Plague Pandemics Research Articles

New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China

Yunnan Province, China is thought to be the original source of biovar Orientalis of Yersinia pestis, the causative agent of the third plague pandemic that has spread globally since the end of the 19th century. Although encompassing a large area of natural plague foci, Y. pestis strains have rarely been found in live rodents during surveillance in Yunnan, and most isolates are from rodent corpses and their fleas. In 2017, 10 Y. pestis strains were isolated from seven live rodents and three fleas in Heqing County of Yunnan. These strains were supposed to have low virulence to local rodents Eothenomys miletus and Apodemus chevrieri because the rodents were healthy and no dead animals were found in surrounding areas, as had occurred in previous epizootic disease. We performed microscopic and biochemical examinations of the isolates, and compared their whole-genome sequences and transcriptome with those of 10 high virulence Y. pestis strains that were isolated from nine rodents and one parasitic flea in adjacent city (Lijiang). We analyzed the phenotypic, genomic, and transcriptomic characteristics of live rodent isolates. The isolates formed a previously undefined monophyletic branch of Y. pestis that was named 1.IN5. Six SNPs, two indels, and one copy number variation were detected between live rodent isolates and the high virulence neighbors. No obvious functional consequence of these variations was found according to the known annotation information. Among genes which expression differential in the live rodent isolates compared to their high virulent neighbors, we found five iron transfer related ones that were significant up-regulated (| log2 (FC) | > 1, p.adjust < 0.05), indicating these genes may be related to the low-virulence phenotype. The novel genotype of Y. pestis reported here provides further insights into the evolution and spread of plague as well as clues that may help to decipher the virulence mechanism of this notorious pathogen.

Plague Dot Text: Text mining and annotation of outbreak reports of the Third Plague Pandemic (1894-1952)

The design of models that govern diseases in population is commonly built on information and data gathered from past outbreaks. However, epidemic outbreaks are never captured in statistical data alone but are communicated by narratives, supported by empirical observations. Outbreak reports discuss correlations between populations, locations and the disease to infer insights into causes, vectors and potential interventions. The problem with these narratives is usually the lack of consistent structure or strong conventions, which prohibit their formal analysis in larger corpora. Our interdisciplinary research investigates more than 100 reports from the third plague pandemic (1894-1952) evaluating ways of building a corpus to extract and structure this narrative information through text mining and manual annotation. In this paper we discuss the progress of our ongoing exploratory project, how we enhance optical character recognition (OCR) methods to improve text capture, our approach to structure the narratives and identify relevant entities in the reports. The structured corpus is made available via Solr enabling search and analysis across the whole collection for future research dedicated, for example, to the identification of concepts. We show preliminary visualisations of the characteristics of causation and differences with respect to gender as a result of syntactic-category-dependent corpus statistics. Our goal is to develop structured accounts of some of the most significant concepts that were used to understand the epidemiology of the third plague pandemic around the globe. The corpus enables researchers to analyse the reports collectively allowing for deep insights into the global epidemiological consideration of plague in the early twentieth century.

Средневековые пандемии чумы

In this work, on the basis of a comprehensive analysis in the field of world history, history of medicine, religious studies, a study of two medieval plague pandemics, features of their distribution, course and consequences was carried out. A close relationship is shown between the appearance of the plague pandemic and the deviations of the church and people from the gospel principles and laws.

Itineraries and Transformations: John of Burgundy's Plague Treatise.

As one of the most popular medieval plague treatises produced during the Second Plague Pandemic, John of Burgundy's tract offers an excellent example of how medical books changed over time and place: in their material formats (such as manuscript to print), their textual contents and meanings, the people involved in their production, their readership, and sometimes even their purpose. The seemingly formulaic structure and medical contents of plague tracts has contributed to a long-standing perception that they were largely static or even ahistorical, one treatise easily exchanged for another. However, by examining copies of the treatise as individual and unique productions, rather than simply seeing the apparent uniformity of a few exemplars (or even the entire genre), we can begin to trace the itineraries through which they traveled and the rich tapestries of change that mark their life stories.

