GCRF_NF98_Building an Early Warning System for community-wide infectious disease spread: SARS-CoV-2 tracking in Africa via environment fingerprinting

Lead Research Organisation: University of Bath
Department Name: Chemistry

Abstract

Mitigating the rapid global spread of Covid-19 requires real-time data on community infection prevalence in order to guide targeted intervention measures on regional, national and global scales. Individual diagnostic testing is of paramount importance for short- and long-term management of the pandemic, but limits on capacity (both of kits and trained workers) mean that healthcare settings are prioritised over the community.
Here we propose a novel supplemental low-resource approach for broad community-wide surveillance of SARS-CoV-2 infection prevalence. We aim for a real-time Covid-19 risk prediction platform for community-wide diagnostics via wastewater-based epidemiology (Figure 1). Disease markers present in domestic wastewater can reveal the health status of contributing population, and we propose that this includes the infection prevalence by SARS-CoV-2. Real-time spatiotemporal estimation of this novel coronavirus in urban water across several sites in South Africa (Cape Town) and Nigeria (Lagos) will provide a broad picture of community infection prevalence, even for asymptomatic cases, as well as the level of acquired immunity, thus identifying hotspots for priority testing, contact-tracing and quarantine and will provide more accurate projections of the spread of the virus and the infection fatality rate. As communities contribute directly to wastewater, we will be able to estimate true infection rate at the community level, including also asymptomatic and pre-symptomatic people. The virus loading levels will be used to establish status and time trends. This would enable rapid identification of hot spots for management via targeted intervention measures and potentially support important decisions regarding entry into and exit from 'lockdown' periods as well as focussed screening of selected communities.
 
Description Output 1: Methods for SARS-CoV-2 quantitative analysis developed

Sample collection (sampling), preparation and analysis methods have been developed in three countries and are currently used for quantification of SARS-CoV-2 in wastewater. Extensive quality control and standardisation work has been carried out with respect to sample storage, RNA extraction and RT-qPCR. We have also spent time focusing on controlling for quantitative changes over time in the size of the population contributing to the wastewater signal.

Output 2: Spatiotemporal monitoring of SARS-CoV-2 in South Africa, Nigeria and in the UK

Longitudinal surveillance in three countries undertaken for a minimum of 6 months. Samples were analysed for SARS-CoV-2 and other indicators.

Output 3: Datasets collated

Datasets were collated, both on wastewater SARS-CoV-2 prevalence as well as public health data on case incidence and prevalence A laboratory information management system was developed for the wastewater measurements and metadata to create an auditable, robust framework for data storage and analysis.

Output 5: Modelling tools
Data science workflow for validating and integrating laboratory results with public health data with continuous updating put in place. Software for addressing the mismatch between WWTP catchments and public health reporting areas produced. Models for predicting incidence and prevalence of SARS-CoV-2 using WBE-methods developed and assessed using external data.
Exploitation Route The impact and value of this project, and its GCRF-funded predecessors (ReNEW and EDGE) has been demonstrated by the Covid pandemic, since a strong - multidisciplinary team with shared interest in WBE was already in place and collaborating when the need for wastewater surveillance was acknowledged by the respective Governments. The strong existing collaboration provided a core leadership group (at least in South Africa) that could immediately play a pivotal role in the rapid assembly of a national task team 'South African Collaboration COVID-19 Environmental Surveillance System (SACCESS)' with important partners, amongst others the South African Water Research Commission (WRC), the City of Cape Town Metropolitan Municipality (CCT), National Department of Health, National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), South African Medical Research Council (SAMRC), as well as our industrial partner ERWAT and various South African academic- and private research institutions. Further evidence of impact is the weekly reporting to senior management at Stellenbosch University on wastewater surveillance at both their Main Campus (Stellenbosch, Western Cape, South Africa), as well as the Tygerberg Medical Campus (Cape Town, Western Cape, South Africa). The project further allowed for the potential to collaborate with other international peers such as those from Monash University's Department of Civil Engineering (Australia). Moreover, the establishment of strong working relationships between UoB, SU, SAMRC, ERWAT and CCT that was made possible by this project allowed for the available foundations that is needed for the expansion and/or continuation of future routine wastewater-based risk assessment interventions.
Sectors Environment,Healthcare

