The mechanisms used by pathogens to generate antigenic variation can be roughly sub-divided into two categories: Random or unprogrammed variation and Programmed variation (antigenic variation sensu stricto). Both mechanisms require several conditions:

• Errors in DNA or RNA replication/repair.
• Recombination between non-identical genes (non-homologous recombination).
• Reassortment of gene segments if the genome is not in one piece.

• A family of genes encoding proteins with the same or similar functions (paralogous genes).
• The ability to express only one of the gene family members at a time and to alter the member expressed over time.

Unprogrammed variation refers to the fact that genome transfer from parents to progeny is not perfect. This imperfection creates antigenic drift, the substrate for selection and evolution.

Programmed variation refers to the existence of specific mechanisms to generate gene diversity. The underlaying concept is that genes can be activated by being moved to a position downstream of an active promoter. There are several mechanisms known to accomplish this goal, including those involved in recombination and in sequence length variation.

All mechanisms of recombinational control restrict expression to a single member of the gene family; there is only a single promoter and only the gene directly downstream of that promoter is active.

This is the simplest way to move genes relative to a fixed location, and can involve either gene or promoter inversion (Figure 1). The inversion is catalyzed by a site-specific DNA recombinase that recognizes a short DNA segment flanking both sides of the invertible segment. A more sophisticated mechanism involves several segments that can be rearranged in different ways, yielding different products (Figure 2). It is hypothesized that sequence specific recombinases catalyze this kind of inversion, but no putative candidate has been found to date.

Reciprocal recombination is used for genes near the telomeres (Figure 3), providing a versatile mechanism in pathogens with large numbers of chromosomes or linear plasmids, e.g. trypanosomes, Pneumocystis and Borrelia.

Also known as the cassette mechanism, as a gene is inserted behind a single promoter in an expression site like a cassette inserted into a tape recorder. The first cassette mechanism described involved a site-specific endonuclease, but whether a dedicated endonuclease is also involved in antigenic variation in African trypanosomes, the pathogen using this mechanism most extensively, is under debate. The high rate of switching and the limited sequence homology available for gene conversion suggests, but does not prove, the involvement of a dedicated endonuclease, but this enzyme remains to be found.

Found in Borrelia, this mechanism requires arrays of antigen genes to be inserted into an active expression site through recombination. If each gene is followed by a strong transcriptional stop, removing the first gene in the array by deletion thereby activates the second one. Such mechanisms can work only if antigen genes are introduced into the expression site in an asymmetrical fashion, i.e. an array of genes replacing a single gene. Otherwise, the gene would be entirely lost from the genome and the gene repertoire would rapidly shrink.

Varying the length of simple repeat tracts allows control of gene expression at the transcriptional (Figure 6) and translational levels (Figure 7).