Human ectoparasites and the spread of plague in Europe during the Second Pandemic

Emerging patterns in rodent-borne zoonotic diseases

Rodents are ubiquitous and typically unwelcome dwellers in human habitats worldwide, infesting homes, farm fields, and agricultural stores and potentially shedding disease-causing microbes into the most human-occupied of spaces. Of the vertebrate animal taxa that share pathogens with us, rodents are the most abundant and diverse, with hundreds of species of confirmed zoonotic hosts, some of which have nearly global distributions. However, only 12% of rodent species are known to be sources of pathogens that also infect people, and those rodents that do are now recognized as tending to share a suite of predictable traits. Here, we characterize those traits and explore them in the context of three emerging or reemerging rodent-borne zoonotic diseases of people: Lassa fever, Lyme disease, and plague.

Differential pathogenicity and lethality of bubonic plague (1720-1945) by sex, age and place

COVID-19 brought back to the attention of the scientific community that males are more susceptible to infectious diseases. What is clear for other infections-that sex and gender differences influence both risk of infection and mortality-is not yet fully elucidated for plague, particularly bubonic plague, although this knowledge can help find specific defences against a disease for which a vaccine is not yet available. To address this question, we analysed data on plague from hospitals in different parts of the world since the early eighteenth century, which provide demographic information on individual patients, diagnosis and course of the disease in the pre-antibiotic era. Assuming that the two sexes were equally represented, we observe a worldwide prevalence of male cases hospitalized at any age, a result which seems better explained by gender-biased (thus cultural) behaviours than biological sex-related factors. Conversely, case fatality rates differ among countries and geographic macro-areas, while globally, lethality appears slightly prevalent in young females and older adults (regardless of sex). Logistic regression models confirm that the main risk factor for bubonic plague death was the geographical location of the cases and being older than 50 years, whereas sex only showcased a slight trend.

Symptom propagation in respiratory pathogens of public health concern: a review of the evidence

Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.

Curiosities take the stage - role-play in parasitology teaching

Careful observation of parasites, masters of camouflage, reveals an ingenious and fascinating world. However, students often perceive parasitology as impenetrable. What if a flamboyant flea circus director passionately introduced the multidimensional contexts of this discipline? Will role-play capture the imagination of students and guide them in their future learning?

Antimicrobial therapies administrated during the Third Plague Pandemic in Europe

Plague raged in Europe for over 1400 years and was responsible for three major pandemics. Today, plague still poses a serious threat to global public health and surveillance is imperative. Plague is still present in natural reservoirs on several continents, including Africa, Asia and the Americas, and sometimes causes local cases and epidemics. The Third Plague Pandemic caused millions of deaths worldwide, including in Europe. Plague arrived in Europe in the autumn of 1896 mostly through maritime trade routes, where it spread with several epidemic events until 1945, when, in the port city of Taranto, the last known outbreak was recorded. In this paper, we present an overview of the natural history and pathogenicity of Yersinia pestis, the bacterium responsible for plague, its spread from Asia to Europe during the Third Pandemic, and the therapies used to treat and prevent the disease in Europe, with particular focus on the case of Taranto. In Taranto, the Pasteur Institute's antiserum antimicrobial therapy, and vaccination were used to treat and stop the advance of the bacterium, with mixed results.

Yersinia pestis can infect the Pawlowsky glands of human body lice and be transmitted by louse bite

Yersinia pestis, the causative agent of plague, is a highly lethal vector-borne pathogen responsible for killing large portions of Europe's population during the Black Death of the Middle Ages. In the wild, Y. pestis cycles between fleas and rodents; occasionally spilling over into humans bitten by infectious fleas. For this reason, fleas and the rats harboring them have been considered the main epidemiological drivers of previous plague pandemics. Human ectoparasites, such as the body louse (Pediculus humanus humanus), have largely been discounted due to their reputation as inefficient vectors of plague bacilli. Using a membrane-feeder adapted strain of body lice, we show that the digestive tract of some body lice become chronically infected with Y. pestis at bacteremia as low as 1 × 105 CFU/ml, and these lice routinely defecate Y. pestis. At higher bacteremia (≥1 × 107 CFU/ml), a subset of the lice develop an infection within the Pawlowsky glands (PGs), a pair of putative accessory salivary glands in the louse head. Lice that developed PG infection transmitted Y. pestis more consistently than those with bacteria only in the digestive tract. These glands are thought to secrete lubricant onto the mouthparts, and we hypothesize that when infected, their secretions contaminate the mouthparts prior to feeding, resulting in bite-based transmission of Y. pestis. The body louse's high level of susceptibility to infection by gram-negative bacteria and their potential to transmit plague bacilli by multiple mechanisms supports the hypothesis that they may have played a role in previous human plague pandemics and local outbreaks.

New records of pathogenic bacteria in different species of fleas collected from domestic and peridomestic animals in Spain. A potential zoonotic threat?

