Introduction
Background
During the COVID-19 pandemic, most of the cities’ administration’s response have been city-wide and universal such as (i) with city-wide lockdowns as containment measures, (ii) testing and tracing symptomatic cases and (iii) universal roll out of vaccination programs. The cities have also been responding on a day to day basis the hospitalisations and positivity rates through RT-PCR tests.
During the first wave, there was an acute shortage of tests, high turn-around time, and no way to know if the city as a whole was seeing trends geo-spatially or temporally.
After the Nature article on COVID in April 2020 , following the study by KWR Water Research Institute in March 2020, COVIDActionCollab jumped into action and gathered a multidisciplinary group from various sectors and countries to think through, what this might mean for metropolitan over crowded resource constrained cities in India who have sewered and non-sewered connections. Would a system like this serve as early warning, or a proxy to the incidence of COVID in the population?
How does wastewater surveillance help monitor COVID outbreaks?
The concept of wastewater surveillance is not new, it has existed since the 1930s. Wastewater surveillance is the process of monitoring the wastewater (sewage) generated by a population to look for contaminants. In the current scenario, the most pertinent example would be looking for the SARS-CoV-2 virus in the sewage of a population.
There is an established science that SARS-CoV-2 virus can be detected from an infected person through fecal shedding, much earlier than the nasal respiratory symptoms occur. Hence, if the wastewater containing *** of an infected person is sampled and tested, it may detect the virus from the wastewater and indicate the risk of infection spread within the population much earlier than the infection outbreaks, thus providing an early warning and also regular sample testing can help monitor the presence of virus in the wastewater.
While all the wastewater surveillance for COVID has been in treatment plants or sewersheds ( pre-treatment at the treatment plants)
Introduction to the Promising Practice
Precision Health, a wastewater surveillance platform, is a joint effort by individuals and organisations under the umbrella of #COVIDActionCollab with the aim to promote systematic wastewater surveillance for early detection and prevention of disease outbreaks by creating an early warning surveillance system.
In the city of Bangalore, this surveillance platform has been set up as an Early Warning System for COVID outbreaks, known as Precision Pandemic Surveillance Initiative. This initiative helps understand the trends of SARS-CoV-2 infections within the city and to support the local municipal administration by informing them about the trend of infection within the population. The surveillance system has proven to be effective in disseminating early warning signals to city administration and health officials for further actions and to also contribute as one of the many surveillance tools of the city's overall public health management systems for COVID control.
The platform has been actively collecting and analysing wastewater samples from open drains of Bengaluru city since April 2021 to detect and monitor the presence of SARS-CoV-2. From January 2022 onwards, the platform has also included the wastewater treatment plants as a sampling site for Bengaluru city through collaboration with TIGS-NCBS-Biome which were conducting wastewater surveillance from WWTPs.
The data from Precision Health mirrors the peak of the second wave in May, and the recent uptick in cases, in terms of the percentage of samples that were positive for SARS-CoV-2. The current findings from wastewater testing show that at the ward level, around half the wards are showing an increasing trend. This also seems to portend a further increase in per-day cases in the coming weeks.
Objective of the Initiative:
- To support the city administration in controlling and managing COVID infection rate in Bangalore
- To provide evidence-based indication of increasing or decreasing infection rates in the city population
- To supplement COVID surveillance through a preliminary information of infection rate in specific areas of the city
- To provide information on emerging variants of COVID in the population.
How can you replicate or adapt this promising practice?
The program can be replicable in most resource-constrained urban settlements and serve as a strong example for the cities to invest in such surveillance systems. The technology of selecting the sites, collecting the sample and transporting the fragile sample to the labs, testing and data entry-powered by a digital backbone can easily be replicated to other cities- with the use of Standard Operating Procedures (SOPs) & guidelines and technical support. The digital backbone can be used and scaled to other cities. The sense making platform will need specialists like epidemiologists, clinicians, data scientists and bureaucrats to be able to translate into city-wide policies and action.
As a platform for public health, apart from COVID-19, this cost-effective system can also track other pathogens of pandemic potential, illicit opioids, and antimicrobial resistance (also known as a slow pandemic). Environmental surveillance for COVID is possible both for sewered and non-sewered connections.
As a pioneering and innovative city-wide approach, the precision pandemic surveillance approach can be scaled up across India and other countries, influencing surveillance policies.
The platform provides SoPs and handholding support and its data architecture to replicate in their own cities or residential townships, universities with residences etc.
How was this promising practice implemented?