URL https://ewsresearch.com/our-projects/ews-C19/
 
Description The impact and value of this project, and its GCRF-funded predecessors (ReNEW and EDGE) has been demonstrated by the Covid pandemic, since a strong - multidisciplinary team with shared interest in WBE was already in place and collaborating when the need for wastewater surveillance was acknowledged by the respective Governments. The strong existing collaboration provided a core leadership group (at least in South Africa) that could immediately play a pivotal role in the rapid assembly of a national task team 'South African Collaboration COVID-19 Environmental Surveillance System (SACCESS)' with important partners, amongst others the South African Water Research Commission (WRC), the City of Cape Town Metropolitan Municipality (CCT), National Department of Health, National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), South African Medical Research Council (SAMRC), as well as our industrial partner ERWAT and various South African academic- and private research institutions. Further evidence of impact is the weekly reporting to senior management at Stellenbosch University on wastewater surveillance at both their Main Campus (Stellenbosch, Western Cape, South Africa), as well as the Tygerberg Medical Campus (Cape Town, Western Cape, South Africa). The project further allowed for the potential to collaborate with other international peers such as those from Monash University's Department of Civil Engineering (Australia). Moreover, the establishment of strong working relationships between UoB, SU, SAMRC, ERWAT and CCT that was made possible by this project allowed for the available foundations that is needed for the expansion and/or continuation of future routine wastewater-based risk assessment interventions.
First Year Of Impact 2021
Sector Communities and Social Services/Policy,Environment,Healthcare
Impact Types Societal,Policy & public services

 
Title Protocol for Viral RNA concentration and isolation from influent wastewater 
Description Influent wastewater (sample) is 'spiked' with internal positive control. Sample is heat inactivated. Sample is clarified (centrifugation). Sample is concentrated (centrifugation + PEG/PBS). RNA is extracted from sample (TRIzol extraction). RNA is prepared for quantification by e.g. qPCR/dPCR/sequencing 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact Use of methodology for COVID-19 outbreak tracking through analysis of community wastewater samples. Contribution to national and international efforts to build an early warning system for infectious disease outbreaks and monitor the COVID-19 pandemic. 
 
Description 1. Kasprzyk-Hordern, Global practices on environmental surveillance for public health tracking and forensics, WRC WORLD ENVIRONMENTAL HEALTH DAY WEBINAR, ENVIRONMENTAL HEALTH, A KEY PUBLIC HEALTH INTERVENTION IN DISEASE PANDEMIC PREVENTION 23 September 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Seminar focussed on Wastewater-based epidemiology
1. Kasprzyk-Hordern, Global practices on environmental surveillance for public health tracking and forensics, WRC WORLD ENVIRONMENTAL HEALTH DAY WEBINAR, ENVIRONMENTAL HEALTH, A KEY PUBLIC HEALTH INTERVENTION IN DISEASE PANDEMIC PREVENTION 23 September 2020
Year(s) Of Engagement Activity 2020
 
Description AQUA˜360: Water for All - Emerging Issues and Innovations", talk entitled: 'Water-based chemical mining for environmental and public health assessment, 21/08/2021 (keynote) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk entitled: 'Water-based chemical mining for environmental and public health assessment
Year(s) Of Engagement Activity 2021
URL http://www.aqua360.net
 
Description Advances made in South Africa on chemical- and molecular biomarker profiling using Wastewater-Based Epidemiology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Third sector organisations
Results and Impact An in-person attendance of a hybrid conference that were organized by the University of Queensland, Brisbane, Australia. The conference was attended by local students from Queensland University, as well as industry partners involved in water quality and epidemiology. Furthermore, the conference was attended by more than 50 participants on the virtual platform of the conference. The results from the EWS-C19 project from the South African component was presented.
Year(s) Of Engagement Activity 2021
URL https://qaehs.centre.uq.edu.au/ttw-conference
 