Climate change is causing many vectors of infectious diseases to expand their geographic distribution as well as the pathogens they transmit are also conditioned by temperature for their multiplication. Within this context, it is worth highlighting the significant role that fleas can play as vectors of important pathogenic bacteria. For this purpose, our efforts focused on detecting and identifying a total of 9 bacterial genera (Rickettsia sp.; Bartonella sp.; Yersinia sp.; Wolbachia sp., Mycobacterium sp., Leishmania sp., Borrelia sp., Francisella sp. and Coxiella sp.) within fleas isolated from domestic and peridomestic animals in the southwestern region of Spain (Andalusia). Over a 19-months period, we obtained flea samples from dogs, cats and hedgehogs. A total of 812 fleas was collected for this study. Five different species were morphologically identified, including C. felis, C. canis, S. cuniculi, P. irritans, and A. erinacei. Wolbachia sp. was detected in all five species identified in our study which a total prevalence of 86%. Within Rickettsia genus, two different species, R. felis and R. asembonensis were mainly identified in C. felis and A. erinacei, respectively. On the other hand, our results revealed a total of 131 fleas testing positive for the presence of Bartonella sp., representing a prevalence rate of 16% for this genus identifying two species B. henselae and B. clarridgeiae. Lastly, both Y. pestis and L. infantum were detected in DNA of P. irritans and C. felis, respectively isolated from dogs. With these data we update the list of bacterial zoonotic agents found in fleas in Spain, emphasizing the need to continue conducting future experimental studies to assess and confirm the potential vectorial role of certain synanthropic fleas.

Head lice as vectors of pathogenic microorganisms

Body lice and head lice are the most common ectoparasites of humans. Head lice (Pediculus humanus capitis) occur worldwide in children and their caretakers, irrespective of their social status. In contrast, body lice (Pediculus humanus corporis) are confined to marginalized population groups in countries of the Global South, homeless people, and refugees. Body lice are known to transmit an array of bacterial pathogens, such as R. prowazekii, R. rickettsii, C. burneti, B. quintana, B. recurrentis, and Y. pestis. The vector capacity of head lice is still a matter of debate. The objective of the review was to scrutinize the existing evidence on the vector capacity of head lice for the transmission of bacterial pathogens. The PUBMED database was searched using a combination of the terms "pediculus humanus" OR "body lice" OR "head lice" AND "pathogen" OR "Rickettsia prowazekii" OR "Bartonella quintana" OR "Borrelia recurrentis" OR "Coxiella burneti" without a time limit. Data from epidemiological studies as well as historical observations demonstrate that body lice and head lice can carry the same array of pathogens. Since the presence of a bacterial pathogen in an arthropod is not sufficient to state that it can be transmitted to humans, and since experimental models are lacking, as yet one cannot conclude with certainty that head lice serve as vectors, although this review presents circumstantial evidence that they do. Adequately designed experimental and epidemiological studies are needed to ascertain the exact transmission potential of head lice.

Historical microbiology: researching past bioevents by integrating scholarship (re)sources with paleomicrobiology assets

The analysis of past epidemics and pandemics, either spontaneous or of human origin, may revise the physical history of microbiota and create a temporal context in our understanding regarding pathogen attributes like virulence, evolution, transmission and disease dynamics. The data of high-tech scientific methods seem reliable, but their interpretation may still be biased when tackling events of the distant past. Such endeavors should be adjusted to other cognitive resources including historical accounts reporting the events of interest and references in alien medical cultures and terminologies; the latter may contextualize them differently from current practices. Thus 'historical microbiology' emerges. Validating such resources requires utmost care, as these may be susceptible to different biases regarding the interpretation of facts and phenomena; biases partly due to methodological limitations.

Overview of Yersinia pestis Metallophores: Yersiniabactin and Yersinopine

The pathogenic anaerobic bacteria Yersinia pestis (Y. pestis), which is well known as the plague causative agent, has the ability to escape or inhibit innate immune system responses, which can result in host death even before the activation of adaptive responses. Bites from infected fleas in nature transmit Y. pestis between mammalian hosts causing bubonic plague. It was recognized that a host's ability to retain iron is essential in fighting invading pathogens. To proliferate during infection, Y. pestis, like most bacteria, has various iron transporters that enable it to acquire iron from its hosts. The siderophore-dependent iron transport system was found to be crucial for the pathogenesis of this bacterium. Siderophores are low-molecular-weight metabolites with a high affinity for Fe3+. These compounds are produced in the surrounding environment to chelate iron. The siderophore secreted by Y. pestis is yersiniabactin (Ybt). Another metallophore produced by this bacterium, yersinopine, is of the opine type and shows similarities with both staphylopine and pseudopaline produced by Staphylococcus aureus and Pseudomonas aeruginosa, respectively. This paper sheds light on the most important aspects of the two Y. pestis metallophores as well as aerobactin a siderophore no longer secreted by this bacterium due to frameshift mutation in its genome.

Global Catastrophic Biological Risks in the Post-COVID-19 World: Time to Act Is Now

Global Catastrophic Biological Risks (GCBRs) refer to events with biological agents that can result in unprecedented or catastrophic disasters that are beyond the collective response-abilities of nation-states and the existing governance instruments of global governance and international affairs. This article offers a narrative review, with a view to new hypothesis development to rethink GCBRs after coronavirus disease 2019 (COVID-19) so as to better prepare for future pandemics and ecological crises, if not to completely prevent them. To determine GCBRs' spatiotemporal contexts, define causality, impacts, differentiate the risk and the event, would improve theorization of GCBRs compared to the impact-centric current definition. This could in turn lead to improvements in preparedness, response, allocation of resources, and possibly deterrence, while actively discouraging lack of due biosecurity diligence. Critical governance of GCBRs in ways that unpack the political power-related dimensions could be particularly valuable because the future global catastrophic events might be different in quality, scale, and actors. Theorization of GCBRs remains an important task going forward in the 21st century in ways that draw from experiences in the field, while integrating flexibility, versatility, and critically informed responses to GCBRs.

