EPA’s New PFAS Biosolids Risk Assessment: Understanding The Impact And Implications

EPA is slightly more than halfway through its public comment period for its PFAS biosolids risk assessment which ends on 17 March 2025. As 18 February 2025 it has exactly 9 comments including one asking for more time; the PFAS drinking water regulation had over 120,000 for comparison. Given the low levels of public engagement, I thought it may be beneficial to explore what biosolids are, how they’re used, what this risk assessment means and why all this matters, then finally my own comment and thoughts. It may help to check out other articles I’ve written on PFAS or wastewater. I am acting in my own capacity; my views are my own and do not represent my employer. Nothing here constitutes legal or professional advice; if you would like professional advice please contact me.

Biosolids Basics

Biosolids are what’s leftover after cleaning your poop. Until treated for safety, biosolids are just sewage sludge. In more technical terms, biosolids are organic leftovers from wastewater treatment that have undergone stabilization to reduce odor and pathogens as well as vector attraction. The term organic leftovers should trigger a thought that biosolids are mostly the result of biological processes which in this case is accurate.  That’s because, in the mildly contumelious words of a former teacher of mine, microbes work even cheaper than immigrants. As a former underpaid stranger in a strange land that hits hard.

Den lille Havfrue or The Little Mermaid Statue is a famous Copenhagen landmark, sitting just in front of Copenhill, the municipal waste incinerator to the back right. Image from Free Walking Tours.

She’s not quite a mermaid—see?—and she’s not quite human. She sits on land, where she has chosen to stay . . . and she stares eternally out to sea, homesick and forever lonely for what she left behind. She’s everybody who ever made a difficult choice. […] She doesn’t regret her choice, but she must pay for it; every choice must be paid for. The cost to her is not only endless homesickness. She can never be quite human; when she uses her dearly bought feet, every step is on sharp knives

Robert A. Heinlein, Stranger in a Strange Land

Brief Biosolids Use Cases

The term “biosolids” was first formally recognized in 1991 by the Water Environment Federation, however, have been used for hundreds of years and even have their own popular science promotional book. Biosolids historically have been used as fertilizer (“soil enrichment”) because of their high nitrogen and phosphorous content, for land reclamation either from the ocean or from erosion, and for restoring degraded areas such as mines. A more recent and modern use of biosolids is for biogas production. In 2014, Germany produced 3,050 GWh or enough to power about 305,000 homes (assuming 10,000 kwh per home), a city the size of Mannheim. Biosolids were one of the original pieces of a circular economy, which is a tremendous idea that helps shift waste from a cost center to a revenue driver making compliance a byproduct of maximizing value. I can’t express what a boon that would be for maintaining a clean environment, it’s simply indispensable to a sustainable future.

A city this size powered by poop, and only a fraction of Germany’s biosolids are used for anaerobic digestion and power production. Photo credit to Philip Koschel.

Biosolids Production

Every water treatment process produces residuals of some kind. Safe and cost-effective residuals management is one of the biggest challenges in every industry and wastewater is no exception. Solids are produced during primary treatment which is generally grit or things caught on a sieve, sometimes known as “screenings.” In secondary treatment, microbes eat the waste, technically called either dissolved or suspended solids depending on the wastes’ physical state; then these microbes and some settleable solids settle out in the primary clarifier. Biomass (microbes) also go to a secondary clarifier and can settle out there in the more quiescent water. Sometimes, tertiary treatment is required to meet environmental guidelines, this often involves chemical or physical treatment which can produce a different type of biosolids. Most biosolids are produced in the clarifiers. The additional biosolids from chemical precipitation are normally contained within either primary or secondary sludge. Tertiary filter backwash contains large volumes of water. Often this residuals stream is recycled through the liquid treatment processes to concentrate the biosolids. Ultimately, a single concentrated biosolids stream consisting of combined sludge is produced. Following wastewater treatment, the solids are then treated to stabilize the readily putrescible materials, reduce volume and destroy pathogens. The final biosolids composition primarily consists of microbial cells and biomass. In particulate form, this biomass contains around 40% carbs, 30% proteins, and 30% lipids. Biosolids can contain organic residues, as well as heavy metals like Ni, Pb, Cr, and Zn, alongside various hazardous pollutants including endocrine disruptors, insecticides, pharmaceuticals, and personal care products. Monitoring is normally required for heavy metals and pathogens but not the other potential hazards.

This handmade schematic shows simplified wastewater collection and treatment.

Biosolids Regulation in the USA

A heavily modified image generated by ideogram-v2 with the prompt “Create a modern infographic-style image titled ‘Biosolids Regulation in America.’ The design should feature a stylized U.S. map in the background and regulatory symbols (such as a scroll or law book) on top. Use a clean, professional color palette dominated by blues, greens, and whites, with subtle red accents. The overall style should be clear, informative, and suitable for a blog post about environmental policy and sustainable waste management.” Not quite right but good enough!

