A Refined Phylochronology of the Second Plague Pandemic in Western Eurasia

Abstract

Although dozens of ancient Yersinia pestis genomes and a vast corpus of documentary data are available, the origin and spread of consecutive outbreaks of the Second Plague Pandemic in Europe (14th-18th c.) are still poorly understood. For the majority of ancient genomes, only radiocarbon dates spanning several decades are available, hampering an association with historically recorded plague outbreaks. Here, we present new genomic evidence of the Second Pandemic from 11 sites in England, Estonia, the Netherlands, Russia, and Switzerland yielding 11 Y. pestis genomes with >4-fold mean coverage dating to between 1349 and 1710. In addition, we present a novel approach for integrating the chronological information retrieved from phylogenetic analysis with their respective radiocarbon dates, based on a novel methodology offering more precise dating intervals. Together with a fine-grained analysis of documentarily recorded plague outbreaks, this allows us to tentatively associate all available Y. pestis genomes of the Second Pandemic with historically documented plague outbreaks. Through these combined multidisciplinary analytical efforts, our newly sequenced genomes can be attributed to the Black Death in Cambridge (England), the pestis tertia or pestis quarta in the late 14th century (Estonia), previously unknown branches emerging in the 15th century (Estonia, the Netherlands and England), and a widespread pandemic in Eastern Europe around 1500 (western Russia), which all seem to have originated from one or multiple reservoirs located in Central Europe. While the latter continued to harbour a major Y. pestis lineage at least until the 1630s, represented by new genomes of the Thirty Years' War plague (Switzerland), another lineage consecutively spread into Europe between the 17th and 18th century from the Ottoman Empire, as evidenced by a genome associated with the Great Northern War plague (Estonia). By combining phylogenetic analysis with a systematic historical reconstruction based on textual sources and an innovative phylogenetically informed radiocarbon modelling (PhIRM), we offer a new groundbreaking interdisciplinary approach that solves several fundamental methodological challenges associated with phylogenetic and spatio-temporal reconstruction of historical pandemics.

Clostridium tetanibacteraemia in the plague area in France: two cases

“…Indeed, in this situation, Ind-7 but not Ind-44 tested positive for the plague agent Y. pestis, in line with previously reported detection of Y. pestis aDNA in this site (5). Present report is therefore one more illustration of dual infection in the course of documented plague, after cases of co-infection with Y. pestis has been reported with Treponema pallidum complex in a post-medieval and 17 th individual (26,27); with Haemophilus influenzae serotype b in 540 to 550 CE individual (28); with Bartonella quintana in individuals buried in a 11th-15th site in France (29). Furthermore, nine cases of Streptococcus spp.-Y.…”

Genetic history of Cambridgeshire before and after the Black Death

“…This might limit our power to detect changes after the Black Death. None of the individuals in the pre– or post–Black Death groups are among those tested positive for Yersinia pestis previously ( 10 , 35 , 36 ). Our analyses of genetic ancestry ( Figs.…”

First glimpse of infectious diseases in medieval and early modern Estonia based on human osteological material

“…Such signs may indicate an infectious disease, such as venereal syphilis. The aDNA analysis confirmed that the deceased was infected by Treponema pallidum and the individual died because of plague (Yersinia pestis; Keller et al 2023). In addition, skeletons with venereal syphilis have been identified among those buried in the burial grounds of the Russian garrison in Kazan churchyard and in the hospital cemetery of the navy and army garrison in the 18th-century Tallinn.…”