Is this or other similar Archaeal species, perhaps undiscovered, pathogenic and contributing to the chronic disease burden of society?

We do not see any value in becoming overconcerned about such primitive organisms and their place in things. For the same reason they are obscure and difficult to isolate, they have much less impact on your planet overall than more complex viruses. For the same reasons, the interlopers have used the more sophisticated viruses to imbue with harmful properties as bioweapons because, as a starting point, such viruses are more robust and successful in competing with other life forms and this makes them inherently more dangerous with respect to their potential for causing harm to host cells. What makes viruses dangerous is the ability to be recognized by the immune system, primarily because fighting back causes the collateral damage of many, many chronic illnesses and their symptoms. The presence of the virus is so minute it is little danger functionally in many cases. To be pathogenic, there is usually a manipulation in the extraterrestrial laboratories to add some kind of aggravating characteristic, like a surface protein that is toxic in some way, to get the immune system activated and in fighting mode, and that will lead to symptoms.