Can Water-Only DNA Extraction Reduce the Logistical Footprint of Biosurveillance and Planetary Health Diagnostics? Toward a New Method

The coronavirus disease-2019 (COVID-19) pandemic has raised the stakes for planetary health diagnostics. Because pandemics pose enormous burdens on biosurveillance and diagnostics, reduction of the logistical burdens of pandemics and ecological crises is essential. Moreover, the disruptive effects of catastrophic bioevents impact the supply chains in both highly populated urban centers and rural communities. One "upstream" focus of methodological innovation in biosurveillance is the footprint of Nucleic Acid Amplification Test (NAAT)-based assays. We report in this study a water-only DNA extraction, as an initial step in developing future protocols that may require few expendables, and with low environmental footprints, in terms of wet and solid laboratory waste. In the present work, boiling-hot distilled water was used as the main cell lysis agent for direct polymerase chain reactions (PCRs) on crude extracts. After evaluation (1) in blood and mouth swabs for human biomarker genotyping, and (2) in mouth swabs and plant tissue for generic bacterial or fungal detection, and using different combinations of extraction volume, mechanical assistance, and extract dilution, we found the method to be applicable in low-complexity samples, but not in high-complexity ones such as blood and plant tissue. In conclusion, this study examined the doability of a lean approach for template extraction in the case of NAAT-based diagnostics. Testing our approach with different biosamples, PCR settings, and instruments, including portable ones for COVID-19 or dispersed applications, warrant further research. Minimal resources analysis is a concept and practice, vital and timely for biosurveillance, integrative biology, and planetary health in the 21st century.

Ecological interactions, local people awareness and practices on rodent-borne diseases in Africa: A review

Several anthropogenic activities exposure humans to the risk of rodent-borne diseases. These activities are but not limited to logging, clearing land for crop cultivation, and consuming rodents. Rodents are a highly diverse mammalian group and harbor many zoonotic diseases. This review focuses on dominant rodent-flea species, rodent-borne zoonotic diseases and awareness and management practices against rodent-borne diseases in Africa. Relevant academic literature spanning from 1974 to 2021 was analysed. Dominant rodent species reported in Africa included:- Mastomys natalensis and Rattus rattus, while dominant flea species included Xenopsylla brasiliensis and Xenopsylla cheopis. Rodents were reported as hosts to a wide range of parasites which can be passed to humans. Rodents were also reported as hosts to some protozoans, trematodes, cestodes, nematodes, bacteria and viruses which are transmissible to humans. Some studies conducted in West Africa revealed good knowledge and practices on plague and Lassa fever diseases among respondents, whereas other studies reported poor practices on Lassa fever management. In part of Southern Africa, some studies reported poor knowledge and practices on plague disease. Further research on rodent-borne disease awareness and management strategies in African countries is desirable.

No evidence for persistent natural plague reservoirs in historical and modern Europe

Caused by Yersinia pestis, plague ravaged the world through three known pandemics: the First or the Justinianic (6th-8th century); the Second (beginning with the Black Death during c.1338-1353 and lasting until the 19th century); and the Third (which became global in 1894). It is debatable whether Y. pestis persisted in European wildlife reservoirs or was repeatedly introduced from outside Europe (as covered by European Union and the British Isles). Here, we analyze environmental data (soil characteristics and climate) from active Chinese plague reservoirs to assess whether such environmental conditions in Europe had ever supported "natural plague reservoirs". We have used new statistical methods which are validated through predicting the presence of modern plague reservoirs in the western United States. We find no support for persistent natural plague reservoirs in either historical or modern Europe. Two factors make Europe unfavorable for long-term plague reservoirs: 1) Soil texture and biochemistry and 2) low rodent diversity. By comparing rodent communities in Europe with those in China and the United States, we conclude that a lack of suitable host species might be the main reason for the absence of plague reservoirs in Europe today. These findings support the hypothesis that long-term plague reservoirs did not exist in Europe and therefore question the importance of wildlife rodent species as the primary plague hosts in Europe.

Misleading estimates of economic impacts of biological invasions: Including the costs but not the benefits

The economic costs of non-indigenous species (NIS) are a key factor for the allocation of efforts and resources to eradicate or control baneful invasions. Their assessments are challenging, but most suffer from major flaws. Among the most important are the following: (1) the inclusion of actual damage costs together with various ancillary expenditures which may or may not be indicative of the real economic damage due to NIS; (2) the inclusion of the costs of unnecessary or counterproductive control initiatives; (3) the inclusion of controversial NIS-related costs whose economic impacts are questionable; (4) the assessment of the negative impacts only, ignoring the positive ones that most NIS have on the economy, either directly or through their ecosystem services. Such estimates necessarily arrive at negative and often highly inflated values, do not reflect the net damage and economic losses due to NIS, and can significantly misguide management and resource allocation decisions. We recommend an approach based on holistic costs and benefits that are assessed using likely scenarios and their counter-factual.

Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health

The SARS-CoV-2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human-to-wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non-human primates or large, long-lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent "secondary spillover" back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non-human primates and human-proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human-to-wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human-to-wildlife pathogen transmission.