АНТРОПОЛОГИЧЕСКИЙ ВЗГЛЯД НА ЭПИДЕМИИ ЧУМЫ В ИСТОРИЧЕСКОМ ПРОШЛОМ

At many times in their history, humans have faced major epidemics. The “Black Death”, which broke out in the middle of the 14th century, is believed to be the deadliest one. The total number of the deceased population and the scale in many ways had a dramatic impact on the course of subsequent historical events. Until recently, the myths dating back to the Middle Ages have prevailed in scientific circles. They have remained unrevised despite the latest achievements in the research on the plague bacterium Yersinia pestis, the history of climate and medicine, and the extensive published data, making it of an interest to both reconsider certain established dogmas and reconstruct the algorithm of the course of major plague epidemics from the historical past using the results of the available paleogenetic, epidemiological, and climatological studies. This triggered our discussion on the nonlinear nature of the course of plague pandemics. The analysis of the historical sources showed that the scale and speed of the spread of plague epidemics in new territories directly depended on the degree of inclusion of cities and regions of the Afro-Eurasian space in the economic system of the Great Silk Road, the proximity to various epidemic centers of plague. The decisive influence of the anthropogenic factor on the duration and main directions of the spread of plague epidemics was revealed. The multivariate onset and course of pandemic plague waves were recognized. Therefore, it is difficult to pinpoint the exact place where the spread of the plague epidemics ended or to identify their consequences.

FRANCESCO DATINI IN EPISTOLARY REFLECTION

The article attempts to reconstruct the mentality of the medieval burgher Francesco Datini (1335-1410) on the materials of his epistolary archive in order to study his inherent reflexive practices in the context of time and life circumstances. The period of Datini’s life (XIV-XV centuries) was marked by a number of cataclysms, among which the Great Plague Pandemic of the middle of the XIV century seems to be the most global phenomenon. People of the “Old World” who survived these shocks felt irreversible social and mental changes. Their habitual way of life seemed to go into an irrevocable past, the established group and individual identity was destroyed. At the same time, a new model of life behavior and identity has not yet taken shape. As a methodological basis for the research undertaken, we chose the methods of emotive history, which allowed us to concentrate research efforts on emotions and value orientations, as well as the theory of liminality, which focuses on studying the states impact of uncertainty on groups of people and individuals. Datini’s correspondence was divided into two parts, official — with his business partners and private — with his foster mother Monna Piera di Pratese Boschetti, his wife Monna Margarita and his closest friend, notary and judge, Ser Lapo di Macei. In business correspondence, Francesco Datini appears to be occupied exclusively with thoughts on income, prone to maxims and evil irony. In private correspondence, the religious motivation of his actions, emotions, doubts, fears and fears are revealed, which were reinforced by the eschatological expectations of the transitional period. These observations made it possible to characterize the reflexive practices of Francesco Datini as liminal. Datini’s reflexive experience turned out to be very multidimensional, reflecting the catastrophic nature of the time he lived through, which prompted him in the last years of his life to turn to charity, long fasts and asceticism.

The Justinianic Plague and Global Pandemics: The Making of the Plague Concept

Abstract This article explores how plague—as an idea—became an ahistorical independent agent of historical change. It focuses on the case of the Justinianic Plague (ca. 541–750 c.e.), the first major recorded plague pandemic in Mediterranean history, which has increasingly been used to explain significant demographic, political, social, economic, and cultural change during late antiquity (ca. 300–800 c.e.). We argue that the Justinianic Plague retains its great historiographic power—namely, its supposed destructive impact over two centuries—because it evokes a terrifying myth of what plague should do rather than because of conclusive evidence of what it did. We define this historiographic power as the plague concept. It includes three key features: extensive chronology (lasting for two centuries), mortality (catastrophic death toll), and geography (global). The plague concept is built on three interdisciplinary types of evidence (here termed truisms): rats, climate, and paleogenetics. Our article traces how scientists constructed the plague concept in the first half of the twentieth century, and how historians entered the discussion in the last third of that century. As historians engaged in Justinianic Plague research, they used the plague concept to frame their arguments without problematizing its presence or contesting features that scientists had constructed decades earlier.

