Dangers of Noncritical Use of Historical Plague Data

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.

Mapping the plague through natural language processing

Pandemic diseases such as plague have produced a vast amount of literature providing information about the spatiotemporal extent, transmission, or countermeasures. However, the manual extraction of such information from running text is a tedious process, and much of this information remains locked into a narrative format. Natural Language processing (NLP) is a promising tool for the automated extraction of epidemiological data, and can facilitate the establishment of datasets. In this paper, we explore the utility of NLP to assist in the creation of a plague outbreak dataset. We produced a gold standard list of toponyms by manual annotation of a German plague treatise published by Sticker in 1908. We investigated the performance of five pre-trained NLP libraries (Google, Stanford CoreNLP, spaCy, germaNER and Geoparser) for the automated extraction of location data compared to the gold standard. Of all tested algorithms, spaCy performed best (sensitivity 0.92, F1 score 0.83), followed closely by Stanford CoreNLP (sensitivity 0.81, F1 score 0.87). Google NLP had a slightly lower performance (F1 score 0.72, sensitivity 0.78). Geoparser and germaNER had a poor sensitivity (0.41 and 0.61). We then evaluated how well automated geocoding services such as Google geocoding, Geonames and Geoparser located these outbreaks correctly. All geocoding services performed poorly - particularly for historical regions - and returned the correct GIS information only in 60.4%, 52.7% and 33.8% of all cases. Finally, we compared our newly digitized plague dataset to a re-digitized version of the plague treatise by Biraben and provide an update of the spatio-temporal extent of the second pandemic plague outbreaks. We conclude that NLP tools have their limitations, but they are potentially useful to accelerate the collection of data and the generation of a global plague outbreak database.

Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic

The Black Death (1347–1352 ce) is the most renowned pandemic in human history, believed by many to have killed half of Europe’s population. However, despite advances in ancient DNA research that conclusively identified the pandemic’s causative agent (bacterium Yersinia pestis), our knowledge of the Black Death remains limited, based primarily on qualitative remarks in medieval written sources available for some areas of Western Europe. Here, we remedy this situation by applying a pioneering new approach, ‘big data palaeoecology’, which, starting from palynological data, evaluates the scale of the Black Death’s mortality on a regional scale across Europe. We collected pollen data on landscape change from 261 radiocarbon-dated coring sites (lakes and wetlands) located across 19 modern-day European countries. We used two independent methods of analysis to evaluate whether the changes we see in the landscape at the time of the Black Death agree with the hypothesis that a large portion of the population, upwards of half, died within a few years in the 21 historical regions we studied. While we can confirm that the Black Death had a devastating impact in some regions, we found that it had negligible or no impact in others. These inter-regional differences in the Black Death’s mortality across Europe demonstrate the significance of cultural, ecological, economic, societal and climatic factors that mediated the dissemination and impact of the disease. The complex interplay of these factors, along with the historical ecology of plague, should be a focus of future research on historical pandemics.

Historical accounts of the mortality outcomes of the Black Death plague pandemic are variable across Europe, with much higher death tolls suggested in some areas than others. Here the authors use a ‘big data palaeoecology’ approach to show that land use change following the pandemic was spatially variable across Europe, confirming heterogeneous responses with empirical data.

Regional Patterns of Late Medieval and Early Modern European Building Activity Revealed by Felling Dates

Although variations in building activity are a useful indicator of societal well-being and demographic development, historical datasets for larger regions and longer periods are still rare. Here, we present 54,045 annually precise dendrochronological felling dates from historical construction timber from across most of Europe between 1250 and 1699 CE to infer variations in building activity. We use geostatistical techniques to compare spatiotemporal dynamics in past European building activity against independent demographic, economic, social and climatic data. We show that the felling dates capture major geographical patterns of demographic trends, especially in regions with dense data coverage. A particularly strong negative association is found between grain prices and the number of felling dates. In addition, a significant positive association is found between the number of felling dates and mining activity. These strong associations, with well-known macro-economic indicators from pre-industrial Europe, corroborate the use of felling dates as an independent source for exploring large-scale fluctuations of societal well-being and demographic development. Three prominent examples are the building boom in the Hanseatic League region of northeastern Germany during the 13th century, the onset of the Late Medieval Crisis in much of Europe c. 1300, and the cessation of building activity in large parts of central Europe during armed conflicts such as the Thirty Years’ War (1618–1648 CE). Despite new insights gained from our European-wide felling date inventory, further studies are needed to investigate changes in construction activity of high versus low status buildings, and of urban versus rural buildings, and to compare those results with a variety of historical documentary sources and natural proxy archives.

