COVID-19 Wastewater Monitoring


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COVID-19 Wastewater Monitoring

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Wastewater Monitoring In Chicago

The Chicago Department of Public Health (CDPH) has developed a wastewater monitoring system to measure citywide levels of SARS-CoV-2, the virus that causes COVID-19 illness. Wastewater, also referred to as “sewage,” contains human waste from households, facilities, and other public spaces. Research shows that individuals infected with SARS-CoV-2 can shed SARS-CoV-2 in their solid waste, regardless of whether they have symptoms. So, monitoring levels of SARS-CoV-2 virus in Chicago’s wastewater system can help us to better understand the amount and duration of COVID-19 activity in communities over time.

A sewershed is an area of land in which all wastewater flows to a single point. Chicago’s wastewater infrastructure is complex and consists of many different, and often overlapping, sewersheds. Different sampling locations are associated with unique sewersheds, which can represent waste from a small segment of Chicago to over a third of the city! CDPH’s wastewater surveillance strategy collects data from multiple different locations.

  1. CDPH, in partnership with the Illinois Department of Public Health (IDPH), collects samples from wastewater flowing into treatment plants. Each of the wastewater treatment plants cleans wastewater for more than a million people. This is the most ‘zoomed out’ scale of wastewater surveillance in Chicago and provides information about general trends across the Chicago region.
  2. CDPH collects samples from local sewersheds using manholes in various parts of Chicago across each of the six Healthy Chicago Equity Zones. Additional sites were selected according to their vulnerability to COVID-19 and the relative availability of clinical testing (prioritizing communities with less access to COVID-19 testing). These sites provide some information on ‘neighborhood level’ trends.
  3. CDPH also samples from pumping stations, which service population sizes between local sewersheds and treatment plants. These are the “mid-size” sites that are sampled to obtain information on larger portions of the city and fill the gaps between local sewershed sites.
  4. Testing also occurs at specific high-risk facilities (including O’Hare Airport). This is the most ‘zoomed in’ scale – it can be useful in the detection of new variants, or for specific public health responses in large congregate facilities experiencing outbreaks of COVID-19. 

Samples are generally collected twice weekly – this reflects a cross-departmental effort to identify viable sampling locations (e.g., manholes), map those locations to the communities living in the vicinity, and collect and test those wastewater specimens.

Data from CDPH’s wastewater surveillance system is used – alongside various other forms of public health surveillance data – to inform the City’s COVID-19 response, for example by prioritizing communities for enhanced COVID-19 testing or vaccination services. Chicago data is also shared with CDC partners and posted to their dashboard as part of the National Wastewater Surveillance System. 


Wastewater Monitoring Dashboard


Chicago’s wastewater dashboard displays concentrations of SARS-CoV-2 in wastewater samples (represented as dots) with an overlaid smoothing line (LOESS regression) using these values to show overall trends in concentration levels. Users can access data for the 8 local sewersheds, 3 pumping stations, and 3 treatment plants (Stickney is divided into North and South sections).

The dashboard displays concentration data for two important “targets”, or viruses of interest.

  • We use SARS-CoV-2 N1 gene concentration levels to determine the presence and concentration of the SARS-CoV-2 virus.
  • We also look for a virus called PMMoV (Pepper Mild Mottle Virus). This is a virus common to pepper plants, which cannot infect humans, but is found in the waste of most healthy people. We use PMMoV to estimate how many people are “contributing” to any given sewershed.

Data displayed are “normalized” which means that we have adjusted concentrations from different sites so that we can roughly compare across sites. Because the amount of wastewater flowing changes over time, and the number of people using different sewersheds is different, we must normalize the data so that they can be roughly compared.

  • Site concentrations are normalized by dividing the N1 gene copies per liter by the PMMoV copies per liter resulting in a unitless ratio of virus to people contributing to wastewater at that site. This ratio is then multiplied by the average concentration of PMMoV at a given site to make the value easier to interpret.

Data are displayed on a log scale to better visualize the change in concentration over time and reduce the impact of extreme values on the regression line. Outliers (values that are much higher or lower than surrounding data points) are potentially due to the changes in the number of people contributing to the sewer system at a given time, variation in viral shedding of SARS-CoV-2 between individuals with COVID-19, or even limitations in the sampling/laboratory methods. We are still learning more about how wastewater data is best used and interpreted.

The Chicago wastewater surveillance system has been collecting data on Chicago wastewater since February 2022. Historical data can be found on the Chicago Data Portal. Data are updated every Wednesday.


National Wastewater Surveillance System

CDC COVID Wastewater Surveillance Map

Visit https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/wastewater-surveillance.html for more information.  


Reports

As of April 2023, data will be available through the CDPH Wastewater Monitoring Dashboard.

