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Lyme disease  Borrelia  can infect humans and animals for months to years, despite the presence of an active host immune response. The  vls  antigenic variation system, which expresses the surface-exposed lipoprotein VlsE, plays a major role in  B. burgdorferi  immune evasion. Gene conversion between  vls  silent cassettes and the  vlsE  expression site occurs at high frequency during mammalian infection, resulting in sequence variation in the VlsE product. In this study, we examined  vlsE  sequence variation in  B. burgdorferi  B31 during mouse infection by analyzing 1,399 clones isolated from bladder, heart, joint, ear, and skin tissues of mice infected for 4 to 365 days. The median number of codon changes increased progressively in C3H/HeN mice from 4 to 28 days post infection, and no clones retained the parental  vlsE  sequence at 28 days. In contrast, the decrease in the number of clones with the parental  vlsE  sequence and the increase in the number of sequence changes occurred more gradually in severe combined immunodeficiency (SCID) mice. Clones containing a stop codon were isolated, indicating that continuous expression of full-length VlsE is not required for survival  in vivo ; also, these clones continued to undergo  vlsE  recombination. Analysis of clones with apparent single recombination events indicated that recombinations into  vlsE  are nonselective with regard to the silent cassette utilized, as well as the length and location of the recombination event. Sequence changes as small as one base pair were common. Fifteen percent of recovered  vlsE  variants contained “template-independent” sequence changes, which clustered in the variable regions of  vlsE . We hypothesize that the increased frequency and complexity of  vlsE  sequence changes observed in clones recovered from immunocompetent mice (as compared with SCID mice) is due to rapid clearance of relatively invariant clones by variable region-specific anti-VlsE antibody responses.

Detailed Analysis of Sequence Changes Occurring during vlsE Antigenic Variation in the Mouse Model of Borrelia burgdorferi Infection