Category Archives: smallpox

Autumn Reading

Autumn 15

While autumn is not officially over yet, December always seems like winter to me so here is my reading review from autumn.
This season I’m introducing a book review rating system. On my scale, an average book would get three scopes; a good book, four; and only the extraordinary book gets five scopes. I probably will not rate translations because I don’t feel qualified to evaluate them.


Paul Kelton. Epidemics and Enslavement: Biological Catastrophes in the Native Southeast, 1492-1715. University of Arizona Press, 2007.   microscope23 (1)microscope23 (1)microscope23 (1)microscope23 (1)

Catherine Cameron, Paul Kelton, and Alan Swedlund, eds. Beyond Germs: Native Depopulation in North America. U of Arizona Press, 2015. microscope23 (1)microscope23 (1)microscope23 (1)microscope23 (1)microscope23 (1)

Pseudo-Dionysius of Tel-Mahre: Chronicle, Part III edited by Withold Witakowski, Liverpool University Press, 1997. (includes the largest section of John of Ephesus’ Church History/History of the Plague)

Zlata Blažina Tomic and Vesna Blažina  Expelling the Plague: The Health Office and the Implementation of Quarantine in Dubrovnik, 1377-1533. McGill-Queens University Press, 2015.microscope23 (1)microscope23 (1)microscope23 (1)microscope23 (1)

Dorothy Crawford. Deadly Companions: How Microbes Shaped Our History. Oxford University Press, 2007. microscope23 (1)microscope23 (1)microscope23 (1)

Susan Mattern. The Prince of Medicine: Galen in the Roman Empire. Oxford University Press, 2013. microscope23 (1)microscope23 (1)microscope23 (1)microscope23 (1)


Meier, D. (2004). Man and environment in the marsh area of Schleswig–Holstein from Roman until late Medieval times. Quaternary International, 112(1), 55–69.


Stanley, J.-D., Bernasconi, M. P., & Jorstad, T. F. (2008). Pelusium, an Ancient Port Fortress on Egypt’s Nile Delta Coast: Its Evolving Environmental Setting from Foundation to Demise. Journal of Coastal Research, 242, 451–462.

Schats, R. (2015). Malaise and mosquitos: osteoarchaeological evidence for malaria in the medieval Netherlands. Analecta Praehistoricaleidensia, 45, 133–140.

MacMaster, T. J. (2015). “Not With a Bang?” The Economics of Trade and the End of Byzantine North Africa. In M. Di Rodi, P. Frankopan, M. Lau, & C. Franchi (Eds.), Landscapes of Power: Selected Papers From the XV Oxford University Byzantine Society International Graduate Conference (pp. 73–91).

SHWARTZ, L. (2013). Gargano Comes to Rome: Castel Sant“Angelo”s Historical Origins. The Journal of Ecclesiastical History, 64(03), 453–475. (Blogged about here: St Michael, the Plague and Castel Sant’ Angelo,  in 2012 after his Kalamazoo talk. I just found in in print much as I remembered in the blog post.)

Rasmussen, S., Allentoft, M. E., Nielsen, K., Orlando, L., Sikora, M., Sjögren, K.-G., et al. (2015). Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell, 163(3), 571–582. (See the previous post on this blog!)

Sun, Y.-C., Jarrett, C. O., Bosio, C. F., & Hinnebusch, B. J. (2014). Retracing the Evolutionary Path that Led to Flea-Borne Transmission of Yersinia pestis. Cell Host and Microbe, 15(5), 578–586.

McCormick, M. (2015). Tracking mass death during the fall of Rome’s empire (I). Journal of Roman Archaeology, 28, 325–357.

Daniel Melleno. (2014) North Sea Networks: Trade and Communication from the Seventh to the Tenth Century. Comitatus. 45:65-90.

microscope23 (1)Icon made by Freepik from

Siberian Mummy Yields 300-year-old Smallpox DNA

Five mummies in one grave. Benigini et al. NEJM, 2012. DOI: 10.1056/NEJMc1208124

It was the mass grave that got their attention. Four bodies crammed into one casket, with one child outside but with the casket. Multiple graves are not common in Yakutia, Siberia. Examination of the late 17th to early 18th century mummies indicates that burial came quickly after death. The casket contains one adult male over age 30, an adult female, an adult female under age 23,  a male child about 5 years old, and outside the casket a child about 4 years old.

The French and Russian team led by Philippe Biagini undertook pathological and genetic analysis of all five mummies. They were able to confirm that the older woman is the mother of  the young adult woman and the adult male. They took lung and tooth specimens from each mummy at the site (in situ). Finding iron inclusions in the lungs of the young female (mummy 2), suggested to the team that she suffered a pulmonary hemorrhage shortly before death. They don’t say how they jumped from there to screening for smallpox or what other pathogens were considered.  Oddly, they make no mention of any smallpox lesions on the mummy. (Without other bioarchaeological data, is it possible that this team only received the tooth and lung specimens, but not the remainder of the mummy?)

The DNA was divided among three labs. Three short sections of Variola  (smallpox) genome were amplified by at least two labs each. They failed to amplify long stretches of the virus, suggesting that there are no intact virons left in the mummy. Their phylogenetic analysis grouped this virus, PoxSib, with Variola but distinct from both clade 1 and clade 2. They suggest that PoxSib could be an ancestral strain to both clade 1 and clade 2 or a strain that has not been previously sampled. Biagini et al. suggest this virus may have come to Siberia with the Russian conquest in early 18th century, possibly connected with a documented outbreak in 1714. This grave comes from the same culture as previously analyzed graves that isolated the first ancient whooping cough.


Biagini, P., Thèves, C., Balaresque, P., Géraut, A., Cannet, C., Keyser, C., Nikolaeva, D., Gérard, P., Duchesne, S., Orlando, L., Willerslev, E., Alekseev, A., de Micco, P., Ludes, B., & Crubézy, E. (2012). Variola Virus in a 300-Year-Old Siberian Mummy New England Journal of Medicine, 367 (21), 2057-2059 DOI: 10.1056/NEJMc1208124 See supplemental appendix for most of the detail.

Mapping Smallpox, Malaria, and Leprosy

Contagion by Haisam Hussein of Lapham's Quarterly (Click the map to enlarge)

I love looking at infection maps. Hat-tip to Michael Walsh at Germscape for finding this map. There is a lot of information on this map and unfortunately any text that might have come with it at Lapham’s Quarterly is not readily available. So we have the map to figure out without any explanation. The red arteries represent the origin of Leprosy in central Africa and the blue veins represent the origin of smallpox in northern Africa and its spread. Transmission lines for malaria are not shown; the yellow areas seem to represent modern endemic malaria. The geographic highlights either document transmission events or major steps in the study of malaria, smallpox and leprosy.

Malaria deaths in the United States, 1870 census.

At the height of its expansion, there are few places on earth that malaria did not penetrate. Today malaria is found primarily in tropical regions but that wasn’t always so. The map to the right illustrates the malarial deaths listed in the 1870 US federal census. Malaria once was endemic, at one time or another, in most of the United States east of the Mississippi River and around the Gulf of Mexico. Likewise it was endemic in parts of 19th century Britain. In temperate regions of the world it is the humans who carry the parasite through the winter and infect the spring mosquitoes. Contrary to general knowledge, most malaria in the United States dwindled long before the arrival of DDT. Improving the standard of living and eliminating unnecessary standing water are the most important ways to decrease malaria. Early American physician Benjamin Rush knew this over two centuries ago.