Shelter collies have cough and runny nose

we just got two border collie lab mix puppys from a shelter 3 days ago. they are 12 weeks old and had there first shots. the day we brought them home our female had a really runny nose and a dry cough, it has died down since then. 2 days later our male woke up and has the same cough but much worse and he has muscle spasms with whining fits…he will throw himself on the floor and acts like his whole body itches badly. it seems to help him when we rub him constantly. i do know that there was a sick dog at the shelter but i dont know what was wrong with it. no one we have asked has been able to help. thank you