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

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

Dear all,

We are starting this discussion on how to develop a protocol for testing sewage as an early warning method for COVID-19 in India. Research from past SARS epidemics has suggested fragments of the viruses from infected human beings are found in wastewater and sewage. These can be isolated and analysed to determine if there are infections in a particular geographic area. In India, this can be especially useful for herd surveillance in densely populated urban residential areas, and factory clusters, where individual testing and social distancing is improbable or impossible. Some such residential areas have community toilets (CTs) connected to a sewer line, or septic tank that is periodically emptied, from where samples can be obtained. This testing can be a sensitive tool to monitor circulation of the virus in a population.

The central problem statement is - 

There exists no ‘Indian’ 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.

Methodology
A few assumptions are necessary in this protocol.
  1. The densely-populated urban residential areas or factory clusters need to have a sewer system. This can be a shallow, narrow-bore system. IHHLs, CTs and other toilets are connected to this
  2. Industrial waste does not mix with sewage
  3. There have been active/cured COVID-19 case in the area; ideally there should active cases
  4. Laboratory facilities for testing exist and are accessible
There is some early research that suggests a method to collect, transport and test sewage samples. A paper from the KWR Water Research Institute, The Netherlands, is one such source. Additional sources will be identified and incorporated into a literature review. CNN reports that  Biobot and universities in New York have developed methods as well.

For sampling, to develop the protocol  Swasti can reach out to communities through grassroots organizations in densely-populated urban residential areas. Such areas include tenements with about 50-80 families per building sharing 1-2 toilets and bathrooms. Some are sewered but others have storage pits emptied by suction machines. Both are amenable to the proposed surveillance method. These areas are surrounded by factory clusters, usually comprising small and medium enterprises. While most industrial estates are sewered, it is unclear if the sewers carry both sewage and effluents.

For the sewered areas, the area needs to be mapped to determine collection points using Google Maps. A suitable ‘catchment’ population can be defined. Using the existing CT norms, this can be  30 people per sample collection point. The collection points need to be marked to develop a collection schedule. Successive samples will be taken in rotation to cover as much of the area as possible within a reasonable time frame. The collection norms will consider the feasibility, periodicity, capacity of the laboratory, capacity of the community and costs.

The collection and transport procedure recommended by KWR is defined in the paper. Biobot also suggests similar procedures. However, these will require modification for Indian temperatures and transport times, that impact sample degradation. The paper states the samples collected in The Netherlands were transported to laboratories on melting ice; a suitable substitute will have to be found for India.

The sampling rate must be statistically significant. The exact size will be determined from the size of the population/number of factories at a 95% confidence interval. From the areas, samples need to be transported to the nearest laboratory that meets bio-safety level 3 (BSL-3)
norms. This will mean having a cold chain – ice or similar method – to reach the laboratory. That laboratory must be able to test for COVID-19 fragments at high levels of dilution and contamination.  

If a sample is found COVID-19+, a community outreach procedure will be required to inform and educate people about the findings and precautions required. This will include setting up a community level institution, messaging, finance and governance. These are crucial to the continued success of the project both in terms of collection and testing, and outreach with the people on the results.

This discussion is divided into the following parts.

Part A: Thematic e-discussion Questions
  1. What can be a protocol for surveillance and action at the ULB level for herd surveillance of COVID-19 through sewage testing for the virus?
  2. Specifically, we need a localised method of sample collection, transport and testing
The topic lead is Arunabha Majumder, Jadavpur University. This topic will open on 8th May and continue till 22nd May
  1. What can be standard operating procedures for community outreach based on evidence?
The topic lead is Malini Reddy, Administrative Staff College of India. This topic will open on the 22nd and continue till 31st May

The second part will be a webinar, proposed to be held on 22nd May. We will share the concept note closer to the date.

Arunabha will share his opening comments today. Look forward to an exciting discussion.

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

Hello everybody, I am Arunabha Majumder, Professor-Emeritus with Jadavpur University’s School of Water Resources Engineering, Former Director and Professor, All India Institute of Hygiene & Public Health, Life-Fellow- Indian Water Works Association & Institute of Public Health Engineers (India).  

As far back as 2005, a study was conducted to assess the concentration and detection of SARS Corona virus in sewage from hospitals by Wang XW et.al (2005) . This drew attention to the possible transmission of the virus by the sewage system because laboratory studies  showed that patients excreted Corona-virus RNA in their stools.  To explore whether the stools of SARS patients or the sewage containing the stools would transmit SARS-CoV, the researchers used a style of electropositive filter media particle to concentrate the SARS-CoV from sewage of hospitals receiving SARS patients. They also used cell culture, semi-nested RT-PCR and sequencing of genes to detect and identify the virus from sewage. In the said study, researchers found the virus can survive for 14 days in sewage at 4◦C, but 2 days at 20◦C and its RNA can be detected for 8 days though the virus has been inactivated.

