Sewage Pooling Test for SARS-CoV-2
SSewage Pooling Test for SARS-CoV-2
Ritam Guha , Anik Sengupta *2 , and Ankan Dutta ∗ [email protected], Department of Computer Science and Engineering,Jadavpur University, India [email protected], Department of Electronics and CommunicationEngineering, Heritage Institute of Technology, India [email protected], Department of Mechanical Engineering, Jadavpur University,India May 2020
Abstract
CoVID-19 is currently one of the biggest threats to mankind. To date,it is the reason for infections of over 35 lakhs and death of over 2 lakhhuman beings. We propose a procedure to detect CoVID-19 affected local-ities using a sewage mass testing and pooling mechanism which has gainedground in recent times. The proposed method named Sewage Pooling Al-gorithm tests wastewater samples from sewage systems to pinpoint theregions which are affected by maximum chances of the virus spread. Thealgorithm also uses a priority-based backtracking procedure to performtesting in sewage links depending on the probability of infection in thesub-areas. For places with very rare CoVID cases, we present a gradient-based search method to prune those areas. The proposed method has lesshuman intervention and increases the effective tests/million people overcurrent in-place methods.
Keywords:
Covid-19, Sewage testing, Pooling, Priority-based backtracking,Gradient-based searching, RT-qPCR. ∗ authors contributed equally a r X i v : . [ q - b i o . O T ] M a y Introduction
The main routes of transmission of CoVID-19 are respiratory droplets and directcontact. Current evidence suggests that the virus may be excreted in faeces,regardless of diarrhoea or signs of intestinal infection. Studies have shown thatCoVID-19 viral RNA fragments can be detected more accurately from patient’s(even asymptomatic patient’s) stool specimen [6]No one knows about the actual number of people affected with COVID-19. We are only aware of the status of those infectious people who have beentested. Testing is our only window to handle this pandemic situation as weget aware of the way virus is spreading and also actual number of infectiouspeople.In the asymptomatic infectious cases in the community or when peopleare not sure whether they are infected or not, community sewage detectioncould determine whether there are CoVID-19 carriers in an area so that effectiveintervention can be taken as soon as possible. The present testing mechanismis too slow, cost prohibitive and sometimes provide negative results even if theperson is infectious. As of now in INDIA, number of samples being tested is0.03 per thousand people [5]. The proposed mechanism of wide sewage testing isdaunting yet more manageable. Studies have shown that SARS COV-2 is highlysimilar to SARS COV-1 genetically [7]. Now because of the genetic similarity,detection method remains quite similar, and there have been studies regardingthe detection method of SARS COV-1 from sewage samples [8].
To understand the proposed methodology, it is essential to get an overview ofthe sewage structure adapted in various places. The most common schematicdiagram of a sewage system is presented in Figure 1. From the structure, it canbe seen that many links are interconnected to form a backbone of the sewagesystem.These links carry waster water from different areas to the backbonestructure which is finally dumped in a place which is marked as Initial Pointin the Figure. Sometimes, this initial point is a Waster Water Treatment Plant(WWTP) which refines the waste water and passes it to rivers, ponds etc.At any point of any link, the entire area whose wastewater passes throughthat point is known as the catchment area of the point. So, a particular link isresponsible to carry the waste water of its catchment area. For easy explanationand references, the proposed method labels the links in terms of a labellingsystem. The links emanating from the initial point are level − level − , level − , . . . , level − n ).All the level − ( i + 1) links connected to a level − i link are called the child linksof that level − i while level − i link is called the parent link of its child links.2igure 1: Schematic diagram representing a Sewage System In the present scenario, composite or integrated sewage samples are collectedwith sampling covering a period usually no longer than 24 hrs using an auto-matic or mechanical sampler. Throughout this report we assume the sampletaken at any link to be an equally probable sewage collection of any individualof the sample population of that region represented as the catchment area ofthat link. To facilitate this statement with higher certainty, we need to assureproper mixing of sewage via making the flow more turbulent and by increasingthe sampling frequency and volume. Satisfactory results are also obtained bycollecting a portion of uniform size each time a predetermined amount of flowhad passed the sampling station [3].For detection of CoVID-19 from sewage, rapid test kit cannot be used asmost of them are based on antibody test. Through the faeces of the humanbody, RNA fragments of the virus are excreted and not the antibody generatedinside the body. One-step quantitative reverse transcription PCR (RT-qPCR)is decided to be used to achieve a faster and highly reproducible test. Recentstudies of sewage test using RT-qPCR has shown better prediction of CoVIDcases and is currently being used in few countries [9, 4, 2]. One such is approvedby ICMR is TRUPCR R (cid:13) SARS-CoV-2 RT-qPCR kit, based on real-time PCRtechnology, for the qualitative detection of (SARS-CoV-2) specific RNA [1].The precision of RT-qPCR is important to determine the largest samplingpopulation the method can encounter or in other words, the initial point atwhich the pooling method in sewage context can start iterating. Suppose a3ewage sample of a CoVID positive person is tested with t viral particles perml. We add the sample with sewage of other n − t/n viral particles perml. This value decreases with increasing the sample size n till we get a maximal n ∗ till which the equipment can detect the virus. We then group the regionwith a maximum pool size n ∗ . The initial points will be links in sewage systemwhich can capture the population of n ∗ independently. For proper functioning of the proposed procedure, it is important to retrievethe latest set of information available in the market. Some very important pa-rameters like number of Covid patients already present in the locality, rate ofincrease in the catchment area, number of infants and aged inhabitants of thearea, population density of area etc. may play a very important role in selectingthe most optimal set of paths for testing. So, the process needs access to thelatest information in terms of these parameters and current test results. Thisshould be done by a system which updates the information after regular inter-vals.
