Trench Fever: An Ancient Zoonosis

Rhesus macaque (Photo by J.M. Garg, CC)

Trench fever is an ancient disease with a surprisingly short history. Named after its discovery in the trenches of World War I, its case history is only about a century old. Yet, the louse transmitted Bartonella quintana that causes trench fever has been found in human remains as old as 4000 years and is one of the most common infectious organisms found in human ancient DNA (for example). Once thought of as a self-limited moderate ‘five-day’ fever (aka quintana) it is now known that it can also cause endocarditis and a chronic bacteremia. It persists today in most countries anywhere that human body lice are common, often among the homeless.

After the chance discovery of trench fever in captive macaques transported in both directions between the United States and China, a Chinese team investigated the extent of Bartonella quintana in macaques in captive primate centers in China (1). They collected blood from Rhesus macaques at three geographically distant primate centers and cynomologus macaques from one additional primate center. They found Bartonella quintana in macaques from all four centers with enough genetic diversity to suggest multiple sources originating in the wild (1). By Multilocus sequence typing (MLST), a type of genetic fingerprinting, they found more genetic diversity just in the macaques from these centers than from all human isolates analyzed to date around the world. This suggested to the Chinese team that the macaques are the likely original host population of an ancient zoonosis (1). The limited genetic variation in humans suggests that the zoonotic transmission events occurred in the distant past and are not continuing today at a level detected in human populations. Further, the Bartonella quintana sequences fell neatly into three groups that corresponded to the species they were isolated from, suggesting to the Chinese group that B. quintana has co-evolved with species specific exoparasites, mostly lice (1).

Phylogeny of Bartonella quintana. Group 1 is found in humans, group 2 in cytomolgus macaques and group 3 in  rhesus macaques. (Li et al, 2013, Ref. 1)

Although they found B. quintana in a high percentage of macaques in all of these facilities, the conditions at the primate centers could account for the high incidence rate. A related study also found that B. quintana spread very easily within the captive Rhesus macaque centers through the macaque specific louse Pedicinus obtusus (2). They were also able to demonstrate that the macaques developed the chronic bacteremia found in humans suggesting some evolved tolerance (2). Samples from wild macaques will have to be sampled to determine what the natural carrying load of these species are. Rhesus macaques have a range from China to Afghanistan with a large population in India. Other macaque species extend the historic range of possible carriers to the Mediterranean and North Africa.

References:

1. Li H, Bai JY, Wang LY, Zeng L, Shi YS, Qiu ZL, Ye HH, Zhang XF, Lu QB, Kosoy M, Liu W, & Cao WC (2013). Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever. Molecular ecology, 22 (8), 2118-27 PMID: 23517327
2. Li H, Liu W, Zhang GZ, Sun ZZ, Bai JY, Jiang BG, Zhang YY, Zhao XG, Yang H, Tian G, Li YC, Zeng L, Kosoy M, & Cao WC (2013). Transmission and maintenance cycle of Bartonella quintana among rhesus macaques, China. Emerging infectious diseases, 19 (2), 297-300 PMID: 23347418

Asymptomatic Plague: Qinghai, China, 2005

Now that we know the Tibet-Qinghai plateau region is where Yersinia pestis originated and the region where subsequent pandemics arose, I think its time to look more closely at regional outbreaks and case studies.

In this region, the marmot (Marmota himalayana) is the primary reservoir for Yersinia pestis. This large communal burrowing rodent is hunted by local Tibetan tribesmen for both meat and pelts. Butchering marmots has long been considered a risk factor for contracting plague via their fleas, aerosols or skin abrasions. To investigate the exposure of marmot hunters to plague, Chinese epidemiologists collected serum from 120 Qinghai villagers, 68 male hunters and 52 female family members, along with 120 negative controls from the non-endemic area of Beijing. None of the villagers or controls reported having a fever within the last two years.

The results are eye-opening and illustrates the importance of occupational exposure. Over a third of the male villagers had an antibody response to Yersinia pestis. Only 2% of their female family members produced an antibody response. Wether two fever-free years are enough time to determine if they had symptomatic plague in the past is an open question. Their letter to Emerging Infectious Diseases does not provide much information on the test subject’s histories or oral reports.

