Category Archives: biogeography

Expanding the Historical Plague Paradigm

When the first complete genomic sequence of Yersinia pestis was published on October 4, 2001 the world was naturally focused elsewhere, on anthrax bioterrorism — the Amerithrax incident was then in its second week– and the September 11 attacks were just over three weeks old. As the world redeveloped bioterrorism assessments and plans, plague was placed on lists along with anthrax, smallpox and yes, ebola as agents of national security concern and response.  Although plague produced more annual cases than most agents on the category A bioterrorism list, it was placed on the list primarily based on its historical reputation and past attempts to weaponize it (also based on its reputation). Yet, in 2001 there was a fierce debate ranging among historians and others on whether Yersinia pestis was the agent of the Black Death at all.

It would take another ten years before genomics would revolutionize our understanding of the historical plague. On October 12, 2011 the first draft sequence of an ancient plague genome was published. Finally, adding to the detection of Yersinia pestis DNA tests previously done on remains, the draft sequence isolated from the East Smithfield Black Death cemetery in London solidified consensus that Yersinia pestis is the agent of the Black Death pandemic.  Meanwhile, the phylogenetic tree of Yersinia pestis had been constructed based on the genetic sequence of isolates from all over the globe. Ancient and modern Yersinia pestis genomes were opening a new window into the history of the species.

As fundamental as genomic analysis is to the new understanding of historical plague, it is a skeleton of data that is open to many different historical interpretations. Science can’t adequately explain the historic plague epidemics alone; it takes historical context. In the inaugural double issue of The Medieval Globe,  Pandemic Disease in the Medieval World: Rethinking the Black Death (open access) begins this process. The eleven articles in this issue take the genetic identification of Yersinia pestis  as the agent of the Black Death as foundational and integrate modern biological and epidemiological information into a new global Old World assessment of the history of the Black Death and subsequent epidemics. Each of these articles lays the groundwork for future interdisciplinary work between historians, anthropologists, biologists, epidemiologists and others.

In my own contribution to this issue, “The Black Death and the Future of the Plague” I discuss why plague is still important in the modern world and for our future. Plague has played an integral role in the development of the re-emerging infectious diseases paradigm and is an agent of biosecurity concern. I review the current state of plague around the world, what we have learned about plague epidemiology and transmission, and how it can be applied to historic epidemics. I also make my case for why the study of the entire history of plague is uniquely important and why the sciences and humanities must move forward together.  I hope we can engage in a discussion on these issues here in the comments section, on twitter or by email.

My own interest and awareness of the issues surrounding the study of the plague was transformed when I had the great fortune to be invited by Monica Green to participate in a session at the American Historical Association annual meeting in New Orleans, January 2013. The group of plague scholars gathered there has largely remained in contact and expanded our network into an informal working group that has enriched all of our scholarship.  No one can become fully conversant with all of the disciplines involved in the study of even one epidemic, much less the entire history of the plague.  Working in disciplinary seclusion will not produce a satisfying paradigm or widespread consensus. It takes work, patience and some tolerance of how other disciplines work, but I have found it to always be worth it. I hope you will agree.

Some references for the milestones mentioned:

Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T., Prentice, M. B., et al. (2001). Genome sequence of Yersinia pestis, the causative agent of plague. Nature, 413(6855), 523–527. doi:10.1038/35097083

Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., et al. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics, 1–20. doi:10.1038/ng.705

Little, L. K. (2011). Plague Historians in Lab Coats. Past & Present, 213(1), 267–290. doi:10.1093/pastj/gtr014

Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., et al. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 1–5. doi:10.1038/nature10549

Pandemic Disease in the Medieval World: Rethinking the Black Death. Edited by Monica Green. The Medieval Globe, 1 (1), 2014.

General Principles of Zoonotic Landscape Epidemiology

Zoonoses, pathogens with animal reservoirs, exist as part of a complex system of interactions between animal reservoirs, vectors, ecological factors and human interaction. Landscape epidemiology has existed as a field of study since Russian epidemiologist E.N. Pavlovsky coined the term and laid the groundwork in the 1960s. Landscape epidemiology is in essence the study of environmental foci of zoonotic disease, what Pavlovsky called a nidas. Many of the variables have been identified and studied in individual pathogen systems.