Poliomyelitis eradication was a challenge to the whole world. Polio vaccines need to be given to the babies to control and eradicate the disease. India did a wonderful job to make the country polio-free. Wastewater /sewage monitoring has been used for decades to assess the success of vaccination campaign against polio-virus. Wastewater/sewage can be also monitored to assess the prevalence of infective Hepatitis A, rota-virus, etc. Recently, by sampling sewage across Greater Paris (reported on April 21, 2020) for more than one month,  researchers have detected a rise and fall in the Novel Corona virus concentration that corresponds to the shape of the COVID-19 outbreak in the region, where a lock-down is now suppressing spread of the disease. The PCR test identifies fragments of RNA from SARS-CoV-2 that causes COVID-19. The concentration of the virus in waste water /sewage is proportional to the number of infected people who contribute to the sewerage system.  

A structured study if carried out through real-time monitoring basis (sewage/sullage sampling and testing) can predict presence of Corona virus-infections (symptomatic and asymptomatic people) in a locality/ ward/zone/slum/ gated community/city or town as well as village in rural area. The study can also predict the possibility of a second wave of outbreak of COVID-19. Extent and magnitude of COVID-19 outbreak can be assessed by extensive sewage / sullage sampling and testing. I am recommending the following samples should be analyzed:
  1. Stool of COVID-19 patients
  2. Sewage samples fromCOVID-19 hospitals (where sewerage is existing)
  3. Sewage samples from Septic Tanks of COVID-19 hospitals (where U/G sewerage does not exist)
  4. In cities, Sewerage network may be divided in small zones and sewage samples may be collected from exit point of each zone
  5. Sewage samples from quarantine centres
  6. Sewage samples from isolation centres
  7. Raw sewage sample(influent) entering to Sewage Treatment Plant
  8. Treated sewage samples
  9. In un-sewered town, sewage samples from septic tanks (hospitals, Quarantine Centres, Isolation Centres) , sullage samples from surface drains  are to be collected for testing.
  10. In villages, sewage samples are to be collected from on-site sanitation systems (Two-pit Pour Flush Toilets, Septic tanks, etc). 
Samples can be collected 2-3 times a week for assessment and prediction.

Can you please suggest the sampling method, sampling time, sample preservation, transport, and precaution/safety against hazard or hazardous events? 

This will help to develop the first part of the protocol. 
Regards,
Arunabha Majumder
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

what will the sampling procedure, the detection method and how to quantify the infected people with respect to sample analysis. can we use the treated water sample from sewage treatment plant or at the inlet of STP. ( before treatment)
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  • Thakur
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Thanks for sharing this important agenda. I would like to add /make a query on this as below

The sensitivity/effectiveness/reliability of available detection methods (cost, time, false negative/positive, % of samples to be tested for representation of the population/herd)- Categorization of viruses potentially exsiting in the embient environment (wastewater/garbage dumped into wastewater) and hosts (human, animals, insects, etc.)- Validation/verification of the test methods with approved / certified protocols (takes time to validate)- Establishing correlation of prevailing disease cases (of different origin, severity, reporting) with the test results and tracing mechanism- Practical collaboration with health agencies (Epidemiology dept.)

If these aspects are also covered, I think the use of wastewater testing method can be applied for EWS for disease outbreaks in general. But for COVID19 in particular, it may still remain having reliability issues for days/months to come. Thanking you and I will be interested to learn more from this discussion.  

With Regards, 
Thakur Pandit
Thakur
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  • msvkvprasad
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

As of now we are believing that quarantine period of covid-19 patients was 14 to 21 days before they leave the hospital. If we collect samples  every 3 days, then average around 5 times when the patient was in hospital, of course new patients being admitted or some cured patients left the hospital.

In my view, the ideal time to collect the samples would be around 8:00AM, the method of collection from the septic tanks with well protected masks and in glass bottles with chlorination, the personnel  should wear personal protection suits to avoid any contamination. The samples should be sealed properly and kept in boxes either made with iron or aluminum so that no sun radiation falls on the samples during transportation. Once the samples reaches the laboratory the wet and dry part of the stool should be separated as of waste water treatment methods. Both should  be subjected for microbial testing and for present covid-19 protocol we should consult WHO.

