Topic 1 Protocol to test sewage for early warnings about COVID-19

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  • Carol McCreary
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Hi Members of Working Group 6

PHLUSH has been tracking this methodology at a distance. I am happy to share our resource list on Wastewater-based Epidemiology.  

In our region, the City of Albany, Oregon and Clean Water Services, which manages WWTPs for Washington County, Oregon are partnered with BioBot and a participating laboratory at Oregon State University in Corvallis. 
 
Carol

2020 List - Wastewater-based Epidemiology for COVID-19
Also known as SCIM (Sewage Chemical-Information Mining), Environmental Wastewater Virus Detection, sewer monitoring, sewer surveillance, and simply wastewater epidemiology.  Update of 5/18

Sections (please suggest changes)
  1. Academic (peer-reviewed; pre-COVID-19; some marked Background) 
  2. Academic (Current non-peer-reviewed, preprints, viewpoints, and news)
  3. Investigative (details, links, names of labs and researchers etc)
  4. Popular overviews  (Science writing, local reports, videos, useful for advocacy etc)
1. Academic (peer-reviewed; pre-COVID-19 marked Background) 

https://reader.elsevier.com/reader/sd/pii/S0048969720323925?token=C0480AE2B601A83A156DA1B7CFA0374DFE7B81BF20C5B7997DD65A24A4D23FA3034A0B1F95F073D3E505A3240278A6E5   Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility,economy, opportunities and challenges Olga E.Harta, a, Rolf U.Haldena,b,c,  In Science of the Total Environment, 730 (2020) 138875. April 22, 2020. Free Download.a Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, AZ 85287-8101, USA b OneWaterOneHealth, Arizona State University Foundation, 1001 S. McAllister Avenue, Tempe, AZ 85287-8101, USA c AquaVitas, LLC, 9260 E. Raintree Dr., Ste 140, Scottsdale, AZ 85260, U  HIGHLIGHTS Wastewater was computationally examined as a matrix for detection of SARS-CoV-2. One infected individual theoretically is detectable among 100 to 2,000,000 persons. Temperature and in-sewer travel time severely impact virus detectability.  2.1 billion people could be monitored globally in 105,600 sewage treatment plants.Combined use of WBE followed by clinical testing could save billions of US dollars. 5/5

https://www.medrxiv.org/content/10.1101/2020.04.05.20051540v1
SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. Fuqing Wu, Amy Xiao, Jianbo Zhang, Xiaoqiong Gu, Wei Lin Lee, Kathryn Kauffman, William Hanage, Mariana Matus, Newsha Ghaeli, Noriko Endo, Claire Duvallet, Katya Moniz, Timothy Erickson, Peter Chai, Janelle Thompson, Eric Almdoi: https://doi.org/10.1101/2020.04.05.20051540 This article is a preprint and has not been peer-reviewed.. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice. 5/7

https://reader.elsevier.com/reader/sd/pii/S0048969717331601?token=8E976E4E4E86FF3C842807AAE5A8C8670DF18125EABFA33B70E7B4B82C275D2E20CA252A376AABBF7564DD77F45A2784
Monitoring wastewater for assessing community health: Sewage Chemical-Information Mining (SCIM).  Christian G.Daughton Journal of Science of the Total Environment. 2018. Open Source. Downloadable. This nascent approach can be referred to as Sewage Chemical-Information Mining (SCIM) and involves the monitoring of sewage for the information that resides in the form of natural and anthropogenic chemicals that enter sewers as a result of the everyday actions, activities, and behaviors of humans. 5/5

https://pubs.acs.org/doi/10.1021/acs.est.6b04846
Aerosolization of Ebola Virus Surrogates in Wastewater Systems. Kaisen Lin, Linsey C. Marr. Environ. Sci. Technol. 51, 5, 2669-2675. Publication Date (Web):January 26, 2017 Background. Free pdf. This paper investigated the potential for aerosolization of viruses from wastewater collection systems such as toilet flushing, sewer systems, and wastewater treatment plants. The emission rates of two viruses, the non-enveloped single stranded RNA bacteriophage MS2, and enveloped double-stranded RNA bacteriophage Phi6, were determined in a flushing toilet, a lab-scale aeration basin, and a lab-scale sewer model of converging pipes. The results showed aerosolization can occur to varying extents in the different systems. Flushing toilets did generate aerosols, but in low amounts. Aerosolization from an aeration basin resulted in viable virus being released, as did the converging flows from a small-scale sewer system. The researchers concluded for a specific virus, the amount of virus aerosolized should depend on its concentration in wastewater, and that while aerosolization from toilets appeared to present a low risk, aerosolization from sewer systems and wastewater treatment plants may be of concern if an infectious virus is present. 5/7

