United Kingdom – A government-led programme to test sewage for traces of COVID-19 has ramped up genomic sequencing to help rapidly detect outbreaks of variants of concern.
The Environmental Monitoring for Health Protection (EMHP) Programme, led by the Joint Biosecurity Centre (JBC), a part of the newly-formed UK Health Security Agency (UKHSA), has reached a new milestone of testing wastewater for COVID-19 and variants across more than two thirds of the population in England.
A new laboratory in Exeter opened last month dedicated to analysing wastewater, making it one of the biggest wastewater processing labs in the world.
Analysts from the JBC are using this insight to help build a better picture of where the virus is circulating, particularly asymptomatic COVID-19 infections that may otherwise go undetected.
Increased genomic sequencing of these sewage samples will provide more clues to where variants of concern may be circulating undetected in communities.
It can pick up evidence of variants from infected people and continue to monitor sewage after surge testing has ended in an area. This helps provide reassurance the variant is no longer circulating in that community.
The JBC shares this insight with local authorities, NHS Test and Trace and Public Health England who take action to prevent outbreaks.
Insights from the programme have already been used in Bristol and Luton to provide timely understanding of the spread of variants in their communities and help to provide reassurance that local outbreak control measures are working.
Wastewater sequencing is another tool to shield communities against the threat of new variants, as the country follows the roadmap out of national restrictions.
Chief Executive of the UK Health Security Agency Dr Jenny Harries said:”
This innovative programme supports the work of Public Health England and NHS Test and Trace to help us understand where the virus may be circulating undetected.
Sequencing wastewater samples provides an additional detection system for variants of concern, enabling us to respond more effectively to outbreaks and better protect citizens.”
Programme lead at the Joint Biosecurity Centre Dr Andrew Engeli said:”
Testing wastewater for traces of COVID-19 gives us an overall picture of national and local infection rates and is a great complement to the work that happens in the wider NHS Test and Trace programme.
As infections fall and we head out of national restrictions, analysing wastewater to detect variants early on is important to help local authorities and NHS Test and Trace act quickly to stop variants from spreading in communities.”
Wastewater samples are taken from around 500 locations in England and sent to the EMHP Laboratory at Exeter Science Park. Environment Agency scientists analyse the samples to quantify the amount of COVID-19 present.
Some of these samples are then sent to other university labs, working with the Centre for Environment, Fisheries and Aquaculture Science (CEFAS), or to CEFAS laboratory partners who sequence the samples to identify variants.
The EMHP programme is a non-invasive way of providing insight for potential spikes in infection in an area. Testing takes place at sewage treatment works and the sewage network across England to understand infection levels at both national and local scales.
Without the need to rely on individuals coming forward for swab tests, monitoring in a catchment area is able to pinpoint outbreaks to smaller areas and neighbourhoods.
There are also pilots analysing the wastewater from specific institutions such as within the food supply chain and prisons. It is not possible to trace back the samples of COVID-19 to specific individuals and no personal information is collected.
Environment Agency Chief Executive James Bevan said:”
From the start of the pandemic, the Environment Agency has supported the nation’s efforts to tackle COVID-19. The join-up between our scientists in the Environment Agency, water companies, government colleagues, public health officials and the academic community has delivered results that have had a real impact in the fight against the virus.
Chief Scientific Adviser at the Department for Environment, Food and Rural Affairs (DEFRA) Professor Gideon Henderson said:”
Rapid ramping up of laboratory capacity has been fundamental to the success of the wastewater COVID-19 programme. This has only been possible through teamwork between government departments and agencies – the Environment Agency and CEFAS – and universities, and demonstrates the broad strength of UK science.
The resulting laboratory infrastructure allows early detection of outbreaks and powerful tracking of variants from genomic sequencing. It will continue to provide valuable information as social distancing restrictions ease and to monitor for future disease.”
Scientists and academics from across the UK are collaborating on their findings, coordinated by the Joint Biosecurity Centre, and sharing data to build up a picture of cases across the UK.
Wastewater testing carried out by Environment Agency scientists and their counterparts across the UK is one of a number of tools used to closely monitor the evolution of COVID-19, from symptomatic testing to surveillance studies and genomic sequencing of new variants.
It will also play a crucial role in tracing other viruses in the future, including the flu, and understanding the impact viruses may have on local NHS systems.
The EMHP programme is led by the Joint Biosecurity Centre in the UK Health Security Agency, in collaboration with DEFRA, the Environment Agency, CEFAS, water companies, Water UK and academic partners.
The programme is coordinated with similar programmes run by the Northern Ireland Executive, Scottish Government and Welsh Government.