Sewage samples are being tested to determine which Covid-19 variants are most prevalent across regions accounting for two-thirds of England’s population.

The Department of Health and Social Care (DHSC) said the programme had helped identify the need for surge testing in areas such as Bristol and Luton. On Wednesday, the health secretary, Matt Hancock, said testing and vaccinations were being surged in six areas as a result of wastewater analysis.

“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,” said Andrew Engeli, who is leading on the wastewater testing scheme at the Joint Biosecurity Centre, part of the newly formed UK Health Security Agency.

The programme genome-sequences any samples that have traces of the virus to identify whether it is a variant of concern, such as the B.1.617.2 strain first detected in India. Sewage is then monitored after surge testing to ensure the variant is no longer circulating in the area.

Sewage testing works because although coronavirus predominantly infects cells lining the respiratory tract, it is also shed in the faeces of some infected individuals. By collecting samples from wastewater treatment plants, scientists can use PCR (polymerase chain reaction) machines to detect and quantify the amount of RNA from Sars-CoV-2 in different areas.

The wastewater scheme was piloted last summer, and has since been expanded to include hundreds of sites across England, Wales, Scotland and Northern Ireland. It is now thought to cover 70% of England’s population.

The DHSC said that monitoring in a specific area can pinpoint localised outbreaks, including within specific institutions such as food manufacturing sites or prisons, without relying on residents to come forward for swab testing.

Although wastewater monitoring is not accurate enough to establish the number of infected individuals, it can indicate where variants are circulating and provide an early warning of escalating cases. This can be followed up with additional community testing and messaging, or the sewage equivalent of surge testing – where manhole covers are lifted up and samples taken from sewers in specific areas to try to narrow down the source of the outbreak.

After the pandemic, the DHSC may continue to use sewage testing to monitor other viruses such as influenza, enabling the NHS to predict major outbreaks.

Last month, a dedicated wastewater testing lab opened in Exeter, and is now receiving samples gathered by Environment Agency scientists from 500 locations across England.

The DHSC said: “It is not possible to trace back the samples of Covid-19 to specific individuals and no personal information is collected.”