Table 1: Plague antibody assays (Li et al, 2005)

The epidemiologists explained this high level of immune protection to the use of prophylactic antibiotics by marmot hunters. They suggest the presence of tetracycline or sulfamethaoxazole, common prophylactic antibiotics in Tibet, in  their system at the time of exposure would be enough to prevent a symptomatic infection while still giving them an immunizing dose of bacteria.

The use of prophylactic antibiotics is, of course, a double-edged sword. It is clearly preventing symptomatic infections and probably outbreaks. The Chinese epidemiologists credit  most outbreaks in Qinghai to marmot hunters who either a lack of prophylactic antibiotics or have ineffective antibiotics.  On the other hand, the use of antibiotics is possibly encouraging them to harvest the easier to catch, sicker marmots. The use of prophylactic antibiotics also promotes antibiotic resistance in Yersinia pestis.

Li, M., Song, Y., Li, B., Wang, Z., Yang, R, Jaing, L., and Yang, R. Asymptomatic Yersinia pestis, China. Emerging Infectious Disease, 2005, 11 (9): 1494-1496.

Molecular Confirmation of Yersinia pestis in 6th century Bavaria

Erasing any lingering doubts about the agent of the Plague of Justinian, a group of German biological anthropologists have shown conclusively that Yersinia pestis caused an epidemic in a 6th century Bavarian cemetery at Aschheim. Harbeck et al (2013) provide a convincing refutation of previous theories about the etiologic agent of the Plague of Justinian.   Returning to the same cemetery where plague was previously reported, two independent labs using the most modern standards to prevent contamination confirmed Yersinia pestis from multiple burials within the cemetery making this the best characterized Early Medieval plague cemetery.

The cemetery, called Aschheim, is in Bavaria outside of Munich. It contains the remains of 438 people with an unusually high number of multiple graves but no disordered mass graves. The 19 multiple burials contained two to five individuals arranged in lines. The cemetery was dated archaeologically to 500-700 AD with remains being carbon dated ranging from 530 to 680, all consistent with the 541 pandemic and its aftermath. Harbeck et al (2013) tested 19 individuals from 12 multiple graves. From these, there were eight positive samples, but only one produced enough aDNA to do some SNP genotyping. Added to the previous paper, this makes 11 positive individuals from this cemetery. Given the tenuous survival of aDNA, 11 positive individuals out of 21 tested in the two combined papers is a very good success rate. This is a cemetery that the F1 antigen test would be interesting since it could be used on the entire cemetery without great cost or labor. More sensitive than aDNA, the antigen test could tell us the percentage of plague deaths in the cemetery.

Individual A120 was screened with several SNPs that mapped it to an early region of the phylogenetic tree in the 0.ANT section. This makes the Plague of Justinian isolate ancestral to the Black Death isolates (yellow boxes below) from East Smithfield. This section whose only point of diversity is 0.ANT1 at node 4. Date predictions for the nodes of diversity in the tree fits with the Plague of Justinian falling in this region.  Modern isolates that  form this region of the phylogenetic tree all come from central Asia (around Tibet), suggesting that like the Black Death, the Plague of Justinian also originated in Asia. Overall, everything fits in well with expectations for the first pandemic.

(Harbeck et al, 2013. Fig. 1)

Reference:

Harbeck M, Seifert L, Hänsch S, Wagner DM, Birdsell D, et al. (2013) Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague. PLoS Pathog 9(5): e1003349. doi:10.1371/journal.ppat.1003349

Wiechmann I, & Grupe G (2005). Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.). American journal of physical anthropology, 126 (1), 48-55 PMID: 15386257

Fleshing out Yersinia pestis

Up until a few months ago there were a few representative samples of the Yersinia pestis genome. Important windows into its secrets, but windows none the less. In January a Chinese group remedied this situation by expanding the number of fully sequenced genomes from 15 to 133 (Cui et al, 2013).  China supplied 107 genomes selected from over 900 genotyped specimens collected since 1955 to represent bacterial and host diversity. To these, 11 additional isolates from Mongolia, Myanmar (Burma), the former Soviet Union, and Madagascar were fully sequenced. For the analysis, the previously sequenced 15 genomes were added bringing the total up to 133 including the ancient specimens from 14th century London.

