Category Archives: Asia

Presentations on the Plague from the European Association of Archaeologists, Vilnius, Lithuania, 2016

I just discovered that most of the presentations from the “Plague in Diachronic and Interdisciplinary Perspective” session of the Europan Association of Archaeologists meeting in Vilnius, Lithuania on 2 September 2016 are now on YouTube.  I think I have collected them all here. Enjoy 3 hours of plague talks!

Introduction-Plague in diachronic and Interdisciplinary perspective by Marcel Keller

From Mild to Murderous: How Yersinia pestis Evolved to Cause Pneumonic Plague by Wyndham Lathem (30 min)

Reconstructing ancient pathogens – discovery of Yersinia pestis in Eurasia 5,000 Years Ago by Simon Rasmussen (15 min)

Plague in the eastern Mediterranean region 1200-1000 BC? by Lars Walloe (15 min)

Placing the Plague of Justinian in the Yersinia pestis phylogenetic context by Jennifer Klunk (15 min)

A demographic history of the plague bacillus revealed through ancient Yersinia pestis genomes by Maria Spyrou (15 min)

Analysis of a High-coverage Yersinia pestis Genome from a 6th Century Justinianic Plague Victim by Michal Feldman (15 min)

Early medieval burials of plague victims: examples from Aschheim and Altenerding (Bavaria, Germany) by Doris Gutsmiedl-Schumann (15 min)

Fleas, rats and other stories – The palaeoecology of the Black Death by Eva Panagiotakopulu (15 min)

Plague in Valencia, 546: A Case Study of the Integration of Texts and Archaeology by Henry Gruber (15 min)

Germany and the Black Death: a zooarchaeological approach by M.A. Paxinos

War as a Driver in Tuberculosis Evolution

by Michelle Ziegler

Russia has been all over the news lately. Beyond our recent election, increased Russian activity on the world stage has public health consequences for Europe and farther afield. It has been known for a long time that post-Soviet Russia had and continues to have serious public health problems. One of their particular problems that they have shared with the world is their alarmingly high rate of antibiotic resistant tuberculosis. There is no mystery over the root cause of their antibiotic resistance woes — poor antibiotic stewardship (Garrett, 2000; Bernard et al 2013).

A study by Vegard Eldholm and colleagues that came out this fall sheds light on the origins of particularly virulent tuberculosis strains with high rates of antibiotic resistance that recently entered Europe.  A large outbreak among Afghan refugees and Norwegians in Oslo, Norway, provided a core set of 26 specimens for this study that could be compared with results generated elsewhere in Europe (Eldholm et al, 2010). The Oslo outbreak clearly fits within the Russian clade A group that is concentrated to the east of the Volga River in countries of the former Soviet Union. They name this cluster the Central Asian Clade, noting that it co-localizes with region of origin of migrants carrying the MDR strains of tuberculosis reported in Europe.

Figure 5. Phylogeny of the Afghan Strain Family (ASF). Colored boxes represent the country of origin: Afghanistan is orange; other countries are gray. (Eldholm et al, 2016)

When the Oslo samples are added to the family tree, phylogeny, of recent tuberculosis isolates from elsewhere in Europe a distinctive pattern emerges. The branches on the family tree are short and dense, suggesting that this is recent diversity, that they calculate to have occurred within approximately the last twenty years (Eldholm et al, 2016).

The Central Asian Clade spread into Afghanistan before drug resistance began to develop, probably during the Soviet-Afghan war (1979-1989) producing the Afghan Strain Diversity clade. Slightly later, the Central Asian Clade still in the former Soviet states begins to accumulate antibiotic resistance as the public health infrastructure crumbles in the wake of the dissolution of the USSR. The invasion of Afghanistan by the US and its allies in 2002 toppled the Afghan state, crippling infrastructure and spurring refugee movements within and out of Afghanistan. The lack of modern public health standards in Afghanistan since their war with the introduction of these strains by the Soviets in the 1980s provided fertile ground for the establishment and diversity of tuberculosis in the country. Instability has been pervasive throughout the entire region sending refugees and economic migrants from both Afghanistan and the former Soviet states into Europe.