https://pubs.acs.org/doi/pdf/10.1021/acs.est.6b00876?ref=vi_coronavirus-survival-behavior
 Survivability, Partitioning, and Recovery of Enveloped Viruses in Untreated Municipal Wastewater. Yinyin Ye, Robert M. Ellenberg, Katherine E. Graham, and Krista R. WiggintonEnviron. Sci. Technol. 50, 10, 5077-5085  April 25, 2016.  9pg. Free pdf. Background The genes of enveloped viruses such as coronaviruses have been detected in the feces of infected individuals and in wastewater biosolids, but the survival of enveloped viruses is largely unknown. Investigating the longevity of human-enveloped viruses in human excrement is therefore an important area of research. This paper investigated the inactivation rates of human enveloped virus surrogates mouse coronavirus MHV and bacteriophage Φ6 and two non-enveloped bacteriophages in pasteurized and non-pasteurized wastewater. The paper describes methods to preserve, extract and concentrate enveloped and non-enveloped viruses from wastewaters and solid wastes in order to study their persistence and inactivation times in these matrices. 

https://pubs.acs.org/doi/pdf/10.1021/acs.est.7b01296?ref=vi_coronavirus-survival-behavior
 Evaluation of Phi6 Persistence and Suitability as an Enveloped Virus Surrogate, Nathalia Aquino de Carvalho, Elyse N. Stachler, Nicole Cimabue, Kyle Bibby. Environ. Sci. Technol. 51, 15, 8692-8700. June 28, 2017. Free pdf. Background. There is mounting evidence that human-enveloped viruses, including members of the Coronavirus family SARS and MERS, can survive in the urban water cycle following release from infectious patient waste, ranging from a few hours to months depending on the environmental conditions. This study highlights the variability in survival and persistence of an enveloped bacteriophage Phi6, a human coronavirus surrogate, under aqueous conditions. The study confirmed that the enveloped phage, Phi6, displayed different persistence behavior in aqueous environmental samples depending on the temperature, biological activity and aqueous media composition. The study highlights the value of working with the virus of interest for environmental persistence studies due to the high variability in survivability in different environments.

2. Academic (Current non-peer-reviewed, preprints, viewpoints, and news)

https://www.eawag.ch/en/news-agenda/news-portal/news-detail/tracking-the-course-of-the-pandemic-in-wastewater/   Tracking the course of the pandemic in wastewater. Eawag (blog post) April 30, 2020.  Researchers at EPFL and Eawag are now working to optimise the methodology to develop a system which could warn of a resurgence of cases earlier than clinical diagnostic tests.

https://www.medrxiv.org/content/10.1101/2020.04.05.20051540v1
  SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases  Fuqing Wu, Amy Xiao, Jianbo Zhang, Xiaoqiong Gu, Wei Lin Lee, Kathryn Kauffman, William Hanage, Mariana Matus, Newsha Ghaeli, Noriko Endo, Claire Duvallet, Katya Moniz, Timothy Erickson, Peter Chai, Janelle Thompson, Eric Alm doi: https://doi.org/10.1101/2020.04.05.20051540   Preprint Non-peer-reviewed We tested wastewater collected at a major urban treatment facility in Massachusetts and found the presence of SARS-CoV-2 at high titers in the period from March 18 - 25 using RT-qPCR. We then confirmed the identity of the PCR product by direct DNA sequencing. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of March 25. The reason for the discrepancy is not yet clear, however, and until further experiments are complete, these data do not necessarily indicate that clinical estimates are incorrect. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. 5/7

https://www.medrxiv.org/content/10.1101/2020.04.12.20062679v1
. Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases.Sebastien Wurtzer, Vincent Marechal, Jean-Marie Mouchel, View ORCID ProfileLaurent Moulindoi: https://doi.org/10.1101/2020.04.12.20062679 . Preprint. Non peer-reviewed 5/5

https://pubs.acs.org/doi/10.1021/acs.est.0c01102?ref=pdf An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19) Guangbo Qu, Xiangdong Li Ligang, Hu Guibin Jiang. Environ. Sci. Technol. 54, 7, 3730-3732. March 23, 2020.  Non-peer reviewed. This just-published viewpoint examines the interdisciplinary research needed to understand the complex interplays of environmental factors influencing the survival, transmission and severity of human responses to novel infectious diseases, with a call for urgent, multi-disciplinary, collaborative research efforts. 5/7
https://pubs.acs.org/doi/pdf/10.1021/acs.est.0c01174?ref=vi_coronavirus-survival-behavior  Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?Kang MaoHua Zhang, Zhugen Yang. Environ. Sci. Technol. 54, 7, 3733-3735. March 23, 2020.3pg  Free pdf. Non-peer reviewed.  This just-published viewpoint describes a novel approach to overcoming the current logistical challenge of rapid and effective screening of mass numbers of the population to determine numbers of infected individuals. Using a multi-faceted paper-based screening tool, the presence of a virus can be detected in wastewaters to provide rapid and real-time community infection statistics, aiding the quick and effective implementation of quarantine measures at the local scale. 5/7

