Cases of the Indian variant of coronavirus in the UK have risen by more than 2,000 in the space of a week, according to official figures.

Public Health England (PHE) said the latest weekly data showed there were 3,424 cases of the B1617.2 mutation – an increase of 2,111 on the previous week.

While most cases were concentrated in the North West – particularly Bolton – and London, PHE said it was seeing “clusters of cases” across the country.

Dr Meera Chand, the Covid-19 incident director at PHE, said it was essential people in the worst-affected areas who had yet to receive their second dose of the vaccine came forward as soon as it was offered.

“This is vitally important in the light of our current assessment that (B1617.2) has grown rapidly in England and may be highly transmissible,” she said.

“PHE will continue to monitor all variants closely, paying particular attention to the impact on hospitalisations and deaths which will help us to understand the protective effects of the vaccine.”

PHE said it was also investigating another new variant after 49 cases were identified, mostly in Yorkshire and the Humber region.

So far, there is no evidence that it causes more severe disease or renders the vaccines less effective.

At the same time NHS Test and Trace said 15,202 people in England tested positive for Covid-19 in the week to May 12 – up 5% on the previous week and the first seven-day increase since early January.

The latest figures came after Boris Johnson said on Wednesday that there was “increasing confidence” in Government that the vaccines were effective against the Indian variant.

The Prime Minister’s official spokesman said that the daily case rates had not shown any “sharp increases or significant areas of concern”.

The rise in cases of the Indian variant came as a leaked document suggested the rapid spread of the strain was at least partially due to failures at NHS Test and Trace.

The report seen by the BBC said for three weeks in April and May, eight local authorities in England did not have access to the full data on positive tests in their area, meaning more than 700 cases were not reported and traced locally.

Among the areas affected was Blackburn with Darwen – one of the areas where the Indian strain is most prevalent.

Downing Street said that only a small number of authorities had been involved and that the issue had been “quickly resolved”.

However, Labour said it showed the Government was continuing to make the same mistakes in its handling of the pandemic.

Shadow health secretary Jonathan Ashworth said: “It beggars belief that yet again local health experts on ground have been left in the dark for two weeks when we know acting with speed is vital to containing an outbreak.”

“Ministers need to explain what’s gone wrong and provide local health directors with all the resources they need to push infections down.”

According to a report by officials at one of the councils affected, seen by the BBC, the central Test and Trace system failed to notify its staff of the missing cases, meaning their contacts could not be traced.

The document went on to state that the rapid spread of Indian variant cases may be “partially or largely attributable to risks in the international travel control system”.

It added: “These were exacerbated by the sporadic failure of the national Test and Trace system.”

The latest disclosures came as a member of the Government’s Scientific Advisory Group for Emergencies (Sage) warned the country could be seeing the start of a third wave of the pandemic.

Professor Andrew Hayward, an infectious diseases expert at University College London, said he was “very concerned” about the rise of the Indian variant and new measures could be required to bring it under control.

He said it would become apparent over the next one to two weeks whether localised outbreaks of the variant would become more generalised.

“Obviously we’re doing everything we can to contain the spread of that, but it’s likely that more generalised measures may start to be needed to control it,” he told the BBC.

“So whilst I think we’ve always thought that we would have another wave of Covid, the size of that wave is going to very much depend on how transmissible the variant that causes it is and what proportion of the population have been vaccinated when it hits.

“Fortunately we’ve had a good proportion of the population vaccinated, but there’s still people who aren’t vaccinated in high-risk groups, the vaccine isn’t 100% effective, and also even in the younger groups, if you get many, many thousands or hundreds of thousands of cases, then you will expect a lot of hospitalisations and deaths to result from that.”