The Core-Genome and the Pan-Genome

Even for a bacterium like Yersinia pestis that is considered to have little genetic diversity, its genome is more elastic than any eukaryote (everything but bacteria). The bacterial genome can be divided into its core genome, found in all members of the species, and the accessory genome, sequences found only in some strains. Plasmids are part of the accessory genome but not all of it. Extra genes are also found on the bacterial chromosome. The core genome is 3.53 Mb long with 3450 genes; the accessory genome has 1.92 Mb with 1249 genes (including 451 on the six known plasmids) (Cui et al, 2013, Table S1). So the accessory genome contains 26% of genes found in the species. This may seem like a lot, but more promiscuous species like Escherishia coli (E. coli) have many more accessory genes than core genes. With E. coli the more specimens that are sequenced, the larger the accessory genome gets with no end in sight.

Combining all of the genes found in Yersinia pestis (core and accessory genome), we have the pan-genome. The pan-genome is 5.46 Mb with 4699 genes (Cui et al, 2013).  No one strain has all of these genes. So different strains do have significant differences in their functions but, as far as I know, there are no significant differences in human prognosis. Hopefully, there will be more study in the future that cross-references strain type  or particular genes with human prognosis, transmission routes (% bubonic vs pneumonic), hosts etc.

Branching Out

Using known and new SNPs, the phylogenetic tree has finally been fleshed out into a healthy looking tree . We couldn’t keep the sickly looking Charlie Brown tree of the past forever! Even so, the tree below represents only the main branches.

Click to enlarge, (Cui et al, PNAS, 2013)

To my mind, the most important aspect of the new tree is that nodes of increased diversity are much more apparent. The authors are the most excited by node 7 where there is a four-way branch, adding two new branches  (3.ANT1 and 4.ANT1) to the main stem of the tree. They refer to this diversity point as the ‘big bang’. This node gains the most attention because the 14th century London genomes are just one step off of node 7 down the 1.ANT1 branch. So it stands the reason that node 7 represents a period of diversity that produced the second pandemic. Yet, looking at their diagram, other locations like node 12 have greater diversity. The 1.IN strains are intermediary on the same lineage between the second the third pandemic. Node 14 is the initial diversity that produced the third pandemic.  Calling node 7 a ‘big bang’ seems to me to have more to do with it producing the second pandemic rather than the diversity at the node itself. The new third and fourth branch (3.ANT and 4.ANT) are concentrated in Mongolia, putting emphasis on the importance of doing such deep sequencing in other Central Asian regions. It is impossible to tell which host species these bursts of diversity occurred within, almost certainly not humans. It’s not that diversity can’t be generated in humans especially during a pneumonic plague, but since it is not endemic in humans,  it must make it back to a reservoir to be preserved anywhere other than in ancient DNA.

Biogeography shows clustering of related strains in regions as would be expected, though they are fairly well mixed within the circled zone in the map above. Samples seem to follow ancient roads, although keep in mind all of these strains have been isolated within the last 60 years.   I do wonder why they were not able to identify a route for the eastern branch two isolates. All of the branch two isolates appear to be running along a fairly straight line from southwest to northeast China (extending trade route III to Manchuria). The 107 Chinese specimens were chosen from > 900 strains identified from 5000 isolates for their diversity revealed by genotyping, host diversity and geography (Cui et al, 2013). It would have been interesting to see a map with all 5000 on it as a measure of abundance (with or without typing).

The oldest strain 0.PE7 is found only on the Qinghai-Tibet plateau in China, an area framed by the ancient trade routes along which most of the western strains are found. This has led Cui et al, 2013 to postulate that the  Qinghai-Tibet plateau as the origin of  Yersinia pestis.

Unsteady Molecular Clocks

Estimating ages from genetics can be a very risky business. To estimate years since the last common ancestor, it requires a steady molecular clock , measured in base changes per unit of time. In theory all of the genes from the core genome should have changed to the same degree from the common ancestor, but that is not the case at all. The number of SNPs in the Yersinia pestis core genome varies greatly. Even excluding the most divergent Angola (0.PE3) strain, there is “a nearly 40 fold difference between the slowest and the fastest evolving branches” (Cui et al, 2013). An unsteady molecular clock was also suggested by previous data from Madagascar, though the discussion was buried in the supplementary material (Morelli et al, 2010, p. S10-s18). Mutator phenotypes do occur (Rajanna et al, 2013), though Cui et al, 2013 assure us that none of these strains are mutators.  On the other hand, a Georgian group suggest that the mutator phenotype, a single point mutation, could naturally reverse (back mutate) altering the predictability of the lineage age (Rajanna et al, 2013). The Chinese group concluded that the faster clock rates for some branches are due to a higher reproduction rate, probably due to more or larger epidemics in the lineage (Cui et al, 2013). The types of genetic changes (SNPs) indicate neutral selection, so the increased reproduction rate is not due to the genetic changes.