The source of the Black Death in fourteenth-century central Eurasia

The origin of the medieval Black Death pandemic (AD 1346-1353) has been a topic of continuous investigation because of the pandemic's extensive demographic impact and long-lasting consequences1,2. Until now, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan1,3-9. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338-1339 state 'pestilence' as the cause of death for the buried individuals9. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’

Tracking of Mammals and Their Fleas for Plague Surveillance in Madagascar, 2018-2019

Plague, a zoonotic disease caused by the bacterium Yersinia pestis, remains a major public health threat in Madagascar. To better understand the risk of transmission to humans and to guide targeted plague prevention and control measures, a survey of Y. pestis infection and exposure in mammals and their fleas was implemented. Small mammals were captured in five districts of Madagascar ranging in levels of plague endemicity, as measured by notified cases, from none to active foci. Blood and spleen samples and fleas were collected from small mammals for the detection of anti-Y. pestis F1 antibodies by ELISA, F1 antigens by rapid diagnostic tests, and pla, caf1, and inv genes by polymerase chain reaction. Some rodent fleas were kept alive and reared in the insectary to assess susceptibility to insecticides. Blood was also collected from 15 dogs and tested for anti-F1 antibodies. A total of 557 spleens, 484 sera, and 1,539 fleas were collected from 557 rodents and shrews. Nineteen (3.4%) spleens were positive for F1 antigen, most from Toamasina (N = 13), a historical plague focus. One dog was also found seropositive in Toamasina. Twenty-two (4.5%) serologic specimens from small mammals were positive for anti-F1 antibodies. The flea index was highest in the city of Antananarivo (8.8). No flea was positive for Y. pestis DNA. Flea populations exhibited resistance to various insecticides weakening the efficacy of vector control. This study highlights the potential use of animal-based surveillance to identify the risk of plague transmission in endemic and nonendemic foci for targeted prevention and control.

The plague’s impact paleodemographic and genetic measures in 15th to 16th century Gdańsk

Yersinia pestis caused plagues and haunted Gdańsk several times during the 15th and 16th centuries. This study focuses on the following demographic effects: 1/ distributions of deceased by age in a plagued city, 2/ parameters of the life tables, 3/ estimation of the natural increase. To assess genetic effects of the plague, measures of the opportunity for natural selection were considered. Skeletal remains of 283 people from the 15th – 16th century ossuary 3009 from the Dominican Monastery in Gdańsk provided research material. Yersinia pestis DNA in this skeletal material has already been found (Morozowa et al. 2017, 2020). Distributions of the deceased by age in the study sample were compared with those for Gdańsk before the plague and with those for the mass burial of plague victims in the 14th century Lübeck. Neither catastrophic mortality was found in the material studied, nor selective nature of the plague with regard to sex and age had been demonstrated. Using the Weiss method, the rate of natural increase r=–0.005 was reconstructed. With the wide dating range of the ossuary and the fact that it contains results of both the epidemic and “normal” mortality, the natural increase value at this level seems justified. There was a deterioration in the values of life tables parameters, especially life expectancy. Newborn life expectancy dropped to 19.5–22.6 years and for a 20-year-old to 17.7 years. The measures of opportunity for natural selection also deteriorated primarily due to child mortality: the biological state index Ibs values were low (within the 0.3–0.4 range) and values of the Im Crow’s index about 1.0. Natural selection also acted on adults as evidenced by values of the gross potential reproduction rate Rpot below 0.7. Demographically the study sample was at the level of the early Middle Ages rather than the Rennaisance.

Digital risk distribution and COVID-19: How contact tracing is promoted as a solution to equilibrate public health and economic prosperity during pandemics

Digital contact tracing appears as an ideal solution to tackle long-term economic damage due to necessary lockdown measures during a pandemic. This essay shows that the challenge of balancing citizen's health and a functioning society is not just coming up today. Commercial centres were already in the Middle Ages worried about their economic prosperity and adopted isolation measures. Although there are much more data available today, pandemic preparedness remains constrained by temporal and spatial realities, thus limiting public health management to the national state. Based on the examples of China and Switzerland, we elaborate on how individual and collective needs can be balanced differently regarding the implementation of a digital contact tracing system. While China's Health Code App is close to social surveillance, Switzerland has turned away from Europe to develop its own Swiss solution due to disagreement about data protection. It becomes clear that the attempts to properly balance public health and economic prosperity during a pandemic must be constantly readjusted and cannot simply be delegated to a digital technology.

Differential word expression analyses highlight plague dynamics during the second pandemic

Research on the second plague pandemic that swept over Europe from the fourteenth to nineteenth centuries mainly relies on the exegesis of contemporary texts and is prone to interpretive bias. By leveraging certain bioinformatic tools routinely used in biology, we developed a quantitative lexicography of 32 texts describing two major plague outbreaks, using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome, comprising overrepresented terms in plague-related texts, indicated that 'buboes' and 'carbuncles' are words that were significantly associated with the plague and signalled an ectoparasite-borne plague. Moreover, plague-related words were associated with the terms 'merchandise', 'movable', 'tatters', 'bed' and 'clothes'. Analysing ancient texts using the method reported in this paper can certify plague-related historical records and indicate the particularities of each plague outbreak, which can inform on the potential sources for the causative Yersinia pestis.

Genetic Evidence of the Black Death in the Abbey of San Leonardo (Apulia Region, Italy): Tracing the Cause of Death in Two Individuals Buried with Coins

The Abbey of San Leonardo in Siponto (Apulia, Southern Italy) was an important religious and medical center during the Middle Ages. It was a crossroads for pilgrims heading along the Via Francigena to the Sanctuary of Monte Sant’Angelo and for merchants passing through the harbor of Manfredonia. A recent excavation of Soprintendenza Archeologica della Puglia investigated a portion of the related cemetery, confirming its chronology to be between the end of the 13th and beginning of the 14th century. Two single graves preserved individuals accompanied by numerous coins dating back to the 14th century, hidden in clothes and in a bag tied to the waist. The human remains of the individuals were analyzed in the Laboratorio di Antropologia Fisica of Soprintendenza ABAP della città metropolitana di Bari. Three teeth from each individual were collected and sent to the Istituto Zooprofilattico Sperimentale di Puglia e Basilicata to study infectious diseases such as malaria, plague, tuberculosis, epidemic typhus and Maltese fever (Brucellosis), potentially related to the lack of inspection of the bodies during burial procedures. DNA extracted from six collected teeth and two additional unrelated human teeth (negative controls) were analyzed using PCR to verify the presence of human DNA (β-globulin) and of pathogens such as Plasmodium spp., Yersinia pestis, Mycobacterium spp., Rickettsia spp. and Brucella spp. The nucleotide sequence of the amplicon was determined to confirm the results. Human DNA was successfully amplified from all eight dental extracts and two different genes of Y. pestis were amplified and sequenced in 4 out of the 6 teeth. Molecular analyses ascertained that the individuals buried in San Leonardo were victims of the Black Death (1347–1353) and the data confirmed the lack of inspection of the corpses despite the presence of numerous coins. This study represents molecular evidence, for the first time, of Southern Italy’s involvement in the second wave of the plague pandemic.

