Antigenic variation is caused by long plasmid segment conversion in a hard tick-borne relapsing fever Borrelia miyamotoi.

Borrelia miyamotoi is a hard tick-borne spirochete genetically related to relapsing fever Borrelia and the etiological agent of an emerging infectious disease in humans. Like relapsing fever Borrelia, B. miyamotoi carries clusters of gene cassettes encoding variable major proteins (Vmps) on multiple linear plasmids and shows antigenic variation in mammalian hosts by switching the expression vmp gene cassette. However, it remains unknown how the switch occurs in B. miyamotoi. Here we determined the whole genome sequences of Japanese B. miyamotoi strains to identify the repertoire and arrangement of vmp gene cassettes on five linear plasmids, and based on this information, analyzed B. miyamotoi clones reisolated from experimentally infected mice. Our analyses revealed that the switch occurred by replacing the expression cassette and its downstream silent cassettes with the long segment from archival plasmid. As the result of this long segment conversion, the first cassette became the expression cassette. Notably, this phenomenon was not due to single gene conversion but the replacement of a long (up to 16 kb or more) plasmid segment. We also show that while bacterial elimination depended on the presence of specific antibodies, the segment conversion was detected at five days post-infection, earlier than antibody production in mice, and even in severe combined immunodeficient mice. These results provide novel insights into the mechanisms that Borrelia evolved to survive and persist in mammalian hosts.