https://news.umich.edu/a-sewage-surveillance-effort-to-track-covid-19/
A sewage surveillance effort to track COVID-19. March 26, 2020. Contact is  Nicole Casal Moore This email address is being protected from spambots. You need JavaScript enabled to view it..  With a rapid response grant from the National Science Foundation, a research team from the University of Michigan and Stanford University is exploring this and other questions about how the novel coronavirus behaves and moves through the environment. Project leader is Krista Wigginton, associate professor of civil and environmental engineering at U-M and currently a visiting professor at Stanford. 5/7

3. Investigative (details, links, names of labs and researchers etc)

https://www.politico.com/news/2020/05/01/cdc-human-waste-coronavirus-222253?mc_cid=ce9fe77808&mc_eid=322767800e   Poop could help stop the pandemic. Really.  By Betsey Woodruff Swan, Daniel Lippman and Annie Snider.  Politico. May 1, 2020.  Monitoring wastewater for the presence of the RNA as a marker for whether or not COVID-19 in the community is a practice that’s been done for decades to look for reemergence of polio viruses in parts of the world where polio has been eradicated. In the U.S., it has been used more recently to track opioid use within communities. A spokesperson for the CDC confirmed that the agency is eyeing wastewater as part of its response to the pandemic, though it is not yet doing so. EPA is currently coordinating sewage sampling and storage protocols with CDC to start sewage surveillance of SARS-CoV-2 with wastewater utilities in multiple cities with a high number of current confirmed cases.  Another example is Clean Water Services, a wastewater utility serving the suburbs west of Portland, Ore. Mark Jockers, head of government and public affairs for the utility, said the utility is working with the startup Biobot to collect and analyze samples with its primary interest being “to track the relative increase or decrease of evidence of COVID-19 in the samples over time.” His utility is also working with researchers at Oregon State University to do finer-scale sampling in hopes of tracking the virus at specific sources like schools, hospitals and retirement homes.

https://www.eenews.net/stories/1063065235
  How sewage reveals 'real numbers' on scale of outbreak. Tamara Ward, E&E News (Essential news for energy and environment professionals). Wednesday, May 6, 2020. To measure the scope of the outbreak, BioBot sends sampling kits and collection protocols to wastewater facilities. MIT's Alm Lab tests the samples to detect the virus, and Biobot communicates the results back to participating communities. Since launching the national campaign in March, Biobot now has over 150 wastewater treatment plants participating and is testing about 10% of the U.S. population on a weekly basis.  HRSD Virginia Beach launched a SARS-CoV-2 water surveillance campaign on March 9 to assist local public health officials in determining the "true illness burden."  HRSD calculates the total load of the genetic material from the virus in wastewater, divided by the amount of the virus normally excreted in the stool of one infected person.  EPA research focuses on understanding viral loads, how much of the virus is present, whether it is in an infectious state and how it moves through wastewater systems.  As for the CDC, environmental microbiologist Amy Kirby said the agency is exploring the methodology.

https://www.epa.gov/newsreleases/epa-expands-research-covid-19-environment EPA Expands Research on COVID-19 in the Environment April 20, 2020  EPA Administrator Andrew Wheeler is asking for a rapid review with the Science Advisory Board (SAB) to provide feedback on research needs identified by EPA’s researchers. This research will enhance and build on the Agency’s capabilities to address the environmental and human health impacts from the virus that causes COVID-19. Environmental Wastewater Virus Detection: The researchers are studying whether SARS-CoV-2 can be detected in wastewater at levels that could inform public health strategies. They will focus on understanding viral loads, or how much of the virus is present, whether it is in an infectious state, and how it moves through the wastewater system. This information will help public health agencies by acting as an early warning system and can identify if there is an outbreak in a specific community. Public health agencies can then take early action to reduce the spread of COVID-19.  EPA also announces research in Cleanup and Disinfection and Salivary Antibody Assay Development

https://medium.com/@biobotanalytics/how-many-people-are-infected-with-covid-19-e7e8c6195d6b
  How many people are infected with Covid-19? Sewage suggests that number is much higher than officially confirmed By Biobot Analytics Medium April 8. 2020 3 min read "At this time, our prevalence estimates are a back of the envelope exercise "  BioBot's laboratory protocols are open source. 1. Sample pasteurization We subject sewage samples to a 60C heat bath over 60 minutes to inactivate coronaviruses. 2. Virus concentration  We remove bacterial cells, and we use a PEG-based precipitation method to concentrate viruses in the sewage sample. 3. RNA extraction.  We extract RNA, since SARS-CoV-2 has an RNA genome. This RNA is used to create cDNA through a reverse transcription assay. 4. qPCR. Finally, we use qPCR to quantify the level of SARS-CoV-2 virus in the sewage sample. We use the virus genome to make a standard curve. And we end up with copies / mL of sewage.

