Liverpool has the second highest rate, up from 287.1 to 456.4, with 2,273 new cases.
Other areas recording sharp increases include; 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).
Dr Duncan Robertson, lecturer in management sciences and analytics at Loughborough University and fellow of St Catherine’s College, Oxford, said the error was “an absolute scandal”.
He tweeted: “These individuals will not have had their contacts identified and those contacts may have become infectious and may have been spreading the virus.”
Paul Hunter, professor of health protection at the University of East Anglia, said “there will be occasional glitches” in a system this size, but added: “I think the thing that surprised me was the size of it – almost 16,000 results going missing over the course of a week is quite alarming I think.”
Prof Hunter told BBC Radio 4’s Today programme: “If you’re going to do your contact tracing, there is a very short time frame in which you can do it effectively.
“And the reason is that we know now that this infection is most infectious at around the time people develop symptoms – so very early on in the illness – and if you’re going to therefore identify contacts… it really needs to be done within a matter of a day or so if you’re going to actually have any effect.”
It is understood the Excel spreadsheet reached its maximum file size, which stopped new names being added in an automated process, but has now been split into smaller multiple files to prevent the issue happening again.
Shadow health secretary Jonathan Ashworth said the error was “shambolic”, adding that “people across the country will be understandably alarmed.”
Health Secretary Matt Hancock was to make a Commons statement on Monday afternoon on the issue.