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CalMac' s Campbeltown-Ardrossan service has been cancelled while the MV Caledonian Isles is deep cleaned.
The company said crew members who are close contacts of those who tested positive are also being replaced.
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Two additional return sailings will be run on the MV Isle of Arran so that people can get on and off the island, which has seen tourist reach their peak summer high.
Tommy Gore, Area Operations (Clyde) said: “Two crew members on board MV Caledonian Isles have received positive Covid tests. According to current protocol, which is in place to protect passengers and staff from the chance of infection, we need to replace crew members who have been identified as close contacts and get the vessel deep cleaned as soon as possible.
“In order to ensure booked passengers can still get on and off the island, MV Isle of Arran will run operate two additional return sailings Ardrossan-Brodick today. All affected passengers have been contacted and made aware of this change.
“Extra sailings will also run today between Lochranza and Claonaig as an alternative crossing and we would encourage customers to use this route if at all possible.
“Unfortunately, this means that the Campbeltown-Ardrossan service today has had to be cancelled, with a replacement bus service for foot passengers running in its place. We apologise for this inconvenience and thank passengers for their understanding.”
The MV Caledonian Isles is expected to return to service tomorrow.
The latest interruption to ferry services on the Firth of Clyde come days after police were called to deal with passengers who refused to leave the Brodick ferry terminal after they were left stranded on Arran when the last ferry back to the mainland was cancelled on Thursday evening.
the problem arose when the MV Caledonian Isles, due to sail at 16.40 was diverted to assist a mayday distress call from a yacht that had lost its power around 4 pm.
It was stood down and returned to service, the 19.00 sailing was cancelled due to bad weather.
Up to 40 passengers were left without accommodation, with some being forced to sleep in their vehicles during the bad weather.
For those on foot, they were told to seek alternative accommodation, even though the buses that could take them further out into the island had finished.
Police Scotland said there were no complaints made with regard to how the incident was dealt with by its officers on the scene.
A spokesperson said: "Around 6.50 pm on Thursday, August 12 2021, police attended the ferry terminal at Brodick after the last ferry sailing had been cancelled due to weather conditions and some passengers were refusing to move from the pier.
"Officers offered advice and assistance and local arrangements were made, via police and Visit Scotland, to accommodate stranded passengers.”
The spokesperson added that no further police action was taken or required.