Squirrel Pox Outbreak Action Plan in Place
Traps are being offered to the public in order to catch and kill grey squirrels in the area.
The virus has no apparent effect on the greys but is invariably fatal to their red counterparts.
Scotland is one of the UK's last red squirrel strongholds, with the south of the country seen as being on the frontline of conservation efforts.
The organization Red Squirrels in South Scotland said post mortem examinations had confirmed the outbreak around the River Tweed.
The public has been advised not to put out garden feeders as a measure to help stop the disease spreading.
Estates on both sides of the river have already removed a number of the animals.
General Manager - Staff Entomologist