates and community disease prevalence has been an ongoing challenge throughout the pandemic. Contributing to the well-established underreporting of swab-based Covid-19 cases include: asymptomatic carriers, the “window period” during which individuals are infectious but asymptomatic, non-reporting from home-based testing and the large number of factors that prevent symptomatic carriers from testing. As governments loosen Covid-19 protocols and pandemic fatigue sets in, fewer people are reporting for swab-based testing, further skewing incidence estimates.

One potential alternative for epidemiological surveillance has risen to prominence internationally: wastewater-based epidemiology (WBE). While WBE is a broad term referring to anything from toxin to drug level monitoring, in the case of Covid-19 it refers to monitoring the level of viral particles in the sewerage system (specifically, viral RNA, detected using RT-qPCR), to gain an idea of the relative disease prevalence in the “drainage area” of the monitoring site. Testing wastewater sidesteps many of the issues of swab-based testing because it does not rely on human behaviour, and one “test” can monitor many people, cutting down on some of the resource requirements. Foladori et al (2020) provide a detailed summary of the theory behind Covid-19 WBE.

So will detecting COVID-19 viral particles in wastewater solve COVID-19 surveillance?

The answer, as for any health sciences initiative, is not an unequivocal “yes”.  This article by Zhang et al. published in January this year provides an excellent summary of the many issues that can affect the quality of wastewater-based Covid-19 surveillance. The genetic material that the test depends on has limited survival outside the body, and the detergents and chemicals used in toilets and in sewerage treatment further impact survival. Temperature, perhaps particularly relevant in a relatively warm country such as South Africa, can also have a huge impact on viral survival. Differing travel distances and inconsistent wastewater dilution make it very difficult to compare sites, and complex mixing between drainage areas can make it almost impossible to identify the source of any particles detected. Furthermore, individuals shed different amounts of viral particles in faeces depending on the type and severity of symptoms, viral strain and where in the course of their illness they are. Additionally, if the number of people in a particular drainage area fluctuates, so too will the relative viral levels. Finally, it is also worth considering that not all waste may go through the formal sewerage systems in places with poor hygiene and sanitation infrastructure.

As a result of all these confounders, it becomes almost impossible to quantify the number of individual cases that have resulted in the viral load detected in wastewater downstream. Furthermore, without one-to-one testing, WBE can inherently never pinpoint infected individuals who need to self-isolate and/or who may need care.

That said, monitoring for large-scale changes in relative viral levels can be of use in identifying new waves (when monitoring at a community or national level) while most cases are still in the asymptomatic phase, or identifying local hotspots where targeted testing campaigns should be implemented (e.g., a specific hostel or building, when monitoring relatively close to the source). These kinds of initiatives have shown very promising anecdotal results across several countries and different implementations.

What were the challenges faced by a local waste-water monitoring initiative?

At the start of the year, Wimmy was asked to analyse the initial results of an outsourced Covid-19 wastewater monitoring initiative for a large organisation with dedicated wastewater management. The initiative had been collecting data for six months across five sites and a downstream wastewater treatment plant. One sample was reportedly taken per site every 72 hours, although there was a median of 4 days (average of 4.8) between samples in the data.

We compared the levels of two different viral genetic sequences (RNA sequences “2019 nCOV_N1” and “2019 nCOV_N2“) with in-house swab testing results for the area and with national Covid-19 levels to understand their relative dynamics. Local swab data was provided on a daily basis.

By synthesising the literature, reviewing the initiative methodology, and analysing the initial collected data, Wimmy provided the following insights in how to maximise the effectiveness of the wastewater monitoring initiative:

1) To be effective, a WBE initiative cannot have “data silos” and reporting must be real-time.

As wastewater monitoring cannot provide reliable prevalence estimates, and can only provide vague relative indicators, its primary function is as an early warning system. This function, however, relies on an efficient and effective reporting structure. Decision-makers and policy implementers who can drive changes to non-pharmaceutical interventions and swab-based testing initiatives in the face of a new wave must be alerted in real-time of any warning signals from the data. This is often a challenge when wastewater testing is done by a third party, as this requires data infrastructure interactions, particularly if the wastewater data is to be linked to swab testing data from another source.

2) Although quantitative linking of wastewater viral levels to case numbers will likely not be achievable, several actions can improve the reliability of the data points.

These include measuring dilution (through the use of tracers), temperature, pH, solvent levels, etc. Providing multiple readings per sample, analysing multiple simultaneously collected samples per site, and sampling along more points in a sewerage system can reduce uncertainty. Reducing uncertainty means that when elevated or decreased viral levels are seen, it is more likely that that measurement reflects a true increase or decrease in case numbers. Another consideration is to ensure that the viral markers used for viral detection are still present and as effective in new viral strains.

3) Effective monitoring and evaluation of a wastewater intervention require coordinated wastewater and swab-based testing programmes.

To understand how wastewater viral levels map to true case numbers, another proxy for case numbers must be used for comparison; in the case of Covid-19, this is typically swab-based testing. Ideally, the swab-testing should occur in the upstream population of the wastewater sample site. For example, if the wastewater of a residence is monitored, cases from that residence should also be identifiable. In this way, the ability of wastewater to predict and/or monitor cases can be clearly shown. Both testing modalities should also occur at similar frequencies, and anything less than weekly testing will diminish the predictive value of wastewater monitoring.

So what does this mean?

Wastewater monitoring for Covid-19 may be a crucial part of epidemiological disease monitoring in the face of declining swab-based testing rates, allowing for early warning signs for new waves on a large scale, and smaller outbreak areas that require targeted testing campaigns on a smaller scale. However, it’s inherent limitations and the complexities of implementation must be properly evaluated when designing a WBE initiative.

It must be well understood that wastewater monitoring complements traditional testing methods but cannot replace them, as individuals will still need a diagnosis, and wastewater viral levels have too many confounding variables to be able to provide incidence or prevalence figures in terms of how many individuals are affected.

Finally, if wastewater monitoring is to fulfil its role as an early-warning system for waves or outbreaks, real-time reporting and linking to swab-based testing data is necessary. As with any health initiative, monitoring and evaluation systems should be built in from the start, with an understanding of how to minimise variance and uncertainty in the results.

Crucially, this case highlighted the importance of an early efficacy assessment. Unforeseen pitfalls in implementation will always arise, limiting usefulness and stalling monitoring and evaluation. By addressing these pitfalls early in the implementation cycle, goals can be achieved sooner, and massive resource wastages can be prevented.

References and Resources

Foladori, P., Cutrupi, F., Segata, N., Manara, S., Pinto, F., Malpei, F., Bruni, L., & La Rosa, G. (2020). SARS-CoV-2 from faeces to wastewater treatment: What do we know? A review. The Science of the total environment, 743, 140444. https://doi.org/10.1016/j.scitotenv.2020.140444

Shah, S., Gwee, S., Ng, J., Lau, N., Koh, J., & Pang, J. (2022). Wastewater surveillance to infer COVID-19 transmission: A systematic review. The Science of the total environment, 804, 150060. https://doi.org/10.1016/j.scitotenv.2021.150060

Zhang, D., Duran, S., Lim, W., Tan, C., Cheong, W., Suwardi, A., & Loh, X. J. (2022). SARS-CoV-2 in wastewater: From detection to evaluation. Materials today. Advances, 13, 100211. https://doi.org/10.1016/j.mtadv.2022.100211

The South African Medical Research Council provides a publicly accessible COVID-19 wastewater surveillance dashboard at the link below: 

https://www.samrc.ac.za/wbe/