Annual Reports

Monthly Reports

  • 03/23/2023 - Monthly Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 02/17/2023 - Monthly Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English

Data Reports

  • 01/18/2023 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 12/16/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 12/01/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 10/19/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 8/22/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 7/29/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 6/21/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English
  • 5/11/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English |  Spanish
  • 3/16/2022 - Data report: Monitoring COVID-19 in Wastewater in the Chicago region: English |  Spanish 


Partners

CDPH contracts with the Discovery Partners Institute (DPI), part of the University of Illinois System, which builds off work that began in 2020, funded by the Walder Foundation (read more about the Chicago Prototype Coronavirus Assessment Network Node here). In building this surveillance system, DPI coordinates expertise from multiple partners to identify possible collection sites, collect samples, conduct SARS-CoV-2 testing and quantification, and to conduct genomic sequencing to identify variants in wastewater samples. These partners include other City departments (e.g. the Department of Streets and Sanitation), the Metropolitan Water Reclamation District of Greater Chicago, and scientists at Northwestern University, Argonne National Laboratory and the University of Chicago.



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Frequently Asked Questions

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Chicago has established a monitoring program to track COVID-19 by measuring the amount of SARS-CoV-2 RNA in wastewater. The initiative is a collaboration between the Chicago Department of Public Health (CDPH) and the University of Illinois System’s Discovery Partners Institute (DPI). Additional partners include the University of Illinois-Chicago, Northwestern University, Argonne National Laboratory, CDM Smith and Current Innovations.

The program aims to deliver actionable information to public health decision-makers identify trends in COVID-19 infections levels and SARS-CoV-2 variants of concern. It also supports City efforts related to pandemic preparedness.

People infected with COVID-19 may be contagious before symptoms appear and/or an individual obtains a clinical diagnostic test, which means the virus could be present and moving undetected through the community. Genetic material from the SARS-CoV-2 virus that causes COVID-19 is excreted in the feces and urine of infected people even if they have no symptoms. Wastewater systems collect sewage from throughout the city, providing an efficient and anonymous way to monitor the presence of COVID-19 in the community.

Wastewater data are analyzed as trends over time and some wastewater samples are also analyzed by genome sequencing to understand variants circulating in a community. This provides useful information for communities where timely COVID-19 clinical testing is underutilized or unavailable. In other locations, SARS-CoV-2 has been detected in wastewater before infections led to increases in case counts or hospitalizations, providing an early warning of COVID-19 increase in a community, though wastewater data does not always precede clinical data. Community and public health leaders can use this information to make decisions about protective actions to help limit further spread of the disease.

It is anticipated that wastewater monitoring will only become more important with the increasing prevalence of at-home testing. It also provides important data during a downtown in the pandemic when testing may become less frequent.

No. Wastewater surveillance is population-level surveillance and does not yield information on specific individuals. The term “surveillance” refers to keeping an eye on the virus and its transmission.

The initial sites included in the Chicago Wastewater Monitoring Program were selected during an 18-month research program led by the Discovery Partners Institute through a grant received from the Walder Foundation and in partnership with the Chicago Department of Public Health.

Sites were selected in late 2020 with the goal of understanding the relationship between public health outcomes and wastewater. Sites were selected across the city for research purposes, including areas with both high and low COVID-19 rates at the time. Some sites are in locations where relative vulnerability has changed since late 2020.

CDPH is re-evaluating sites on an ongoing basis to support City of Chicago health equity goals.

Samples are collected in 50 mL tubes from specific sampling locations across the city. The program partners with the Metropolitan Water Reclamation District of Greater Chicago, Chicago Department of Aviation, Cook County Sheriff’s Office, Department of Water Management, Current Innovations and CDM Smith in selecting and facilitating the collection of samples. Although sampling design may change according to the priorities of CDPH, samples are currently collected three times a week to help understand fluctuations in the quantity of the virus as well as the profile of SARS-CoV-2 genomic variants.

Samples are taken to a lab at the University of Illinois-Chicago for processing and analysis to quantify viral remnants in the water, which are measured in gene copies/liter. Samples are then sent to Argonne National Laboratory for genetic sequencing to identify the variants of the virus.

Per CDC guidelines, the twice-weekly samples are analyzed every Friday to determine 2- and 4-week trends (up, down, neutral). The results of this analysis are discussed each week with CDPH, who in turn incorporate the trend information into their planning processes.

CDPH will determine how to respond to data collected from each site. Wastewater sampling will not be used alone to make policy and will complement clinical data (i.e., nasal/saliva swabs).

No. This data alone will not drive public health interventions. Rather, it is information for the community to use along with other resources to help protect their citizens.

When public health officials determine that COVID-19 risks are very low, it is anticipated that samples will still be taken, though less frequently. Wastewater monitoring will be especially helpful for understanding disease prevalence as at-home testing increases since public health systems do not receive these results.