While I understand that calculating divergence dates an important exercise to people who focus on phylogenetics, for the understanding of historical plague it is not useful. It is not solid or specific enough to base historical events upon alone. Predictions are just that; all of these groups have been proven wrong, sometimes later by themselves, too often.  Most importantly, it appears that it will eventually be trumped by ancient DNA analysis with an archaeological and/or documentary context. As far as I’m concerned, the Angola strain is a genetic and geographic outlier of uncertain provenance. We don’t know important factors like how long it was kept in active culture before it was made into a stock or the conditions of storage. Both of these can effect mutation rates and the molecular clock (Rajanna et al, 2013).  I’m sure the Angola strain’s story is interesting but unlikely to be useful for understanding the whole species unless it turns up in ancient DNA.

Gaining and Loosing Diversity

Returning to these starburst points on the tree, called polytomys, where multiple lineages share the same ancestor, we have some of the most valuable information in the new phylogenetic tree. Epidemics (and presumably epizootics) are believed to have an increased reproduction rate over enzootic plague. Since the mutation rate is directly tied to the reproduction rate, increased reproduction rates predict an increased mutation rate and, therefore, production of genetic diversity.  The team predicts that “higher clock rates are an indicator of epidemic disease, even in the absence of historical evidence” (Cui et al, 2013). It is unclear how an epidemic can be differentiated from an epizootic by genetics alone. We know from modern observations that not all epizootics spill over into the human population. Yet, major polytomys can at least be used to estimate how many bursts of growth the bacterium has gone through in China. We should see other polytomys with increased sequencing of other Central Asian regions.

While these polytomys show a starburst of new lineages, there is also a loss of diversity during every epidemic. Most of the new lineages produced during an epidemic (or epizootic) will die out (become extinct) when the epidemic ends. If the changes are truly neutral, then which lineage survives to endure in the reservoir will be completely random (as will be the number of surviving lineages). We should also remember that clinical isolates  during an epidemic and ancient DNA can preserve lineages that become extinct (and this is normal). In the four individuals they sequenced from 14th century East Smithfield, they found two different clones, with the second being derivative of the first. Both of these clones may only be found in ancient DNA, not in any living specimen. The more time that passes the greater the likelihood that the minor lineages will become extinct. This tends to make the earlier sections of the pylogenetic tree look cleaner by stripping off side branches.

Another recent study by Vogler et al (2013), supports their scenario on a finer scale during the 9 year epidemic in a port town of Mahajana,  Madagascar from 1991 to 1999. Over a decade we can compare the incidence of plague vs. the genetic diversity. Yersinia pestis evolution can be plotted with great precision. In the lower diagram, clones are color coded to the year of isolation. From 1995 to 1999 it is possible to see the next year’s primary clone emerge in the previous year’s epidemic, which supports local cycling within the city. At the same time, most of the diversity generated is not represented in later outbreaks.

Vogler et al, 2013

Vogler et al, 2013

Host Diversity

Host genus vs Y. pestis strain collected (Cui et al, 2013).

The hosts of these 107 strains give us a glimpse into the host diversity for Yersinia pestis within China (Cui et al, 2013). The figure to the right gives an indication of strain diversity within each host but does not tell us abundance or location within China. What jumps out at me, is that humans and marmots have the most strain diversity. The high strain diversity in humans including 0.PE7, the strain closest to the most recent common ancestor, suggests to the Chinese team that Yersinia pestis has been pathogenic to humans since it evolved (Cui et al, 2013). Thus, at no point in its evolution did it gain the ability to infect humans. The few strains that can not infect humans are hypothesized to have lost their ability to infect humans possibly as a function of purifying selection for voles as hosts. It is interesting that the 1.ORI strains of the third pandemic are only found in humans, rats and mice.  We have to be careful about taking this figure to represent abundance or importance of a particular host. The great gerbil, Rhombomys opimus, is a primary host throughout central Asia is is represented by only one strain in this figure.