After testing i believe 'incineration' should be done and the ash stored in steel container and lastly underground as of radioactive material used in cancer treatment.
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  • arraghuw
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Nitya

Regarding surveillance - CPCB already prepared a document and sent across to state pollution control boards for online real time monitoring of inflow quality and treated effluent quality of the STP's, CETPs - way back in year 2012- But it is still not implemented at all. Further in context of in India following are observations which would impact this methods
  1.  The old network are fairly efficient but recent sewer networks are of poor workmanship and high rate of infiltration or leakage in system
  2. Connectivity issues - sewer networks are laid but properties are not connected or existing septic tanks are connected instead of direct waste water pipes
  3. toilets are built to some extent we declared our self ODF. I don't have actual figure, but i can say that half them are on paper.
  4. Their construction quality are so bad that most of them are now not existent after 1-2 years of construction
Further this could be good to have surveillance system subject to seriousness and implementation of public health dept or the state govt. When we are still in situation of low cost / least cost system - these all papers are used for having Bhelpuri' or some parts samosa and chutney.

Not even a metro city have 80 percent sewer network coverage and most of sewer mains are openly drained in the open drains. These sewers in some of development are not have even a provision of septic tanks - just simply draining in open rivers ( now become nallah). 

Only hope is if severity of this type of analysis is considered important than only framing SOP's, methodology, protocols works.
Regards
Arvind S Raghuwanshi
Water and Wastewater Engineer
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  • drgs
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

COVID-19 is unprecedented in scale and spread to any other pandemic. With human populations nearing 8 billion, it is unique in the history of Earth. 
I shall bring forward a few aspects of information in scientific decision making and the overall context of society before taking up this effort (Sewerage testing for early warning about #Covid-19)
  1. VoI- Value of Information: A metric and mechanism to assess what the additional data/information shall do to the decision tree.
  2. Sensitivity & Specificity- How a new test, data/information addresses the reliability aspect
  3. Applicability- How the validity or expiry of data/information applies to decisions
Applicability: A standard HbA1c, Typical Lipid Profile, TSH  test have 3-6 month validity. Troponin T (hs-cTnT1) is a diagnostic criterion for an AMI at the instant of attack. The Covid-19 tests are all small longevity tests. E.g. President Trump today moves around without safety as his tests came negative. Whereas, the virus spreads in the White House 2, notwithstanding numerous regular ‘negative’ test results. 
→ Any test today is valid only until 3-5 days.
→ Continuous repeated tests only can screen (more like a IoT sensor on DCS or SCADA)
→ Their Sensitivity and Specificity are poor (too many blind shots)
 
Sensitivity & Specificity: A hs-cTnT level > the 99th percentile (0.014 ng/mL), had a sensitivity, specificity, with different positive and negative predictive values. It is a nearly certain diagnostic measure to take action on the patient. The current diagnostic laboratory tests for Covid-19 themselves are struggling with too many False (+) and False (-). 
→ Sewer testing can not become more specific or sensitive. It can only open up for Lab-Tests.
→ Yet, the mechanism to identify a virus or antibody or antigen is equally complex in sewer sample (as tough and expensive as in nasal fluid or blood)

VoI: This now opens the Value of such a Sewer test result (+ or -) to further decision making. What is the further decision making flow? How does this ‘sewer data’ assist in the decision tree. At what reliability and affordability?
For this, a schematic decision flow diagram is needed. I made a quick and dirty effort. 
https://docs.google.com/drawings/u/0/d/sktuYP6ZuW_bidbWryG0DEw/image?w=624&h=449&rev=772&ac=1&parent=15V19QKhFh6VinbCOjOGTmeoJI-xo_pTUKGolW2N1TwI

At this juncture, at this level of management of the Pandemic, at this economic and resource scenario - conducting systematic reliable pathological tests itself is a huge challenge. There are competing needs contesting for money, resources and attention. 

One needs to rank the VoI and its position among various “Critical’ and ‘Essential’ needs at this juncture of #Covid-19 management in India. Any further effort needs to clearly assess these and prioritise. 
Thanks

India Scene
https://lh6.googleusercontent.com/kIVoOUozSa0pvHkJUWkDJuxmvj5MElpLQreXC0SD9e8a0RzWPYYUtAMRyYA8RXmbo40-PHSHXOvOunPeUx7pTM0A0hwkK19zOqeTfL59Pt0yj_FpB-UZ-9rvw1sqLBRjBvHZJQ_D
Logarithmic rise from 1-10-100-1000-10000 in typically 2 weeks each. 10000-100000 (104-105-106) need to wait3  

References (Links)
1.  www.ncbi.nlm.nih.gov/pmc/articles/PMC3627711/
2.  www.express.co.uk/news/world/1279840/Cor...over-19-katie-miller
3.  http://a.msn.com/01/en-in/BB13IHrb?ocid=st2  
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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  • AjitSeshadri
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Members.

