DATA issues that stopped almost 16,000 coronavirus cases being recorded in England – delaying contact tracing efforts – should never have happened, the Health Secretary has said.

Matt Hancock told MPs that a technical problem over the weekend occurred with the system “that brings together” data from NHS test sites and tests processed by commercial firms.

Public Health England (PHE) told the PA news agency that the issue had been caused by an Excel file maxing out during an automated process.

The issue resulted in 15,841 cases between September 25 and October 2 being left out of figures.

It said files had now been broken down into smaller, multiple files to avoid the issue happening again.

It is understood that data from labs was being pulled into Excel templates by PHE so it could then be uploaded to a central system and made available to NHS Test and Trace.

Hancock said it had been decided in July that the PHE “legacy system” needed an upgrade, with contracts for a new system awarded in August.

He said 51% of people testing positive had now been contacted by the system, telling the Commons: “Contact tracing of these cases began first thing Saturday.

“We brought in 6500 hours of extra contact tracing over the weekend and I can report to the House as of 9am today 51% of the cases have now been contacted a second time for contract tracing purposes.

“I want to reassure the house that outbreak control in care homes, schools and hospitals has not been directly affected because dealing with outbreaks in these settings does not primarily rely on this PHE system.”

Hancock said it was “critical that we work together to fix these issues that were themselves identified by PHE staff working hard late on Friday night.”

He added: “This incident should never have happened but the team has acted swiftly to minimise its impact and now it is critical that we work together to put this right and make sure it never happens again.”

Regarding the scale of the pandemic, Hancock said the Government’s assessment has “not substantially changed” after the error, which was being investigated fully.

“This morning the Joint Biosecurity Centre (JBC) presented to me their updated analysis of the epidemic based on the new figures,” he said.

“The chief medical officer, Chris Whitty, has analysed that our assessment of the disease and its impact has not substantially changed as a result of this data.

“The JBC has confirmed that this has not impacted the basis on which decisions about local action were taken last week. Nevertheless, this is a serious issue that is being investigated fully.”

Analysis by the PA news agency shows that the weekly rate of new Covid-19 cases has soared in dozens of areas of England following the blunder.

Manchester now has the highest rate in England, with 2927 cases recorded in the seven days to October 2 – the equivalent of 529.4 cases per 100,000 people, up from 246.4 in the previous week.

Knowsley in Merseyside has the second highest rate, up from 324.1 to 498.5, with 752 new cases, and Liverpool is in third, up from 306.4 to 487.1, with 2426 new cases.