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.


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.
  • 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.
  • 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.

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