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

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

I realise this thread is specifically about the situation in India, but perhaps it's nevertheless interesting to see how other countries are approaching this. To this end, I'd like to share with you an article in The Guardian that I saw today about my country of residence (Australia):
https://www.theguardian.com/world/2020/may/13/sewage-and-wastewater-the-key-to-finding-hidden-clusters-of-coronavirus

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Sewage and wastewater: the key to finding hidden clusters of coronavirus
Wastewater testing is already used to estimate illegal drug usage, and from June will play a critical role in Australia’s Covid-19 response

Testing sewage and wastewater for coronavirus could be the next step in Australia’s response to the Covid-19 pandemic.
On Monday, Victoria’s chief health officer, Prof Bret Sutton, announced that sewage testing was “important” and would be rolled out across the state. The  CSIRO and the University of Queensland  have developed a way to do it, and trialled it in small areas in Queensland, and brought praise from the federal health minister, Greg Hunt, and the science minister, Karen Andrews.
On Tuesday, the Victorian health department confirmed to Guardian Australia that results and “routine testing” would start from June.

But what is wastewater testing and will it actually be used in Australia?
How does it work? Scientists can detect fragments of the RNA (a virus’s DNA) of Sars-Cov2, the virus that causes Covid-19, in our sewage.

Researchers from the University of Queensland and the  CSIRO  have developed a method of sampling sewage from water treatment plants and spotting the “specific nucleic acid fragments” of the virus.

This will help health authorities spot hidden clusters of coronavirus – if a high amount is detected in a region’s wastewater, they can start large-scale testing and quarantine.

On Monday, Sutton described it as “another tool in our surveillance that will tell us how much virus is out there”.
“Even if we are not getting cases notified, if we detect it in sewage, we know that there are active cases out there,” he said. “It might tell us about places where we’ve got gaps in surveillance, that people need to come forward for testing or we need to look harder for active cases.”

Wastewater tracking has already been used for years for tracking polio and for estimating how many illegal drugs we take as a country.

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(read the rest of the article at the link above)

In our state of Queensland we have nowadays very few new cases of infections (thankfully), usually zero up to 6 new cases per day (in the last two weeks). So the sewage testing will either find nothing, or it might uncover hidden/undiagnosed cases.
So it's a very different situation to India, but probably the sampling and analytical techniques would still be similar.

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

This looks like a really good initiative. Well done.
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  • nityajacob
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dzifa wrote: Hello Nitya, 
What you are trying to do is not very clear to me. Maybe more clarification on the objective and expected outcome will be good. 
For now, from what you have written I am thinking you are trying to determine the presence of COVID19 in faeces and its survival in onsite sanitation systems (OSSs), whiles looking at how the virus can be transferred from these OSSs into communities with users been carriers due to the bad designs of these OSSs?
Please clarify.


Hi Dzifa and Paresh,

I'm trying to work out how testing sewage samples for COVID-19 could be used as an early warning system for infections in a community. For instance, if we collect sewage from a location and find it has fragments of the COVID virus' RNA, it means somebody in the system's catchment has been infected or is a asymptomatic carrier of the disease. If there are no traces of the RNA, the community is free from infection. If infections are found, the people can go for individual testing. In effect, this could replace individual or mass testing that is expensive and slow.

One of the problems is this requires sewer systems to work effectively. Collecting and testing samples from OSS will require more effort than current individual testing methods and won't be practical.

Hope this clarifies.

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

Again, though not relevant only to India, thought this piece  will help understand the need of wastewater surveillance regime. 
  • Surveillance of wastewater could help determine the true scale of the spread of the virus:

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

  • Regular surveillance of wastewater could serve as an early-warning sign:

Infection-control measures, such as social distancing, will probably suppress the current pandemic, but the virus could return once such measures are lifted. Routine wastewater surveillance could be used as a non-invasive early-warning tool to alert communities to new COVID-19 infections

Studies have also shown that SARS-CoV-2 can appear in faeces within three days of infection, which is much sooner than the time taken for people to develop symptoms severe enough for them to seek hospital care — up to two weeks — and get an official diagnosis, says Tamar Kohn, an environmental virologist at the Swiss Federal Institute of Technology in Lausanne. Tracking viral particles in wastewater could give public-health officials a head start on deciding whether to introduce measures such as lockdowns, she says. “Seven to ten days can make a lot of difference in the severity of this outbreak.

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

Hi,

I am sharing the collection method used by KWR in The Netherlands. It is meant for automatic sampling and will need to be adapted.

Regards
Nitya

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

Workflow and successful process of Wastewater Based Epidemiology (WBE) is now established. There are 2 aspects to this:
  1.  Tracing chemical and bio markers in Wastewater --> Proved consistently in various problems
  2. Administrative response to any health or social problems from Wastewater study. Interruption in catchment or provenance using the study results --> Not traceable
In Chennai, where I live "locked-in", the Health Secretary or Special Government official issues guidelines and interruptions to social conduct. The Medical process for handing Covid-19 patients is a specialized facet of this administrative overview.
 
I studied the entire paper from CSIRO and some overlapping work on WBE. Some points from CSIRO work are:
  1.  9 samples studied using 2 different protein assay methods (18 investigations); Covid-19 RNA detected in 2. (Fig-2, Table-2)
  2. The Monte Carlo model estimates are in excess of actual clinical reports (This pattern seems to be confirmed by others also)
  3. Authors conclude it as "Proof of Concept of detection". Their claim of "establishing quantitative predictions" is weak.
 