Movements of the Central Asian Clade (CAC) since c. 1960 and the subsequent Afghan Strain Family (ASF). (Eldholm et al, 2016)

Their dating of the last common ancestor for the Central Asian Clade to c. 1961 is significantly younger than the previous dating of 4,415 years before present for the Russian clade A (CC1) of the Beijing lineage of Mycobacteria tuberculosis. They account for this difference by noting differences in their methods of assessing sequence differences and note that their method is in line with other recent evolutionary rates for other tuberculosis clades.  The diagnosis dates and length of the arms on their reconstructed phylogeny suggests that there were multiple, independent introductions of the cases from Afghanistan and the former Soviet republics. This is consistent with a repeated periods of refugee movements from central Asia into Europe.

The rapid proliferation and diversification of the Afghan Strain Family may be explained by a known syndemic between tuberculosis and war (Ostrach & Singer, 2013). Conditions of war everywhere disrupt food systems, destroy critical infrastructures such as electricity and water systems, interrupts medical supplies, and the human public health infrastructure of the country. Malnutrition and stress are known contributors to immune suppression. Many pathogens flourish simultaneously in these conditions increasing the infectious challenges the population must fend off. Diarrheal diseases are the most acute and demanding of rapid attention, allowing longer-term diseases like tuberculosis to slip through the overburdened healthcare system. Afghanistan has experienced nearly forty years of war, political instability, and repeated infrastructure destruction. Thus, they were primed for both the establishment of new tuberculosis strains during the Afghan-Soviet war in the 1980s along with the proliferation and diversification of tuberculosis during the Afghan-American war of the last sixteen years.

Established syndemics between tuberculosis and war have been made retrospectively following the Vietnam war and the Persian Gulf war of 1991 (Ostrach & Singer, 2013). In Vietnam, prolonged malnutrition caused an eruption of tuberculosis along with malaria, leprosy, typhoid, cholera, plague, and parasitic diseases.  A WHO survey in 1976 found that Vietnam had twice the incidence of tuberculosis over all of its neighboring countries (Ostrach & Singer, 2013). When the military intentionally targets water infrastructure as it did in Vietnam and Iraq, the production of civilian infectious disease is a tactic of war. In both Vietnam and post-Gulf war Iraq, more civilians died of malnutrition and infectious disease than enemy soldiers died of all causes (Ostrach & Singler, 2013).

It seems likely that this is just one of the first studies to establish a link between serious infectious disease developments and the Afghan wars. The current war zones throughout central Asia and the Middle East already have ramifications for the public health of the entire world that walls along borders will not be able to stop. Most of the cases in the Oslo outbreak were Norwegians, not Afghan immigrants. Diseases will spread beyond the migrants so country of origin screening will be of little use before long.


Eldholm, V., Pettersson, J. H. O., Brynildsrud, O. B., Kitchen, A., Rasmussen, E. M., Lillebaek, T., et al. (2016). Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 201611283–16.

Ostrach, B., & Singer, M. C. (2013). Syndemics of War: Malnutrition-Infectious Disease Interactions and the Unintended Health Consequences of Intentional War Policies. Annals of Anthropological Practice, 36(2), 257–273.

Bernard, C., Brossier, F., Sougakoff, W., Veziris, N., Frechet-Jachym, M., Metivier, N., et al. (2013). A surge of MDR and XDR tuberculosis in France among patients born in the Former Soviet Union. Euro Surveillance: Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 18(33), 20555.

Keeping Bronze Age Yersinia pestis in Perspective

by Michelle Ziegler

Graphic abstract from ____
Graphic abstract from Rasmussen et al, 2015.

The latest plague news to splash across headlines is the discovery of Yersinia pestis aDNA in seven Bronze Age remains from Eurasia.  The most important findings in this new study are not anthropological; they are evolutionary. This paper allows us to drop a couple more evolutionary mile markers. Finding  7% of the tested remains  (7 out of 101) positive for plague is surprising, but I’m not yet ready to believe that it was endemic over such a huge area scattered over 2000 years. Not yet anyway.