https://www.pugetsoundinstitute.org/2020/04/coronavirus-found-in-tacoma-sewage-could-help-scientists-track-the-pandemic/
The coronavirus has been found in Tacoma sewage. It could help scientists track the pandemic  by Jeff Rice. Puget Sound Institute. David Hirschberg's group received permission from the City of Tacoma to test sewage in the hope of developing a “tripwire” for tracking the outbreak.  Hirschberg said the levels of the virus were very low and “we don’t think it is infectious,” but the presence of the virus may help scientists in the battle to identify infection hot spots around the world. The evidence was found in raw sewage influent referred to as “water sludge” by wastewater treatment officials.

https://www.nature.com/articles/d41586-020-00973-x
  How sewage could reveal true scale of coronavirus outbreak. Wastewater testing could also be used as an early-warning sign if the virus returns.  Smriti Mallapaty Nature.  April 3,2020  Monitoring influent at this scale could provide better estimates for how widespread the coronavirus is than testing, because wastewater surveillance can account for those who have not been tested and have only mild or no symptoms, says Medema, who has detected SARS-CoV-2 genetic material — viral RNA — in several treatment plants in the Netherlands. “Health authorities are only seeing the tip of the iceberg.”  But to quantify the scale of infection in a population from wastewater samples, researchers say the groups will need to find out how much viral RNA is excreted in faeces, and extrapolate the number of infected people in a population from concentrations of viral RNA in wastewater samples. Researchers will also need to ensure that they are looking at a representative sample.

4.  Popular overviews  (Science writing, local reports, videos, useful for advocacy etc)

https://www.oregonlive.com/coronavirus/2020/04/poop-may-tell-us-when-the-coronavirus-lockdown-will-end.html Poop may tell us when the coronavirus lockdown will end. By Rosanna Xia, Los Angeles Times. Apr 29, 2020.Current and quotes key players. Good overview para: The amount of virus detected in the sewage can, in essence, mirror the timing and scale of an outbreak in ways that more delayed (and more expensive) in-person testing cannot, experts say. All this information, when pieced together, is critical to informing and validating public health decisions — such as where to allocate medical supplies and when to reopen schools, restaurants and other public gathering spaces.  And as cities start loosening stay-at-home orders in the coming weeks and months, some say monitoring sewage could also provide early warnings if the virus suddenly makes a comeback. In addition to BioBot, team at Stanford University just recently received a rapid grant from the National Science Foundation.  BioBot researchers, do the weekly (sometimes biweekly) analysis pro bono and hope to work with 10,000 facilities to create a more comprehensive picture of how the virus is spreading or “flattening” in different parts of the United States.

https://www.kgw.com/article/news/local/tracking-coronavirus-covid19-in-sewage/283-68e6204d-8a44-462b-b0e6-20324ffcac22
The proof is in the poo: What your sewage can tell you about coronavirus hot spots. Chris McGuinnes for KGW8 (Portland) April 14, 2020. 100 communities  participating in 12-week BioBot study include Albany and Washington County. Weekly samples are concentrated and pasteurized for safe handling and shipped to Biobot in MA. Washington  County's Clean Water Services serves 600,000 customers. CWS is partnering with Oregon State University for hyper local testing. 5/7

https://www.popsci.com/story/health/poop-sewage-covid-19-coronavirus/
Poop could be the key to tracking COVID-19 outbreaks. Searching wastewater for the coronavirus is fast, cheap, and anonymous. Kate Baggaley. Popular Science. April 27, 2020.   Researchers at Harvard University recently estimated that the country would have to perform up to 20 million diagnostic tests daily to fully reopen the economy. COVID-19 may be most contagious early in the disease, before people are even aware that they are sick. And it can take more than a week before some people start feeling ill, which means there is a lag between when somebody gets infected and when they receive an official diagnosis.

https://www.youtube.com/watch?v=QqWWEFc-Z1M&t=4s&app=desktop
What Your Toilet Flush Reveals About Covid-19. 6-min video. Ashlee Vance, Senior Writer, Bloomberg Businessweek. May 7, 2020 interviews BioBot Co-Founders.  Mariana Matus and Newsha Ghaeli explain their work testing wastewater to analyze COVID-19 infection in 1% of the US population.