PREFACE

PREFACE

A brief outline of the history of world epidemics-pandemics. Part I

Pandemics in human history led to losses of millions of people and a significant decline in economic and social life. At the end of autumn 2019, humanity once again «unexpectedly» ran into the manifestations of mass infectious defeat. But the alarming reports of doctors were not heard by society. Unfortunately, what they predicted soon became a bitter reality of our time.The article traces and partially analyzes the consequences of epidemics-pandemics that occurred in ancient Athens during the Peloponnesian War, the plague of Antoninus, the plague of Justinian and the «black death» in the fourteenth century. To cope with the pandemic, cities and rulers sought out and lured doctors, paying for their services six months or even a year in advance. At that time, the saying appeared «the presence of a doctor in the city is a blessing from God!» The predecessors of modern infectious disease doctors, the «plague doctors», also appeared. For the first time, quarantine was used as an anti-epidemic protection. Its high efficiency is evidenced by the fact that 600 years later the WHO recognizes quarantine as the only possible effective way to combat the coronavirus pandemic.Dogmatic medicine, which was completely defeated in the fight against the plague, began to change in favor of the conclusions of doctors with practical knowledge, who not only tried to prevent the disease but also to cure it, and surgery received a significant impetus for its further development.After partial recovery from the plague pandemics, at the end of the 15th century in Spain and Italy, an epidemic of a «new» infection broke out unexpectedly. In a record short time, it captured residents of all other countries of Europe and Asia, regardless of age, gender and social status. In view of the result, it was first called «sexual plague», and later — more familiar to us — «syphilis». This epidemic-pandemic with certain periods of its extinction and revival continues to this day, affecting hundreds of thousands of people worldwide each year.At the beginning of the seventeenth century epidemics were not only in Europe but also in the colonies of the Spanish crown. With a strange pattern they arose in the 20s of almost every century. This particular year, a pandemic of a dangerous infectious disease, smallpox, broke out.That is, from antiquity to the beginning of the eighteenth century the society, with great human and economic losses, suffered several epidemics-pandemics, which not only significantly slowed down its progress, but also allowed the human community to redefine the further vector of its existence and development.

A millennium-long ‘Blue Ring’ chronology from the Spanish Pyrenees reveals severe ephemeral summer cooling after volcanic eruptions

‘Blue Rings’ (BRs) are distinct wood anatomical anomalies recently discovered in several tree species from different sites. While it is evident that they are associated with a cooling-induced lack of cell wall lignification, BRs have yet to be evaluated systematically in paleoclimate studies. Here, we present a continuous wood anatomical assessment of 31 living and relict pine samples from a high-elevation site in the central Spanish Pyrenees that span the period 1150–2017 CE at annual resolution. While most BR years coincide with cold summer temperatures and many BRs follow large volcanic eruptions, some were formed during overall warm summers. We also see a differential response between eruptions: the Samalas eruption is followed by 80% BRs in 1258, but only a modest signal is evident after the 1815 Tambora eruption, and there are no wood anatomical effects of the Laki eruption in 1783–1784. Apparently linked to a cluster of tropical eruptions in 1695 and 1696 CE, 85% BRs occurred in 1698. This new wood anatomical evidence is corroborated by the record of sulphur deposition in polar ice cores, and corresponds with catastrophic famine and unprecedented mortality in Scotland. The extremely rare occurrence of consecutive BRs in 1345 and 1346 marks the onset and spread of the Black Death, Europe’s most devastating plague pandemic. In their ability to capture severe ephemeral cold spells, as short as several days or weeks, BR chronologies can help to investigate and understand the impacts of volcanism on climate and society.

Post-Pandemic City: Historical Context for New Urban Design

Cities have been almost completely unprepared for the COVID-19 pandemic. Urban history has known many epidemics and pandemics, and there are clear historical parallels between the 13th and 19th century plague pandemics and cholera epidemics and the 21th century COVID-19 pandemic, from an administrative point of view. However, the cities’ public administration did not take into account the experience of the cities of the past to be prepared for the future problems. This requires developing flexible pandemic strategies and focusing on the decentralization of urban space through an even distribution of population in the urban environment. The COVID-19 pandemic will change the city, as previous pandemics and epidemics did. Urbanism v.3.0. will emerge, combining a green vector of development and digital technologies to ensure the autonomy and sustainability of buildings, districts and cities. At the same time, the role of culture will increase, which will become an effective tool for consolidating the soft power of the city in order to attract new people as the opposition of nowadays trend for living in the countryside.

The \u03ba-statistics approach to epidemiology

A great variety of complex physical, natural and artificial systems are governed by statistical distributions, which often follow a standard exponential function in the bulk, while their tail obeys the Pareto power law. The recently introduced kappa -statistics framework predicts distribution functions with this feature. A growing number of applications in different fields of investigation are beginning to prove the relevance and effectiveness of kappa -statistics in fitting empirical data. In this paper, we use kappa -statistics to formulate a statistical approach for epidemiological analysis. We validate the theoretical results by fitting the derived kappa -Weibull distributions with data from the plague pandemic of 1417 in Florence as well as data from the COVID-19 pandemic in China over the entire cycle that concludes in April 16, 2020. As further validation of the proposed approach we present a more systematic analysis of COVID-19 data from countries such as Germany, Italy, Spain and United Kingdom, obtaining very good agreement between theoretical predictions and empirical observations. For these countries we also study the entire first cycle of the pandemic which extends until the end of July 2020. The fact that both the data of the Florence plague and those of the Covid-19 pandemic are successfully described by the same theoretical model, even though the two events are caused by different diseases and they are separated by more than 600 years, is evidence that the kappa -Weibull model has universal features.

