A genomic and historical synthesis of plague in 18th century Eurasia

Discussion

The introduction of post-Black Death plague to Europe has been subject to debate in previous studies (10⇓–12, 18). The main points of contention are the number of introductions from outside of Western Europe and the location of the reservoir(s) feeding the Y. pestis lineage, which established itself following the Black Death epidemic. One of the currently predominant hypotheses in the literature (14) suggests that a reservoir was established in Western Europe, potentially in the alpine region, and gave rise to the post-Black Death lineage prior to diversification. The lineage diversification possibly resulted in the establishment of multiple European reservoirs. However, the lineage lacked any non-European representative and chronologically ended with the last large outbreak recorded in Western Europe, the great plague of Marseille (1720 to 1723), which is documented to have been imported from the Eastern Mediterranean. Here, we propose an alternative hypothesis based on our synthesis of historical and genomic data. Evidence in the form of the genomes from Pestbacken and particularly the genome from Maist points toward the possibility of multiple waves of plague stemming from a single main reservoir situated outside of Western Europe. Following the apparent “diversification” of the post-Black Death lineage in our updated phylogeny, the post-Black Death lineage gives rise to four more outbreaks, the representative genomes of which all carry a large deletion and show an increase in substitution rate (14). Contrary to the Alpine clade (Landsberg, Brandenburg, Stans), which now also carries the Italian SPN genomes, these genomes stem from various locations in Eurasia (England, Sweden, France, and Chechnya, Russia). In the following paragraphs, we will summarize historical sources for the introduction routes, which support the genomically documented plague outbreaks of the 18th century in Western Europe.

Strain PEB10 was isolated from a skeleton from the plague cemetery of Pestbacken, dated numismatically to 1710 to 1711, in Southern Sweden, where plague had devastated the regions of Skåne and Blekinge in 1710 to 1711. The eastern and northern European plague outbreak of 1702 to 1713 was the last continental-scale plague epidemic to affect Western Europe. Set during the Great Northern War (1700 to 1721) and the War of the Spanish Succession (1701 to 1714), this plague epidemic took a heavy toll on the eastern European population, which was already suffering from a series of bad harvests and ensuing famines (32). The concurrent large-scale wars also involved massive soldier movements across the entire continent, which helped propagate plague over large distances in short periods of time (24). The epidemic is said to have entered Europe around the turn of the century in multiple waves via the Ottoman Empire through the Balkans and Transylvania. In 1709, the disease reached the southern Baltic coast, where the Swedish army was engaged in military actions against Russia. From there, Swedish military vessels brought plague to Karlskrona, where it spread from the barracks to the whole region of Blekinge and Näsum, Scania, ∼12 km from Pestbacken, via returning soldiers (23⇓⇓–26). Plague continuously persisted in Blekinge until the end of 1711 (26). Strikingly, this epidemic event was the first documented outbreak in Sweden since the mid-1600s and the last documented plague outbreak to affect Scandinavia altogether (25, 26, 33).

Previously published genomes from Marseille l’Observance (10) can be dated to 1722 and therefore postdate the genome from Pestbacken by 12 y. According to historical sources, plague reached Marseille over the sea in 1720, where it persisted for almost 2 y. The boat associated with the outbreak, the “Grand-Saint-Antoine,” had visited Lebanon, Syria, and Cyprus before arriving in Marseille and had lost multiple passengers to plague along the way (27⇓⇓–30). The genomes are derived from the plague pits dug in the Convent of l’Observance between May and September 1722 (10, 34). By then, the city had been isolated from the rest of the country for about 2 y, and individuals attempting to escape were killed upon sight. Spread to the rest of Europe had successfully been limited to the neighboring regions by the establishment of a cordon sanitaire by one-fourth of the French army and a range of other measures, such as the construction of a 36-km wall across the Vaucluse countryside (13, 28, 30).

