{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T04:54:20Z","timestamp":1789102460391,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011404","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,8,10]],"date-time":"2023-08-10T00:00:00Z","timestamp":1691625600000}}],"reference-count":71,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T00:00:00Z","timestamp":1689638400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004189","name":"Max-Planck-Gesellschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["771234"],"award-info":[{"award-number":["771234"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["805268"],"award-info":[{"award-number":["805268"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p><jats:italic>Pestis secunda<\/jats:italic> (1356\u20131366 CE) is the first of a series of plague outbreaks in Europe that followed the Black Death (1346\u20131353 CE). Collectively this period is called the Second Pandemic. From a genomic perspective, the majority of post-Black Death strains of <jats:italic>Yersinia pestis<\/jats:italic> thus far identified in Europe display diversity accumulated over a period of centuries that form a terminal sub-branch of the <jats:italic>Y<\/jats:italic>. <jats:italic>pestis<\/jats:italic> phylogeny. It has been debated if these strains arose from local evolution of <jats:italic>Y<\/jats:italic>. <jats:italic>pestis<\/jats:italic> or if the disease was repeatedly reintroduced from an external source. Plague lineages descended from the <jats:italic>pestis secunda<\/jats:italic>, however, are thought to have persisted in non-human reservoirs outside Europe, where they eventually gave rise to the Third Pandemic (19<jats:sup>th<\/jats:sup> and 20<jats:sup>th<\/jats:sup> centuries). Resolution of competing hypotheses on the origins of the many post-Black Death outbreaks has been hindered in part by the low representation of <jats:italic>Y<\/jats:italic>. <jats:italic>pestis<\/jats:italic> genomes in archaeological specimens, especially for the <jats:italic>pestis secunda<\/jats:italic>. Here we report on five individuals from Germany that were infected with lineages of plague associated with the <jats:italic>pestis secunda<\/jats:italic>. For the two genomes of high coverage, one groups within the known diversity of genotypes associated with the <jats:italic>pestis secunda<\/jats:italic>, while the second carries an ancestral genotype that places it earlier. Through consideration of historical sources that explore first documentation of the pandemic in today\u2019s Central Germany, we argue that these data provide robust evidence to support a post-Black Death evolution of the pathogen within Europe rather than a re-introduction from outside. Additionally, we demonstrate retrievability of <jats:italic>Y<\/jats:italic>. <jats:italic>pestis<\/jats:italic> DNA in post-cranial remains and highlight the importance of hypothesis-free pathogen screening approaches in evaluations of archaeological samples.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011404","type":"journal-article","created":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T17:31:18Z","timestamp":1689701478000},"page":"e1011404","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["14th century Yersinia pestis genomes support emergence of pestis secunda within Europe"],"prefix":"10.1371","volume":"19","author":[{"given":"Cody E.","family":"Parker","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alina N.","family":"Hiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria A.","family":"Spyrou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunnar U.","family":"Neumann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Slavin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Nelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Nagel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xandra","family":"Dalidowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Friederich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9144-3920","authenticated-orcid":true,"given":"Johannes","family":"Krause","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-1166","authenticated-orcid":true,"given":"Alexander","family":"Herbig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2475-2007","authenticated-orcid":true,"given":"Wolfgang","family":"Haak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2937-3006","authenticated-orcid":true,"given":"Kirsten I.","family":"Bos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,7,18]]},"reference":[{"key":"ppat.1011404.ref001","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/35097083","article-title":"Genome sequence of Yersinia pestis, the causative agent of plague","volume":"413","author":"J Parkhill","year":"2001","journal-title":"Nature"},{"key":"ppat.1011404.ref002","first-page":"578","article-title":"Retracing the Evolutionary Path that Led to Flea-Borne Transmission of Yersinia pestis. 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