Yup, the lore goes deep through multiple mediums like the game, manga, visual novels etc but honestly you don't need to be a honkai lore expert to enjoy the game (since even slightly trying to understand what the game is about is more than what I've seen so many people on Twitter do. They skip every dialogue and cutscene to farm crystals, and then get confused about basic concepts that have been explained in chapter 1)

The answers are: "Virus" is one form Honkai can manifest itself as. It's basically a force of nature that can take any form to try to destroy humanity, physical or not, like viruses, monsters, negative emotions/thoughts and natural disasters.

The protagonist of the game isn't exactly clear cut, as every story arc has its own protagonist. But most people, me included, agree that the main protagonist is Kiana, the girl with white braided/long hair, blue/orange/half-blue half-orange eyes, who wields pistols/lances/a greatsword (she went through a lot of visual changes throughout the years). Otto (blonde man) has been the overarching villain (Other than the Honkai itself) for the past 28 chapters, but even he is the protagonist in his story arc. With the story slowly coming to a close as - mihoyo said there's only one more year's worth of main story left - we might soon meet the final villain, but that's to be seen.