To date, COG-UK have focused their sequencing might on samples from people with COVID-19 by accessing discarded samples after PCR tests performed in the mega-labs and NHS hospitals. This gives detailed information on viral variants present in individuals but may not provide a comprehensive community level overview, since this misses cases who are not tested, including people who have no symptoms and those not accessing healthcare.
Wastewater, such as sewage effluent, has long been used for poliovirus surveillance in many countries globally. Traces of SARS-CoV-2 virus are present in the faeces of those with COVID-19 and can be detected in small quantities in the resulting sewage output. This makes the detection of viral RNA fragments in wastewater from a particular community a cost-effective way of determining burden of disease and could be used as an early warning system to detect outbreaks.
Like patient testing, wastewater testing uses the PCR method. The question now is whether sequencing of material generated by the PCR test can be used to define the viral variants circulating in tested populations.
Why use wastewater to study SARS-CoV-2 transmission?
Wastewater (sewage) treatment is an essential part of a strong public health infrastructure. A comprehensive wastewater network exists across the United Kingdom to collect and treat water from toilets, baths, sinks and washing machines from domestic and residential premises, industrial wastewater discharges to sewers and rainwater.
Environmental surveillance based on testing of wastewater has been used for many years to detect poliovirus and more recently to study antimicrobial resistance. Studies have also demonstrated that this can detect enteric viruses such as norovirus, hepatitis A and E, adenovirus and rotavirus [Ref 1].
SARS-CoV-2 is shed in the faeces of people with asymptomatic and symptomatic infection [Ref 2] and testing is being developed and rolled out in numerous countries to detect RNA from SARS-CoV-2 shed into wastewater.
Detecting fragments of viral RNA in untreated wastewater is achieved by molecular tests, similar to one of the common technologies used to test people for COVID-19. Specifically, this is a quantitative Polymerase Chain Reaction with a reverse transcriptase step (RT-qPCR), which targets specific genes in the virus. The readout is the number of RNA copies in the sample, and data is reported as gene copies per litre of wastewater sample collected. This is important, as it gives some measure of the number of people infected. Current estimates are that this type of testing can detect 1 infected person in 1000, although this is influenced by local plumbing and on the significant variability in faecal shedding rates of SARS-CoV-2 from individuals [Ref 3].
This approach does not identify those individuals who are infected. But it provides a surveillance mechanism that can be used to monitor the presence of COVID-19 in populations and can provide data on trends over time. This captures people with symptoms, people who have mild or no symptoms, or people who have not sought a test, which is more comprehensive than is possible with our current diagnostic testing approach.
A summary of wastewater COVID-19 monitoring in the UK was prepared in Nov 2020 by the Department for Environment, Food and Rural Affairs (Defra) and the Joint Biosecurity Centre (JBC), and is available on the gov.uk website. This provides a technical overview of wastewater-based epidemiology and its application for COVID-19, a summary of the UK Wastewater Programmes and presentation of some results and data use-cases from the English programme.
Where does COG-UK fit in?
Sequencing of wastewater samples that have flagged as positive by PCR can reveal the genetic code of fragments of the SARS-CoV-2 genome. This may be sufficient to capture viral genome diversity between and within cities; that is, what virus variant is circulating in a given area. Although further work is required to define how accurate the approach is, it may also be possible to detect variants of interest that have particular properties. At the moment, this is focused on the ‘Variant of Concern 202012/01’, which has rapidly spread around the UK and is associated with an upsurge in the number of people with COVID-19.
In December 2020, COG-UK convened a seminar on the detection of SARS-CoV-2 in wastewater. The purpose was to share knowledge and foster collaboration. Key sequence-related discussion topics were how to use existing and developing technologies for sequencing; how to determine the main variants circulating and their change in prevalence change over time; and whether it is possible to identify emerging new variants and their source.
Several COG-UK research groups are exploring these issues. One group has used the ARTIC protocol and the Grid ION sequencing instrument, whilst another is using Illumina technology. Their work is currently focused on detecting mutations in the fragments and comparing these with entire genome information generated from patient samples to determine if the lineage in wastewater can be defined.
Finally, sequencing proceeded in a COG-UK lab over the holiday season, an important activity that evaluated whether wastewater could detect mutations associated with our latest and most worrying variant, Variant of Concern 202012/01.
These are early days of technical development and research. In the coming months, sequence data generated from UK wastewater will be compared with the COG-UK and clinical epidemiology datasets to establish how the wastewater data and data from people matches up.
It will be important to find ways to link and analyse human and wastewater data, which will involve further development of the MRC-CLIMB genome data repository and analysis infrastructure used by COG-UK.
- Bosch, A., 1998. Human enteric viruses in the water environment: a minireview. Int Microbiol, 1(3), pp.191-6.
- Wu, Y., Guo, C., Tang, L., Hong, Z., Zhou, J., Dong, X., Yin, H., Xiao, Q., Tang, Y., Qu, X. and Kuang, L., 2020. Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. The lancet Gastroenterology & hepatology, 5(5), pp.434-435.
- Jorgensen, A.U., Gamst, J., Hansen, L.V., Knudsen, I.I.H. and Jensen, S.K.S., 2020. Eurofins Covid-19 sentinel TM wastewater test provide early warning of a potential COVID-19 outbreak. MedRXiv.
COVID-19 Genomics UK (COG-UK)
The current COVID-19 pandemic, caused by the SARS-CoV-2, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.
Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, 15 academic partners providing sequencing and analysis capacity, and the central sequencing hub of the Wellcome Sanger Institute. A full list of collaborators can be found here. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.
COG-UK was established in April 2020 supported by £20 million funding from the COVID-19 rapid-research-response “fighting fund” from Her Majesty’s Treasury (established by Professor Chris Whitty and Sir Patrick Vallance), and administered by the National Institute for Health Research (NIHR), UK Research and Innovation (UKRI), and the Wellcome Sanger Institute. The consortium was also backed by the Department of Health and Social Care’s Testing Innovation Fund on 16 November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the winter period.