https://www.popsci.com/city-health-sewage/
  Scientists are scrutinizing city sewage to study our health; It's not just useless crap. By Kate Baggaley. Popular Science July 5, 2017. Excellent background article on wasterwater-based epidemiology. Scientists track drug abuse, pathogens, chemical exposure, and markers for certain illnesses.  “The wastewater treatment plant is the one point where everything flows together,” says Rolf Halden, an environmental engineer and sustainability researcher at Arizona State University in Tempe "...sewers the undiscovered information superhighway,” Halden says. “...we’re already used to analyzing urine and stool for medical purposes. This just takes it to a different scale.”  Other experts in sewer epidemiology include Dan Burgard of the University of Puget Sound in Tacoma, Washington and Kevin Bisceglia, of Hofstra University in Hempstead, New York. Halden's 2002 research  In 2002 found triclocarban from antibacterial soaps is not broken down during wastewater treatment so the sewage sludge used to fertilize crops finds its way "right back to our dinner plates." Halden also found  a second hormone disruptor from antibacterial soap, which is not more effective than regular soap. FDA banned the chemicals from OTC soaps in 2016. Polio and Zika have also been tracked. Tracking germs over time can also provide information about anti-bacterial resistance. Nicotine, opiate, morphine, cocaine, and ecstacy, Adderall, and cannabis use are also tracked. Fentanyl is more potent but harder to track use in population. 

https://biodesign.asu.edu/rolf-halden/research
  National Sewage Sludge Repository (NSSR) Run by the Laboratory of Dr. Ralf  Halden at Arizona State University. NSSR contains sludge samples from more than 200 American wastewater treatment plants, representing more than 32 million people. See list of studies for these topics: Urban Metabolism Assessment Informed by Sewage Epidemiology; Bioremediation of Environmental Contaminants; Pharmaceuticals and Personal Care Products (PPCPs) in the Environment; Environmental Proteomics; Health Effects of Human Exposure to Toxic Pollutants; and Renewable Energy from Biological Systems

https://www.sciencenews.org/article/coronavirus-covid-19-infection-contagious-days-before-symptoms-appear
  COVID-19 may be most contagious one to two days before symptoms appear. More than 4 in 10 coronavirus cases are spread by those not obviously sick, a study suggests. By Tina Hesman Saey. Science News. April 15, 2020.  Pairs of people in which one person definitely caught the coronavirus from the other, an estimated 44 percent of cases likely spread from person to person before symptoms appear. Analyzing 77 infector-infectee pairs allowed researchers to calculate when people are most contagious. The team estimates that contagiousness starts 2.3 days before symptoms begin and peaks 0.7 days before symptoms start. 

https://www.washingtonpost.com/climate-environment/2020/05/01/coronavirus-sewage-wastewater/
An early warning system for coronavirus infections could be found in your toilet. By Brady Dennis.  Washington Post. May 1, 2020. From the U.S. to Europe to Australia, scientists have detected the virus in wastewater ahead of spikes in local cases.
Carol McCreary
Public Hygiene Lets Us Stay Human (PHLUSH)
1240 W. Sims Way #59, Port Townsend, Washington 98368 USA

Toilet availability is a human right and well-designed sanitation systems restore health to our cities, our waters and our soils.
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  • drgs
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Nitya 
Chris Zurbrügg, has pointed to EAWAG news portal page which states the realistic expectations to launch any WBE in the middle of Pandemic. 
  1. Tracking infection trends - not absolute numbers
  2. Goal: Early Warning
Essentially, WBE based detection of Covid-19 is non-issue. What to do with the data is the real issue

I have done a hypothetical case-study of 10-day WBE sampling and data from a community. It is a moderately sized catchment to make some inference and decision. It could be a Dharavi or Royapuram (both Hot spots) or A village in Kancheepuram. 

Attached in the same PDF file is the 10 day data-set (taken from the CSIRO paper) and rational choices for ACTIONABLE DECISION by the Collector of the District. 

Any ACTION needs to be useful or meaningful to overall management of society, control transmission (spread) or assist in treatment of Covid-19.  

If only some rational action can be taken with such data, then 1.4 billion population of India may be divided into groups of 1000-100000 and WBE done. Otherwise, WBE is only a proven scientific method of unknown potential. 

Please give a thought to this.
Certifying Oil & Gas Reserves helped in realizing the fallibility of lot of Science and Technology. I believe that reliable and sustainable science needs integrity and commitment. Disbelief in science is originating from - i) Pseudo-Science; ii) Inconsistency and conflict in scientific doctrine; and iii) Weak Evidence: Data, Process, Review and Results.
Data Intensive Scientific Discovery (DISD) is the new paradigm for growth.