Descriptive understanding and prediction in COVID-19 modelling

COVID-19 has substantially affected our lives during 2020. Since its beginning, several epidemiological models have been developed to investigate the specific dynamics of the disease. Early COVID-19 epidemiological models were purely statistical, based on a curve-fitting approach, and did not include causal knowledge about the disease. Yet, these models had predictive capacity; thus they were used to ground important political decisions, in virtue of the understanding of the dynamics of the pandemic that they offered. This raises a philosophical question about how purely statistical models can yield understanding, and if so, what the relationship between prediction and understanding in these models is. Drawing on the model that was developed by the Institute of Health Metrics and Evaluation, we argue that early epidemiological models yielded a modality of understanding that we call descriptive understanding, which contrasts with the so-called explanatory understanding which is assumed to be the main form of scientific understanding. We spell out the exact details of how descriptive understanding works, and efficiently yields understanding of the phenomena. Finally, we vindicate the necessity of studying other modalities of understanding that go beyond the conventionally assumed explanatory understanding.

Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information

The second plague pandemic started in Europe with the Black Death in 1346 and lasted until the 19th century. Based on ancient DNA studies, there is a scientific disagreement over whether the bacterium, Yersinia pestis, came into Europe once (Hypothesis 1) or repeatedly over the following four centuries (Hypothesis 2). Here, we synthesize the most updated phylogeny together with historical, archeological, evolutionary, and ecological information. On the basis of this holistic view, we conclude that Hypothesis 2 is the most plausible. We also suggest that Y. pestis lineages might have developed attenuated virulence during transmission, which can explain the convergent evolutionary signals, including pla decay, that appeared at the end of the pandemics.

The influence of temperature on the seasonality of historical plague outbreaks

Modern plague outbreaks exhibit a distinct seasonal pattern. By contrast, the seasonality of historical outbreaks and its drivers has not been studied systematically. Here, we investigate the seasonal pattern, the epidemic peak timing and growth rates, and the association with latitude, temperature, and precipitation using a large, novel dataset of plague- and all-cause mortality during the Second Pandemic in Europe and the Mediterranean. We show that epidemic peak timing followed a latitudinal gradient, with mean annual temperature negatively associated with peak timing. Based on modern temperature data, the predicted epidemic growth of all outbreaks was positive between 11.7°C and 21.5°C with a maximum around 17.3°C. Hence, our study provides evidence that the growth of plague epidemics across the whole study region depended on similar absolute temperature thresholds. Here, we present a systematic analysis of the seasonality of historical plague in the Northern Hemisphere, and we show consistent evidence for a temperature-related process influencing the epidemic peak timing and growth rates of plague epidemics.

Poor vector competence of the human flea, Pulex irritans, to transmit Yersinia pestis

Background

The human flea, Pulex irritans, is widespread globally and has a long association with humans, one of its principal hosts. Its role in plague transmission is still under discussion, although its high prevalence in plague-endemic regions and the presence of infected fleas of this species during plague outbreaks has led to proposals that it has been a significant vector in human-to-human transmission in some historical and present-day epidemiologic situations. However, based on a limited number of studies, P. irritans is considered to be a poor vector and receives very little attention from public health policymakers. In this study we examined the vector competence of P. irritans collected from foxes and owls in the western United States, using a standard protocol and artificial infection system.

Methods

Wild-caught fleas were maintained in the laboratory and infected by allowing them to feed on human or rat blood containing 2 × 10⁸ to 1 × 10⁹Y. pestis/ml. The fleas were then monitored periodically for infection rate and bacterial load, mortality, feeding rate, bacterial biofilm formation in the foregut (proventricular blockage), and ability to transmit Y. pestis after their single infectious blood meal.

Results

P. irritans were susceptible to infection, with more than 30% maintaining high bacterial loads for up to 20 days. Transmission during this time was infrequent and inefficient, however. Consistent with previous studies, a low level of early-phase transmission (3 days after the infectious blood meal) was detected in some trials. Transmission at later time points was also sporadic, and the incidence of proventricular blockage, required for this mode of transmission, was low in fleas infected using rat blood and never occurred in fleas infected using human blood. The highest level of blockage and transmission was seen in fleas infected using rat blood and allowed to feed intermittently rather than daily, indicating that host blood and feeding frequency influence vector competence.

Conclusions

Our results affirm the reputation of P. irritans as a feeble vector compared to rodent flea species examined similarly, and its vector competence may be lower when infected by feeding on bacteremic human blood.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04805-3.

