Yes, they can, but dirty cages and drafty conditions can also lead to respiratory disease as well. Coming in contact with rats infected with viruses and then handling your rats without taking precautions can also be a problem.
The ammonia in urine is said to irritate the lungs, so don't let your cages get too wet and dirty.
Cedar can also cause liver and kidney damage. So can pine. See above section on bedding.
More info HERE.
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