We added an historical Y. pestis genome from the Caucasus region to the phylogeny. The sample CHE1 stems from the site of Maist, which is located in close proximity to today’s Chechnya–Georgia border. The region houses multiple plague foci, which makes it a key area for plague activity today (21, 35, 36). Based on the phylogeny, the genome isolated from individual CHE1 appears to stem from the same lineage as the strains circulating in Europe until the 18th century. While no exact dates or related historical sources are available for this sample (SI Appendix), the isolated genome postdates the genomes from the plague pit of Marseille l’Observance (1722), based on the phylogeny, potentially dating well into the 18th century or even later, e.g., in the context of the Caucasian War (1817 to 1864). Considering that the disease did not advance far into France during the Great Plague of Marseille, it seems unlikely that the lineage introduced into Europe in 1720 was reintroduced from there to the Caucasus region and then reached Chechnya. Instead, we propose that the disease reached Chechnya directly on a separate route via land or that the region is located close to the wildlife reservoir that is responsible for the plague lineage documented in Europe following the Black Death (Fig. 2). For example, known modern plague foci are situated in neighboring Georgia, where written sources describing cases of bubonic plague date from the 11th century CE until after the start of the Third Plague Pandemic (1894) (35).

While it was not possible to identify a modern representative of 14th to 18th century lineage, recent studies have demonstrated the high genomic diversity found among the wildlife reservoirs of the Caucasus region (21). Considering the wealth of lineages unearthed in the Caucasus region alone, we can assume that much of Y. pestis diversity remains undiscovered. Additionally, more data from other regions of the world, which remained affected by plague beyond the outbreak of Marseille l’Observance in 1720, are needed to gain insights into the global diversity of lineages during the Second Plague Pandemic.

Recent ancient genomes predating the Second Plague Pandemic also emphasize the historical importance of Western and Central Asia for plague expansion. A genome from Tian Shan (Kyrgyzstan, 186 CE), recently published by Damgaard et al. (37), is the most basal genome of the first Plague Pandemic lineage to date (38⇓–40) and actually predates the pandemic by more than 300 y. This study also described a second sample for which a full genome could not be assembled from North Ossetia–Alania (Russia, sixth and the ninth century CE), close to the Georgian border and the site of Maist (Chechnya, Russia). The dating of this genome has recently been contested (41), placing it closer to the polytomy of branches 1 to 4 and therefore chronologically closer to the Black Death. Although it is difficult to draw parallels across pandemics, as they can exhibit significant changes in dynamics, the importance of Western and Central Asia and the regions surrounding the Black Sea is pronounced across pandemics as far back as the Neolithic (2).

While the wildlife reservoir responsible for the post-Black Death lineage could be situated anywhere in Eurasia, we propose, based on our synthesis of historical sources and phylogeny, that the reservoir was not situated in Western Europe, but instead was close to Europe, specifically in Western Asia or the Black Sea region. From there, plague was introduced into Europe in multiple waves. We do not expect CHE1 to have originated in the European Alps, nor do we think it is likely that, following the Great Plague of Marseille, Y. pestis retreated to the East. In fact, historical sources for all of the 18th century genomes support the possibility of introduction through the Eastern Mediterranean and the Black Sea region. This would be plausible considering that the Second Plague Pandemic was not an exclusively European phenomenon (42) and, with the addition of CHE1, neither is the post-Black Death lineage. The Alpine clade could be the results of extended circulation during larger epidemics (e.g., the plague epidemics associated with the Thirty Years’ War, during which regions of today’s Germany are known to have lost up to 50% of their population (6, 29, 43) or by the establishment of short-lived secondary reservoirs, as all clade lineages seemingly became extinct in the 17th century. A similar clade formation could be expected following the addition of more strains from the Great Northern War epidemics, with Pestbacken representing one of the final outbreaks and being situated on its northernmost expansion. However, more data are needed to validate this hypothesis.

Historians have concluded that the 17th century saw a major shift in plague dynamics around the 1630s (5⇓–7). In Europe, this period of change was dominated by the Thirty Years’ War, a period defined by large soldier movements and mass mortality by both war and disease. Considering that increases in mutation rates evidently occur in large transmission chains during epidemic events (44), mass movements and mortality could explain the increase in substitution rate, assuming constant circulation. However, the Alpine clade, which is at least partially chronologically contemporary to this branch, does not show such drastic rates (14). The early 17th century was also a period of crisis throughout the Ottoman Empire (45, 46). Two time periods stand out. The first crisis, dated between the 1570s and the 1610s, is marked by social unrest (Celali Rebellion) and demographic shifts, which were caused by sudden massive population loss and climatological events. The second one spans the period from the 1670s to the 1710s and falls within the Late Maunder Minimum. Both intervals were characterized by climate changes associated with the Little Ice Age, which have to be differentiated from the ones traditionally observed in the West. Instead of increased humidity, these periods are marked by historical reports of extended periods of drought, which led to food shortages, famine, and unrest (45, 46). However, a lack of high-quality, high-resolution climate reconstructions for this region does not allow any robust assessment of climate–plague interaction. Nonetheless, the history of the Ottoman empire, its Eastern reach, and its vast trade connections cannot be ignored when discussing plague introduction.

