No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy

The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory. [Display omitted] •DNA screening of 26 individuals from a 1629-1630 French Alps cemetery for plague•Sequencing two Yersinia pestis plague genomes at 2.3- and 13.7-fold coverage•These genomes are phylogenetically closest to those from the 1636 Italian outbreak•No genetic changes explain the particularly increased spread of the disease in Italy Paleontology; Genomics; Microbiology