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

Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

Volcanism and global plague pandemics: Towards an interdisciplinary synthesis

Understanding the prevalence and dissemination of bacterial pathogens such as Yersinia pestis, the bacterial agent of plague, is key to identifying the origins and demographic impact of historic pandemic episodes and mitigating future risk. Climate may influence the spread of Yersinia pestis through impact upon bacterial, vector, and rodent host populations prior to human infection. Large climate-forcing volcanic eruptions have the potential to influence global climate for several years following the eruption with evidence increasingly suggesting that, through oceanic feedback mechanisms, some eruptions can influence climate for decades to centuries. This article assesses the potential mechanistic links between some of the largest volcanic eruptions of the Common Era and the three recorded plague pandemics. The article uses proxy records of climate and volcanic forcing along with historic data to suggest mechanisms by which each of the pandemic episodes may have been influenced by volcanism. Commonalities between the pandemic episodes are surprisingly rare, but it is suggested that the influence of volcanism on climate may be an important factor and may aid in understanding the complex array of factors which caused plague pandemics.

Pandemics and the development of scientific methods in the history of epidemiology

&#x0D; The Covid-19 pandemic has made me see the history of epidemiology differently. Pandemics are such impressive events that they can exert urgent pressure to identify new modes of research and new methodologies to replace methods that have failed in the past. Some examples seem to corroborate this idea.&#x0D; The plagueThere is no doubt that one of the most important events in the history of science occurred in the 17th century when population thinking was discovered. All human and social sciences such as sociology, demography, Darwinian biology, political economy, statistics and epidemiology, have their origin in the discovery that dictates that events in populations can be predictable and have a probability of occurrence. Then the occurrence of events in populations can be quantified, can be compared between populations and can be the source of scientific knowledge. This true revolution in scientific thought is a consequence of changes in society that occurred due to plague pandemics.Since the great pandemic of the 14th century, outbreaks of plague in Europe caused great confusion in cities and increasingly threatened existing powers. It was the case of the monarchical society of England. In the event of an outbreak of plague in London, the nobles, the wealthy, and the army left the city, where only the poor remained. The situation became chaotic in London. It was quickly clear that there was a certain chronological regularity in the outbreaks. They started with a small but growing number of deaths in some parishes before spreading throughout the city. In the 16th century the city of London began to collect data on the number and location of pest deaths. The system was improved in the 17th century and extended to all causes of death, making it possible -by the end of the century- to organize orderly outings from London in the event of an outbreak of plague, preventing chaos. These data were printed and placed on the walls of the city. They were called the “Bills of mortality”, death posters. In this process, a temporal series of mortalitydata was established in London over decades.

Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic

Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of pla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.

