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Most of the<jats:italic>Y. pestis<\/jats:italic>strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of<jats:italic>Y. pestis<\/jats:italic>sequences in four remains, confirming that the buried individuals were victims of plague. In two samples,<jats:italic>Y. pestis<\/jats:italic>DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop\u00a0in coverage of the pPCP1 plasmid region containing the<jats:italic>pla<\/jats:italic>gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the<jats:italic>pla<\/jats:italic>gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The<jats:italic>pla<\/jats:italic>\u00a0gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of<jats:italic>pla<\/jats:italic>-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.<\/jats:p>","DOI":"10.1038\/s41598-020-71530-9","type":"journal-article","created":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T10:04:10Z","timestamp":1599127450000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic"],"prefix":"10.1038","volume":"10","author":[{"given":"Julian","family":"Susat","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanna H.","family":"Bonczarowska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"El\u012bna","family":"P\u0113tersone-Gordina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Immel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Almut","family":"Nebel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guntis","family":"Gerhards","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben","family":"Krause-Kyora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,9,3]]},"reference":[{"key":"71530_CR1","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.cell.2015.10.009","volume":"163","author":"S Rasmussen","year":"2015","unstructured":"Rasmussen, S. et al. 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