As mentioned, before treatment biosolids are sewage sludge. Treatments which transform sewage sludge into biosolids include anaerobic or aerobic digestion and composting, chemical processes such as lime treatment, and physical processes such as pasteurization, thermal hydrolysis, thermal drying, and air/solar drying. Biosolids are often categorized as “Class A″ or “Class B″ based on the extent of pathogen reduction achieved. The Clean Water Act Section 405(d) requires EPA to create regulations for sewage sludge disposal which are found in 40 CFR Part 503.  The Ocean Dumping Ban Act of 1988 did what its name suggests and banned ocean dumping in the United States after 1992 as well as requiring study of the 106-mile Dumpsite, so named because it lies 106 nautical miles southeast of New York Harbor.

Selected Worldwide Biosolids Regulations

In the European Union, the Sewage Sludge Directive (86/278/EEC) encourages sewage sludge use in agriculture whenever harmful effects on soil, vegetation, animals and humans are avoided. In the Netherlands, Switzerland, and South Korea, the biosolids use in agriculture is completely prohibited over concerns stemming from heavy metals, pathogens and organic pollutants. Here sewage sludge is incinerated or used as a component in cement. In Australia, there is no federal sewage sludge recycling and disposal regulation, and guidelines are set out on a state basis. In Brazil, as of 2014 only about 39% of wastewater is actually treated; federal legislation defines the criteria and procedures for biosolids use in agricultural areas through Resolution 375 from August 29th, 2006.

My first ever AI generated image! The prompt was: “A pair of hands lovingly letting biosolids run between the fingers in realistic, natural lighting” using a “photorealistic portrait” with “Juggernaut XL” on OpenArt.AI. I probably should have read the tutorials and guides first.

Biosolids Disposal

EPA requires Biosolids Annual Reports from larger wastewater treatment facilities and data can be accessed publicly through ECHO – Enforcement and Compliance History Online, one of EPA’s data warehouses. Biosolids reports come from roughly 2,500 larger facilities in the U.S in the 41 states where the EPA is the permitting authority. Nine states (Arizona, Idaho, Michigan, Ohio, Oklahoma, South Dakota, Texas, Utah, and Wisconsin) are authorized through the National Pollutant Discharge Elimination System (NPDES) Program to be the permitting authority for biosolids. Through phase 2 of the NPDES eRule, these 9 states should start electronically reporting biosolids data by December 2025. For 2022, EPA Managed: ~3.76 million dry metric tons (dmt) of sewage sludge; this compares with total generation of 292.4 million tons of municipal solid waste in 2018 or about 1% of total waste produced was biosolids.

From EPA’s Biosolids Annual Reports
  1. ~2.12 million dmt was land applied
    • ~1.17 million dmt was on agricultural land
    • ~39,000 dmt was used for reclamation
    • ~906,000 tons had other uses (home garden, landscaping, golf course etc.)
  2. ~600,000 dmt was incinerated
  3. ~1 million dmt was landfilled
    • ~895,000 dmt was disposed of in a municipal solid waste landfill
    • ~111,000 dmt was surface disposed in a monofil
  4. ~40,000 dmt were managed through other practices including deep well injection and storage

In the European Union About 37% of sewage sludge produced is applied to agricultural land, 12% is used for land reclamation and restoration, and 11% is incinerated. The rest is landfilled (mostly) or used for biogas (rarely).

How does PFAS get into Biosolids?

Traditional wastewater treatment does not really remove PFAS however, some PFAS does sorb to sewage sludge and in fact the protein content is currently the best known simple indicator of PFAS sorption for biosolids. Additionally, PFAS is contained in consumer products such as toilet paper, which winds up in biosolids. The dewatering process could also provide two avenues for PFAS to enter biosolids, it could leave behind some PFAS from the dewatering process itself and finally it provides opportunities for fluorinated precursors to biodegrade to PFOA or PFOS, which are terminal degradants. Examples of precursors to PFOS include perfluorooctane sulfonamidoethanol-based phosphate diester (sAmPAPs) containing carbon-chain moieties with at least eight fluorinated carbons, N-ethyl perfluorooctane sulfonamidoethanol (NEtFOSE), N-ethyl perfluorooctane sulfonamidoacetic acid (NEtFOSAA), perfluorooctane sulfonamidoethanol (FOSE), perfluorooctane sulfonamidoacetic acid (FOSAA), N-ethyl perfluorooctane sulfonamide (NEtFOSA), and perfluorooctanesulfonamide (PFOSA). Commonly detected precursors to PFOA include fluorotelomer alcohols (FTOHs), polyfluoroalkyl phosphoric acids (PAPs) and polyfluorinated iodides (PFIs) that contain a fluorinated carbon chain moiety with at least eight carbons in the chain (i.e., 8:2 FTOH). Sidechain fluorotelomer-based polymers (FTPs), especially those used on textiles, could also be significant sources of PFOA to wastewater treatment plants.

A soil washing facility in Australia courtesy of Enviro Wiki. The basic idea is to take PFAS out of soil and put it into water then treat the water; one of the treatment methods with the least potential for creating new unknown problems.

How large of a problem are PFAS in Biosolids?

We currently don’t know how big of a problem this is although EPA is trying to find out through its National Sewage Sludge Survey, which was last held in 2006. The National Sewage Sludge Survey is working in collaboration with the publicly owned treatment works (POTW) Influent PFAS Study and will focus on PFAS. The EPA collects biosolids annual reports from roughly 2,500 facilities in the 41 states where the EPA is the permitting authority.

