COVID 19 - SARS-CoV-2 in Sewage Treatment Works: Environmental Impact, Infectivity and Prevalence Modelling

Lead Research Organisation: Imperial College London
Department Name: Life Sciences


Given that SARS-CoV-2 RNA is detectable in faeces for prolonged periods (even for otherwise asymptomatic individuals), efforts have so far concentrated on trying to map its prevalence using sewage samples, e.g. via our partners at Bangor University (NERC Urgency Grant NE/V004883/1). Because live viruses have also been detected in the stools of patients affected by COVID19, there is growing concern about the risks of faecal-oral transmission to humans and/or wildlife (where the virus first originated) via sewage outflows and overspill. This is particularly worrying as, for example, hundreds of tonnes of raw sewage enter the Thames each year when sewers overflow during rainstorms, effectively bypassing sewage treatment works (STWs) when they exceed capacity. We combine expertise from Life Sciences and Mathematics at Imperial College, corona virology at Nottingham University, and a network of collaborators to fill this gap and to complement ongoing work in related (but not overlapping) areas. We have also already secured £49K of internal funding from Imperial College to prime the lab work, as a direct in-kind contribution. First, the potential for sewage (via effluent discharge, storm overflows, and other forms of run-off) to contribute to transmission to humans and wildlife will be measured by assessing RNA concentration and viral infectivity from environmental samples, from sewage outflows down to rivers, estuaries, and faeces from wildlife. Second, using data on concentrations of SARS-CoV-2 RNA in sewage and in the environment, we will provide models of population-level prevalence of COVID19 and elucidate key environmental transmission routes for management.
Description The presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated freshwaters is still poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. We investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over 8 months for SARS-CoV-2 RNA and infectious virus. Bivalves were sampled as sentinel species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. We found no evidence of SARS-CoV-2 RNA or infectious virus in UK samples, in contrast to RNA positive water and sediment samples from Serbia. Furthermore, we show that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for < 3 days, while RNA remained detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that infectivity should be embedded in future risk assessments of pathogen spillover.
Exploitation Route Bats in rehabilitation, whose rehabilitators have confirmed SARS-CoV-2 infections, require testing before release back into the wild; we have provided a new protocol for doing so in line with current guidelines.
Several studies have suggested SARS-CoV-2 originated from a viral ancestor in bats, but whether transmission occurred directly or via an intermediary host to humans remains unknown. Concerns of spill-over of SARS-CoV-2 into wild bat populations is hindering bat rehabilitation and conservation efforts in the UK and elsewhere. Current protocols state that animals cared for by individuals who have tested positive for SARS-CoV-2 cannot be released into the wild and must be isolated to reduce risk of transmission to wild populations. In collaboration with the Department for Environment, Food & Rural Affairs (DEFRA),
the Animal and Plant Health Agency (APHA), and the Bat Conservation Trust, we have
designed a reverse transcription - quantitative polymerase chain reaction (RT-qPCR)-based protocol for detection of SARS-CoV-2 in bats, using faecal sampling. Bats from the UK were tested following suspected exposure to SARS-CoV-2 and tested negative for the virus. With current UK and international legislation, the identification of SARS-CoV-2 infection in wild animals is becoming increasingly important, and protocols such as the one developed here will help improve understanding and mitigation of SARS-CoV-2 in the future.
Sectors Environment


Description Bats in rehabilitation have been tested for SARS-CoV-2 before release into the wild
First Year Of Impact 2021
Sector Environment
Impact Types Policy & public services

Description 'COVAIR': Is SARS-CoV-2 airborne and does it interact with particle pollutants?
Amount £515,964 (GBP)
Funding ID EP/V052462/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2021 
End 12/2022
Description How can NCS healthcare data be connected with wastewater surveillance of COVID-19 in a privacy-preserving fashion to inform epidemiological models and democratise data access?
Amount £56,330 (GBP)
Funding ID HDRUK2020.147 
Organisation Health Data Research UK 
Sector Private
Country United Kingdom
Start 01/2021 
End 06/2021
Description Animal and Plant Health Agency 
Organisation Animal and Plant Health Agency
Country United Kingdom 
Sector Public 
PI Contribution We have worked on Testing bats in rehabilitation for SARS-CoV-2 before release into the wild and designed a novel protocol submitted for publication to Conservation Science and Practice
Collaborator Contribution Provided expertise on policy and legal issues surrounding the release of bats and zoonoses
Impact publication still in revision
Start Year 2021
Description Bat Conservation Trust 
Organisation Bat Conservation Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Analyses of bat samples for SARS-CoV-2 before release after rehabilitation
Collaborator Contribution Provided bat faecal samples for testing for coronaviruses
Impact paper in revision
Start Year 2020
Description DEFRA 
Organisation Department For Environment, Food And Rural Affairs (DEFRA)
Country United Kingdom 
Sector Public 
PI Contribution Report findings to fortnightly meetings chaired by DEFRA with representatives of Public Health England, Environmental Agency, NERC, PIs of NERC Covid Grants, Water Companies, Office of National Statistics, Joint Biosecurity Centre, etc
Collaborator Contribution Link with DEFRA Chief Scientist and Chief Vet for policy development
Impact Fortnightly meetings
Start Year 2020
Description The UKRI COVID-19 AHI meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Led by BBSRC (Elizabeth Treadwell), a workshop was organised - the UKRI COVID-19 AHI meeting - with representatives from UKRI, but also DEFRA, APHA and a wider range of COVID grant grantees in comparison to TWEG. Again, the meeting was aimed at exchanging ideas and results, and PI Savolainen presented our results. A second follow-up such meeting is scheduled in April 2022 where PI Savolainen will provide further results on potential bat-human spillover in the UK more relevant to policies, as discussed already with DEFRA and APHA and which led to a policy paper in Conservation Science and Practice.
Year(s) Of Engagement Activity 2021
Description Transmission of Covid-19 in the Wider Environment Group (TWEG) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact PI Savolainen has attended monthly online meetings of the 'Transmission of Covid-19 in the Wider Environment Group (TWEG)' chaired by members of DEFRA's Chief Scientist, usual Dan McGonigle), with representatives from UKRI, water companies, PIs from NERC COVID grants, the Office for National Statistics (OST) and other relevant policy makers and analysists. These meetings have permitted exchange of ideas, protocols and results, contributions to major press releases, and avoiding of duplicated efforts; PI Savolainen reported on our progress each time.
Year(s) Of Engagement Activity 2020,2021