Protection against severe infectious disease in the past

Before the 20th century many deaths in England, and most likely a majority, were caused by infectious diseases. The focus here is on the biggest killers, plague, typhus, smallpox, tuberculosis, cholera, typhoid, dysentery, childhood infections, pneumonia, and influenza. Many other infectious diseases including puerperal fever, relapsing fever, malaria, syphilis, meningitis, tetanus and gangrene caused thousands of deaths. This review of preventive measures, public health interventions and changes in behavior that reduced the risk of severe infections puts the response to recent epidemic challenges in historical perspective. Two new respiratory viruses have recently caused pandemics: an H1N1 influenza virus genetically related to pig viruses, and a bat-derived coronavirus causing COVID-19. Studies of infectious diseases emerging in human populations in recent decades indicate that the majority were zoonotic, and many of the causal pathogens had a wildlife origin. As hunter-gatherers, humans contracted pathogens from other species, and then from domesticated animals and rodents when they began to live in settled communities based on agriculture. In the modern world of large inter-connected urban populations and rapid transport, the risk of global transmission of new infectious diseases is high. Past and recent experience indicates that surveillance, prevention and control of infectious diseases are critical for global health. Effective interventions are required to control activities that risk dangerous pathogens transferring to humans from wild animals and those reared for food.

Didelphis spp. opossums and their parasites in the Americas: A One Health perspective

Medium sized opossums (Didelphis spp.) are among the most fascinating mammals of the Americas, playing important ecological roles (e.g., dispersal of seeds and control of insect populations) in the environment they inhabit. Nevertheless, as synanthropic animals, they are well adapted to human dwellings, occupying shelters within the cities, peripheral areas, and rural settings. These marsupials can harbor numerous pathogens, which may affect people, pets, and livestock. Among those, some protozoa (e.g., Leishmania infantum, Trypanosoma cruzi, Toxoplasma gondii), helminths (e.g., Ancylostoma caninum, Trichinella spiralis, Alaria marcianae, Paragonimus spp.) and arthropods (e.g., ticks, fleas) present substantial public health and veterinary importance, due to their capacity to cause disease in humans, domestic animals, and wildlife. Here, we reviewed the role played by opossums on the spreading of zoonotic parasites, vectors, and vector-borne pathogens, highlighting the risks of pathogens transmission due to the direct and indirect interaction of humans and domestic animals with Didelphis spp. in the Americas.

How epidemics end

As COVID-19 drags on and new vaccines promise widespread immunity, the world's attention has turned to predicting how the present pandemic will end. How do societies know when an epidemic is over and normal life can resume? What criteria and markers indicate such an end? Who has the insight, authority, and credibility to decipher these signs? Detailed research on past epidemics has demonstrated that they do not end suddenly; indeed, only rarely do the diseases in question actually end. This article examines the ways in which scholars have identified and described the end stages of previous epidemics, pointing out that significantly less attention has been paid to these periods than to origins and climaxes. Analysis of the ends of epidemics illustrates that epidemics are as much social, political, and economic events as they are biological; the "end," therefore, is as much a process of social and political negotiation as it is biomedical. Equally important, epidemics end at different times for different groups, both within one society and across regions. Multidisciplinary research into how epidemics end reveals how the end of an epidemic shifts according to perspective, whether temporal, geographic, or methodological. A multidisciplinary analysis of how epidemics end suggests that epidemics should therefore be framed not as linear narratives-from outbreak to intervention to termination-but within cycles of disease and with a multiplicity of endings.

History of the Plague: An Ancient Pandemic for the Age of COVID-19

During the fourteenth century, the bubonic plague or Black Death killed more than one third of Europe or 25 million people. Those afflicted died quickly and horribly from an unseen menace, spiking high fevers with suppurative buboes (swellings). Its causative agent is Yersinia pestis, creating recurrent plague cycles from the Bronze Age into modern-day California and Mongolia. Plague remains endemic in Madagascar, Congo, and Peru. This history of medicine review highlights plague events across the centuries. Transmission is by fleas carried on rats, although new theories include via human body lice and infected grain. We discuss symptomatology and treatment options. Pneumonic plague can be weaponized for bioterrorism, highlighting the importance of understanding its clinical syndromes. Carriers of recessive familial Mediterranean fever (FMF) mutations have natural immunity against Y. pestis. During the Black Death, Jews were blamed for the bubonic plague, perhaps because Jews carried FMF mutations and died at lower plague rates than Christians. Blaming minorities for epidemics echoes across history into our current coronavirus pandemic and provides insightful lessons for managing and improving its outcomes.

Yersinia pestis: the Natural History of Plague

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe

Yersinia pestis, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of Y. pestis have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled Y. pestis genomes from Eastern Europe (Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern Y. pestis strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial Y. pestis genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning Y. pestis transmission and its evolutionary history in Eastern Europe. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

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.

Estimating the basic reproduction number for the 2015 bubonic plague outbreak in Nyimba district of Eastern Zambia

BACKGROUND

Plague is a re-emerging flea-borne infectious disease of global importance and in recent years, Zambia has periodically experienced increased incidence of outbreaks of this disease. However, there are currently no studies in the country that provide a quantitative assessment of the ability of the disease to spread during these outbreaks. This limits our understanding of the epidemiology of the disease especially for planning and implementing quantifiable and cost-effective control measures. To fill this gap, the basic reproduction number, R0, for bubonic plague was estimated in this study, using data from the 2015 Nyimba district outbreak, in the Eastern province of Zambia. R0 is the average number of secondary infections arising from a single infectious individual during their infectious period in an entirely susceptible population.

METHODOLOGY/PRINCIPAL FINDINGS

Secondary epidemic data for the most recent 2015 Nyimba district bubonic plague outbreak in Zambia was analyzed. R0 was estimated as a function of the average epidemic doubling time based on the initial exponential growth rate of the outbreak and the average infectious period for bubonic plague. R0 was estimated to range between 1.5599 [95% CI: 1.382-1.7378] and 1.9332 [95% CI: 1.6366-2.2297], with average of 1.7465 [95% CI: 1.5093-1.9838]. Further, an SIR deterministic mathematical model was derived for this infection and this estimated R0 to be between 1.4 to 1.5, which was within the range estimated above.