Each system seems so complex and unique that it can be easy to think that they each exist as separate entities with little to do with each other. It is necessary to develop some general principles to both see the bigger picture, and guide research and response to less studied and newly discovered pathogens. Lambin et al. set out to do just that by doing a meta-analysis of eight regional case studies of zoonotic diseases in Europe and East Africa: West Nile Virus in Senegal, Tick-borne Encephalitis in Latvia, Sandfly abundance (leishmaniasis vector) in the French Pyrenees, Rift Valley Fever in Senegal, West Nile Virus hosts in Camargue, Rodent-borne Puumala hantavirus in Belgium, human cases of Lyme borreliosis in Belgium, and risk of malaria re-emergence in Camargue. Obviously, as indicated, not all of these studies look at all factors involved in landscape epidemiology so validation is not solely based on the number of case studies that support each principle.

The ten proposed principles by Lambin et al are shown graphically below where they fit into the system of variables.

Graphical representation of the landscape determinants of disease transmission. The numbers refer to the ten propositions formulated in this paper. Lambin et al. International Journal of Health Geographics 2010 9:54   doi:10.1186/1476-072X-9-54
Graphical representation of the landscape determinants of disease transmission. The numbers refer to the ten propositions formulated in this paper.
Lambin et al. International Journal of Health Geographics 2010 9:54 doi:10.1186/1476-072X-9-54

Proposed general principles (Lambin et al, 2010):

  1. Landscape attributes may influence the level of transmission of an infection” This proposal is found in all case species. Features of the landscape influence vector and host distribution across the region of study. Distribution and type of water (fresh, brackish, or salt water) is a common landscape feature that influences density of insect vectors.
  2. Spatial variations in disease risk depend not only on the presence and area of critical habitats but also on their spatial configuration“.   The sheer size of the critical area is not the only or necessarily the most important characteristic to determine risk in an area. Some vectors like ticks thrive along border zones between ecosystems, like edges between woodland and grasslands.
  3. Disease risk depends on the connectivity of habitats for vectors and hosts” Creating contact zones or contiguous zones that create linked areas are also important. The spatial configuration can create corridors for disease persistence in harsh landscapes. Type and connectivity of  vegetation is as important as terrain for vector habitats. Connectivity between suitable habitat for rodents and insects allows the disease to spread from one patch to the next amplifying the pathogen to a level that increases risks of human transmission. Connections between patches of critical habitats allows for recolonization after local extinction.
  4. The landscape is a proxy for specific associations of reservoir hosts and vectors linked with the emergence of multi-host disease.” Their principle could be better fleshed out; their primary evidence coming from West Nile Virus (WNV). Like other multi-host pathogens, WNV has some hosts that are much more important than others for transmission across wide regions. In WNV migratory birds are a key to understanding its spread and epidemic dynamics. WNV is also an example of a disease with different proxies and amplification hosts in different regions of the world.
  5. To understand ecological factors influencing spatial variations of disease risk, one needs to take into account the pathways of pathogen transmission between vectors, hosts, and the physical environment.” Vector-borne diseases require direct contact between humans and the vector. For other zoonoses like hantavirus contact between humans and animal hosts can be via aerosols of material with rodent feces or dust containing rodent remains. For example, people have contracted hantavirus by vacuuming up rodent remains in homes. When estimating risk of transmission to humans, abiotic (non-living) environmental conditions that can preserve or transmit to humans have to be considered. Climate and moisture content of the soil are common abiotic factors to be concerned about. Additional support for this principle comes from the role of the rodent burrow system on plague (Yersinia pestis) hosts and vectors.
  6. The emergence and distribution of infection through time and space is controlled by different factors acting at multiple scales” In their discussion of this principle, they focus on human interaction with the environment and particularly urbanization altering disease risk. They note that climate change and natural environmental change do not account for all emerging and re-emerging disease but the activities of humans including urbanization and ecological change like deforestation. Ben-Ari et al‘s study on plague and climate change also looks at the many factors at all levels from micro to macro scales effect the abundance and likelihood of transmission of the plague.

