#FEMSmicroBlog: Wastewater samples to predict viral outbreaks


To tackle the COVID-19 pandemic, one central challenge has been the timely and cost-effective tracking of cases. Fortuitously, concentrations of SARS-CoV-2 in domestic wastewater reflect the rise and fall of COVID-19 cases in communities. Hence, tools for wastewater monitoring have been implemented and improved throughout the pandemic. A new study published in FEMS Microbes now presents a mathematical framework to relate SARS-CoV-2 RNA signals in sewerage to case rates in a community served by the wastewater treatment facility. Alessandro Zulli and Jordan Peccia explain for the #FEMSmicroBlog how these models could help us tackle the current pandemic but also prepare for upcoming ones. #BehindThePaper


Why wastewater monitoring is important

Wastewater monitoring for viral agents is not a new idea. It has been implemented to detect poliovirus infections in several countries and to understand the effectiveness of vaccination campaigns. Mild or asymptomatic poliovirus infections are common and the virus is shed in the stool of infected individuals.

Similarly, SARS-CoV-2 is ideally suited for wastewater surveillance due to its ability to replicate in the human gut – also referred to as gut tropism. In prior metagenomic surveys of viruses in wastewater, our group determined elevated concentrations of endemic coronaviruses.

SARS-CoV-2 is suited for wastewater surveillance because it replicates in the human gut.

In early 2020, we then demonstrated that SARS-CoV-2 concentrations in wastewater reflect case rates and hospital admissions. Based on our findings, wastewater surveillance became a leading indicator of COVID-19 outbreaks. At the same time, wastewater monitoring techniques, such as RT-qPCR, were improved and adapted to follow the SARS-CoV-2 pandemic.

Wastewater monitoring has at least three advantages over the use of established COVID-19 clinical tests to track community outbreaks. The first of them is the timeliness of wastewater results. From sample collection to the measured signal, wastewater can be processed in a single day. In comparison, individual testing, from sample collection, processing to aggregation of data often take days. This means that wastewater surveillance can provide information a few days before clinical tests.

Second, wastewater testing can have similar costs as clinical PCR tests. While one wastewater sample can give information about an entire community served by a treatment plant, a PCR test can only do so for one individual.

Third, COVID-19 testing programs are subject to personal availability, might lag during periods of high infection over holidays and may overlook asymptomatic cases. In comparison, wastewater production is steady and independent of these factors.


How to use wastewater monitoring to predict COVID-19 cases

In our study “Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments” published in FEMS Microbes, we demonstrated the relationship between wastewater concentrations of SARS-CoV-2 RNA and COVID-19 case rates – cases per 100,000 people – derived from a well-run testing program. The strong correlation between the two factors shows the public health significance of wastewater SARS-CoV-2 concentrations. Hence, to make this information more accessible to the affected community, we developed a model that converts the signals into case rates.

Predictive models for wastewater monitoring of SARS-CoV-2
Wastewater monitoring to estimate COVID-19 case rates. From Zulli et al. (2022).

For our study, we collected over 1700 daily sludge samples from six municipalities in Connecticut (USA) and measured their SARS-CoV-2 RNA levels. Using RNA level data from the last 5 days, we created predictive case rate models. These models have proven highly accurate, with coverage probabilities between 94%-96%.

Therefore, our model could accurately predict the case rates in a municipality using only wastewater concentrations. As the world’s clinical testing infrastructure slowly dissolves due to expenses and the rise of home test kits, our model allows for municipalities to estimate case rates using wastewater surveillance.


Wastewater monitoring beyond COVID-19

Wastewater surveillance can be most effective when COVID-19 testing programs were limited by financial resources. This approach is also an efficient alternative for pathogens for which clinical testing did not exist. Even in the presence of a strong clinical COVID-19 testing and reporting system, the wastewater approach provides a low-cost, early indicator of COVID-19 outbreak dynamics.

Our aim was to develop a modelling framework that can be applied to other wastewater monitoring programs to predict case rates. This information could empower public health officials to make timely decisions about resource allocation and preventative measures.

Wastewater monitoring programs empower public health officials to make timely decisions.

Even during periods of low viral activity, local governments could carry on tracking progress. Monitoring programs would continue while individual testing could wind down, thus improving the allocation of resources.


About FEMS Microbes

FEMS Microbes is a new open-access journal we are introducing to help meet the latest needs of researchers as authors and readers. FEMS Microbes is our new community journal for sharing research findings. In particular, it will be a venue for early-career scientists to read, publish, and contribute – we intend to recognize the crucial, and often unnoticed, contribution to peer review by Early Career Scientists. FEMS Microbes welcomes both direct submissions and manuscripts transferred from other FEMS journals, including both full-length research articles and short reports of broad significance in the field of microbiology and related disciplines.

About this blog section

#BehindThePaper posts on the #FEMSmicroBlog aim to bring the science closer to different audiences and to tell more about the scientific or personal journey to come to the results.

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