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  • nityajacob
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Carol
This is a really comprehensive list. Thank you.

Dear Srikanth,
Thank you for the PDF - will go through and comment.

Regards
Nitya
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Nitya
Susana.in has announced a Webnair towards getting some SMAC direction with WBE of Covid-19.

Technical ability to detect Covid-19 in sewage is pure laboratory process and easy to define. There is no further doubts on it. Just an SOP document using worldwide success reports will meet the needs.

The action Matrix with any such data is still beyond my grasp. There is no clear proof of value through administration intervention in any published case study.  

Appreciate the Webnair authors are pointed to these points to give their view point

I hope they get to read this forum posts.
Thanks
Certifying Oil & Gas Reserves helped in realizing the fallibility of lot of Science and Technology. I believe that reliable and sustainable science needs integrity and commitment. Disbelief in science is originating from - i) Pseudo-Science; ii) Inconsistency and conflict in scientific doctrine; and iii) Weak Evidence: Data, Process, Review and Results.
Data Intensive Scientific Discovery (DISD) is the new paradigm for growth.
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Narayanan,
The point of low coverage/fragmented sewage systems is very pertinent to India. This protocol will need to recognize that draw boundaries on where it can and cannot be applied. As you say, transposing a western concept here will not work. Instead, we will need to divide the town into zones and map sanitation systems before testing.
Regards
Nitya

ncn wrote:  As an add-on to the current discussions let me raise some fundamental and practical questions for discussion: 

(1) Before getting into methods, can we discuss the epistemology of this idea? Are we transposing a western/industrial economy based strategy here?  (a) will it not be problematic and partial because of the limited coverage in small towns and disruptions in the network? 
(b) can it then capture an appropriate picture of the spread and hot spots? 
(2) If you are keen on taking this forward, then we need to understand/dis aggregate the town into zones, understand the sanitation systems and then have a sampling strategy of 
(i) single/representative OSS,
(ii) connected grids and fall of points (
iii) continuous networked sewerage.

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  • paresh
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear All,
The 2nd part of the this thematic discussion, that is, the webinar will be held on 22nd May 4-5 pm IST (GMT+530), more details can be found here  

Regards
paresh
Paresh Chhajed-Picha
Researcher at Indian Institute of Technology - Bombay, India
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Mam/Sir
We agree to the need and as a Start up company in Clean tech area, we have been working on validation of following protocol developed by us.

The problem statement is There exists no ‘Indian’ customized protocol to test sewage and develop an action plan based on the evidence to manage COVID-19 infections in  densely populated urban residential areas or factory clusters. Currently, urban local bodies (ULBs) have no alternate means to detect COVID-19 infections other than mass testing/herd testing. The wastewater-based epidemiology (WBE) approach could provide an effective and rapid way to predict the potential spread of novel coronavirus pneumonia (COVID-19) by picking up on biomarkers in feces and urine from disease carriers that enter the sewer system

A. Sampling of positive samples in sewage /wastewater/fecal matter In India, this can be especially useful for herd surveillance intensely populated urban residential areas, and factory clusters, where individual testing and social distancing is improbable or impossible. Keeping this in mind we will collect sample from following sites which have reported active/cured COVID-19 case in the area; ideally there should active cases or positive cases
  • Residential areas have community toilets (CTs)connected to a sewer line. For the sewered areas, the area needs to be mapped to determine collection points using Google Maps.
  • Residential areas have community toilets (CTs)connected to a septic tank.
  • Sewage samples from COVID-19 hospitals / quarantine/ isolation centres (where sewerage is existing)
  • Sewage samples from Septic Tanks of COVID-19 hospitals/ quarantine/isolation centres
  • Inlet(s) of municipal wastewater treatment plant (WWTP) of hotspot area as raw wastewater.
  • Sludge samples before Biological treatment   tank.
  • Sludge sample from or after the Biological treatment tank.
  • Treated sewage samples
B. Collection and transportation of sample to Laboratory for testing.Sample has to be transported in cool pack container (normal ice container can be used) to lab for minimizing sample degradation within 1 hr after collection. Although similar protocol are recommended by various agencies international yet these will require modification for our local resources  and transport times has to be minimized, to test for COVID-19 fragments at high levels of dilution and contamination.  

C. Development of community outreach procedure.After testing of samples areas found COVID-19+, messaging to community level institution the Measure of the outbreak independent from patient testing or hospital reporting, and including data on asymptomatic individuals is crucial for the success of the project. This information will provide decision support for officials determining the timing and severity of public health interventions to mitigate the overall spread of the disease. Track the effectiveness of interventions and measure the wind-down period of the outbreak. Provide an early warning for reemergence of the coronavirus (if it does indeed have a seasonal cycle) and to take action to educate people about the findings and precautions required.