It is clear that a lot of sewerage conveyance in India is not in order. As most of the non -sewered lines are open and flows into main river thro waste-streams.( locally called nallahs)
It is here, that  ULBs and Rural boards need to apply pertinent process and containment and removal solid sludges Etc. at point source.

Dewats type process - large dugouts and float traps on surface are done and manual methods are employed to reduce pollution in rivers Etc. 

All the sludge matter removed may be taken for co composting to have a closed loop aiding sustainable mode.

Well wishes.
Prof. Ajit Seshadri, Senior Faculty in Marine Engg. Deptt. Vels University, and
Environment Consultant (Water shed Mngmnt, WWT, WASH, others) Chennai, India
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  • nityajacob
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Hi Swapnil
Those are the questions we are trying to work out. Please suggest ways to do so.
Nitya
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  • nityajacob
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Hi Srikanth,

This is most informative. I have a few questions about the VoI and diagramme.

Is there a reason you suggest retesting at the intervals specified? Can these be changed and how will it affect results?

The RT-PCR test is commonly used. Do you suggest using that or some other type of test? There are cost implications for this. How will the choice of test determine or affect the sewage collection methods?
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  • nityajacob
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Hi
Yes I am aware of the CPCB document for online monitoring but little has happened in that regard. Your points 2-4 have a bearing on the collection methods, given that more than a third of toilets are connected to onsite sanitation. How can one collect samples here? This was a problem we had when we started out, as sampling individual septic tanks and toilets defeats the 'early warning' idea of the activity.
Regards
Nitya

arraghuw wrote: Dear Nitya

Regarding surveillance - CPCB already prepared a document and sent across to state pollution control boards for online real time monitoring of inflow quality and treated effluent quality of the STP's, CETPs - way back in year 2012- But it is still not implemented at all. Further in context of in India following are observations which would impact this methods

  1.  The old network are fairly efficient but recent sewer networks are of poor workmanship and high rate of infiltration or leakage in system
  2. Connectivity issues - sewer networks are laid but properties are not connected or existing septic tanks are connected instead of direct waste water pipes
  3. toilets are built to some extent we declared our self ODF. I don't have actual figure, but i can say that half them are on paper.
  4. Their construction quality are so bad that most of them are now not existent after 1-2 years of construction
Further this could be good to have surveillance system subject to seriousness and implementation of public health dept or the state govt. When we are still in situation of low cost / least cost system - these all papers are used for having Bhelpuri' or some parts samosa and chutney.

Not even a metro city have 80 percent sewer network coverage and most of sewer mains are openly drained in the open drains. These sewers in some of development are not have even a provision of septic tanks - just simply draining in open rivers ( now become nallah). 

Only hope is if severity of this type of analysis is considered important than only framing SOP's, methodology, protocols works.

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

VoI - Value of Information allows assessing the entire DATA and INFORMATION in the context of the DECISION that it shall influence.
The line of thought in this discussion is -
  1. " Sewage testing of patients in the hospital".  I do not see why that is needed as the patient is available and direct test can be done easily.  After all the complications of sampling sewage and testing it - what is that decision that can be taken (will be taken by the CMO) based on the sewage results?
  2. "Sewage testing of households or hot-spot areas". I assumes there is some VoI proposition here. My note went on this line of thought. I have a hot-spot area of say, 50 households and want to see early evidence of them getting infected. Without scaring them, I test their septic tank or sewage line to short-list 5-10 households (example) to do proper Covid-19 test.  
The {2} has some potential to become USABLE. If and Only If the Sewage test is far simpler, faster and cheaper. 

Coming to the Applicability of Covid-19 test itself --
These are highly 'Temporal' or 'Time-Sensitive' data.  Closest I could think of its equal is Troponin T test during Myocardial Infraction.  The {+} means cardiac trauma now.' {-} itself does not rule out there will be no cardiac event for next 15 days or 3 months. Same way, COVID-19 tests are valid to the moment of time when the test sample was taken. 
Example = A family with high levels of exposure: 1 Covid-19 patient in hospital; 4 other members tested {-} on Monday. Next Monday, 2 or them become {+} and by end-of-month all 4 {+} --- alternately till the standing incubation period of 3 weeks, all 4 remain {-}. Only way anybody can know is testing regularly these high-risk candidates. 

In summary, I see sewage testing needs a CLEAR DIRECTION and CLARITY of what decision it will influence {At what cost and demand of resources}. 
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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