Well we don’t really know but if you wanted to you could pick up this poster from Etsy for about $5

Final thoughts on PFAS in Biosolids

This brings us to the crux of the point; PFAS may be the final nail in the coffin for biosolids. Biosolids have a number of concerns historically related to endocrine disruptors, insecticides, pharmaceuticals, and personal care products but none of these are quite as pernicious as PFAS. None of these as anywhere near as stable as PFAS so applying them to a particular area at a set rate could eventually reach an equilibrium depending on application rate. With PFAS, because they essentially don’t degrade, the only way to reach an equilibrium is to stop the input. Some of the largest contaminated sites in Germany, Rastatt and Arnsberg, come from soil amendments. In Rastatt, over 1,200 hectares were contaminated. In Arnsberg illegal disposal of sewage sludge from paper industry in a biowaste mixture resulted in about 40,000 residents exposed to PFOA at 500-640 ng/L in drinking water which is 125-160x the legal limit in the United States. In general, a centralized source is much much easier to treat and model than diffuse sources such as spreading lots of contaminated soil everywhere. Even worse, PFAS can partition favorably onto and into plants creating a risk for whatever consumes those; even traditional biosolids use despite tight regulation still poses a risk. In this risk assessment, the EPA did not estimate risk associated with occasionally consuming products or drinking water impacted by land application of contaminated sewage sludge nor foods that come from a variety of sources ( e.g., milk from a grocery store that is sourced from many farms and mixed together before being bottled). Additionally, the majority of food produced in the U.S. is not grown on fields where sewage sludge is land applied. However, while true on a national scale, on a local scale this could be problematic, as the risk assessment identifies. Finally, sewage sludge monitoring based on EPA methods (e.g., EPA Method 1633) can be used to test for 40 PFAS but does not include precursors such as sAmPAPs and diPAPs. According to EPA’s risk assessment, several studies using soil columns and non-targeted analysis have found that most of the environmental loading to biosolids will come from these precursor chemicals.

Another AI generated image, I can’t quite tell what all the words on it are but it did identify heavy metals and nutrient runoff as other problems associated with biosolids application. Image from imagen-3.0-generate-002 with the prompt “create an image of PFAS being the final nail in the coffin of biosolids.” Thanks Google.

My Comment on the PFAS in Biosolids Risk Assessment

My comment on this risk assessment is that this risk assessment is based on credible well established and supported science and is a good initial step in recognizing the hazards PFAS can pose in biosolids. While diverting all sewage sludge to other means of disposal instead of beneficial reuse represents a large increase in total waste produced and will be more costly, it is easier to contain and treat centralized sources than diffuse sources. As this risk assessment points out, PFAS travel through the environment and have been found in areas with almost no human activity to include the blood of Greenlandic polar bears. This risk assessment fails in only taking PFOA and PFOS into account. While it does mention most of the environmental loading to biosolids comes from precursors, these precursors are not currently tested by EPA methods nor monitored by FDA in the food supply and since an updated National Sewage Sludge Survey isn’t out we don’t know the true extent of the problem posed. Given the difficulties in treating PFAS once in the environment, we need to rethink the biosolids program.

I used ideogram-v2 with the prompt “create an image of PFAS being the final nail in the coffin of biosolids.” The unique risks PFAS creates may well be the end of biosolids.

Conclusions

To me it is insane that photolithography can use extreme ultraviolet light to etch 3 and 5 nm process nodes onto silicon wafers but mankind’s first solution to waste would generally be recognizable to our Neanderthal ancestors, dig a hole dump it in shrug and walk away. While today’s landfills are a far cry from ancient midden heaps often with liners, leachate collection, and monitoring in place for gases, leachate, and leaks, the basic concept is the same which underpinned the Culleenamore shell middens. While land application of biosolids is a good example of the circular economy, it needs to be safe and it does not appear to be so. Biosolids disposal poses a significant challenge and PFAS just made it harder.

This high-NA extreme ultraviolet lithography system at an Intel facility in Hillsboro, Oregon costs roughly $380M which is roughly what a landfill the size of Monaco would cost. Photo from the Taipei Times.

Covid-19 Wastewater Update

Wastewater and public health potentials
Photo from Farkas, K., Hillary, L. S., Malham, S. K., McDonald, J. E., & Jones, D. L. (2020). Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19. Current Opinion in Environmental Science & Health.

Since my previous article on wastewater based epidemiology (WBE) for SARS-Cov-2 monitoring, there have been rapid developments. According to the World Health Organization’s 12 September 2020 update there have been over 28 million confirmed cases and 900,000 deaths worldwide making it a serious global pandemic. For comparison, last year about 1.7 million people acquired AIDS and 700,000 died. There is growing evidence that built environmental systems, particularly ventilation systems and residential plumbing systems, contribute to SARS-Cov-2 spread.