The new phylogenetic tree places Y. pestis in humans since the Bronze Age and the origin of the species as far back 50,000 years ago.  It also opens up questions on the original reservoir species and the location of the birth of the species, although central Asia is still the most likely location.

Stretching out the Yersinia pestis tree. Blue arrows are gains and red arrows are losses. (Rasmussen et al, 2015)

So let’s look at the genetic results in three areas highlighted by Rasmussen et al: flea transmission, Pla activity, and suppression of the immune response stimulating flagellin production. These traits are critical to producing bubonic plague as we know today.

Late phase flea transmission of modern Yersinia pestis is dependent on the ability to survive in and colonize the flea. The Bronze Age strains have all of the plasmids and virulence genes of modern strains except one, the ymt gene that encodes the murine toxin. The basic tool set of modern strains also have deactivated or knocked-out the protein products of three ancestral genes that hinder Yersinia pestis biofilm formation. Remnants of these genes persist as pseudogenes in modern strains. (A pseudogene is the corpse of a former gene.) This genetic combination allows Y. pestis to survive in the mid-gut of the flea, persist longer and form a biofilm; a necessity for late phase flea transmission. However, as Monica Green reminded me,  ymt is not required for early phase flea transmission, dirty-needle style (Johnson et al, 2014). In fact, since Y. pestis does not need to persist long or multiply at all, there are no known genes needed to be present or absent for early phase transmission.  As I recently reviewed, early phase transmission is very common and effective (see Eisen, Dennis & Gage, 2015). Based on the dates of their samples, they estimate that ymt was gained in about 1000 BC. In the RISE509 strain from Afanasievo Gora in southern Siberia, the pde3 is inactive but the other two, pde2 and rcsA, are still functional. Taken together this genetic combination should allow early phase flea transmission but not late phase flea transmission that requires biofilm formation. They are still mid-way in developing late phase flea transmission. This makes sense for a microbe being transmitted dirty-needle style, providing the opportunity for natural selection to develop late phase transmission bit by bit. While early phase transmission can support regional epizootics and epidemics,  late phase flea transmission is probably important for long distance transmission by fleas in grain or textiles, or by sea.

The recent discovery of the Pla gene in Citrobacter koseri and Escherichia coli, other enteric opportunistic flora, but not found in Yersinia pseudotuberculosis, suggests that lateral gene transfer  brought the plasmid to the young Y. pestis while still in the enteric environment (Hänsch et al, 2015) . This is consistent with Y. pestis Pla and Salmonella enterica PgeE both evolving from the same ancestral omptin ancestor in an enteric environment (Haiko et al, 2009).  This suggests that Y. pestis may have remained an enteric organism for some time after it split from Y. pseudotuberculosis.

Six of seven Bronze Age Y. pestis strains contain the Pla gene required for deep tissue invasion and bubo formation. Rasmussen et al (2015) suggest that the strain lacking the Pla gene has lost it and that this gene has been lost more than once in the phylogenetic tree. In other words, Pla was present in the common ancestral strain. However, to support development of bubonic plague Pla needed to gain a mutation at position 259 that these strains lack (Haiko et al, 2009). So the Pla gene without the mutation at position 259 can support pneumonic plague but not bubonic in the Pestoides F strain (0.PE2) of Y. pestis (Zimbler et al, 2015).  On the other hand, Sebbane et al (2006) showed that strains completely lacking Pla can still develop primary septicemic plague following flea transmission. They can envision an “evolutionary scenario in which plague emerged as a flea-borne septicemic disease of limited transmissibility”(Sebbane et al, 2006).  Without the polymorphism at position 259, bubo formation should be retarded, if not suppressed.

A third genetic difference of possible significance is the apparent ability to produce flagellin, a major activator of the human innate immune system. Modern Y. pestis strains have deactivated the production of flagellin by a frameshift mutation in the regulatory gene flhD. The Bronze Age strains lack this frameshift and so presumably had normal flagellin production. However, Y. pseudotuberculosis and  Y. enterocolitica down regulate production at mammalian body temperatures. If the ancestral Y. pestis did also then its possible that it wasn’t a factor in human infections.  Experimentally recreating the regulatory environment from  Y. pseudotuberculosis would be much more difficult than simply inserting an intact copy of the gene in a modern strain of Y. pestis.

