A computer glitch in the UK’s Test and Trace system means the true rates of coronavirus in cities such as Manchester, Leeds and Newcastle upon Tyne is far higher than previously thought.

Manchester now has the highest rate in England, with 2,740 cases recorded in the seven days to October 1 – the equivalent of 495.6 cases per 100,000 people, more than double the figure of 223.2 the previous week.

Liverpool has the second highest rate, up in a week from 287.1 to 456.4, with 2,273 new cases, PA Media reports.

Knowsley is in third place, up from 300.3 to 452.1, with 682 new cases.

Delays in tracing the contacts of those infected due to the computer glitch mean potentially tens of thousands of carriers of the virus have not been told to self-isolate.

The problem was caused by an Excel spreadsheet reaching its maximum file size, which stopped new names being added in an automated process, PA Media reported.

Other areas recording sharp increases include Newcastle upon Tyne (up from 256.6 to 399.6, with 1,210 new cases); Nottingham (up from 52.0 to 283.9, with 945 new cases); Leeds (up from 138.8 to 274.5, with 2,177 new cases); and Sheffield (up from 91.8 to 233.1, with 1,363 new cases). 

All but Nottingham are already under some sort of increased local restrictions.

All figures are based on Public Health England data published on Sunday night.

Asked on Monday how many contacts of positive coronavirus cases had been missed as a result of the error, Johnson told reporters in central London: “I can’t give you those figures.

“What I can say is all those people are obviously being contacted and the key thing is that everybody, whether in this group or generally, should self-isolate.”

He said the updated figures meant that the prevalence of the virus was where experts had expected it to be and it would soon be apparent if extra restrictions were having the intended impact.

“The incidence that we are seeing in the cases corresponds to pretty much where we thought we were,” he said.

“And, to be frank, I think that the slightly lower numbers that we’d seen, you know, didn’t really reflect where we thought the disease was likely to go, so I think these numbers are realistic.”

Shadow health secretary Jonathan Ashworth said the error was “shambolic”, adding that “people across the country will be understandably alarmed.”

Health secretary Matt Hancock is to make a Commons statement on Monday afternoon on the issue.