SARS-Cov-2 in the Gastrointestinal Track

The pooled SARS-Cov-2 viral RNA prevalence in stool samples from clinically confirmed cases is only estimated to be around 50% although estimates range from 15% to 84% in this meta-study and review. These studies unfortunately generally did not have many participants; between 9 and 4,243, with most studies having under 60 participants. Likewise, SARS-Cov-2 loads and viral RNA in fecal samples reported between 1,000 and 10,000,000 SARS-Cov-2 copies per fecal milliliter; one study had 153 participants, where only 44 participants (29%) had viral RNA present, while the other studies all had under 50 total participants.  That study indicated that there was, broadly speaking, a traceable general shedding pattern. During the initial SARS-Cov outbreak in 2002-2003 and MERS-Cov outbreak in 2012, viral RNA was still present in stool samples over 30 days after the illness. Similarly, patients with SARS-Cov-2 in their stool continued to shed RNA viral positive fecal samples after showing negative respiratory/nasopharyngeal samples. The estimated continued positive shedding duration and percentage still shedding varied greatly but reported means vary between 11 days and 5 weeks in 20% to greater than 70% of patients that had positive stool samples. There is limited evidence to suggest that viral RNA in stool comes from live infectious viruses instead of deactivated or destroyed viruses however, testing for the live virus is difficult to do and few people try. Most studies suggest that SARS-Cov-2 in urine is rare however, some studies report its presence past negative throat swabs.

Funny image
This guy has about a 50% chance of containing SARS-Cov-2 when excreted from an infected individual

SARS-Cov-2 in potable water distribution

It is extremely unlikely that SARS-Cov-2 can remain viable in potable water systems, especially in the US where 0.2 mg/L chlorine residual minimum must be at temporally farthest tap. While I could not find information on SARS-Cov-2’s survival in chlorinated water, other human coronaviruses are highly susceptible to chlorination. Likewise, I could not find information on SARS-Cov-2’s survival in non-chlorinated tap water which dominates Europe however, other human coronaviruses showed a three log removal (99.9% removal) at 23°C (73.4°F) in 10 days; at 4°C (39.2°F) human coronaviruses do not show a three log removal after greater 100 days. These results are not particularly helpful.  Cold inlet tap water’s temperature is normally 10-15.5°C (50-60°F) but can vary from 3.6-“jacuzzi temperature” 39°C (38.6- ≈100°F) in the United States (low value is Anchorage, Alaska and the high value is Death Valley, California). The temperature depends on several factors: water age, water source (surface or ground), season, processed water storage, pipe depth, and ambient air temperature. In aggregate however, I cannot derive a scenario where SARS-Cov-2 would proliferate enough in potable water systems to make someone sick through showering for instance.

SARS-Cov-2 in sewers

Similar to potable water, I was unable to find information specific to SARS-Cov-2 however, information on other human coronaviruses is available. Other human coronaviruses die rapidly in wastewater with three log removal (99.9%) occurring between 2 and 4 days for all temperatures. I do not believe there is a general standard time for sewage to reach treatment plants however, most sewers are designed with a self-cleaning velocity that should be reached daily (between 0.6 m/s and 1 m/s mainly dependent on specific gravity and pipe diameter) and are generally capped at 3 m/s during max flow to prevent erosion. Rochester, NY takes about 24 hours for sewage to reach its treatment facilities which is normal and a decent average proxy. All reputable sources agree that standard wastewater treatment processes, which are designed for virus and bacteria inactivation among other things, inactivate SARS-Cov-2. Likewise, dilution occurs in sewers which should increase the minimum infective dose by lowering the virus’ concentration.

SARS-Cov-2 in residential plumbing

Sewers, unlike potable water, are not generally pressurized and are ventilated to eliminate smells. This little distinction is critical.  Circumstantial evidence reported in the Annals of Internal Medicine indicated that 9 people became sick with SARS-Cov-2 from fecal aerosols. This is not the first time that a respiratory disease has been tied to sewage waste vents. The 2003 SARS outbreak at Amoy Gardens in Hong Kong was implicated in 321 cases and 43 deaths. During China’s ultra-strict lockdown, Kang complied camera footage indicating no contact between the sick apartment members and the newly infected group who lived on different floors. Among more than 200 air and surface samples collected, the only ones testing positive for SARS-CoV-2 came from the 15th floor family’s apartment and a vacant apartment’s bathroom on the 16th floor directly above. Tracer gas piped into the 15th floor apartment’s drainpipe exited in the 25th and 27th floor apartment bathrooms. Generally, there is a plumbing “trap” (shaped like a U or P) that has water in it to block smells from rising. These however, can dry out leaving a transmission route for disease. Drying out can occur from non-use or air pressure surges. The ethane tracer gas presence indicates that these traps dried out. Contact tracing and other standard causal patterns did not reveal leads. One team member on Kang’s study indicated that there could also be three other outbreak incidents related to waste vent gases. However, while compelling, there is no iron clad evidence and it is possible the disease was contracted elsewhere. Mechanical bathroom exhaust fans and outdoor air conditions can lead to a favorable environment for SARS-Cov-2 to spread through bathroom exhaust. There should be appropriate caution reading these findings. Many factors must fall into place for this kind of residential transmission. For instance, the proposed transmission route relies on viral infectivity in fecal droplets and aerosols. However, building wastewater systems are a potential reservoir for many other viruses and bacteria, even in the absence of SARS-CoV-2.