GEOGRAPHY
In India, the practice is being implemented in the city of Bangalore, Karnataka. Initially, the Precision Pandemic Surveillance Initiative covered only 45 open drain sites, adding one more recently to make the total sites to 46. However, in December 2021, NCBS (National Center for Biological Sciences) with TIGS (Tata Institute of Genetics and Society) and Biome through their work with BWSSB, joined the platform to expand and add 28 STPs from sewersheds. Hence, now the initiative tests samples across 74 sample collection sites covering the 46 open drains and 28 sewersheds. The selection of sites is based on multiple factors including perennial flow of wastewater, presence of population and households near the open drains and accessibility for taking samples throughout the year.
The coverage of open drains and sewersheds ensure comprehensiveness and inclusivity of different population sections in the city. The population in Indian cities is primarily divided into two types, among other distinctions: the households linked with an underground sewer network in which the wastewater drains out to sewersheds through pipes for treatment, and households in which the wastewater drains out in the open stormwater drains, which primarily comprise of slums and unauthorized dwellings where more vulnerable and marginalized communities reside.
Hence, the insights from surveilling wastewater from both sources provide a better picture of infection spread within the city’s population.
PARTNERS AND STAKEHOLDERS
Precision Pandemic Surveillance Initiative involves a group of partners for implementing this practice on ground starting from a project management agency, a laboratory partner for sample testing, sample collection agency and a partner for stakeholder management. The initiative started with engaging different partners with specific roles to play in the implementation. These partners were specialized in their domain. As the implementation largely involves sample collection, testing, results sharing, data analytics and communication, each partner is very critical for a successful operation. Communicating and keeping the stakeholders informed for actions is the ultimate and most vital role in the initiative.
In addition to this, short term consultancy on understanding and explaining the city's sanitation system, site selection, epidemiology and developing data infrastructure becomes very helpful, especially in the designing phase of the project.
The below table shows the main partners which are critical for the initiative:
|
Partner type |
Roles and responsibilities |
|
Project Management |
Project Management and facilitation, Data Management and Analytics |
|
Sample collection agency |
Sample site selection; sample collection and transportation |
|
Laboratory partner |
Laboratory partner,sample processing and testing, technical and clinical support |
|
Stakeholder Engagement |
Sharing the findings and liasioning with Government stakeholders |
The initiative also requires a list of resources including experts like Local sewer and drainage expert, Sanitation expert, Data Analyst, Wastewater Epidemiologist apart from the 4 partners listed above. In order to implement the surveillance system, a list of sample collection sites, sample collection, storage and testing tools, safety gears, testing equipment and other supplies are required.
In Bangalore, the practice is working with Bruhat Bengaluru Mahanagara Palike (BBMP), which is a city corporation accountable for controlling COVID spread in the city. The Corporation has a dedicated nodal person from their COVID war room to review the surveillance data to understand the current scenario and discusses how this data could be added with other surveillance data for better planning of action. The team works closely with them to provide an Early Warning signal in case the site positivity and viral load increases in the city.
COVERAGE
The initiative currently has 46 open drains sites and all the functional 28 sewersheds from where the samples are collected and tested. The frequency of sample collection is twice every week from each open drain site and once in ten days from each sewershed.
The black colored symbols represent 28 sewersheds and 46 blue colored symbols represent open drains in the city.
As the open drains flow through multiple wards and locations within the city, the 45 sites are taken as a proxy for overall city-wide representation. In addition to this, the data from 28 sewershed also represent a specific catchment area and population. Hence, most of the insights shared and reported to the city administration, BBMP is representation of the city's population as a whole.
THE PROCESS
The implementation plan was discussed with partners and consultants in consideration of resources and in context of the city's infrastructure and systems. The standard operating guidelines were developed after a thorough study from various references of other environmental surveillance initiatives, across the world. We adopted European Commission guiding principles for wastewater surveillance to develop the SOPs and other practices as those are more applicable.
The process of wastewater surveillance involves a number of activities and data collection at different stages. A sample is collected from designated sites as per the sample collection plan (prepared following the sample frequency) and delivered to the laboratory. The laboratory processes each sample to extract RNA and then runs the RT PCR test through the qPCR method to detect the viral load (determined by RNA copies/ml). After the sample results are declared, it is analysed with the help of earlier datasets to convert it into data insights for interpretation. The data interpretation is followed through a communication system by the team and shared to the stakeholder for assessment. The overall process takes around 15 hours
The following diagram shows the complete process:
DATA MANAGEMENT AND DIGITIZATION
The data management has been a critical part of the implementation of this initiative. The processes within the initiative have been digitized so as to have the records for each activity which are carried out. Digitization also helps in:
- Check human data entry errors in the implementation process
- Electronic record-keeping of the data is handy to access for future analysis.
