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Passengers on the Eurostar service will be tested for Ebola at terminals in Ashford and Ebbsfleet, according to the government health chiefs.
But in a statement to KentOnline, Eurostar said the government's announcement today was "the first they've heard of it" and the company would be liaising with the relevant authorities.
The news comes after Kent and Canterbury Hospital ran an emergency drill earlier this week to test the hospital's ability to react in case of an outbreak.
The government said screening at airports in Liberia, Sierra Leone and Guinea has been in place for some weeks in an effort to ensure all passengers leaving affected countries are checked.
Handheld thermal scanners, which check body temperature, can be used to identify passengers who have a high fever, one of the symptoms of ebola.
A Downing Street spokesperson said: "Enhanced screening will initially be implemented at London's Heathrow and Gatwick airports and Eurostar terminals and will involve assessing passengers' recent travel history, who they have been in contact with and onward travel arrangements as well as a possible medical assessment, conducted by trained medical personnel rather than Border Force staff."
Passengers will also be given advice on what to do if they develop symptoms later.
P&O Ferries and Eurotunnel both say they have no plans to introduce screening measures unless told to do so by the government.