Covid-19 could now be endemic in some parts of the country that combine severe deprivation, poor housing and large BAME communities, according to a highly confidential analysis by Public Health England.

The document, leaked to the Observer, and marked “official sensitive”, suggests the national lockdown in these parts of the north of England had little effect in reducing the level of infections, and that in such communities it is now firmly established.

The analysis, prepared for local government leaders and health experts, relates specifically to the north-west, where several local lockdowns have recently been put in place following spikes in numbers. But it suggests that the lessons could be applied nationally. Based on detailed analysis of case numbers in different local areas, the study builds links between the highest concentrations of Covid-19 and issues of deprivation, poor and crowded accommodation and ethnicity.

Produced in the last few weeks and containing data up to August, it states: “The overall analysis suggests Bolton, Manchester, Oldham and Rochdale never really left the epidemic phase – and that nine of the 10 boroughs [of Greater Manchester] are currently experiencing an epidemic phase.”

The five worst-hit areas are all currently in the north-west. Bolton had 98.1 cases per 100,000 people last week, with 63.2 in Bradford, 56.8 in Blackburn and Darwen, 53.6 in Oldham and 46.7 in Salford. Milton Keynes, by comparison, had 5.9 per 100,000, and it was 5.2 in Kent and 3.2 in Southampton.

Comparing other English regions, the study says: “Each region has experienced its own epidemic journey with the north peaking later and the NW [north-west], Y&H [Yorkshire and Humber] and EM [East Midlands] failing to return to a near zero Covid status even during lockdown, unlike the other regions which have been able to return to a near pre-Covid state.”

It also questions, under a heading marked for “discussion”, why anyone should expect fresh local lockdowns to work in these areas now: “If we accept the premise that in some areas the infection is now endemic – how does this change our strategy? If these areas were not able to attain near zero-Covid status during full lockdown, how realistic is it that we can expect current restriction escalations to work?”

The comments point to friction between Public Health England and the government over the strategy to tackle local outbreaks as a potential second wave of Covid-19 threatens.

Last night, Gabriel Scally, visiting professor of public health at the University of Bristol and a member of the independent Sage committee, described the findings of the leaked report as “extremely alarming” after being shown them by the Observer.

“The only way forward is to build a system which provides much better, more locally tailored responses,” Scally said. “There is no integrated find, test, trace, isolate and support system at the moment. The data on housing is extraordinarily important. Overcrowded households are part of public health history. Housing conditions are so important and always have been, whether it was for cholera or tuberculosis or Covid-19.

“Doing something about housing conditions for someone who has an active infection is extremely important and it is not something that can be handled by a call centre run by a commercial company hundreds of miles away.”

Scally said that helping people to isolate by giving financial support was also crucial: “Taking two weeks off if you are on a zero-hours contract is not an option for people.”

Matthew Ashton, director of public health at Liverpool city council, said on seeing the study: “This report shows a strong link between our most deprived areas, our BAME communities and poor housing communities, and that can lead to the virus becoming endemic. I absolutely agree with that. But I think it is also more complicated in that there are different types of outbreaks and different types of ways in which the virus could become endemic, such as opening the night-time economy and young people getting the virus asymptomatically and then passing it on.”

Last night, amid continuing confusion over rules on quarantining when returning to the UK, Labour called for a “rapid review” to restore public confidence. In a letter to the home secretary, Labour is urging the government to consider introducing a “robust testing regime in airports” that could help to safely minimise the need for 14-day quarantine.

There have been more than 340,000 confirmed cases of coronavirus so far in the UK, and more than 40,000 people have died, according to government figures.

Local lockdowns are now being implemented or relaxed across the country in response to surges. The most recent have seen Norfolk, Rossendale and Northampton added as “areas of enhanced support”, meaning the government will work with local authorities to provide additional resources – such as testing or contact tracing – to help bring infection numbers down.

Improvements in Newark and Sherwood in Nottinghamshire, Slough in Berkshire and Wakefield. West Yorkshire, mean they have been removed from the watchlist. Restrictions already in place in parts of Greater Manchester, Lancashire and West Yorkshire have been eased.

In Scotland, restrictions on visiting other households were reintroduced this week in Glasgow, West Dunbartonshire and East Renfrewshire.