To progress the contribution of wastewater surveillance of the COVID-19 virus SARS-CoV-2, a group of international partners have established a global collaborative repository for data. By Joan B Rose, Gertjan Medema, Colleen Naughton, Panagis Katsivelis and Vajra Allan.
With the rapid rise in interest in the COVID-19 virus SARS-CoV-2 in wastewater, Michigan State University, KWR Water Research Institute, the University of California Merced, Venthic Technologies, and PATH are collaborating to develop the Wastewater SARS Public Health Environmental REsponse, or W-SPHERE. This is a new global centre for data and for public health use cases on SARS-CoV-2 in wastewater. Its mission is to advance environmental surveillance of sewage, informing local and global efforts for monitoring and supporting public health measures to combat COVID-19.
History of COVID and monitoring
Over the one-and-a-half years since the declaration of the COVID-19 pandemic, there have been more than 236 million cases and 4.8 million deaths. Using methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater-based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater. Unlike data for COVID-19 cases and mortality, there was not a global dashboard to harmonise and follow the databases emerging all over the world to track wastewater monitoring of SARS-CoV-2 RNA.
COVIDPoops19
Into this space, the COVIDPoops19 Twitter account was started in May 2020 and its associated global dashboard for wastewater monitoring of SARS-CoV-2 (https://arcg.is/1aummW) was launched in September 2020.
The methods used to create this inventory for the COVIDPoops19 ArcGIS online dashboard included a Google form submission of wastewater SARS-CoV-2 surveillance information and other dashboards from specific individuals or groups. Information was also gathered from literature reviews, as well as from social media and news keyword searches. Additionally, the team attended webinars worldwide to obtain new data on who is setting up monitoring programmes.
After more than a year of data tracking, the dashboard has documented wastewater surveillance for SARS-CoV-2 in more than 57 countries, 2691 sites, and 263 universities/institutions. A small subset (92) of those monitoring for SARS-CoV-2 in wastewater provide their data publicly, but fewer than 20 provide downloadable data. Of the 57 that are conducting wastewater monitoring, 36 (63%) are in high-income countries, 12 (21%) in upper-middle-income, 8 (14%) in lower-middle-income, and one (2%) is a low-income country.
COVIDPoops19 is actively informing the W-SPHERE global data centre on open data from individual country/city wastewater dashboards and soliciting data submissions and agreements from the research community. These sites are promoting the open sharing of this information and the development of a global approach to wastewater surveillance.
W-SPHERE
W-SPHERE is built upon the current knowledge platform of the Global Water Pathogen Project (GWPP) (www.waterpathogens.org), being directly aligned and synergistic with the GWPP mission to provide knowledge on pathogens in sewage. In the case of enteric pathogens, the goal of GWPP has been to promote better understanding and updates to sewage treatment to meet the UN water-related SDG 6. W-SPHERE is supporting and demonstrating a historic paradigm shift in the use of wastewater monitoring data, moving from waterborne disease probability estimates to the support of community disease surveillance and public health interventions. Using COVIDPoops19 as a starting point, the GWPP website has been revamped with a new look and the addition of a new global repository of the SARS-CoV-2 environmental surveillance data.
Working with dashboards, utilities, scientists and laboratories, our interdisciplinary team of environmental virologists and public health specialists, as well as engineering and IT professionals, have developed this global database. W-SPHERE gathers datasets (Figure 1), along with their metadata and dictionaries, in one centralised location where it is formatted for open access use and sharing across the globe. The data is visualised on dynamic/updated maps on a global and country scale, with options to zoom in regionally at a spatial level that can protect the anonymity of the facility when that has been requested and enable examination of the spatial and temporal trends of SARS-CoV-2 (Figures 2 and 3).
To date, the W-SPHERE has collected 13 datasets representing 655 Sites from 24 countries (see table for example dashboards).
An example of a unique database available is in Malawi where the wastewater facility in Blantyre is being monitored, as well as the river system in the city, to capture the non-sewered population. The support for low- and middle-income countries is needed in order to maximise resources for public health.
