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

Clio Der Sarkissian,Caroline Costedoat,Catherine Thèves,Andaine Seguin-Orlando,Norbert Telmon,Célia Kamel,Love Dalén,Ludovic Orlando,Stéfan Tzortzis,Michel Signoli

doi:10.1016/j.isci.2021.102383

Abstract

SummaryThe 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.

Highlights

With the advent of next-generation DNA sequencing, ancient DNA research has moved from single locus studies to the characterization of the complete genomes of ancient individuals, including from extinct hominids such as Neanderthals and Denisovans
Historians have identified the Justinian plague of the sixth century CE as marking the beginning of the first major plague pandemics, ancient DNA data have revealed that plague pathogens had already started to infect human populations thousand years earlier, between the third and sixth millennium BCE (Before Common Era) (Rasmussen et al, 2015; Andrades Valtuena et al, 2017; Spyrou et al, 2018; Rascovan et al, 2019)
Polymerase chain reaction (PCR) amplifications of a 133-bp fragment located in the pPCP1 pla gene returned positive results on the tooth DNA extracts of these two individuals

Summary

Introduction

With the advent of next-generation DNA sequencing, ancient DNA research has moved from single locus studies to the characterization of the complete genomes of ancient individuals, including from extinct hominids such as Neanderthals and Denisovans (see Orlando et al, 2021 for a review). Genome sequencing has revealed a pathogenic genetic toolkit much different than at the time of the Justinian plague (Wagner et al, 2014; Feldman et al, 2016; Namouchi et al, 2018; Keller et al, 2019) and the infamous Black Death (Bos et al, 2011, 2016; Spyrou et al, 2016, 2019b; Guellil et al, 2020; Morozova et al, 2020; Susat et al, 2020), which marked the beginning of the so-called second pandemic by decimating 30-60% of the European population in the 14th century CE (Eckert, 1978; Benedictow, 2004).

Results

Conclusion