In the middle of the 14th Century of the Christian era, bubonic plague spread through Eurasia, claiming millions of lives from China to Western Europe. The terrible plague came to be known as "the Black Death."
The 14th Century was, in the Jin Yong universe, the era of HSDS. As the plague lasted for decades, its effects likely continued to spread well into the 15th Century, after the foundation of the Ming Dynasty, which might put it into the time period of SPW and a number of Gu Long's stories as well.
The Black Death/Great Plague is never addressed in any work of wuxia. Having the plague as the backdrop/setting for a wuxia story might lead to some interesting and unprecedented storytelling ideas. No matter how great a martial artist's prowess, his/her skill in martial arts would be all but useless against the plague. After all, one can't use a dagger, sword, or even internal energy against bacteria.
Even the great healers of wuxia, who are seemingly able to heal a variety of apparently hopeless ailments, would likely be able to do little against the plague: if traditional Chinese medicine has an Achilles' Heel, it would be infectious disease.