SARS-Cov-2 in toilets

Virus-containing fecal aerosols can be produced during toilet flushing after index patient use. These bioaerosols can settle onto surfaces and remain infective. There was a case where a South Korean woman most likely contracted Covid-19 from an airplane toilet. She self-quarantined in complete isolation for three weeks before the flight, did not use public transport to get to the airport, wore an N-95 mask for the entire flight except a visit to the bathroom, all passengers sat two meters (six feet) from each other during boarding, and quarantined for two weeks by South Korean officials on landing. The one asymptomatic sick passenger on the plane used the toilet before her. The most likely transmission route was encountering contaminate surfaces because the airplane used high-efficiency particulate arresting systems. According to Dr. Joseph Allen from Harvard’s T.H. Chan School of Public Health, about 1,000,000 additional particles per air cubic meter are generated when a toilet is flushed with the lid up. These particles can settle on surfaces or linger in the air until someone breaths them in.

Protecting yourself

There are some easy common-sense protective measures you can take to protect yourself. Ensure bathrooms you use are well ventilated, turn on an exhaust fan when entering a bathroom and leave it on when you leave. Make sure the P or U trap isn’t dried out; a bad smell indicates a dry trap. Close the lid when flushing the toilet to help prevent bioaerosols from spreading. Clean and disinfect bathroom surfaces. Most importantly, wash your hands when leaving the bathroom, then try and use a paper towel to touch surfaces including the door handle on your way out.

Potential WBE Advances

To date SARS-Cov-2 Wastewater Based Epidemiology (WBE) relies on the same analytical platforms used in clinical diagnostic testing (eg PCR or antigen testing). WBE does not need to be limited to the monitoring the infectious agent’s nucleic acid or antigens. WBE could target endogenous biomarkers that are significantly elevated in diseased states. This could reduce analytical costs and broaden availability (through immunoassays) or better serving as leading infection indicators (earlier alerts). Urine (as opposed to fecal) biomarkers would also simplify sampling and sample preparation. Since Covid-19 can cause extensive inflammatory damage, biomarker for systemic oxidative stress such as the prostaglandin-like class of substances called isoprostanes are currently being proposed. These biomarkers may be more universally excreted among infected individuals, better track the infection severity, have tighter per-capita excretion ranges (allowing for better case count calibration and estimation), and avoiding a potential under-appreciated problem with using PCR, where RNA fragments may not be originating from viable virus, but rather from virus remnants (litter) from cleared infections. That last issue could overestimate infection incidence or intensity. It is also speculated that patient repeat infection reports are caused by this.

WBE could also be used to test hypotheses involving correlating various community-wide population demographics with the magnitude and duration of SARS-CoV-2 measurements to probe inter-community disparities such as race, culture, income, healthcare availability, and occupation. WBE data could also be examined for correlations with drug manufacturer geographic prescribing data — notably for drugs suspected to improve or exacerbate Covid-19 therapeutic outcomes. WBE could also determine which SARS-CoV-2 subtypes dominate in given populations.

WBE Other Shortcomings

In addition to the difficulties I outlined in my first article on WBE, I have learned about some additional difficulties. Population size estimations are difficult because populations fluctuate due to travel and commuters. The standard approach to this is to measure certain endogenous biomarkers such as cortisol or cotinine then calculate those as daily loads normalized to population sizes. However, some unique population fluctuations have negligible catchment impacts leading to higher uncertainties in smaller populations. Other standard population estimating wastewater parameters used such as Chemical Oxygen Demand, Biochemical Oxygen Demand, or ammonia can reduce uncertainties but can be strongly influenced by the wastewater’s composition. Another is that biomarkers must be relatively stable not only in the sewer system but also through the sampling and storage processes.

Another shortcoming is wastewater itself makes it extremely difficult to extract and quantify biomarkers and chemicals. PCR inhibitors include fats and proteins, as well as humic and fulvic acids. New digital PCR techniques use Poisson distributions, via partitioning samples into reaction wells to lessen these effects.

Previously Unmentioned Successes

WBE can distinguish differences between prescription and consumption of a pharmaceutical. Investigating parent compounds to metabolites ratios or ratios between compound enantiomers in wastewater can distinguish human excretion from direct pharmaceutical disposal in sewers. This distinction ability is important because prescriptions do not necessarily correlate to use. Delayed prescribing is a strategy where doctors prescriptions available but ask patients to delay using them to see if symptoms improve. These initiative successfully reduced antibiotic use in New Zealand, Norway and England; WBE can distinguish how many antibiotics were actually used as opposed to prescribed.