- Check typos in data entry to reduce the data cleaning during data analysis
- Facilitate data analytics through a structured database
- Real-time updates through online dashboards
The initiative has an end to end online data entry system, which helps in managing and analysing the data easily and quickly. The initiative operates a data entry system through a complete package of ArcGIS, consisting of a data entry and management tool (Survey123 app), data analysis & visualization tool (ArcGIS dashboards) and data presentation and web services (AcGIS story map). This helps in complete digitization of the initiative with more readily available data for further analytics.
The Survey123 app has an inherent feature of tracking the geo-coordinates and hence, when the data is entered for sample collection, it automatically tracks the location’s geo coordinates and auto-populates the location entry for each sample.
The below table demonstrates how data is been managed in the initiative:
|
Processes |
Sample Collection Plan |
QR code for sample identification |
Data Collection Tool (ArcGIS Survey123) |
Data repository and visualization - online dashboard (ArcGIS Survey123) |
Report findings and insights |
|
Tool |
Calendar | QR code | ArcGIS, Calendar | Digital Mapping Tool | Google Slides, Tableau |
|
Data/ Details captured |
1. Date and time of the visit 2. Allocation of sites among sample collectors 3. Geo-coordinates of the sites 4. Sample number |
1. Name of the initiative 2. Site identifier 3. Sample number |
1. QR code scanner 2. Date and time 3. Location of each site (Geo- coordinates) |
1. Web map of Bangalore on viral load trends 2. Time series graph on viral load trend for each site |
1. Dashboards on week-wise positive sites 2. Week-wise city-wide viral load trend |
|
Significance/ usage |
1. Helps in review and evaluation 2. Helps in effective project management |
1. Check typos and data entry errors 2. Increase time efficiency 3. Easy to use 4. Helps identify each sample |
1. Digitized data collection 2. Facilitates data analytics and visualization 3. Easy to store and protect |
1. Facilitates data interpretation 2. Facilitates comprehensive view of the findings |
1. Facilitates possible actions for COVID infection control 2. Provides additional insights on infection spread within the city |
To avoid typos and other human errors on data entry, QR codes are used to enter data in the data collection form. Once the sample collection plan is prepared, each sample which is planned is alloted a unique sample ID. This sample ID consists of the name of the site and the number of the sample and this sample ID is linked with QR code. Once the QR code is scanned, the app automatically detects the site source with the linked sample ID and populates some of the required entries and thus manual entry is not required. This QR code is pasted in the outer surface of each bottle in which the sample is collected.
- Sample Collection: With the pre-decided sample collection plan and frequency, the sample collector visits the site and collects the sample. The records for each activity are entered through the Survey123 app.The collected sample is stored in an ice box with ice packs to ensure the quality of the sample for testing. The RNA structure of the virus tends to degrade in high temperatures.
- Sample delivery: After collecting samples from each planned site, it is delivered to the lab through the ice box.
- Sample receiving, processing and testing: After the lab receives the samples, the lab staff process each sample for RNA extraction and finally sends them for PCR testing, where the final results (positive/negative/invalid) and viral load calculation is conducted.
- Analytics: After the results are entered, it automatically gets analysed by the system and dashboard showing viral loads for each site gets updated on real time.
- Communication: The results are also observed and analyzed with different analytical tools for better interpretation. After the interpretation, a sense-making communication is developed which is more crisp, comprehensible and action oriented to the stakeholder (BBMP) to arrive at a conclusion and a possible action.
DATA ANALYTICS
Data visualization: The dashboards developed for sharing the insights are embedded in the initiative’s web link, which is updated regularly for public view. This helps the viewer (both govt and general public) to understand the trend of infection in the city. As per the data sharing system, the initiative provide the following findings which are updated on a regular basis:
- City-wide positivity
It shows and determines the week-wise trend of site positivity in the city level.
The above graph shows the percentage of sites of which the samples were tested positive out of the total samples covering all sites within a week. This indicates if the number of sites tested positive has increased or decreased from the last week. Hence, when the percentage of the site positivity increases in a week from its preceding week, it indicates a warning of infection spreading within the city.
- City-wide viral load trend
It shows a cumulative (aggregated) viral load trend of all sites taken together, which determines the increasing or decreasing concentration of RNA copies in a sample. The viral load is determined by RNA copies/ml.
The above graph shows the cumulative VL in the city’s wastewater. The increasing trend indicates the concentration of RNA copies in the sample is increasing, whereas the decreasing trend shows the same decreasing.
