The Catriona plague, named after the Nilfgaardian ship that brought it to the Northern Kingdoms, is a disease which is extremely similar to the bubonic plague. Its appearence in the North is a result of a time-travelling paradox.
During her escape from the world of Aen Elle, Ciri travelled through the time-space continuum and one of her stops was likely medieval Europe in our World during the plague epidemic of the 14th century. She entered a port town (perhaps Genoa or another Mediterranean port) and was immediately repelled by the place because of the corpses of people and animals lying in the streets. There were also many fleas and many burned buildings marked by white crosses.
She escaped to another point in the time-space continuum, but before she was able to do so, a few fleas attached themselves to her jacket. Her next stop was another unnamed port town. She was able to discern that the port laid somewhere in Nilfgaard. She decided to quickly leave this place as well, but just before the next time-space jump one of the surviving fleas fell from her jacket and made itself comfortable on an old sewer-rat. This rat boarded an old dirty hulk that set sail Cintra that very evening. The name of the hulk was Catriona. Later in the Saga, there was small note about a dying tomcat who had caught a rat that left that hulk.
In The Witcher computer game
St. Lebioda's Hospital in the Temple Quarter of Vizima is filled with the victims of Catriona, and Shani spends her time trying to help them in Chapters II and III. She probably works in the hospital during Chapter IV, as well, but Geralt is no longer in Vizima to witness this.
According to the old women in the Outskirts, when the plague first came, the first to go were the cats and dogs, then the rats and finally the people. Apparently, the lack of food even drove some of the more desperate to cannibalistic and necrophagic acts and many ghouls were created as a result.
Glossary Entry
Catriona "A disease which quickly spread through all the northern countries after the war with Nilfgaard. Those who suffer from catriona die a terrible death — their convulsions become stronger each day, they vomit blood and mucus, and have bloody diarrhea. After a fortnight or so they die in agony."
In The Witcher 3: Wild Hunt
The plague is rampant across the war-torn countryside in the wake of the invasion of the North by Nilfgaard.