WBE can minimize the tests required to uncover positive cases. Clinical tests need to continually increase test coverage. The ratio between tests required to uncover a single case and total tests is generally the most direct infection extent indicator. A low ratio (when using random sampling) points to a high incidence of infection and therefore the need for more intensive testing until the ratio significantly increases (where increasing testing amounts are required to confirm additional cases). This indicates increasing success in containment or mitigation measures. However, diagnostic tests are never intended for mass surveillance. The tests are generally time-consuming and costly as well as exposing the test administrator. There are two alternatives: increase conventional testing or minimize the tests required to reveal positive cases. Pooled testing procedures increases testing capacity and throughput, especially for PCRs. Pre-targeting subpopulations can help with minimizing the rests required as well. These methods conserve diagnostic tests. Using WBE then can be akin to using a forward observer to improve artillery’s accuracy. This would greatly reduce the demand for diagnostic testing and reduce supply-chain shortages caused by insufficient manufacturing capacity. The metric of success for WBE when used for targeting the use of clinical diagnostic testing would be lower ratios for “Tests Administered” per “Case Confirmed” (counter intuitively, maximize the positivity test rate).

WBE may also be the only way to infer the uninfected population as well as provide perspective on how well diagnostic testing reflects the total population.

Corrections to Previous Article

In my previous article, I mentioned that WBE started around 2001. In the 1980s, Finland, Israel, and Senegal all successfully analyzed sewage samples to assess circulating polio.

Conclusions

You can probably catch Covid-19 from public toilets and in star-crossed circumstances from your neighbor’s toilet. WBE research is developing but remains much more difficult than analyzing for chemicals such as illegal drugs because there are differences in viral shedding patterns, total shedding, viral attenuation during sewer travel, and determining statistically representative sampling. Even in other applications, matrix separations pose difficulties for WBE.  WBE is still an effective epidemiology tool to rapidly monitor disease spread and trends, especially when paired with other contemporary measures. The preponderance of evidence suggests that CoVs are less stable in the environment than other enteric viruses. Water recycling guidelines may have to be revised in light of emergent diseases and viral shedding into sewer systems. Effective surveillance systems are key for the rapid intervention and infectious disease control. WBE is the most effective and cheap near real-time tool available to communities.

Further Reading

  • IWA’s Information resources on water and COVID-19
  • Chan, K. H., Poon, L. L., Cheng, V. C. C., Guan, Y., Hung, I. F. N., Kong, J., … & Peiris, J. S. M. (2004). Detection of SARS coronavirus in patients with suspected SARS. Emerging infectious diseases10(2), 294.
  • Cha, S., & Smith, J. (2020). Explainer: South Korean findings suggest ‘reinfected’ coronavirus cases are false positives. Reuters.
  • Cheung, K. S., Hung, I. F., Chan, P. P., Lung, K. C., Tso, E., Liu, R., … & Yip, C. C. (2020). Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis. Gastroenterology. https://doi.org/10.1053/j.gastro.2020.03.065
  • Foladori, P., Cutrupi, F., Segata, N., Manara, S., Pinto, F., Malpei, F., … & La Rosa, G. (2020). SARS-CoV-2 from faeces to wastewater treatment: What do we know? A review. Science of the Total Environment743, 140444. https://doi.org/10.1016/j.scitotenv.2020.140444
  • Gundy, P. M., Gerba, C. P., & Pepper, I. L. (2009). Survival of coronaviruses in water and wastewater. Food and Environmental Virology1(1), 10.
  • Heller, L., Mota, C. R., & Greco, D. B. (2020). COVID-19 faecal-oral transmission: Are we asking the right questions?. Science of The Total Environment, 138919.
  • Hovi, T., Shulman, L. M., Van Der Avoort, H., Deshpande, J., Roivainen, M., & De Gourville, E. M. (2012). Role of environmental poliovirus surveillance in global polio eradication and beyond. Epidemiology & Infection140(1), 1-13.
  • Kaiser, Jocelyn (2020) Can you catch COVID-19 from your neighbor’s toilet? Science Magazine
  • O’Brien, J. W., Choi, P. M., Li, J., Thai, P. K., Jiang, G., Tscharke, B. J., … & Thomas, K. V. (2019). Evaluating the stability of three oxidative stress biomarkers under sewer conditions and potential impact for use in wastewater-based epidemiology. Water research, 166, 115068.
  • Petrie, B., Youdan, J., Barden, R., & Kasprzyk-Hordern, B. (2016). New framework to diagnose the direct disposal of prescribed drugs in wastewater–a case study of the antidepressant fluoxetine. Environmental Science & Technology, 50(7), 3781-3789.
  • Wolfel, R., Corman, V. M., Guggemos, W., Seilmaier, M., Zange, S., Müller, M. A., … & Hoelscher, M. (2020). Virological assessment of hospitalized cases of coronavirus disease 2019. Nature. https://doi. org/10.1038/s41586-020-2196-x.
  • Wu, Y., Guo, C., Tang, L., Hong, Z., Zhou, J., Dong, X., … & Kuang, L. (2020). Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. The lancet Gastroenterology & hepatology5(5), 434-435. https://doi.org/10.1016/S2468-1253(20)30083-2

Wastewater and Covid-19 Surveillance

Screenshot of Biobot report
Report from Biobot on Livingston County, MI on Covid-19 from wastewater

Covid-19 is currently a hot topic, environmental health and engineering is no exception. Wastewater is now in international news because of it! This Reuters article from 19 June 2020 for example shows that researchers found RNA from Covid-19 in Milan and Turin’s wastewater in December 2019 before China reported the first cases on 31 December 2019! The Italian National Institutes of Health examined 40 sewage samples collected in northern Italy between October 2019 and February 2020 and found that samples in Milan and Turin from 18 December 2019 showed SARS-Cov-2. Monitoring sewage for health purposes is known as “wastewater-based epidemiology” (WBE).