D. Validation/ Establishing correlation, Sensitivity and cost optimization Establishing correlation of prevailing Positive covid-19 patients cases (of different origin, severity, reporting) with the test results and tracing mechanism. And the sensitivity/effectiveness/reliability of available detection methods (cost, time, false negative/positive, % of samples to be tested for representation of the population/herd)

I am looking forward to have discussion with all to further improve and validate and then can used in routine  by operators .

Regards
Dr Vanita Prasad
Founder & Director, CTO
REVY Environmental Solutions Pvt. Ltd.
313-314, Siddharth Upscale,
Vasna Road, Vadodara – 390007
M: +91 8156009652 www.revy.co.in    
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  • drgs
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Very useful compilation. Many Thanks!!
Attached are few pointers from my notes on this subject:

Oldest use of WBE or Sewage Epistemiology is traced to work of 1976 as below:
1. G.C. Alexander, R.J. Stevens, Per capita phosphorus loading from domestic sewage, Water Research, Volume 10, Issue 9, 1976, 757-764, ISSN 0043-1354, https://doi.org/10.1016/0043-1354(76)90093-2 . ( http://www.sciencedirect.com/science/article/pii/0043135476900932 )
 A modern estate with 472 houses was chosen, population 1645; Daily  monitoring the effluent; Predicted "creatinine" loadings, using population data and per-capita excretion values; Correlated  measured values to infer  a per-capita value of 1.8 g day−1 for total phosphorus in domestic sewage.

2. Zuccato, E., Chiabrando, C., Castiglioni, S. et al. Cocaine in surface waters: a new evidence-based tool to monitor community drug abuse. Environ Health 4, 14 (2005). https://doi.org/10.1186/1476-069X-4-14   accessed at https://rdcu.be/b4euJ   
  1. Considered as an ORIGINAL Idea paper on WBE.
  2. Used for assessment of Cocaine
  1. Cocaine and its main urinary metabolite (benzoylecgonine, BE) were measured by mass spectrometry in water samples collected from the River Po and urban waste water treatment plants of medium-size Italian cities.
  2. Italian river Po - carried the equivalent of about 4 kg cocaine per day
[/list][/list] 3. Christian Daughton - https://sites.google.com/site/daughton/publications
  1. The author has worked for many years at EPA (USA) and contributed a number of reports and publications. 
  2. Essential to review his work to appreciate the scope of WBE
 3. Dr. Christian advised to follow the work at - EMCDDA: European Monitoring Centre for Drugs and Drug Addiction


4. Christian G. Daughton, Monitoring wastewater for assessing community health: Sewage Chemical-Information Mining (SCIM), Science of The Total Environment, Volumes 619–620, 2018, Pages 748-764, ISSN 0048-9697,    https://doi.org/10.1016/j.scitotenv.2017.11.102 .
  1. Sewage Chemical-Information Mining (SCIM)
  2. Biomarkers are needed that not only measure disease but also health → Overall health status of a community
  3. Sewershed (WBE or Sewerage Epidemiology catchment area)
  4. BioSCIM = Biomarkers as positive indicators of health (opposed to disease)
  5. WBE or Sewage Epidemiology - mainly explored - targeting metabolites of illicit and licit drugs for - 
   1. Back calculating use or abuse
   2. Various non-drug xenobiotics are recently targeted
   3. Endogenous markers <> direct measures of important physiological processes
   4. Exogenous markers | Xenobiotics <> exposure to parent xenobiotic or its metabolite(s) 

An area that is not yet traceable by me is - How the WBE data is used by -  law or municipal administration  for social, administrative or legal interventions. 

Thanks!
Certifying Oil & Gas Reserves helped in realizing the fallibility of lot of Science and Technology. I believe that reliable and sustainable science needs integrity and commitment. Disbelief in science is originating from - i) Pseudo-Science; ii) Inconsistency and conflict in scientific doctrine; and iii) Weak Evidence: Data, Process, Review and Results.
Data Intensive Scientific Discovery (DISD) is the new paradigm for growth.
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

The Phase-2 Webinar on 22-May-2020 on Protocol to test sewage for early warnings about COVID-19 (in India) raised a question in this thread  (Dr. Malini Reddy, ASCI)

There is no evidence of Covid-19 transmission through faecal matter. The possibility of communication through air (aerosol) is considered important in most investigations. Sewage is not even fresh faecal matter unless in conditions where humans are made to come in contact with such material as it happens in India.  