Description Announcement of the implementation of a wastewater surveillance platform to detect COVID-19 outbreaks on the Stellenbosch University campus 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Media (as a channel to the public)
Results and Impact A press release was done on the Stellenbosch University newsletter that announced the initiation of a wastewater-based epidemiology surveillance program on the two major campuses of Stellenbosch University. The methodology of the surveillance program was explained as well as the value that this may provide as an early warning system to safeguard the health system of campus staff and students. The press release also served as a platform for reaching other media platforms and journalists to expand on the project's communication strategy.
Year(s) Of Engagement Activity 2021
URL https://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8289
 
Description Barbara Kasprzyk-Hordern, Wastewater Based Epidemiology and One Health, Water Security Alliance Series 2021, 1/11/-21-4/11/21 (invited talk) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Barbara Kasprzyk-Hordern, Wastewater Based Epidemiology and One Health, Water Security Alliance Series 2021, 1/11/-21-4/11/21 (invited talk)
Year(s) Of Engagement Activity 2022
 
Description Barbara Kasprzyk-Hordern, Wastewater based epidemiology for environmental and public health assessment, Joint Biosecurity Centre seminar series9/09/2021 (invited talk) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Talk entitled: 'Wastewater based epidemiology for environmental and public health assessment'
Year(s) Of Engagement Activity 2021
 
Description Bath scientists to track COVID-19 through monitoring wastewater in cities in the UK and Africa, 11 September 2020, University of Bath 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release
Year(s) Of Engagement Activity 2020
URL https://www.bath.ac.uk/announcements/bath-scientists-to-track-covid-19-through-monitoring-wastewater...
 
Description Cape Town's sewers offer clues to next Covid-19 wave 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact An online article was performed by a member of the Groundup newsletter that outlined the concept of SARS-CoV-2 surveillance in wastewater and the potential application of this concept to serve as an early warning system for future outbreaks and/or infection waves that was experienced with the SARS-CoV-2 pandemic.
Year(s) Of Engagement Activity 2021
URL https://www.groundup.org.za/article/sewage-is-being-used-to-detect-cape-towns-next-covid-wave/
 
Description Conference Talk (TTW5, Brisbane): Wastewater-Based Epidemiology for Spatiotemporal COVID-19 Outbreak Tracking: Disease Surveillance, Quality Assurance and Modelling in the South West UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Over 100 water researchers from around the world attended this event both in person (Brisbane) and online. This talk sparked professional discussion of sample stability and sources of methodological variability in wastewater-based epidemiology.
James Boxall-Clasby received the Overall Best Student Presentation Award for this talk.
Year(s) Of Engagement Activity 2021
URL https://qaehs.centre.uq.edu.au/files/7441/TTW5%20Program_15_09_21.pdf
 
Description Detecting COVID-19 outbreaks on campus using wastewater-based epidemiology 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact An live interview was conducted by a South African news broadcaster. Dr. Edward Archer provided an overview of the methodology and concept of sewage surveillance for SARS-CoV-2 at student campus residences and wastewater treatment plants, including the mention of the link with the larger South African community on SARS-CoV-2 detection via wastewater (SACCESS) that was initiated at the onset of the COVID-19 pandemic in the country and to date, include more than ten research institutions and more than forty members nationwide that meet on a regular basis to compare insights on sewage surveillance.
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=zS8F2KXE36w
 
Description Explaining the methodology of detecting SARS-CoV virus via wastewater-based epidemiology 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A newsletter in the native Afrikaans language was posted on the methodology and process of sewage surveillance of the SARS-CoV-2 viral fragments to serve as an early warning indicator of ongoing infections and new potential outbreaks in communities. This newsletter was aimed to reach a defined audience within South Africa to explain the process and applicability of this tool to inform on public health.
Year(s) Of Engagement Activity 2021
URL https://www.litnet.co.za/covid-19-en-rioolwater-hoe-om-die-morsige-virus-op-te-spoor/
 
