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The Home Office is being urged to explain why official health data has shown only one case of diphtheria near Manston processing centre in recent months, despite there being 50 instances of the disease linked to the site.

According to weekly figures about cases of infectious diseases in England, known as the notification of infectious diseases data (NOID), there has only been one case recorded since September that is likely to relate to Manston – in Ashford, Kent.

Only nine other cases of diphtheria have been recorded in this published data in recent months in a variety of areas including Manchester, Eastbourne and Southampton. On Saturday, the Home Office said one person at Manston may have died from diphtheria.

Small boat arrivals undergo initial Home Office checks at Manston, a Ministry of Defence site in Kent, which is understood to be currently empty after various controversies. However, new small boat arrivals are predicted for Monday and use of this site is expected to continue.

Home Office sources confirmed to the Guardian there had been 50 diphtheria cases linked to Manston that had come to light in recent weeks.

The UK health security agency (UKHSA), which publishes the data, said the figures relate to cases reported by doctors. But Home Office sources said all those screened for suspected diphtheria had been seen by Home Office medics, who are A&E doctors.

The transport secretary, Mark Harper, told Sky’s Sophy Ridge on Sunday: “My understanding is those cases were people who had that disease before they came to the United Kingdom.”

Andy Baxter, the assistant general secretary of the Prison Officers Association, which has members working at the site, said: “We have consistently raised concerns around the presence of diphtheria at Manston, concerns around the infection control within the facility, and concerns that people were being moved to hotels and onward accommodation without being tested. This failure to test will have seen infected people moved into our communities.

“Our first priority is the safety of our members to ensure they don’t take home an infectious disease to their families, but we have to pose the question: have people working further up the process also been put at an unacceptable level of risk and has public health in general been placed at risk?

“The UKHSA needs to explain why those cases have not all been reported in a timely manner through their NOID published weekly reports.”

The Guardian is aware of at least one confirmed diphtheria case in an asylum seeker who was moved from Manston to a hotel in the north of England before his test results came through. It is understood that, as well as asylum seekers who contracted the infection, at least one person working at Manston tested positive for it and was hospitalised.

According to UKHSA sources, individuals are tested for diphtheria at Manston by Home Office medics if they have “compatible symptoms”. The sources say they are working with the Home Office and continue to keep these recommendations under review.

The Home Office initially said a person who died at Manston did not have diphtheria, but on Saturday said he had tested positive for diphtheria after an initial test produced a false negative. The cause of death has not yet been confirmed.

Dr Trish Mannes, the UKHSA director for the south-east, said: “The risk of diphtheria to the wider public remains very low, due to high uptake of the diphtheria vaccine in this country, and because the infection is typically passed on through close prolonged contact with a case.”

The Home Office said: “We work closely with a range of partners within the community including local authorities and health leads to make sure information is shared in a timely way and that everyone leaving Manston is given access to appropriate treatment.

“We take both the welfare of those in our care and our wider public health responsibilities extremely seriously. As such, we continue to work closely with the NHS and UKHSA to support the individuals affected and limit the transmission of infection.”

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