CONCLUSIONS/SIGNIFICANCE

This estimated R0 for bubonic plague is an indication that each bubonic plague case can typically give rise to almost two new cases during these outbreaks. This R0 estimate can now be used to quantitatively analyze and plan measurable interventions against future plague outbreaks in Zambia.

A digital reconstruction of the 1630-1631 large plague outbreak in Venice

The plague, an infectious disease caused by the bacterium Yersinia pestis, is widely considered to be responsible for the most devastating and deadly pandemics in human history. Starting with the infamous Black Death, plague outbreaks are estimated to have killed around 100 million people over multiple centuries, with local mortality rates as high as 60%. However, detailed pictures of the disease dynamics of these outbreaks centuries ago remain scarce, mainly due to the lack of high-quality historical data in digital form. Here, we present an analysis of the 1630-1631 plague outbreak in the city of Venice, using newly collected daily death records. We identify the presence of a two-peak pattern, for which we present two possible explanations based on computational models of disease dynamics. Systematically digitized historical records like the ones presented here promise to enrich our understanding of historical phenomena of enduring importance. This work contributes to the recently renewed interdisciplinary foray into the epidemiological and societal impact of pre-modern epidemics.

The role of louse-transmitted diseases in historical plague pandemics

The rodent-murine ectoparasite-human model of plague transmission does not correspond with historical details around plague pandemics in Europe. New analysis of ancient genomes reveal that Yersinia pestis was unable to be transmitted by rat fleas until around 4000 Before Present, which challenges the rodent-murine ectoparasite-human model of plague transmission and historical details around plague pandemics in Europe. In this Review, we summarise data regarding Y pestis transmission by human lice in the context of genomic evolution and co-transmission of other major epidemic deadly pathogens throughout human history, with the aim of broadening our view of plague transmission. Experimental models support the efficiency of human lice as plague vectors through infected faeces, which suggest that Y pestis could be a louse-borne disease, similar to Borrelia recurrentis, Rickettsia prowazekii, and Bartonella quintana. Studies have shown that louse-borne outbreaks often involve multiple pathogens, and several cases of co-transmission of Y pestis and B quintana have been reported. Furthermore, an exclusive louse-borne bacterium, namely B recurrentis, was found to be circulating in northern Europe during the second plague pandemic (14th-18th century). Current data make it possible to attribute large historical pandemics to multiple bacteria, and suggests that human lice probably played a preponderant role in the interhuman transmission of plague and pathogen co-transmission during previous large epidemics, including plague pandemics.

Human plague: An old scourge that needs new answers

Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague's resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a "One Health" approach.

Extraordinary curtailment of massive typhus epidemic in the Warsaw Ghetto

The highly dependent interplay of disease, famine, war, and society is examined based on an extreme period during World War II. Using mathematical modeling, we reassess events during the Holocaust that led to the liquidation of the Warsaw Ghetto (1941-1942), with the eventual goal of deliberately killing ~450,000, mostly Jewish residents, many through widespread starvation and a large-scale typhus epidemic. The Nazis justified genocide supposedly to control the spread of disease. This exemplifies humanity's ability to turn upon itself, based on racially guided epidemiological principles, merely because of the appearance of a bacterium. Deadly disease and starvation dynamics are explored using modeling and the maths of food ration cards. Strangely, the epidemic was curtailed and was brought to a sudden halt before winter, when typhus normally accelerates. A far more massive epidemic outbreak was prevented through the antiepidemic efforts by the often considered incompetent and corrupt ghetto leadership and the Herculean efforts of ghetto doctors.

Managing plague on prairie dog colonies: insecticides as ectoparasiticides

Human health practitioners and wildlife biologists use insecticides to manage plague by suppressing fleas (Siphonaptera), but insecticides can also kill other ectoparasites. We investigated effects of deltamethrin and fipronil on ectoparasites from black-tailed prairie dogs (Cynomys ludovicianus, BTPDs). In late July, 2018, we treated three sites with 0.05% deltamethrin dust and 5 sites with host-fed 0.005% fipronil grain. Three non-treated sites functioned as experimental baselines. We collected ectoparasites before treatments (June-July, 2018) and after treatments (August-October, 2018, June-July, 2019). Both deltamethrin and fipronil suppressed fleas for at least 12 months. Deltamethrin had no detectable effect on mites (Arachnida). Fipronil suppressed mites for at least 12 months. Lice (Phthiraptera) were scarce on non-treated sites throughout the study, complicating interpretation. Concentrating on eight sites where all three ectoparasites where found in June-July, 2018 (before treatments), flea intensity was greatest on BTPDs carrying many lice and mites. These three ectoparasites co-occurred at high numbers, which might facilitate plague transmission in some cases. Lethal effects of insecticides on ectoparasite communities are potentially advantageous in the context of plague management.