- Site-wise viral load trend with map
This is a city map highlighting the site-wise viral load trend by comparing the previous VLs for each site.
In the above map, the increasing trend is shown as a red circle as a warning, whereas the decreasing trend is shown by a downward green triangle. Orange and grey circles represent no change and consistent negative samples in the sites, respectively.
COMMUNICATION WITH STAKEHOLDERS
The initiative was developed to set an early warning system for future COVID outbreaks by analysing data trends from wastewater testing. It was meant to support local governments in better understanding the disease trend and have evidence-based decision-making in a resource-constrained environment during public health emergencies like COVID pandemic.
The initiative is focused on providing insights of the city-wide infection trend as the main stakeholder, city’s corporation (BBMP) caters and serves the entire city population.
Hence, the reports which are shared to BBMP on a regular basis, informs them about the early warning and potential risk the population may be at. These early warnings can drive better planning of disease control and resource allocation and deployment in managing the outbreak.
In addition to sharing data and findings to the stakeholder, it was realised that other stakeholder, such as the general public of the city should also be communicated about the situation, so that they can be sensitized about the findings of the initiative and take necessary precautions based on those findings. In this regard, the dashboard displayed in the Initiative’s web link was made publicly accessible and updated real-time every day. In addition to this, a twitter handle, precisi0nhealth was set up from which a post is sent every week on Friday of the weekly findings from the initiative, tagging BBMP and public in general.
So far, the findings from the sample test results and analysed data are shared and presented to the local government, BBMP on a periodical basis. The details of reporting the findings to BBMP is mentioned below:
|
Daily |
Weekly |
Monthly |
|
Online dashboard reflecting viral loads for each site in bangalore.precisionhealth.in
|
Precision Health Twitter handle (https://twitter.com/Precisi0nHealth) Actively followed and re-shared by BBMP COVID Update handle (@BBMP_Covid19)
|
Monthly report to BBMP with:
Key meetings
|
|
Sharing number of positive sites via Precision Health Twitter handle (https://twitter.com/Precisi0nHealth) |
Online Web map with weekly viral load trend for each site |
There are also key meetings with the health officials of BBMP through:
- BBMP expert committee meetings
- One on one ad hoc when there are spikes
- Regular updates with epidemiologists
In addition to this, any Early Warnings which are detected in the initiative are shared to the BBMP on an ad hoc basis.
VARIANT TESTING
Genome sequencing to identify new and emerging variants in the wastewater samples was initiated in June 2021. This helps track evolution of lineages and variants of the RNA virus, which helps the scientist and public health professional in understanding the virus mutation and public health risk from the new variants.
For this, a new and separate map was developed to identify the location of each variant identified after Genome Sequencing.
What are the lessons learned from this Bright Spot?
- The data and findings obtained from the initiative primarily focus on providing preliminary insights on rising infections in the city. Hence, these findings are best placed when it is integrated with the existing surveillance system to augment the effective tracking and control system and to make a smart decision-making system.
- Before the initiative, there were few studies which postulated the effectiveness of environmental surveillance through sample testing from open drains, primarily because most of the studies were conducted in developed countries where sewersheds are more common. Hence, through this initiative, we learned that environmental surveillance works effectively also from open drains.
- City administration’s is vital to translate findings into action. As the initiative largely focuses on an early warning system for infection outbreak, shared sense-making platforms are critical.
- Rapid succession in achieving government’s acquiring of confidence on the concept and subsequently taking action on the findings is critical for the success of the initiative.
- Most important lesson is the public health communication, choice of words, timing, platforms are just as critical, if not more critical than the science itself ( as it was established fairly earlier on). To get from the science to action- one must use trusted relationships to onward accurate ethical and user-sensitive communication.
Precision Health is one of Asia’s first city-wide wastewater surveillance systems for COVID being implemented in Bangalore. The practice has initially prioritized open drains as sample collection sites that cover a larger vulnerable and marginalized population of the city, which are not connected with the underground sewage network. Hence, supporting community surveillance especially of the marginalized communities that can access and afford individual testing.
This is not the only program that conducts environment testing of COVID however, this particular intervention is special because of the kind of partnership, and the science to administrative action loop which is absent in most other initiatives.
Dr. Angela Chaudhuri (angela@catalysts.org ) and Shirish Harshe (shirish@catalysts.org ) can be contacted to learn more about this program/practice.
The individuals part of this promising practice can be found here (bangalore.precisionhealth.in, and precisionhealth.in)
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