For your example: influenza virus actively destroys host cells as part of its replication cycle (lytic cycle), whereas HIV integrates its genome into the genome of its target cells (lysogenic cycle), allowing its replication without the killing of the host cell. Although the infected T-cell is still alive, it loses most function because HIV has mechanisms of switching off normal function in favour of viral replication. In addition, the interferon response is largely suppressed in HIV infection, thus you don’t get quite the same scale of rapid onset inflammation and other indications of disease that are obvious in an influenza infection.
There are many other reasons why one particular microorganism might cause a more severe disease, of course.
This post was edited by GetOnYourKnees on Mar 10 2018 02:19pm