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Persistence is promoted by the VlsE antigenic variation system, which generates combinatorial diversity of VlsE through unidirectional, segmental gene conversion from an array of silent cassettes. Here we explore the variants generated by the <jats:italic>vls <\/jats:italic>system of strain JD1, which has divergent sequence and structural elements from the type strain B31, the only <jats:italic>B. burgdorferi <\/jats:italic>strain in which recombinational switching at <jats:italic>vlsE <\/jats:italic>has been studied in detail. We first completed the sequencing of the <jats:italic>vls<\/jats:italic> region in JD1, uncovering a previously unreported 114\u00a0bp inverted repeat sequence upstream of <jats:italic>vlsE.<\/jats:italic> A five\u2010week infection of WT and SCID mice was used for PacBio long read sequencing along with our recently developed VAST pipeline to analyze recombinational switching at <jats:italic>vlsE <\/jats:italic>from 40,000 sequences comprising 226,000 inferred recombination events<jats:italic>. <\/jats:italic>We show that antigenic variation in B31 and JD1 is highly similar, despite the lack of 17\u00a0bp direct repeats in JD1, a somewhat different arrangement of the silent cassettes, divergent inverted repeat sequences and general divergence in the <jats:italic>vls<\/jats:italic> sequences. We also present data that strongly suggest that dimerization is required for <jats:italic>in vivo<\/jats:italic> functionality of VlsE.<\/jats:p>","DOI":"10.1111\/mmi.14189","type":"journal-article","created":{"date-parts":[[2018,12,23]],"date-time":"2018-12-23T09:40:00Z","timestamp":1545558000000},"page":"750-763","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Antigenic variation in the Lyme spirochete: detailed functional assessment of recombinational switching at <i>vlsE<\/i> in the JD1 strain of <i>Borrelia burgdorferi<\/i>"],"prefix":"10.1111","volume":"111","author":[{"given":"Theodore B.","family":"Verhey","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary Calgary Alberta T2N 4N1 Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mildred","family":"Castellanos","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary Calgary Alberta T2N 4N1 Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9611-2095","authenticated-orcid":false,"given":"George","family":"Chaconas","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary Calgary Alberta T2N 4N1 Canada"},{"name":"Department of Microbiology, Immunology and Infectious Diseases Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary Calgary Alberta T2N 4N1 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