The World Health Organisation (WHO) epidemics expert will be treated at University Hospital Hamburg-Eppendorf (UKE), a spokesman for the Hamburg health authorities confirmed to The Local.
The specially-equipped medical jet from Sierra Leone with the patient on board landed at Hamburg Airport shortly before 11am. The Senegalese medic was then transported in a special isolation vehicle provided by the fire service.
The man was infected while working with Ebola samples in a WHO laboratory in the stricken west African country.
The virus has infected more than 2,600 people and killed 1,427 since reemerging in west Africa this year.
Ebola has a fatality rate of up to 90 percent according to the WHO, but during the current outbreak the survival rate has been 47 percent.
It is transmitted by direct contact with blood and body fluids.
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At the end of July, a medic from Sierra Leone who had contracted the disease was meant to be treated in Hamburg's UKE, but he died before he could be flown to Germany.
The clinic has an isolation ward shut off behind three airlocks designed to stop contaminated material and microbes escaping.