Covid-19 virus structure is relatively simple RNA with ACE2 receptor for infection. It is not clear whether the 'integrity' of the virus is intact when RNA is detected in WBE or Sewage samples. The important think is "infectivity of the virus" in sewer. 

There is no way the virus can further spread or infect again, unless the viral structure is intact. That is it is infectious. RNA detection process actually breaks the virus wall. Unless the virus samples are extracted from sewage in large enough quantities and examined with SEM, the integrity of virus can not be ascertained.

A high-level workflow to examine this is attached. A more competent molecular biology or virology team needs to refine it for any serious investigation.

Thanks.
Certifying Oil & Gas Reserves helped in realizing the fallibility of lot of Science and Technology. I believe that reliable and sustainable science needs integrity and commitment. Disbelief in science is originating from - i) Pseudo-Science; ii) Inconsistency and conflict in scientific doctrine; and iii) Weak Evidence: Data, Process, Review and Results.
Data Intensive Scientific Discovery (DISD) is the new paradigm for growth.

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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear all

I am not expert on wastewater treatment.
However, I am reading lots of papers in which methods are described for assessing quantitatively the COVID-19 presence in wastewater.
One of the more relevant papers is "Regressing SARS-CoV-2 sewage measurements onto COVID-19 burden in the
population: a proof-of-concept for quantitative environmental surveillance", authored by  Itay Bar-Or1+, Karin Yaniv2+, Marilou Shagan2, Eden Ozer9, Oran Erster1, Ella Mendelson1,12, Batya
Mannasse1, Rachel Shirazi1, Esti Kramarsky-Winter2, Oded Nir5, Hala Abu-Ali5, Zeev Ronen5, Ehud
Rinott6, Yair E. Lewis7, Eran Friedler9, Eden Bitkover10 , Yossi Paitan11, Yakir Berchenko4* and Ariel
Kushmaro2,3

You can easily download it from
www.medrxiv.org/content/10.1101/2020.04.26.20073569v1

They describe the method in details, it seems a very interesting both descriptive and predictive method.
I hope it helps.
Ki
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nd regards
Claudia.

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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Prof. Arunabha Majumder

COVID-19 faecal-oral transmission: Are we asking the right questions?

doi: 10.1016/j.scitotenv.2020.138919   raised them - “argue that a comprehensive and more nuanced analysis is required to test this hypothesis, taking into consideration both environmental dynamics and the persistence of viral infectivity.”

I had a reading of Wang XW et.al (2005) . Like the present day evidence of Covid-19 RNA in sewage, the presence of viral RNA detected by RT–PCR for SARS. RT-PCR is a destructive test, where the amputated virus RNA is matched. The authors have stated - “All sewage samples tested for the presence of infectious SARS-CoV in cell culture were negative”. Also, they claimed - “The samples (25,000 ml or 50,000 ml) from the two hospitals were all negative by the infectivity method”. 

Most important question is - any evidence of any virus remaining infectious in sewage.
  1. The determination of the presence of infectious virus is crucial.
  2. Determination of enteric virus infecitivity is important
{ref: https://link.springer.com/chapter/10.1007/978-3-319-30723-7_12

My reasonable effort found no evidence.

Other research on virus infectivity. 
  • PMID: 28501626  DOI: 10.1016/j.virusres.2017.05.004 -- Advances in automated live imaging of cells opened new possibilities for standard virus diagnostic techniques such as neutralization assays. The fluorescent neutralization test is suitable.
  •   DOI //dx.doi.org/10.13070/mm.en.3.207 - Virus Identification and Quantification”, seems to be a good recent summary of available methods.
  • Viruses 2020, 12(3), 318; https://doi.org/10.3390/v12030318 - examined Rotavirus A in Raw Sewage Samples. It avoided any measure of infectivity. 
  • doi: 10.1016/j.jece.2020.104006 - addressed Covid-19 itself as an “Opinion Paper”. It completely avoided the question of infectivity. 
Are Virus RNA in Sewage infectious?

I tried to see whether there is any published EVIDENCE of any kind of infective virus in sewage to give rationale for WBE (Sewage Epidemiology) of Covid-19 in India

Thanks and Warm Regrds
Certifying Oil & Gas Reserves helped in realizing the fallibility of lot of Science and Technology. I believe that reliable and sustainable science needs integrity and commitment. Disbelief in science is originating from - i) Pseudo-Science; ii) Inconsistency and conflict in scientific doctrine; and iii) Weak Evidence: Data, Process, Review and Results.
Data Intensive Scientific Discovery (DISD) is the new paradigm for growth.
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

I love this discussion! Should we find some evidence of covid-19 virus survive in rivers and springs, it would be a game changer in our campaign for ZOD and clean water for all. Thanks for opening this discussion. Sincerely yours, Nelson Philippines
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