Description Kasprzyk-Hordern, Wastewater-based Epidemiology and Environment Fingerprinting for Public Health Assessment, BNet Webinar: Biosensors and Environmental Monitoring - New Developments in Environmental Biotech, 17th November 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Kasprzyk-Hordern, Wastewater-based Epidemiology and Environment Fingerprinting for Public Health Assessment, BNet Webinar: Biosensors and Environmental Monitoring - New Developments in Environmental Biotech, 17th November 2020
Year(s) Of Engagement Activity 2020
URL https://ebnet.ac.uk/biosensors/
 
Description Media piece on wastewater-based epidemiology for public health surveillance 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact A media piece was conducted through a South African news channel that detailed the process of wastewater collection and analysis for disease, such as RNA fragments of the SARS-CoV-2 virus, and pharmaceutical/illicit drugs from communities.
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=-ZM-oGpBl5E
 
Description Modelling spatio temporal COVID-19 trends through wastewater surveillance 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation and interview for the H2020 project MOnitoring Outbreak events for Disease surveillance in a data science context consortium.
Year(s) Of Engagement Activity 2021
URL https://mood-h2020.eu/
 
Description Royal Society of Chemistry Webinar - Wastewater Based Epidemiology entitled Wastewater-Based Epidemiology: past, present and future, 9/09,2021 (invited talk) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk entitled Wastewater-Based Epidemiology: past, present and future.
Year(s) Of Engagement Activity 2022
URL https://www.rsc.org/events/detail/47496/webinar-wastewater-based-epidemiology
 
Description Solayide Adesida, Iseoluwa Akinwumi, Mayowa Fasona, Joseph Minari, Temilola Oluseyi, Esther Oluwole, Sunday Omilabu, Timothy Segun, Temitope Sogbanmu, Detection of SARS-CoV-2 RNA in Wastewater Samples from Anthropic Sites in Lagos Metropolis, Nigeria: Implications for community surveillance and management. 11th International Conference and General Assembly of the Nigeria Young Academy - 24th to 26th August 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Solayide Adesida, Iseoluwa Akinwumi, Mayowa Fasona, Joseph Minari, Temilola Oluseyi, Esther Oluwole, Sunday Omilabu, Timothy Segun, Temitope Sogbanmu, Detection of SARS-CoV-2 RNA in Wastewater Samples from Anthropic Sites in Lagos Metropolis, Nigeria: Implications for community surveillance and management. 11th International Conference and General Assembly of the Nigeria Young Academy - 24th to 26th August 2021
Year(s) Of Engagement Activity 2021
 
Description Virtual event - Stellenbosch University Science Café - Developing a risk prediction platform for COVID-19 using sewage water 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The session was part of the annual Stellenbosch University Science Café that was moved to a virtual platform in 2021 due to the ongoing COVID-19 pandemic. These events are well received on the regional calendar that forms part of the annual Stellenbosch Word Festival. The session contained presentations/dialogue from the EWS-C19 research partners and collaborators that included Dr Edward Archer (Stellenbosch University), Prof. Wolfgang Preiser (Head Medical Virology; Stellenbosch University) and Dr. Rabia Johnson (Senior Researcher; South African Medical Research Council). The methodology of wastewater-based epidemiology was explained to a large audience that attended the virtual event, including the distribution of the session on Youtube that potentially attracted a wider national and international audience.
Year(s) Of Engagement Activity 2021
URL https://www.youtube.com/watch?v=BBVPsQ-c5qs
 
Description Water fingerprinting for environmental and public health assessment, Centre of Research in Biomedical Science (CRIB), UWE, 4th December 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Talk by Kasprzyk-Hordern focussed on 'Water fingerprinting for environmental and public health assessment', Centre of Research in Biomedical Science (CRIB), UWE, 4th December 2020
Year(s) Of Engagement Activity 2020