Antigenic variation can occur through three broadly defined genetic processes: gene mutation, recombination, and switching. In all cases, antigenic variation results in pathogens that are immunologically distinct from the parental strains.

Viruses

The process of antigenic variation occurring in viruses is categorized as either antigenic drift or antigenic shift. Antigenic drift, which is exhibited by a wide range of viruses, is a result of genetic point mutations accumulated by the viral genome over an extended period of time. This drift produces small antigenic changes in the pathogen population which ultimately reduce the efficacy of B and T cell memory during the host immune response.

Antigenic drift has been well characterized in the influenza virus, and is becoming more and more evident in the rapid evolution of rhinoviruses and enteroviruses. The Human Immunodeficiency Virus (HIV) exhibits antigenic drift within the particular host due to its high rate of replication.

Antigenic shift refers to a more immediate and extensive change in genetic information. This can occur when two strains of the pathogen recombine, a process exemplified by Influenza A. In this instance of genetic recombination, whole segments of the virus genomes are swapped when human and avian strains dually infect a single host. The immunological challenges posed by the newly produced influenza strain are the cause for widespread influenza epidemics.

Bacteria

Bacteria in general are phenotypically hypermutable, a characteristic which allows the pathogen to evade the host immune system and develop resistance to therapeutic drugs. Examples of bacteria that undergo high genetic mutation rates and therefore phenotypic variation include Escherichia coli and Salmonella.

Processes of antigenic variation which lead to a more sophisticated mechanism of immune evasion can be seen in Borrelia recurrentis and Neisseria gonorrhoeae. In these bacteria, gene switching and phase variation allow for a high level of epitope variation.

Protozoa