Guest Editor's Introduction

Guest Editor's Introduction William Hirst (bio) when the editor of this journal asked me to guest-edit an issue on cultural trauma, neither she nor I anticipated that the world would be in the grip of the COVID-19 pandemic as the project was winding down. When this special issue was initiated, an exploration of what had become known as "cultural trauma" seemed more of an intellectual undertaking than a plunge into an ongoing crisis. Now, as I write this in early April and the timing of the pandemic's end is still unknown, one cannot read through the contributions to this special issue—most of which were written before anyone had heard of COVID-19—without asking how they might contribute to an understanding of the pandemic and the collective memories society might form of it. A number of contributors to this volume underscore the role social science can play both by revealing the way society responds to suffering and by offering means not just for individuals but for the population at large to cope with this ordeal. Quite a few years ago, in response to the AIDS crisis, Social Research sponsored and published the proceedings of a conference called In Time of Plague: The History and Social Consequences of Lethal Epidemic Disease, which has just been reissued. A similar exploration of the COVID-19 pandemic will need to wait for a time when we have some distance from the current crisis. Nevertheless, the present contributions may offer at least ways of thinking about how to frame this discussion. Without doubt, pandemics can have long-term consequences. During the bubonic plague pandemic of 1349, Jews were scapegoated, accused of poisoning wells, and, as a result, substantial portions of the Jewish populations in many German cities were killed (Benedictow 2004). The result was a mass migration of the remaining Jews to [End Page xxxiii] Poland, permanently changing the demographics of Europe. With the massive death toll it brought, the bubonic plague also altered labor relations, with the wages of workers doubling as a result of the ensuing labor shortage. To a large extent, it led to the end of feudalism as a social system. But my concern when putting this special issue together was not necessarily with such logistical societal consequences. Rather it was with the representations people form of the collective suffering. The two are separable, to a degree. After all, the increase in wages observed after the plague occurred because of the labor shortage itself, not necessarily because of the way the plague was represented by the public. In pursuit of this concern about representation, the contributors to this volume were asked to address questions such as: Does society remember a cultural trauma over the long term? How will society remember it? Will it alter societal actions not just in the near future but also for generations to come? Will it do so in a way that reflects the evolving representation? What are the forces behind shaping these representations? I find these questions to be as important as those about the logistical societal consequences because, in the end, they bear on a community's sense of itself and on the way the community deals with its past—and constructs its future. This evolving sense of identity has profound consequences on the way society itself evolves. The labor shortage following the bubonic plague may have increased wages and put financial strain on the elite class, but the way society reacted to this strain—either by suppressing the laboring class or responding to its demands—reflects, in a major way, how society has come to understand the trauma and its consequences. One might come to see the deaths of a substantial portion of the population as merely an unfortunate natural disaster of little meaning or a tragedy that needs to be responded to. Answers to questions about representations of collective suffering are not straightforward, of course. In what might be viewed as [End Page xxxiv] an enduring mystery, many pandemics seem to be forgotten rather than remembered, at least in the long term. They do not haunt us, generation after generation, much to our collective regret when new pandemics...

Pandemic India: Coronavirus and the Uses of History.

The onset of the COVID-19 pandemic has produced two different narratives in India. One, here described as "historical," looks back to the pandemics of the colonial past-bubonic plague from 1896, influenza in 1918-19-as a source of comparisons, lessons, and dire warnings for the present. This narrative envisages the reenactment of past scenes, including flight from the cities, victimization of the poor, and the questioning of state authority. The other narrative, here called "insurgent," questions the value of historical analogies, doubts that history ever substantially repeats itself, and stresses the specificity of postcolonial Indian politics and health. While recognizing the validity of both narratives, the author urges caution in employing colonial history to critique contemporary events and, while recognizing the 1890s plague as a watershed moment, questions whether even the most devastating pandemics (such as 1918's influenza) necessarily result in profound social, political, and health care changes.

코로나19 시대, 페스트 팬데믹의 역사를 읽다 : (신규환, 『페스트 제국의 탄생』, 역사공간, 2020년)

코로나19 시대, 페스트 팬데믹의 역사를 읽다 : (신규환, 『페스트 제국의 탄생』, 역사공간, 2020년)

The pyrin inflammasome and the Yersinia effector interaction.

Pyrin is a cytosolic pattern-recognition receptor that normally functions as a guard to trigger capase-1 inflammasome assembly in response to bacterial toxins and effectors that inactivate RhoA. The MEFV gene encoding human pyrin is preferentially expressed in phagocytes. Key domains in pyrin include a pyrin domain (PYD), a linker region, and a B30.2 domain. Binding of ASC to pyrin by a PYD-PYD interaction triggers inflammasome assembly. Pyrin is held in an inactive conformation by negative regulation mechanisms to avoid premature inflammasome assembly. One mechanism of negative regulation involves phosphorylation of the linker by PRK kinase which in turn is positively regulated by active RhoA. The B30.2 domain also negatively regulates pyrin. Gain of function mutations in MEFV responsible for the autoinflammatory disease Familial Mediterranean Fever (FMF) map to exon 10 encoding the B30.2 domain. Insights into pyrin regulation have come from studies of several Yersinia effectors, which are injected into phagocytes and interact with the RhoA-PRK-pyrin axis during infection. Two effectors, YopE and YopT, inactivate RhoA to disrupt phagocytic signaling. To counteract an effector-triggered immune response, a third effector, YopM, binds to and inhibits pyrin by hijacking PRK and RSK and directing linker phosphorylation. Inhibition of pyrin by YopM is required for virulence of Yersinia pestis, the agent of plague. Recent results from infection studies with human phagocytes and mice producing pyrin B30.2 FMF variants show that gain of function MEFV mutations bypass inhibition by YopM. Population genetic data suggest that MEFV mutations were selected for in individuals of Mediterranean decent during historic plague pandemics. This review discusses current concepts of pyrin regulation and its interaction with Yersinia effectors.