{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T02:22:13Z","timestamp":1776824533649,"version":"3.51.2"},"reference-count":53,"publisher":"Microbiology Society","issue":"5","license":[{"start":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T00:00:00Z","timestamp":1716508800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004319","name":"Pfizer","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100004319","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,24]]},"abstract":"<jats:p>Lyme disease (LD), caused by spirochete bacteria of the genus <jats:italic>Borrelia burgdorferi sensu lato<\/jats:italic>, remains the most common vector-borne disease in the northern hemisphere. <jats:italic>Borrelia<\/jats:italic> outer surface protein A (OspA) is an integral surface protein expressed during the tick cycle, and a validated vaccine target. There are at least 20 recognized <jats:italic>Borrelia<\/jats:italic> genospecies, that vary in OspA serotype. This study presents a new <jats:italic>in silico<\/jats:italic> sequence-based method for OspA typing using next-generation sequence data. Using a compiled database of over 400 <jats:italic>Borrelia<\/jats:italic> genomes encompassing the 4 most common disease-causing genospecies, we characterized OspA diversity in a manner that can accommodate existing and new OspA types and then defined boundaries for classification and assignment of OspA types based on the sequence similarity. To accommodate potential novel OspA types, we have developed a new nomenclature: OspA <jats:italic>in silico<\/jats:italic> type (IST). Beyond the ISTs that corresponded to existing OspA serotypes 1\u20138, we identified nine additional ISTs that cover new OspA variants in <jats:italic>B. bavariensis<\/jats:italic> (IST9\u201310), <jats:italic>B. garinii<\/jats:italic> (IST11\u201312), and other <jats:italic>Borrelia<\/jats:italic> genospecies (IST13\u201317). The IST typing scheme and associated OspA variants are available as part of the PubMLST <jats:italic>Borrelia<\/jats:italic> spp. database. Compared to traditional OspA serotyping methods, this new computational pipeline provides a more comprehensive and broadly applicable approach for characterization of OspA type and <jats:italic>Borrelia<\/jats:italic> genospecies to support vaccine development.<\/jats:p>","DOI":"10.1099\/mgen.0.001252","type":"journal-article","created":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T15:16:17Z","timestamp":1716563777000},"source":"Crossref","is-referenced-by-count":6,"title":["Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato"],"prefix":"10.1099","volume":"10","author":[{"given":"Jonathan T.","family":"Lee","sequence":"first","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenghui","family":"Li","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorna D.","family":"Nunez","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Katzel","sequence":"additional","affiliation":[{"name":"Pfizer Digital, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B. Scott","family":"Perrin Jr.","sequence":"additional","affiliation":[{"name":"Pfizer Digital, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Varun","family":"Raghuraman","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Urvi","family":"Rajyaguru","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrina E.","family":"Llamera","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lubomira","family":"Andrew","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Annaliesa S.","family":"Anderson","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joppe W.","family":"Hovius","sequence":"additional","affiliation":[{"name":"Amsterdam University Medical Centers (UMC), location Academic Medical Center (AMC), Department of Internal Medicine, Division of Infectious Diseases, Center for Experimental and Molecular Medicine, Amsterdam Institute for Immunology and Infectious Diseases, University of Amsterdam, Amsterdam, Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul A.","family":"Liberator","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raphael","family":"Simon","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8865-7351","authenticated-orcid":false,"given":"Li","family":"Hao","sequence":"additional","affiliation":[{"name":"Vaccine Research and Development, Pfizer, Inc., Pearl River, NY, 10965, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(11)60103-7"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2017.62"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fux047"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1093\/jme\/tjv237"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2019.00401"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2021.101766"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.ss6622a1"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.3201\/eid2702.202731"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/595427"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2017.12.006"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1093\/jme\/tjv199"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1093\/jme\/tjw076"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2016.09.006"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20031960"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0184357"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0113294"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2005.04.066"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0305680101"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199807233390402"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199807233390401"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00917-19"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1017\/s0031182003004694"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1007\/BF00221390"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00116-09"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.31.2.340-350.1993"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1007\/BF02456135"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1002\/9780471729259.mc12c05s34"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.12.4.633"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2007.05.002"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1007\/s00430-003-0196-8"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2006.01.006"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0800323105"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2013.04.009"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.21775\/cimb.042.409"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1186\/1756-3305-7-418"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01447-15"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0524-x"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab120"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty121"},{"key":"R41","article-title":"Pfizer and Valneva Initiate Phase 3 Study of Lyme Disease Vaccine Candidate VLA15: Pfizer; 2022"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.37.12.3965-3970.1999"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2015.02.008"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.052001-0"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1007\/BF01713341"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.36.3.768-776.1998"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1997.tb12669.x"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-007-9029-5"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1111\/j.1348-0421.1996.tb01106.x"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1016\/s0923-2508(00)00155-8"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(15)00464-8"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.11.7203-7216.2005"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1999.tb13745.x"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001252?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T15:16:19Z","timestamp":1716563779000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001252"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,24]]},"references-count":53,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2024,5,24]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001252","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,24]]}}}