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.


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Description We have tested animal faeces and environment samples near sewage outflows (water, sediments) for the presence f SARS-CoV-2 and related coronaviruses.

Animal faeces
50 animal faecal samples (38 bat samples; 12 samples from mustelids and rodents) have been tested for the SARS-CoV-2 E gene. Of these samples, seven samples tested positive. Five positive samples (M.daubentonii (1), Plecotus auritus (1), R. hipposideros (3)) with the largest number of E gene copies were sent to the NEOF Centre for Genomic Research, Liverpool for metagenomic sequencing. Furthermore, 42 of the 50 animal faecal samples were also tested for the SARS-CoV-2 ORF1a and RdRp gene, of which none were positive. Another 19 samples were also test for the SARS-CoV-2 N1 gene. One of these samples was positive and another two were inconclusive. All positive/inconclusive results for the N1 gene were from bats. These results indicate that we have probably identified new coronaviruses for UK bats. Overall, faeces from 11 different bat species has been tested (M.daubentonii, Plecotus auritus, R. hipposideros, E. serotinus, M. bechsteinii, M. nattereri, P. nathusii, P. pipistrellus, P. pygmaeus, R. ferrumequinum, R. hipposideros). Faeces have also been tested from the Eurasian otter, rodents and water voles.

44 sediment samples from 10 sites (5 in Norfolk, 4 in London, 1 in Little Marlow) have been tested for the SARS-CoV-2 E gene. 35 of the 44 samples were also tested for the SARS-CoV-2 ORF1a and RdRp genes. Another 20 samples were tested for the N1 gene. No samples yielded positive test results.

Two water samples from two CSO sites (Little Marlow and Hammersmith) have been tested for the SARS-CoV-2 E and N1 genes. Neither sample was positive.
Exploitation Route It is too early to say as we first need to confirm the identity of the coronaviruses found in UK bat with genome sequencing
Sectors Environment,Healthcare

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 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