Predicting the impact of these ancestral genes is highly conjectural. This combination of genes has never been studied together. Since these strains were isolated from human remains we can assume that there is a path for transmission and pathogenesis. The reliance on early phase flea transmission, the less virulent pla allele and the possible production of flagellin suggest that Bronze Age local (dermal) infections from flea bites would be less virulent (more survivable). Interestingly, these milder local infections may have been immunogenic.

As Y. pestis moved away from an enteric lifestyle, producing a septicemia was necessary for either flea transmission or development of a secondary pneumonia with aerosol transmission. I find it hard to believe that Bronze Age Siberia or Estonia had a large enough population for sustained pneumonic transmission. Since Pulex irritans can transmit Y pestis without development of a biofilm, there is no reason to see humans as a dead-end to flea transmission even as early as the Bronze Age.

Humans could have also contracted septicemic plague by ingesting infected meat. Although natural ingestion infections are very rare today, this mode remains effective. A village size outbreak could easily occur from sharing a large infected animal as happened in Afghanistan in 2007. In that outbreak a single infected camel shared among two villages produced 83 probable cases of plague with 17 deaths, a case fatality rate of 20.5%. (Leslie et al, 2011).  Last but certainly not least, the further back we go in Yersinia pestis‘ evolution the more likely ingestion is to be a mode of transmission like its ancestor Yersinia pseudotuberculosis.

Its takes more than good transmission to cause a demographic changing epidemic over large areas like the Eurasian continent. It also requires a fairly high human density and good trade or communication routes. Humans play the the most important role in transmitting plague of pandemic size. I can’t say if the cultural factors that make such large epidemics possible were in place in Bronze Age Eurasia.

Let’s keep things in perspective before we conjure up the specter of virgin soil epidemics of plague in the Bronze Age. Yersinia pestis is the kind of over achiever that may have been a player in Bronze Age demographics but it would be nice to have a lot more evidence before jumping to that conclusion.


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.

Eisen, R. J., Dennis, D. T., & Gage, K. L. (2015). The Role of Early-Phase Transmission in the Spread of Yersinia pestis. Journal of Medical Entomology, tjv128–10.

Johnson, T. L., Hinnebusch, B. J., Boegler, K. A., Graham, C. B., MacMillan, K., Montenieri, J. A., et al. (2014). Yersinia murine toxin is not required for early-phase transmission of Yersinia pestis by Oropsylla montana (Siphonaptera: Ceratophyllidae) or Xenopsylla cheopis (Siphonaptera: Pulicidae). Microbiology, 160(Pt_11), 2517–2525.

LESLIE, T., WHITEHOUSE, C. A., YINGST, S., BALDWIN, C., KAKAR, F., MOFLEH, J., et al. (2011). Outbreak of gastroenteritis caused by Yersinia pestis in Afghanistan. Epidemiology and Infection, 139(5), 728–735.

Sebbane, F., Jarrett, C. O., Gardner, D., Long, D., & Hinnebusch, B. J. (2006). Role of the Yersinia pestis plasminogen activator in the incidence of distinct septicemic and bubonic forms of flea-borne plague. Proceedings of the National Academy of Sciences of the United States of America, 103(14), 5526–5530.

Zimbler, D. L., Schroeder, J. A., Eddy, J. L., & Lathem, W. W. (2015). Early emergence of Yersinia pestis as a severe respiratory pathogen. Nature Communications, 6, 1–10.

Hänsch, S., Cilli, E., Catalano, G., Gruppioni, G., Bianucci, R., Stenseth, N. C., et al. (2015). The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis. BMC Research Notes, 1–3.

Haiko, J., Kukkonen, M., Ravantti, J. J., Westerlund-Wikstrom, B., & Korhonen, T. K. (2009). The Single Substitution I259T, Conserved in the Plasminogen Activator Pla of Pandemic Yersinia pestis Branches, Enhances Fibrinolytic Activity. Journal of Bacteriology, 191(15), 4758–4766.