The CDPH Wastewater Monitoring Program provides information on the extent of infection that can help local communities intervene with protective measures to slow disease spread.

As each of us weighs the risks of COVID-19 in our daily lives, we look to public health guidelines but many of us also track public data such as the positivity rate of testing or the hospitalizations in our communities. Wastewater trends are useful to provide similar information at the community level.

CDPH will leverage the CDC's national web portal to make the data available to the public. This mechanism will enable interested individuals to not only see what is happening in Chicago but also understand how Chicago compares with other communities in Illinois or elsewhere.

CDPH shares Chicago’s sewershed level data with the public on the Chicago Data Portal.

IDPH also shares statewide data including treatment plants covering Chicago on the Illinois Wastewater Surveillance System website.

The program occasionally experiences logistical difficulties in sample collection related to extreme cold temperatures that may cause equipment to malfunction and other weather-related events. Program sample collectors follow a standard operating procedure to make sure a full faith effort is made to collect samples from every sampling location. Sample collectors and researchers are working together to understand whether other factors may have an impact to the ability to collect samples in certain conditions and modifying sample collection methodology accordingly.

At this time, there is no evidence that a person has become infected with the virus that causes COVID-19 from exposure to wastewater. While genetic evidence of the virus exists in wastewater, researchers have not shown that any virus present in the wastewater is still capable of causing infection. Wastewater still contains many viruses, bacteria, and other microbes that are known to cause other infections in humans and should always be handled with caution.

For sample collectors, both the Centers for Disease Control and Prevention (CDC) and Environmental Protection Agency (EPA) recommend standard protective equipment and procedures associated with working with wastewater.

Wastewater samples are first processed to concentrate and isolate genetic material (RNA) that is present in the sample. RNA sequences specific to SARS-CoV-2 are then detected and quantified using a molecular biology tool called digital polymerase chain reaction (dPCR). During dPCR, a targeted segment of the RNA (most commonly the N1 or N2 gene) is converted to DNA and then amplified (copied many times) so it can be detected by laboratory instruments. Specific methods for sample processing and PCR-based quantification differ among wastewater monitoring projects and analytical laboratories.

There are not presently agreed-upon methods for translating concentration of SARS-COV-2 genetic material in wastewater into a measure of how many people, or even what percentage of a community, have COVID-19. Variability between different wastewater sources, treatment facilities, and

communities makes it difficult to translate the SARS-CoV-2 GC concentration into a measure of how many people are infected in the community. However, an upward or downward trend in SARS-CoV-2 GC/liter generally suggests a similar trend in the number of people infected within a given community.

Because each community has a different mix of wastewater inputs, different populations, and different wastewater systems, it is not appropriate to compare viral gene copy numbers among communities. Instead, trends in SARS-COV-2 GC/liter from a specific community over time can be used to help understand whether cases or hospitalizations are likely to increase or decrease in the community.

There are several factors to consider when interpreting viral data in wastewater. The rate, magnitude, and duration of shedding varies from one person to another, thus how or even whether it is possible to translate viral levels in wastewater into precise community health metrics is an open scientific question. It is only appropriate to monitor and observe the trends of viral gene copies detected in a community over time. The data presented in the tables, graphs and trend assessments shared with you show the concentration of RNA copies in the wastewater area from the community where the wastewater was collected. A significant increase in viral gene copies over time is an indicator that cases may be increasing in the community. Because infected individuals can continue to shed the virus RNA in feces for 20 to 30 days after they are no longer infectious, decreases in the number of viral gene copies in wastewater might lag behind decreases in COVID-19 cases in a community. Trends in viral gene copies should be considered along with community case numbers and other COVID-19-related data to inform decisions about taking actions to help limit disease spread.

The focus is on major trends in the concentration of viral gene copies detected in wastewater. Rapid increases over 1-2 weeks may indicate an area of concern that should be investigated further by evaluating other public health measures of COVID-19 cases and impacts. Increases in wastewater concentrations over multiple weeks may indicate a sustained trend.

Wastewater monitoring methods are being refined to provide more information on the prevalence of COVID-19 in the contributing community and to better compare results between communities. Laboratory analysis methods, data analysis methods, and predictive models are being improved to better relate observations of SARS-CoV-2 RNA in wastewater to health surveillance data, the percentage of infection in communities, and more severe disease outcomes like hospitalization, ventilation, and mortality. Sampling and sample analysis strategies are being improved to make results more comparable between communities. The local factors that cause variations in wastewater detection limits are also being investigated to enable direct comparison of SARS-CoV-2 gene copy concentrations between communities, which will enable better allocation of public health resources to respond to local and regional outbreaks.