Studies published this winter have moved us significantly down the road to fleshing out Yersinia pestis. The genetic survey of Y. pestis in China provides a firm foundation to build on as more ancient DNA becomes available and extensive sequencing is done in other regions. Madagascar continues to be the best laboratory for plague ecology and epidemiology, while the Georgian study begins to address unintended intra-laboratory evolution that may shed light on Y. pestis in the wild. I’ll return to these papers again soon as I continue to examine Y. pestis from different perspectives and ruminate on answers to other questions.

References:

Cui, Y., Yu, C., Yan, Y., Li, D., Li, Y., Jombart, T., Weinert, L., Wang, Z., Guo, Z., Xu, L., Zhang, Y., Zheng, H., Qin, N., Xiao, X., Wu, M., Wang, X., Zhou, D., Qi, Z., Du, Z., Wu, H., Yang, X., Cao, H., Wang, H., Wang, J., Yao, S., Rakin, A., Li, Y., Falush, D., Balloux, F., Achtman, M., Song, Y., Wang, J., & Yang, R. (2013). Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis Proceedings of the National Academy of Sciences, 110 (2), 577-582 DOI: 10.1073/pnas.1205750110

Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, & Achtman M (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature genetics, 42 (12), 1140-3 PMID: 21037571

Rajanna C, Ouellette G, Rashid M, Zemla A, Karavis M, Zhou C, Revazishvili T, Redmond B, McNew L, Bakanidze L, Imnadze P, Rivers B, Skowronski EW, O’Connell KP, Sulakvelidze A, & Gibbons HS (2013). A Strain of Yersinia pestis With a Mutator Phenotype from the Republic of Georgia. FEMS microbiology letters PMID: 23521061

Vogler, A., Chan, F., Nottingham, R., Andersen, G., Drees, K., Beckstrom-Sternberg, S., Wagner, D., Chanteau, S., & Keim, P. (2013). A Decade of Plague in Mahajanga, Madagascar: Insights into the Global Maritime Spread of Pandemic Plague mBio, 4 (1) DOI: 10.1128/mBio.00623-12

Visualizing the Plague of Justinian in the Mediterranean

Browsing through Academia.edu this morning I came across some graphics from the Topographies of Entanglements project from the Austrian Academy of Sciences, Division of Byzantine Research. Unfortunately there is very little explanation with these graphics.

Comparing these two graphs they are not conveying exactly the same information.  How do we define a wave of plague? Does it have to show directional movement? How far does it have to go?  Given the sparse information from this period, accurately defining waves must be tentative.   The second graph, may be a more realistic representation. The second graph charts individual epidemic outbreak records giving a better representation of scale and that the gaps between the waves are not plague-free. Given the sparse records in the early medieval period, we can not take the lack of reports in 580 and 610 to mean that the plague disappeared completely. Plague was also occurring outside of the Mediterranean in these low years. For example the major wave of plague to devastate Britain and Ireland was from 664-668.

From: Visualising waves of Plague epidemics in the Mediterranean and the Near East, 541-750 AD by Topographies of Entanglements. Graphics by Johannes Preiser-Kapeller, 2013. (Here converted from tiff files to jpg.)

They took their data from Dionysios Stathakopoulos, Famine and Pestilence in the Late Roman and Early Byzantine Empire: A Systematic Survey of Subsistence Crises and Epidemics (Ashgate, 2004).

The Great Pneumonic Plague of 1910-1911

The Great Manchurian Plague of 1910-1911: Geopolitics of an Epidemic Disease

by William C. Summers
Yale U Press, 2012

Manchuria was a political mess at the turn of the 20th century. Although it was the homeland of the Qing dynasty, the Chinese considered it a backwater. Japan and Russia on the other hand saw it as potential colonial territory, a beachhead for Japan’s mainland ambitions or access to a valuable ice-free Pacific port for Russia. By 1910 an uneasy truce held giving Russia and Japan corridors to build railroads with stations and towns to support them while technically still in Chinese sovereign territory. The importance of Manchuria to global politics and trade was underscored by the presence of European and American diplomatic representatives in these upstart towns and ports. Into this delicate situation, the discovery that marmot fur could be dyed to pass as ermine brought a flood of primarily Chinese hunters into the region. The drive for furs (and marmot oil) led many to cast aside traditional hunting practices and safeguards, setting the stage for the plague to come.

