Up to three-quarters of new UK Covid cases are now thought to be caused by the variant first detected in India, the health secretary has said.

The variant of concern, known as B.1.617.2, has been linked to a rise in cases in hotspots around the country. Data released on Thursday by Public Health England (PHE) shows 6,959 cases have been confirmed so far in the UK, up from 3,424 the week before.

Announcing the figures, PHE said hospitalisations were rising in some affected areas. “Hospital attendances and admissions are predominantly in unvaccinated individuals, highlighting how crucial it is that people in these areas come forward to receive vaccination,” it added.

Earlier, Boris Johnson said “we may need to wait” for the lifting of all Covid restrictions in England, planned for 21 June. The PM said he saw nothing “currently in the data” to suggest the government would have to delay unlocking but noted the signs of an increase in cases of the variant.

Dr Jenny Harries, the chief executive of the UK Health Security Agency, told a Downing Street press briefing the rise in cases of the variant could, in part, be down to increased testing in affected areas. She added that in some areas outbreaks had been squashed, while efforts continue in the north-west.

“I think it is really, really just on the cusp at the moment, if we see cases rise we are not clear yet quite whether that is a rise in the variant cases taking off or whether it is actually a rise because we are actively, quite rightly, detecting them and then challenging these chains of transmission,” she said.

On Thursday a total of 3,542 people were reported as testing positive for Covid in the UK – the highest figure since 12 April.

The health secretary, Matt Hancock, said on Thursday evening that the vaccine was “severing the link between cases and hospitalisations”.

But experts warned the link was not yet broken because only 44% of adults had received both Covid jabs and the vaccines do not offer 100% protection against hospitalisation. “You can see that in Bolton, but you can see [it] most clearly in Scotland,” said Prof Christina Pagel, the director of University College London’s clinical operational research unit.

Scotland, where there have been outbreaks of the India variant in areas including Glasgow, had 98 patients in hospital with Covid on 26 May, up from 58 on 6 May.

Meanwhile, Bolton NHS foundation trust, which serves an area also hard-hit by the India variant, has seen the number of patients in hospital rise from 11 on 9 May to 41 on 25 May – the latest date for which figures are available.

Earlier in the day Hancock said about one in 10 people in hospital in current Covid hotspots had received both jabs, noting this suggested a “high degree of confidence” that the vaccines are very effective.

While experts have said two doses offer good protection against the India variant, it is somewhat weakened compared with the Kent variant, particularly after the first dose.

Paul Hunter, a professor in medicine at the University of East Anglia, said a link between cases and hospitalisations remained. “If case numbers go up hospitalisations will inevitably go up,” he said. “The issue is whether they go up as far as was the case in the past and that is probably a no.”

A new report from PHE also suggests the link has not yet been completely broken, with hospital admission rates for Covid showing a small rise to a rate of 0.79 per 100,000 in the week ending 23 May, compared with 0.75 per 100,000 in the previous week. Rates were highest in the West Midlands and among those aged 85 and above.

Dr Yvonne Doyle, the medical director of PHE, said it was encouraging that the number in hospitals around the country remains low. “However, we are concerned about the outbreak of the variant first discovered in India and in some areas hospitalisations have slightly risen,” she said.

The news came as PHE released new data on variants in the UK, revealing it has designated a new variant as being under investigation, on the basis of the mutations it contains and “increased importation from a widening international area”. “The C.36.3 variant was first detected in Thailand, in cases who had travelled from Egypt,” the team wrote. So far 109 cases have been detected in the UK.

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