SWOT of this and its application to India needs to be judicious.
STRENGTH : Proved as viable to detect biomarker in Wastewater
WEAKNESS : Models are presumptive; Has never been used in any administrative intervention; Lacks Sensitivity to any such intervention
OPPORTUNITY : Data intensive approach. Needs to build high-performance, fast-track lab processes. Can be used for a variety of health and environmental applications
THREAT : Exposure to other virus/ pathogens; Cost-Value-Proposition
 
WBE is a proven method. It is the future. It is yet to become reliable, actionable and affordable for roll out in the middle of a PANDEMIC. It will compete for scarce resources without clear accountable guidance.

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

  1. Sample from Sewage taken for testing
  2. CSIRO case study points to 2:18 as successful identification ( 9 samples 2 protein assay method)
  3. Positive --> Infection in Catchment
  4. Negative --> Points to NOTHING.
In Australia case study, the catchment was PROVED to be infected at the time of sampling. All Negative results are clearly False-Negatives.

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

The HINDU report of detecting Covid-19 RNA in Chennai sewage is not disclosing their source/ lab information. However, this proves the ease of Wastewater Based Epidemiology (WBM) - detection is easy. What to do with that data (action) is daunting. 
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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  • nityajacob
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear all

(I am posting this on behalf of Dr Kurian Baby)

There is scientific evidence from across the globe, that testing sewage and waste water could be one of the surveillance tool to gauge the extent and prevalence of COVID -19, particularly in the cities. However, for developing protocol, one must take care the following:
  • The evidences of faecal oral transmissions are not robust and clear. The excreta and human waste of all affected people may not invariably indicate COVID presence.
  • Secondly, there are also evidences of community spread in some geographical areas like slums or others.
  • Thirdly,  in developing context , the sewerage coverage is only scanty and most vulnerable areas or hotspots like slums are largely out of the network.
  • Fourthly, the drinking water distribution networks in many places mixes with sewerage/ waste water  lines (leakage and NRW at 35-40%),  the protocol should ensure safe drinking water
  • Fifthly, if managing networks are potentially a challenge under COVID-19, the design and management of drinking water security under pandemic shall incorporate stand-alone self-supply sources, like open wells in Kerala and new design features.
Accordingly, one must be extremely careful in extrapolating the findings of sewerage test in itself as analytical evidence of the extent of spread. At the current level of evidences and methodology, we can at best use the data as a supplementary analytical tool for early warning and surveillance. We may also incorporate the guidance published by the WHO  ( Water, sanitation, hygiene and waste water management for the COVID-19 virus, 23 April 2020) in this regard.   

Dr. V. Kurian Baby

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

Christian Zurbrügg <This email address is being protected from spambots. You need JavaScript enabled to view it.>
Sandec: Department of Water and Sanitation in Developing Countries
Eawag: Swiss Federal Institute of Aquatic Science and Technology
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Nitya

 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.

For this starting point might be a participatory mapping exercise like what we suggested:
N. C. Narayanan, Isha Ray,Govind Gopakumar and Poonam Argade, 2018, Towardssustainable urban sanitation: A capacity-building approach to wastewater
mapping for small towns in India, Journal of Water, Sanitation andHygiene for Development, Volume 8, Issue 2. IWA Publishing.
(3)

If we need to deploy it in scale, we will need to think about dealing with governance institutions. The over-stretched and sometimes under-capacitated bureaucracy in government agencies (ULBs, SPCBs, etc) might not be able to take it up and operationalise it. This will demand a larger network of institutions - academic, think tanks, NGOs, consultancies to come together and assist/capacitate/collaborate with the governance agencies to make it work. 

As suggested in the beginning I am flagging these as complementary points to the technical discussions triggered here.
Best wishes, NC Narayanan, IIT Bombay.
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Re: Topic 1 Protocol to test sewage for early warnings about COVID-19

Dear Dr Kurian and Nitya,
I can not agree more than what you have said. For India where sewerage management is the worst, it will be very difficult to correlate the result with any geographical area. OD and particularly child faeces very easily get mixed with solid waste which ultimately finds a way into the sewer system. On the other hand, may medical waste or waste from the quarantine centers are disposed of openly (perhaps in the back yard pf the center or just outskirts of the city without any treatment which ultimately either through the wind, animal or rag pickers get mixed with the sewage.  In this condition even if you do have the protocol and get the result (and it can be achieved as it is under the control of the trained personnel/institution and other countries have done it), my only worry is the use of the report. Therefore, unless 

1. Majority of the sewers are  controlled and clearly marked the ara served at a particular control point
2. Majority of the city/towns/villages are served with such sewerage system
3. People are using a toilet for defecation (nowadays all are not using the toilet particularly in the rural area even if they have it) 

In absence of the above (which is a reality of today's India) the result may give a falls interpretation-

1) either positive cases are present in the society but not detected as the infected person is outside the sewer service, this will lead to a false impression that community is not infected but actually it is)  
2) Infected solid waste or faeces due to OD of some other area finds its way to the nest area - in this case, the actual geographical area may not be identified
3) Loys of migrant/floating people visit a city and return the same day or after someday. They might be using the facility of hotel/offices/business area/public toilet/institutions and from there tracing the positive people is like finding a needle from in a haystack.


So in my opinion as from an academic point of view, it is ok but from a practical point of view, I doubt how effective it will be.

My suggestion is to go for something that suits the Indian condition.

Regards
Nagendra Prasad Singh
Lucknow 

  in the staying in hotel, 
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