The beginning of the plague was sparsely recorded. Starting in October 1910 scattered reports were sent that plague had appeared at sites along the railway, but concern was slow in coming. Summers credits the nearly annual outbreaks of plague, low concern for locals, and the temporary camps of hunters for the lack of information on beginning of the plague. Deaths quickly jumped into the thousands in towns along the rail line but never spread very far from the lines. Summers notes that of the over 43,000 recorded cases during the outbreak only one single person survived (p. 19). Some estimates place the mortality closer to 60,000 when early cases and locals away from the rail line are included. Summers notes that this puts the death toll in the range of the great London plague of 1665. By February 1911, the plague was over; blatant proof the plague outbreaks can flourish in winter (as it sometimes did in medieval European winters).

This plague has some unique features. First, there is no report of bubonic plague at all; it was exclusively pneumonic. Most plagues are primarily bubonic with flair ups of pneumonic transmission. Etiology was confirmed by autopsy and the then new bacteriological techniques including culture. American doctor Richard Strong, working with the Chinese under Wu Lien-Teh, did 25 autopsies before the International Plague Conference called by the Chinese in Mukden. There is no doubt the Yersinia pestis caused this epidemic.

Without antibiotics, quarantine and isolation were the only effective means of control. The means were brutal but effective. In the Russian zone the Chinese were crowded into train cars and not let out until there were several days with no one displaying any symptoms. If a case of pneumonic plague was locked in the car with others, the prognosis for the others was predictably terrible. Within this relatively small region, we can also see three different national approaches (China, Russia, and Japan) to controlling the epidemic each always subordinated to their respective political anxieties.

The chapter on origins of the plague begins to move toward was Edmund Russell envisioned as evolutionary history in his book of the same name (2011). The most useful information here is the history of marmot activity and traditional hunting. Summers hypothesizes that traditional shaman-like practices may have aided hunters in only taking healthy animals. Concern for the health of the animal was one of the early traditions abandoned by hunters eager for furs. Following the reports of the time, Summers believes the plague originated in the marmots, and was distinct from the third pandemic lineage. In accordance with modern strain maps, Summers predicts that the 1910-1911 Manchurian outbreak strain will belong to either the antiqua or medievalis biovars (p. 128-9). If this is true, as is likely, it’s a relatively modern challenge to our notion that plague during pandemics has a single lineage and origin. It should be possible to type this outbreak from graves of the epidemic (which should be relatively easy to locate at barely a century old) or even tissue archived from the autopsies (if it was saved and can be located).

Summers is clearly in his element when he discusses the politics of turn of the 20th century politics. This is a region and time period that most Americans know very little about but is still critically important for Asian politics today with the still uneasy relationship between China, Korea, Japan, and Russia. Summers account lays out the different approaches to healthcare and attitudes toward the epidemic as a national and economic threat. This carried over to the International Plague Conference that nevertheless managed to focus on science and medicine. While the scientific politics was interesting I would have liked to hear more about the contents of the wide-ranging Conference report.

Summers does a good job of being very diplomatic will all parties concerned. In doing so, he does overlook a major legacy of the Manchurian plague. There seems little doubt that this plague, witnessed and closely reported on by Russia, the United States and Japan, played a role in plague being developed as a biological weapon. This plague illustrated the deadly efficiency and sustained transmission of pneumonic plague. This book should be read as a prologue to Japan’s biological ‘experiments’ during World War II beginning in Manchuria (see Sheldon Harris’ Factories of Death) and the continuing programs of the United States and Russia during the Cold War.

This book makes a valuable contribution to plague studies, and early 20th century public health practices. Yet there are still unanswered questions on genetics, epidemiology, and ecology. I hope this book along with Myron Eschenberg’s Plague Ports(2007) and others are ushering in a new period of focus on the plague in the 19th-20th century.

Reactivation of Ancient Plague Foci in Libya, 2009

Landscape around Oran, Algeria (2003), and Tobruk, Lybia (2009) that produced plague cases. (Cabanel et al, 2013)

Plague has been called a re-emerging disease primarily because cases have begun to appear in areas where plague has been absent for decades. Two recent surprising outbreaks occurred in Algeria, where plague had been absent for over 50 years, and in Libya after a 25 year absence. A team led by the Institut Pasteur explored possible relationships between the recent Libyan outbreak and the Algerian outbreaks. All of the information in this post comes from their report to be published in the February issue of Emerging Infectious Diseases (citation and link below).