Modeling the Justinianic Plague: Comparing hypothesized transmission routes

The Justinianic Plague, the first part of the earliest of the three plague pandemics, has minimal historical documentation. Based on the limited primary sources, historians have argued both for and against the "maximalist narrative" of plague, i.e. that the Justinianic Plague had universally devastating effects throughout the Mediterranean region during the sixth century CE. Using primary sources of one of the pandemic’s best documented outbreaks that took place in Constantinople during 542 CE, as well as modern findings on plague etiology and epidemiology, we developed a series of dynamic, compartmental models of disease to explore which, if any, transmission routes of plague are feasible. Using expected parameter values, we find that the bubonic and bubonic-pneumonic transmission routes exceed maximalist mortality estimates and are of shorter detectable duration than described by the primary sources. When accounting for parameter uncertainty, several of the bubonic plague model configurations yielded interquartile estimates consistent with the upper end of maximalist estimates of mortality; however, these models had shorter detectable outbreaks than suggested by the primary sources. The pneumonic transmission routes suggest that by itself, pneumonic plague would not cause significant mortality in the city. However, our global sensitivity analysis shows that predicted disease dynamics vary widely for all hypothesized transmission routes, suggesting that regardless of its effects in Constantinople, the Justinianic Plague would have likely had differential effects across urban areas around the Mediterranean. Our work highlights the uncertainty surrounding the details in the primary sources on the Justinianic Plague and calls into question the likelihood that the Justinianic Plague affected all localities in the same way.

A Note on Observation Processes in Epidemic Models

Many disease models focus on characterizing the underlying transmission mechanism but make simple, possibly naive assumptions about how infections are reported. In this note, we use a simple deterministic Susceptible-Infected-Removed (SIR) model to compare two common assumptions about disease incidence reports: Individuals can report their infection as soon as they become infected or as soon as they recover. We show that incorrect assumptions about the underlying observation processes can bias estimates of the basic reproduction number and lead to overly narrow confidence intervals.

Real-time forecasting of epidemic trajectories using computational dynamic ensembles

Forecasting the trajectory of social dynamic processes, such as the spread of infectious diseases, poses significant challenges that call for methods that account for data and model uncertainty. Here we introduce an ensemble model for sequential forecasting that weights a set of plausible models and use a frequentist computational bootstrap approach to evaluate its uncertainty. We demonstrate the feasibility of our approach using simple dynamic differential-equation models and the trajectory of outbreak scenarios of the Ebola Forecasting Challenge. Specifically, we generate sequential short-term forecasts of epidemic outbreaks by combining phenomenological models that incorporate flexible epidemic growth scaling, namely the Generalized-Growth Model (GGM) and the Generalized Logistic Model (GLM). We rely on the root-mean-square error (RMSE) to quantify the quality of the models' fits during the calibration periods for weighting their contribution to the ensemble model while forecasting performance was evaluated using the RMSE of the forecasts. For a given forecasting horizon (1-4 weeks), we report the performance for each model as the percentage of the number of times each model outperforms the other models. The overall mean RMSE performance of the GLM and the GGM-GLM ensemble models outcompeted that of participant models of the Ebola Forecasting Challenge. We also found that the ensemble model provided more accurate forecasts with higher frequency than the GGM and GLM models, but its performance varied across forecasting horizons. For instance, across all of the Ebola Challenge Scenarios, the ensemble model outperformed the other models at horizons of 2 and 3 weeks while the GLM outperformed other models at horizons of 1 and 4 weeks.

The Justinianic Plague: An inconsequential pandemic?

Existing mortality estimates assert that the Justinianic Plague (circa 541 to 750 CE) caused tens of millions of deaths throughout the Mediterranean world and Europe, helping to end antiquity and start the Middle Ages. In this article, we argue that this paradigm does not fit the evidence. We examine a series of independent quantitative and qualitative datasets that are directly or indirectly linked to demographic and economic trends during this two-century period: Written sources, legislation, coinage, papyri, inscriptions, pollen, ancient DNA, and mortuary archaeology. Individually or together, they fail to support the maximalist paradigm: None has a clear independent link to plague outbreaks and none supports maximalist reconstructions of late antique plague. Instead of large-scale, disruptive mortality, when contextualized and examined together, the datasets suggest continuity across the plague period. Although demographic, economic, and political changes continued between the 6th and 8th centuries, the evidence does not support the now commonplace claim that the Justinianic Plague was a primary causal factor of them.

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.

Epidemiology of Plague: Problems with the Use of Mathematical Epidemiological Models in Plague Research and the Question of Transmission by Human Fleas and Lice

This article addresses the recent use of mathematical epidemiological SIR or SEIR models in plague research. This use of S(E)IR models is highly problematic, but the problems are not presented and considered. Serious problems show in that such models are used to "prove" that historical plague was a (1) Filoviridae disease and (2) a bacterial disease caused by Yersinia pestis which was transmitted by human fleas and lice. (3) They also support early-phase transmission (by fleas). They purportedly consistently disprove (4) the conventional view that plague is/was a rat-and-rat-flea-borne disease. For these reasons, the focus is on methodological problems and on empirical testing by modern medical, entomological, and historical epidemiological data. An important or predominant vectorial role in plague epidemics for human fleas and lice requires that several necessary conditions are satisfied, which are generally not considered by advocates of the human ectoparasite hypothesis of plague transmission: (1) the prevalence and levels of human plague bacteraemia (human plague cases as sources of infection of feeding human ectoparasites); (2) the general size of blood meals ingested by human fleas and lice; (3) the consequent number of ingested plague bacteria; (4) the lethal dose of bacteria for 50% of a normal sample of infected human beings, LD50; and (5) efficient mechanism of transmission by lice and by fleas. The factual answers to these crucial questions can be ascertained and shown to invalidate the human ectoparasite hypothesis. The view of the standard works on plague has been corroborated, that bubonic plague, historical and modern, is/was a rat-and-rat-flea-borne disease caused by Yersinia pestis. These conclusions are concordant with and corroborate recent studies which, by laboratory experiments, invalidated the early-transmission hypothesis as a mechanism of transmission of LDs to humans in plague epidemics and removed this solution to the problem of transmission by human fleas.