Differential mortality of infectious disease in Italian polities: COVID-19, past plague epidemics, and currently endemic respiratory disease

Coronavirus disease 2019 (COVID-19) has harshly impacted Italy since its arrival in February 2020. In particular, provinces in Italy's Central and Northern macroregions have dealt with disproportionately greater case prevalence and mortality rates than those in the South. In this paper, we compare the morbidity and mortality dynamics of 16th and 17th century Plague outbreaks with those of the ongoing COVID-19 pandemic across Italian regions. We also include data on infectious respiratory diseases which are presently endemic to Italy in order to analyze the regional differences between epidemic and endemic disease. A Growth Curve Analysis allowed for the estimation of time-related intercepts and slopes across the 16th and 17th centuries. Those statistical parameters were later incorporated as criterion variables in multiple General Linear Models. These statistical examinations determined that the Northern macroregion had a higher intercept than the Southern macroregion. This indicated that provinces located in Northern Italy had historically experienced higher plague mortalities than Southern polities. The analyses also revealed that this geographical differential in morbidity and mortality persists to this day, as the Northern macroregion has experienced a substantially higher COVID-19 mortality than the Southern macroregion. These results are consistent with previously published analyses. The only other stable and significant predictor of epidemic disease mortality was foreign urban potential, a measure of the degree of interconnectedness between 16th and 17th century Italian cities. Foreign urban potential was negatively associated with plague slope and positively associated with plague intercept, COVID-19 mortality, GDP per capita, and immigration per capita. Its substantial contribution in predicting both past and present outcomes provides a temporal continuity not seen in any other measure tested here. Overall, this study provides compelling evidence that temporally stable geographical factors, impacting both historical and current foreign pathogen spread above and beyond other hypothesized predictors, underlie the disproportionate impact COVID-19 has had throughout Central and Northern Italian provinces.

Acceleration of plague outbreaks in the second pandemic

Historical records reveal the temporal patterns of a sequence of plague epidemics in London, United Kingdom, from the 14th to 17th centuries. Analysis of these records shows that later epidemics spread significantly faster ("accelerated"). Between the Black Death of 1348 and the later epidemics that culminated with the Great Plague of 1665, we estimate that the epidemic growth rate increased fourfold. Currently available data do not provide enough information to infer the mode of plague transmission in any given epidemic; nevertheless, order-of-magnitude estimates of epidemic parameters suggest that the observed slow growth rates in the 14th century are inconsistent with direct (pneumonic) transmission. We discuss the potential roles of demographic and ecological factors, such as climate change or human or rat population density, in driving the observed acceleration.

Drought-induced spatio-temporal synchrony of plague outbreak in Europe

Plague synchronously swept across separated regions in Europe throughout history. However, the spatio-temporal synchrony of plague and its driving mechanism have not been thoroughly investigated. In this study, we transformed the historical European plague database spanned 1347-1800 CE into country-level time-series that differentiated large-scale plague outbreak from counted data. We found that there are 74 years in which two or more countries in our study region (UK, France, Germany, Spain, and Italy) experienced large-scale plague outbreak in the same year. Our Multivariate Ripley's K-function results showed that the onset year and the cessation year of large-scale plague outbreak are synchronized at the 0-23-year and 0-20-year windows, respectively. The temporal association between such synchrony and climatic forcing was further investigated using the Superposed Epoch Analysis, and drought was found to be responsible for the synchrony. Integrating our results with a literature survey, we suggested that prior to the peak of plague, the occurrence of drought and the subsequent reintroduced rainfall dampened both the rodent community and human society and boosted the number of fleas that carried plague. Such a synthesis facilitated the outbreak of plague. At the same time, high temperature associated with such drought also confined the geographic diffusion of the plague. Hence, although continental mega-drought could initiate the synchrony of plague outbreak, the synchrony actually consisted of a number of localized plague outbreak events scattering across different regions in Europe. According to the projected rising trend of drought in terms of its magnitude, duration, and geographic extent, the risk of synchrony of rodent-borne diseases in Europe will be significantly elevated, especially in France, Italy, and Spain.