Early WBE

Using wastewater to track populations is not a new idea. It was first proposed by Christian Daughton in 2001 to track illicit drug use. You can read his paper here. As a former wastewater teacher of mine, COL Timmes, liked to say: “everyone passes through us.” Generally, he meant that you can’t easily hide from the central sewage system. In more polite terms raw wastewater is a reservoir of excretion products such as: parent compounds, metabolites, and genetic material. The earliest widespread use of WBE (then called “sewage epidemiology”) was in 2005 to monitor for illicit drugs which you can find here. After this early case WBE gained traction. At least Australia, Belgium, Germany, Ireland, Italy, the Netherlands, Norway, Spain, South Korea, the United Kingdom, and the United States use WBE to monitor illicit drug use. After this initial use WBE started to take off in public health circles and WBE started to be used to track broader chemical public health indicators, for instance alcohol consumption in Norway, counterfeit medicine distribution in the Netherlands, and even tobacco use in Italy.

Environmental engineers and public health officials eventually realized that any excreted substance that has known kinetic pathways in wastewater could be used to reverse engineer the initial concentration. All these early methods focused on chemicals and were based around mass spectrometry. WBE was then and is still used to study exposure to chemicals or pollutants such as pesticides, herbicides, and flame retardants. After the sewer’s viability as a surveillance network was established, someone around 2008 realized with some work they could use quantitative polymerase chain reaction methods (qPCR) to amplify, detect, and quantify genetic material.

WBE basics

WBE’s popularity continues to increase because exclusive reliance on testing of individuals is slow, costly, and generally impractical. WBE also often serves as a disease early warning indicator because asymptomatic or prodromal individuals typically don’t get tested and there may be underdiagnosis. In cases like this WBE serves as an unbiased community prevalence estimator. This is especially true with Covid-19 whose asymptomatic period is about a fortnight. Ultimately, WBE allows near real-time cheap monitoring of health indicators such as obesity, diabetes, drug use, microbial antibiotic resistance, and disease outbreak. Its use in disease outbreaks offers particularly rich data on genetic diversity of outbreaks and phylogenic analysis can reveal viral ancestry.

In Australia, the University of Queensland has been linking census data to wastewater samples across the country to see the interrelationship between wastewater chemicals and social and economic measures of a population. Doing that opened the study of socioeconomic influences on chemical consumption. This study showed that caffeine consumption is associated with aspects of financial capability and educational attainment in Australia for instance.

WBE success

WBE is successful in sentinel surveillance providing early outbreak warnings and in determining the efficacy of public health interventions. It is remarkably sensitive at picking up infections and viral load in wastewater. For polio for instance, WBE sensitivity is estimated at about 1 case per 10,000 uninfected people. WBE also allows spatial sensitivity by moving “upstream.” WBE can detect variations in circulating strains through phylogenic analysis allowing for comparisons between region and viral genomic evolution. Another important benefit of WBE is that it enables disease prevalence gauging by circumventing individual stigmatization which can arrive from clinical diagnosis (early AIDS research for instance).

SARS-Cov-2 Simplified WBE Procedure

In general all WBE follows the same process: pretreatment, concentration, recovery, secondary concentration, then detection. Detection normally means either molecular analysis or traditional culturing. In an International Water Association (IWA) webinar on 19 June 2020 Charles Gerba, an environmental microbiologist at the Water, Energy, and Sustainable Technology Center (WEST) in the University of Arizona provided an outline of how they were testing:

  • Gather a 500 mL to 1 L sample of wastewater (grab or composite was not specified)
  • Take a 100-250 mL aliquot to process
  • Spike some samples with 229E to test efficiency
  • Store at -80°C for future analysis
  • Centrifuge to remove solids because some virus are lost to solids – in general about 100 mL would spin down to 1-3 mL
  • RT-qPCR: biomarkers (gene targets) N1, N2, N3, E229. Normally N2 and E229 are used to ensure the signal is specific enough. N1 and N3 are typically dropped

Difficulties in WBE Interpretation

WBE sounds amazing and it truly is. It has already been used successfully to track public health threats from polio to alcohol and all these achievements for a field under 20 years old. Its full potential isn’t even near realized at this point. However, there are several issues in the field. The largest is the lack of standardization and inability to compare results between testing facilities. These two factors are intrinsically linked but one will not necessarily solve the other. Another set of issues revolve around tying total loads to population numbers.

Difficulties with standardization

WBE is still a new field. It has not decided upon standards for many common procedures yet. For instance, some areas preform pre-process techniques to lower the risk of catching Covid-19 from working with SARS-Cov-2. Different pre-processing techniques such as pasteurization or filtration, will produce different signal drops.