The Covid-19 pandemic requires every patient to recover from the disease with-out affecting others around. Even the presence of a single patient may resultinto exponential spread of the virus thereby affecting a large population. So,the main aim of the proposed approach is to make an attempt to identify everyCovid-19 affected locality. For this reason, the proposed model tries to collecttest samples from every sewage link possible and test them but the selection ofthe links is not done blindly. It uses a probability-guided backtracking approachto find the most probable links in the current situation.After finding the starting point of the search procedure, the probability iscalculated for each and every link in the area based on the information extractedfrom the demo-graphical study of the locality. Then the testing starts with the level − Link − Link − Link − level − ( i + 1) links are done with the testing, subsequent levels aretested using the same rule until terminal links are tested in a recursive manner.This procedure is known as Priority-based backtracking as probability is guidingthis searching procedure.The flowchart for the entire procedure is provided inFigure 3. The entire approach is named as Sewage Pooling Algorithm presentedin Figure 4.Figure 3: Flowchart of Priority-based backtracking procedure5igure 4: Flowchart of SPARegarding quarantining, there are mainly two scenarios:1. If the search procedure ends at a terminal link which is tested positive, peo-ple in its catchment area should be quarantined and confirmatory tested.2. If an intermediate node is tested positive, then all the people staying at theunique houses only connected to that intermediate node must be tested. Gradient Searching:
The choice of initial point is dependent on the sensi-tivity of RT-qPCR. In case of very low concentration or probability area whichare being pruned, there will still be cases of CoVID which cannot be ignored inthe long run. Moreover there may be exception when the sample doesn’t reallyabstract the sewage information of the catchment area with equal probability.To tackle these problems we use gradient i.e. difference in concentration acrossdepth-wise links. Suppose to test a sample at link level − n ∗ or level − n ∗ population with m CoVID positive caseswhere m << n ∗ and the mixing doesn’t equilibrate thus over-estimating n ∗ .We find gradient of all links of level − level − level − level − n ∗ . So if there was a positive CoVID case there must be arise in the CoVID level as a percentage. Moreover the concentration must notbe less than precision if even one CoVID case is there as the sample size is muchless than n ∗ . We prune the links where gradient is negative and move forwardwith positive gradient showing the direction. This approach has many advantages over the currently available methods. Theadvantages are outlined in the following portion.1. Currently the process-in-action for CoVID treatment requires affected peo-ple to identify the symptoms, consult doctors, visit hospitals and then ifpositively identified, go for treatment¿ During this entire process, somemore people may get affected if the person is positive. But, the proposedapproach should be performed at Govt. level with little to no effortfrom the affected patients.2. This process can detect asymptomatic patients as well.3.
Reduced number of test are required on an average basis. (There maybe scenarios in which most of the patients are affected in the locality. Inthis exceptional scenario, number of tests will increase)4. Even after the pandemic is over, this process can be used to keep a trackof CoVID in different localities.
This work presents an approach to identify the CoVID affected localities usinga sewage pooling mechanism. The proposed method known as Sewage PoolingAlgorithm tries to identify the affected areas by performing RT-qPCR testingon sewage samples collected from these areas in an informative way. It usesthe data extracted from demo-graphic information of the regions to computethe probability of infections in different sub-areas connected by sewage links.Priority-based backtracking approach is used to perform testing in sub-areaswith higher probability of infection. Although, to the best of our knowledge,it is a very efficient way to detect affected areas using less number of tests, itassumes ideal scenarios in many situations. For example, it requires proper mix-ing of the pooled sewage samples but in reality it may not be the case. Theremay be various organizations in the locality which negatively affects the results.For example, if the area has a hospital treating CoVID patients or a factoryemanating chemicals which may change the nature of the wastewater samples,the result will get badly affected. The procedure needs some modifications tomake it applicable to real-life situations which is not possible without practical7esting and implementations. In future, if this idea gets approved, modifica-tions can be performed over the procedure based on the new set of informationobtained from the practical testing outcomes.
The authors have conflict of interest to declare. AS, AD presented this idea asQuickSolutions to Techstar India start-up weekend and secured the first prizein India Chapter.
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