The outbreaks under consideration were just south of Oran, Algeria in 2003, at Lanhouat, Algeria in 2008 and near Tobruk near the Libyan-Egyptian border in 2009. Another possible outbreak of plague occurred at Tobruk during the Libyan revolution in 2011.  Political unrest prevented a complete disease investigation of the 2011 Libyan epidemic. Past Libyan plague outbreaks have occurred from 1913-1920, 1972, 1976, 1977, and 1984. The largest outbreak in 1917 is credited with 1,449 deaths.

The 2009 Libyan index cases consisted of three children from one nomad family; one child died after two days of intensive care and the other two eventually recovered. Only one child had a tender cervical node. The other two, including the child who died, had signs of a severe infection but no visible buboes. The father reported having axillary lymphadenitis and a couple of sudden deaths in the region in the previous two months. A week after admission Libyan authorities reported 13 possible cases to the World Health Organization and requested assistance. The WHO-Libyan team identified two more women with painful inguinal nodes and “infectious syndrome”, but also concluded the initial estimate overstated the number of cases. There are five confirmed cases. The cases were spread 30-60 km from the index family’s home in Eltarsha, 30 km south of Toburk. Regional response included antibiotic treatment of contact persons, and insect and rodent control measures. No further cases were reported.

Diagnosis was confirmed by standard bacteriological assays and molecular characterization. All five confirmed cases were positive with the F1 antigen dipstick.  Yersinia pestis cultures were isolated from three patients,  all phenotyped to the Medievalis biovar by metabolic assays. Molecular characterization confirmed that all are the same Medievalis strain. Hybridization analysis indicates that it is most closely related to, but distinct from, strains isolated from Iranian Kurdistan in 1947 – 1951.

Using the same methods, the 2003 Algerian isolates were phenotyped to the Orientalis biovar. Molecular characterization confirmed that they are all related but not identical Orientalis strains. Activation of multiple related strains from an ancient foci in the same year suggests an environmental trigger. Comparing the 2003 strains to those isolated in 1944 and 1945 illustrate the complexities of plague foci. The 1944 isolate is a Orientalis strain that belongs to the same cluster of strains as the 2003 isolates and other strains from Morocco and Senegal.  The 1945 strain matched a molecular characterization of  Orientalis isolates from Saigon, Vietnam and is believed to have been transmitted by military transports during World War II.  Cabanel et al conclude that the 2003 Algerian outbreaks were caused by local Yersinia pestis strains. It should be noted that the third pandemic from the turn of the 20th century was a Orientalis biovar (1.Ori1).

Cabanel et al. note this is the only instance they could find of a Medievalis strain in Africa. The spread of cases over a 30-60 km region and isolation of related but different strains support the reactivation of an ancient plague focus. Unfortunately they did not have access to isolates from previous 20th century Libyan outbreaks (if they exist) that could have provided more certainty.

Reactivation of plague foci around the Mediterranean has been associated with climate change. They note that an unusually humid winter and good crops in Libya in 2009 favored rodent and flea abundance. Long dormancies may be part of Yersinia pestis’ natural history particularly in resource limited environments. This possibility will be one of the topics of my next post.

Cabanel et al. note that camel meat and livers have been associated with human plague cases in Libya (1976), Saudi Arabia (1994), Jordan (1997), and Afghanistan (2007). Additional local evidence suggested that the highly susceptible camels contracted the plague from local foci in these instances. Although camels do not survive plague long enough to transmit it very far, camel caravan routes may still have played a role in transmission if only by the other organisms also along the camel caravan route. Camels would have provided an abundant host to amplify the organism along the route. Camel fleas could have been carried among the cargo not unlike rat fleas in ship cargoes. Camel caravans would provide an ancient route for a Medievalis strain to reach Libya from the central Asia.

Reference

Cabanel, N., Leclercq, A., Chenal-Francisque, V., Annajar, B., Rajerison, M., Bekkhoucha, S., Bertherat, E., & Carniel, E. (2013). Plague Outbreak in Libya, 2009, Unrelated to Plague in Algeria Emerging Infectious Diseases, 19 (2), 230-236 DOI: 10.3201/eid1902.121031