The general idea is that there is a virus that's going around. It was rare at first, but it quickly spread. Now there are those who have been altered due to the virus, those who are infected with the virus, those who carry the virus, those who are immune, and those who haven't caught it yet.
Those who have been altered get different physical appearances. They can be fusions, re-colored, gain markings, lose markings, or any number of things. Shinies are not under this category, though, as they were around before the virus took hold.
Those who are infected are stronger, faster, and all around have improved stats. However, with these stat gains also comes lack of mental status. They get easier to enrage, want to kill others, and just aim to gain more power.
Those who are carriers are affected on a much lesser scale. They get spurts of increased stats periodically, but they are still coherent pokemon. Not much has changed about them from before they were introduced to the virus, except for the fact that they can infect others with it. Most carriers don't know they are carriers.
Those who have not been infected are normal pokemon. (Normal or shiny)
Those who are infected tend to get sick when the virus switches from active to dormant and the host becomes a carrier of the virus.