Empirical "integrated disease management" in Ferrara during the Italian plague (1629-1631)

Plague, a highly infective disease caused by Yersinia pestis (Proteobacteria: Enterobacteriales), ravaged Europe from 1347 over the course of more than 450 years. During the Italian Plague (1629-1631), the disease was rampaging in the entire Northern Italy down to Tuscany, but the city of Ferrara was relatively spared, in spite that the economic activities were maintained with highly affected cities, such as Milan, through the relevant salt commerce. The aim of the study is to evaluate the hygiene rules that were effective in preventing the spread of the plague in Ferrara in 1630, by examining historical documents and reports. According to these documents, a kind of empirical "integrated disease management" was carried out, using remedies including compounds with bactericidal, anti-parasite and repellent activity, and by technical strategies including avoidance of possible plague carriers. The anti-plague remedies and technical strategies used in ancient Ferrara are critically analysed using a multidisciplinary approach (pharmaceutic, medical, epidemiologic and entomological) and compared to current prevention protocols.

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.

Is Crohn's Disease the Price to Pay Today for Having Survived the Black Death?

BACKGROUND AND AIMS

Nucleotide Oligomerisation Domain 2 [NOD2] is a key gene of innate immunity which participates in the host defence against pathogens. Several loss-of-function NOD2 mutations are associated with Crohn's disease [CD]. Their high frequencies in populations of European ancestry suggest a model of balancing selection. Because NOD2 deficiency has been associated with a resistance to Yersinia pseudotuberculosis in mice, we hypothesised that NOD2 mutations have been selected during past plague outbreaks due to the closely related bacterium Yersinia pestis.

METHODS

Contemporary frequencies of the main CD-associated NOD2 mutations [R702W, G908R, and 1007fs], measured in healthy people from European and Mediterranean countries, were collected from 60 studies via a PubMed search. Plague exposure was calculated from a dataset providing outbreaks from 1346 to 1860 in Europe and the Mediterranean Bassin. A plague index was built to capture the intensity of plague exposure in the studied geographical areas.

RESULTS

NOD2 mutation frequencies were associated with the past exposure to plague. Statistical significance was obtained for the most frequent mutation [R702W, p = 0.03] and for the pooled three mutations [p = 0.023]. The association remained significant when putative demographic biases were considered.

CONCLUSIONS

This result argues for a selection of CD-associated NOD2 mutations by plague outbreaks and further questioned the role of exposure to enteropathogenic Yersinia species in CD.

Living with plague: Lessons from the Soviet Union's antiplague system

Zoonoses, such as plague, are primarily animal diseases that spill over into human populations. While the goal of eradicating such diseases is enticing, historical experience validates abandoning eradication in favor of ecologically based control strategies (which reduce morbidity and mortality to a locally accepted risk level). During the 20th century, one of the most extensive plague-eradication efforts in recorded history was undertaken to enable large-scale changes in land use in the former Soviet Union (including vast areas of central Asia). Despite expending tremendous resources in its attempt to eradicate plague, the Soviet antiplague response gradually abandoned the goal of eradication in favor of plague control linked with developing basic knowledge of plague ecology. Drawing from this experience, we combine new gray-literature sources, historical and recent research, and fieldwork to outline best practices for the control of spillover from zoonoses while minimally disrupting wildlife ecosystems, and we briefly compare the Soviet case with that of endemic plague in the western United States. We argue for the allocation of sufficient resources to maintain ongoing local surveillance, education, and targeted control measures; to incorporate novel technologies selectively; and to use ecological research to inform developing landscape-based models for transmission interruption. We conclude that living with emergent and reemergent zoonotic diseases-switching to control-opens wider possibilities for interrupting spillover while preserving natural ecosystems, encouraging adaptation to local conditions, and using technological tools judiciously and in a cost-effective way.

The 'light touch' of the Black Death in the Southern Netherlands: an urban trick?

Although the fanciful notion that the Black Death bypassed the Low Countries has long been rejected, nevertheless a persistent view remains that the Low Countries experienced only a 'light touch' of the plague when placed in a broader European perspective, and recovered quickly and fully. However, in this article an array of dispersed sources for the Southern Netherlands together with a new mortmain accounts database for Hainaut show that the Black Death was severe, perhaps no less severe than other parts of western Europe; that serious plagues continued throughout the fourteenth and fifteenth centuries; and that the Black Death and recurring plagues spread over vast territories-including the countryside. The previous conception of a 'light touch' of plague in the Low Countries was created by the overprivileging of particular urban sources, and a failure to account for the rapid replenishment of cities via inward migration, which obscured demographic decimation. We suggest that the population of the Low Countries may not have recovered faster than other parts of western Europe but instead experienced a greater degree of post-plague rural-urban migration.