Datasets that appear on the map are also downloadable through a dedicated ‘Data’ section in W-SPHERE. Currently, download options include samples in tabular (CSV) format, sites information in tabular (CSV) format, and their combined information available in GeoJSON format for map visualisations. W-SPHERE also provides all data through open-access application programme interfaces (APIs). The data will be useful for further analysis and for generating discussion on harmonisation, standardisation, normalisation and visualisation of such datasets.
W-SPHERE encourages researchers to contribute their own data through the website at https://sphere.waterpathogens.org/contribute. This allows researchers to create their own space for visualisations and analysis of their unique datasets while also adding value to the global knowledge of SARS-CoV-2 surveillance in wastewater.
Public health use cases
Around the world, city, state and national leaders are making decisions on how to respond to the pandemic, allocate resources, distribute vaccines and ultimately reopen communities. Sewage provides a window to view trends in community infection, earlier and more objectively and efficiently than other surveillance systems and has the potential to assist in public health decisions. This could benefit society greatly.
W-SPHERE will showcase good examples of the added value of wastewater surveillance and how wastewater data have been used to guide public health decision making on different levels (national, regional, local, building-level) and in sewered and non-sewered settings in high-, middle- and low-income countries.
The first use cases will show how wastewater data provides: early warning of (re)appearance of the virus in a community; confirmation of absence of active virus circulation in a community; an indication of underreported cases in city areas; and a metric for virus circulation in cities that is not sensitive to clinical testing/availability/policy/willingness and therefore represents an objective complement to the data on reported cases.
Through the W-SPHERE website, visitors are encouraged to submit good use cases via a short online form with essential information about their use case and how the wastewater data has been used to support public health actions. For selected use cases, information is collected and used to populate engaging storytelling visualisations that promote the responsible research groups, a summary of their outcomes in numbers and the decisions that were affected by those outcomes.
The future
The W-SPHERE team is currently working on ways to automate data harvesting and the updating of numerous global dashboards, so that it provides fresh versions of datasets in a homogenised format, suitable for meta-analysis. We are actively looking at methods that would allow the connection (mapping) of data dictionaries used globally, so that data harmonisation can happen seamlessly between diverse data sources. Our aim is not to come up with yet another data standard, but to support wastewater monitoring data and global publishing in ways that it will result in meaningful and reusable data products.
The team is also preparing novel visualisation approaches at the level of a dataset and a monitoring location that will enable new, multi-faceted views of the data. Some of the new approaches include: the creation of collated visualisations from multiple datasets in wide regions; high-resolution visualisations of datasets at a building level; overall comparisons of concentrations with local clinical data; visualisation of data on Variants-of-Concern; and data storytelling techniques for the selection of specific monitoring locations in non-sewered settings. •
More information https://sphere.waterpathogens.org
To get in touch with us, please visit: https://sphere.waterpathogens.org/form/contribute
Professor Joan B Rose is at Michigan State University, Professor Gertjan Medema is at KWR Water Research Institute, Dr Colleen Naughton is Assistant Professor at University of California Merced, Panagis Katsivelis is at Venthic Technologies, and Vajra Allan is at PATH.
Example dashboards from W-SPHERE
Catalonia
Sites: 71
Samples: 1630
Gene targets: N1, N2, E, IP4
Time frame: July 6, 2020 – March 9, 2021
Link: https://sarsaigua.icra.cat/
Link: Catalonia Dataset
The Netherlands
Sites: 11
Samples: 1106
Gene targets: N2
Time frame: February 05, 2020 – June 16, 2021
Link: Netherlands Dataset
Ohio
Sites: 65
Samples: 2323
Gene targets: N2Time frame: July 19, 2020 – June 6, 2021
Link: https://coronavirus.ohio.gov/wps/portal/gov/covid-19/dashboards/other-resources/wastewater
Link: Ohio Dataset
Scotland
Sites: 113
Samples: 4176
Gene targets: N1
Time frame: May 28, 2020 – June 23, 2021
Link: https://informatics.sepa.org.uk/RNAmonitoring/
Link: Scotland Dataset
Switzerland
Sites: 6
Samples: 400
Gene targets: N1, N2
Time frame: October 10, 2020 – August 15, 2021
Link: SARS-CoV-2 in Wastewater (https://sensors-eawag.ch/sars/overview.html
Link: Switzerland Dataset