Following the shift in plague dynamics around the 1630, major plague epidemics slowly became less frequent. By the 18th century, quarantine was a widespread norm of surveillance throughout major European port cities, and state-regulated disease surveillance seemed to have successfully decreased the occurrence of major plague outbreaks in Europe (5, 47). Following the Eastern European epidemics of 1702 to 1713, the Austrian Empire established a cordon sanitaire, which was fully enforced by 1770 and spanned from the Adriatic Sea to Transylvania to avoid entry of plague from the Ottoman Empire, with which they had been at war since the 16th century (48). By the time that the Austrian cordon sanitaire started to disintegrate, the Ottoman Empire had established nationwide quarantine measures for the first time following the Napoleonic Wars (1803 to 1815) (5, 48, 49). These measures coupled with improved living conditions, medical care, and hygiene therefore could, to some extent, account for progressive European isolation from plague starting with the 17th century, assuming the source of plague was not situated in Western Europe.

After the Great Plague of Marseille (1720 to 1722), no plague outbreak of comparable scale is documented in Western Europe, but many reports of plague in the Near East and Russia exist, where the Russian–Turkish Wars spread plague within southeastern Europe and Russia, culminating in a devastating epidemic in Moscow in 1770 (42, 50, 51). Overall, the Near East and the Ottoman Empire, where natural plague foci are frequent to this day, were heavily affected by plague epidemics throughout the Second Plague Pandemic (35, 42, 51, 52). The Balkans were also impacted by plague long after its slow disappearance from Europe. This could be attributed to the different quarantine strategies of surrounding countries (47). For example, while mainland Greece was under Ottoman control during the 17th and 18th century, the Ionian Islands were governed by the city-states of the Adriatic Sea and subject to strict quarantine measures (47). Reported imports of plague to the Ionian Islands almost exclusively occurred from mainland Greece, where plague was a constant threat during the 18th century with only 14 recorded plague-free years. The ubiquity of plague in the Balkans during the entire 18th century (47) and its presence until the establishment of quarantine measures throughout the Ottoman Empire at the beginning of the 19th century, as well as documented imports of plague from the Balkans to the West, illustrate the directionality of plague transmission during the 17th and the 18th centuries according to historical sources (5, 47).

While these changes concur with societal changes such as increased disease control, they also seemingly coincide with structural and mutational changes in Y. pestis genomes circulating at the time. We noted that the 49-kbp deletion, which was first detected in the OBS genomes (10, 11, 14), was also present in the genomes PEB10 and CHE1. This deletion has evidently arisen on the branch between the genomes from Ellwangen and London New Churchyard, which is the branch with the highest substitution rate across the lineage (14). However, the effect of the loss of these genes on the overall virulence of the bacterium remains unclear. Considering the high mortality described during the epidemics associated with the genomes from Pestbacken and Marseille, virulence does not seem to have been considerably impaired. Moreover, while the deletion apparently appeared only during the last two centuries of the Second Plague Pandemic in Europe, the Balkans and the Near East continued to be heavily affected by the disease (42, 47). It is also important to note that a similar 49-kbp deletion has recently been reported in a First Plague Pandemic genome from Lunel-Viel (France, 567 to 618) (40) and that these sequences have therefore been lost independently on at least two known occasions. Both affected lineages have no known modern representatives.

Many different hypotheses have been proposed to explain the mechanisms of plague introduction to Europe and its subsequent spread throughout the continent. However, the true processes are likely part of a complex web of dynamics, of which the available data only allow us to elucidate the most general trends. Yet, the data presented in this study allow for interpretations of the current phylogeny and for its assessment with a broader geographic focus. Our multidisciplinary approach hints at the possibility of an extra-European reservoir, which introduced plague to Europe in multiple waves and saw the pathogen evolve within its natural foci. The limited available genomic data, while growing, make thorough historical research indispensable to provide context to the evolutionary processes observed via phylogeographic analyses. Most of the available data remain concentrated in Western Europe. Eastern Europe and much of the Mediterranean remain underrepresented or absent in the Second Plague Pandemic phylogeny and could provide key information in the debate. Further sampling in active plague regions, which have been shown to be genomically diverse, could also help to answer the question of whether the post-Black Death lineage went extinct or is currently undiscovered.