Even the sample collection is very different. In wastewater there are typically two kinds of sampling: grab and composite. Grab sampling reflects a discrete point in time and space; composite sampling essentially is several grab samples pooled together at regular time or spatial intervals. Composite sampling is the most common in wastewater because varying flow patterns cause hydraulic surges followed by intermittent periods of low to no flow. However, that does not necessarily make it the best method for WBE.

The solids amount in the wastewater can also reduce efficacy of RT-qPCR methods; what phase to analyze (particulate or liquid) can affect results. Likewise, different inhibitors used for sample shipment may reduce the signal strength. The specific method chosen as a standard unfortunately must consider cost as well as effectiveness and test time. Likewise decontamination procedures between tests must be considered.

Difficulties with linking viral loads to population cases

Sewers undergo infiltration and inflow (i/i). Infiltration is where groundwater enters the sewer system through joints or breaks, inflow is where water is channeled into a sewer from various sources into the sewer such as downspouts. Without getting too deep, there are combined, separate, and merged sewer systems referring to surface runoff or sewage removal. Most large cities have merged systems were sewers were initially built as combined but started providing separate runoff and sewage systems. In short, a remote lab won’t necessarily have the proper infrastructural or weather contextualization to interpret the RNA signal in testing.

Another significant hurdle for disease monitoring is figuring out each disease’s excretion pattern. While it may seem reasonable that a greater number of sick people or sicker people excrete a higher viral load this is not always the case. Extrapolating the viral load to clinical cases becomes complicated. If the disease already has a well known viral shedding pattern and spread pattern with significant effort based, on where in the outbreak a disease is, you can get a correlation however it would be predicated upon many assumptions. For diseases with well defined correlations between degree of illness and viral shedding combined with disease transmission knowledge it is not possible to distinguish between one moderately sick person and two or more asymptomatic people with any degree of precision. With novel diseases only trend analysis is possible. Given the unknowns around viral shedding it becomes difficult to determine how the RNA signal drop corresponds with prevalence drops in the local community. It also becomes difficult to determine how strong the signal change needs to be to differentiate from statistical noise.

Correlating viral loads with clinically identified cases becomes even more challenging because of variable excretion rates during the infection, temporal delays, inconsistent spatial variability due to travel leading to use of multiple wastewater treatment systems, i/i, inactivation during transport, or infrequent, absent or inadequate clinical testing. Genomic instability in wastewater, sampling variability (grab/composite), and viral concentration efficiency differences compound these problems.

Where the sample was taken from, for instance from the sewage network or treatment plant, is also believed to effect viral recovery making comparisons difficult. The type of upstream user, for example domestic or industrial, will make a large difference as well. Areas with more septic systems then become harder to check. Likewise there is a divide between smaller more rural populations and larger cities; cities tend to create more normalization and may not necessarily be compared to their rural counterparts.

Practical difficulties with WBE

The best monitoring schedule at what frequency and spatial resolutions remain open questions which most likely vary across diseases. Likewise, who pays for the monitoring is an important consideration. Currently, WEST’s price list is between $350 and $1,250 per sample depending on how exactly they perform and analyze the sample. The quantification level can be tricky as well since most PCR techniques were developed for the clinical setting instead of an environmental one. There is also a privacy issue with this sort of monitoring.

Conclusions

WBE is an amazing tool for disease monitoring but is better suited to looking at trends because direct comparisons across catchments remains elusive. Since some aspects rely on data individual to specific catchments (recent precipitation, sewer condition, length of sewer and viral decay in sewer transport etc…) direct comparisons between viral loads may never really be achieved.

Further Resources

US EPA on Coronavirus in water and wastewater

Research Centers:

Papers:

  • Kitajima, M., Ahmed, W., Bibby, K., Carducci, A., Gerba, C. P., Hamilton, K. A., … & Rose, J. B. (2020). SARS-CoV-2 in wastewater: State of the knowledge and research needs. Science of The Total Environment, 139076
  • Nemudryi, A., Nemudraia, A., Surya, K., Wiegand, T., Buyukyoruk, M., Wilkinson, R., & Wiedenheft, B. (2020). Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater. medRxiv : the preprint server for health sciences, 2020.04.15.20066746
  • Venugopal, Anila, Harsha Ganesan, Suresh Selvapuram Sudalaimuthu Raja, Vivekanandhan Govindasamy, Manimekalan Arunachalam, Arul Narayanasamy, Palanisamy Sivaprakash et al. “Novel Wastewater Surveillance Strategy for Early Detection of COVID–19 Hotspots.” Current Opinion in Environmental Science & Health (2020)
  • Ahmed, W., Angel, N., Edson, J., Bibby, K., Bivins, A., O’Brien, J. W., … & Tscharke, B. (2020). First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community. Science of The Total Environment, 138764
  • Gracia-Lor, E., Castiglioni, S., Bade, R., Been, F., Castrignanò, E., Covaci, A., … & Lai, F. Y. (2017). Measuring biomarkers in wastewater as a new source of epidemiological information: Current state and future perspectives. Environment international, 99, 131-150
  • Xagoraraki, I., & O’Brien, E. (2020). Wastewater-based epidemiology for early detection of viral outbreaks. In Women in Water Quality (pp. 75-97). Springer, Cham
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