One of the clearest instances of this occurred around the time that Edward Jenner famously developed his vaccine against the virus in the 18th century.
During this period, the variola virus appears to have split into two strains - variola major and variola minor - which suggests that vaccination, which led to eradication of smallpox, may have changed the selection pressures acting on the virus and caused it to split into two strains.
There are diseases that we do not yet know exist. As much as we have concurred our planet, there is always something hiding in a far corner or just developing or in this case buried so deep in the past that it is not known to us until we stumble upon it. Part of our confidence and ignorance will lead us to believe we have it all understood, but there is always another thing to learn.
Not only are there diseases that we do not know existe, there are also people who have diseases that people have that we have not been able to diagnose. Hopefully whatever virus the child mummy has is not contagious or atleast is so dead that no one will get it.
There were likely many diseases in ancient times that have been abolished. Modern medicine might not know about these diseases. It's possible that the people in those times developed the appropriate medicines to treat the diseases. It's also possible that the people with those diseases died and that is the way the disease was wiped out.