    Plague cycle including hosts and vectors with abiotic influences
    Plague cycle including hosts and vectors with abiotic influences (Ben-Ari et al, 2011).
  7. Landscape and meteorological factors control not just the emergence but also the spatial concentration and spatial diffusion of infection risk” This principle just adjusts the previous principles to take account of primarily rainfall by looking at temporary ponds or wetlands. This particularly affects mosquito abundance, but as the graphic above demonstrates also effects soil moisture.
  8. Spatial variation in disease risk depends not only on land cover but also on land use, via the probability of contact between, on one hand, human hosts and, on the other hand, infectious vectors, animal hosts or their infected habitats” Land use has been long known to affect mosquito abundance and disease transmission. Clearing land for settlements or agriculture always increases standing water in ditches, tire ruts, railroad ditches, animal troughs, incomplete building projects, and due to loss of water absorbing vegetation. A century of malaria research and management has focused on land use and the elimination of standing water.  Mature water management programs for cultivation or flood control can also alter vector abundance and human contact rates. For example flooding fields to grow rice not only provides habitat for mosquito production but also brings people into the fields to cultivate increasing contact rates. Irrigation canals would have a similar effect.
  9. The relationship between land use and the probability of contact between vectors and animal hosts and human hosts is influenced by land ownership” In Lambin et al, they looked at the contact rates between public (state) land and private ownership. In these studies state ownership increased access to forestland over private ownership.By the same token, state ownership could also prevent deforestation and urbanization by preserving the wilderness or reserving the land for other uses. Forest age and maturity also varies significantly between state forests and private land.
  10. Human behaviour is a crucial controlling factor of vector-human contacts, and of infection.”  Humans bring themselves into contact with vectors by risky behavior and can control exposure vectors and infections. Obviously, vaccination is one of the controlling factors of infection, although many zoonotic infections have either no or poor vaccines. Occupational and recreational exposure to vectors often explains gender difference in infection rates.

In conclusion these principles begin to mark out the three sides of a zoonotic triangle: biology of pathogen, vector and host; ecological system where they exist; and human behavior and ecological interaction. Human behavior including land use and constructed environments is as important as the other two sides of the triangle. Humans are not passive victims or collateral damage.


Lambin, E. F., Tran, A., Vanwambeke, S. O., Linard, C., & Soti, V. (2010). Pathogenic landscapes: Interactions between land, people, disease vectors, and their animal hosts. International Journal of Health Geographics, 9(1), 54. doi:10.1186/1476-072X-9-54 [open access]

Ben-Ari T, Neerinckx S, Gage KL, Kreppel K, Laudisoit A, et al. (2011) Plague and Climate: Scales Matter. PLoS Pathog 7(9): e1002160. doi:10.1371/journal.ppat.1002160

Western Iranian Plague Foci Still Active, 2011-2012

In a letter in this month’s Emerging Infectious Diseases, an Iranian and French team of epidemiologists report that the old plague focus in western Iran bordering Kurdistan is still active. Between 1947 and 1966 there were nine human plague epidemics causing 156 human deaths.  The last recorded human case occurred in 1966 and in animals in 1978. No surveys for plague were conducted for the following 30 years. It is unlikely to be a coincidence that the Iranian Revolution also began in 1978.

During the summers of 2011 and 2012, the team captured and tested for the plague F1 antibody 98 rodents and counted their fleas, finding only one rodent with antibodies (1.08%). They also tested 117 sheepdogs finding 4 positive dogs or 3.42%.  In dogs, plague antibodies only last about six months suggesting that these sheepdogs must have had recent infections.  This is enough to suggest that the plague foci is still present in western Iran. Moreover, they believe the number of reservoir rodents and fleas per rodent (Xenopsylla species index 4.10) is “most favorable” circumstances for an epizootic. With plague antibodies found in the only area surveyed in 30 years, it is clear that surveillance needs to not only continue but expand extensively.


Esamaeili S, Azadmanesh K, Naddaf SR, Rajerison M, Carniel E, & Mostafavi E (2013). Serologic survey of plague in animals, Western Iran. Emerging infectious diseases, 19 (9) PMID: 23968721