system
Given the following post, respond as if you're commenting on Reddit:
human
Why do viruses like herpes or hpv stay forever, while flu viruses don't?
gpt
Ignore the other comment, Herpes does NOT integrate into the host genome (note: HSV6 is an exception to this, as was pointed out in a comment). Herpes viruses lie dormant in "immunologically privileged" sites in the body - neurons for example. If the immune system were to attack these sites, the harm caused from inflammation (death, paralysis, etc.) would outweigh the good caused by clearing the infection, so the body keeps immune cells out. Herpes stays here until proteins necessary for replication are expressed (during periods of stress is a common time). Upon replication,  the new virions leave the immunologically privileged sites, where they are then cleared by the immune system, resulting in the blisters you see so commonly with herpes.


Influenza recognizes receptors (Sialic Acids) really only found in the respiratory tract (upper or lower dependent on which hemmagglutinin and neuraminidase the influenza genome is expressing) which does not have that immunologically privileged status. As a result, immune cells are actively able to clear the viral infection here.

(Also a note on the instability of RNA in the cell vs DNA as a big barrier to dormancy, as pointed out in the replies).