Did India and China Escape the Black Death?

One of the few things everyone studying the plague can, I think, agree on is the importance of plague dynamics in Asia. Genetic diversity and biogeography suggest that Yersinia pestis evolved in East Central Asia (S. Russia, Mongolia, N. China) and spread along the Eurasian steppe from the Caspian Sea in Kazakstan to the Mongolia very early, perhaps even before it became a human pathogen [1]. The orange labeled clones in the diagram below represent Y. pestis clones that branched off of the main stem before Y. pestis was a human pathogen. These clones only infect voles [2]. They are spread in a wide belt along the Asian steppe but as these are modern clones, we can’t be sure how early this spread occurred. Pandemic Yersinia pestis, ‘the plague’, could have emerged anywhere along this wide Asian belt. Note the red clones (the “Medievalis biovar”) shadow the Silk Road.

Yersinia pestis isolates across modern Asia. (Li et al, 2009) Click to enlarge

The three main pandemics probably arose from different localities  as clones were slowly spread along the Silk Road and endemic foci emerged and expanded [1,2]. The Plague of Justinian is first recorded in Pelusium Egypt, but it probably arrived via canals linking it to the Red Sea and ultimately the Indian Ocean. The Black Death is first recorded at Caffa on the Black Sea. The third (modern) pandemic began in southern China (purple clones on the figure). Not unsurprisingly it is difficult to trace these pandemics back to an endemic site since as a primarily rodent pathogen, Yersinia pestis can move without effecting humans.

The Black Death (1347-1352) draws all the attention because of its scope and scale, the amount of evidence, and the intensity of its legend. In some parts of the world, legend is nearly all we have (or have so far). Although the scientific evidence points toward an Asian origin for Yersinia pestis, there is precious little documentary evidence of it in Asia before modern times (17th century onwards).

George Sussman set out to examine the evidence of the Black Death in India and China in the current edition of the Bulletin of the History of Medicine. What he found in both enlightening and yet mystifying.

Western legends of the Black Death in the Far East go back to contemporary 14th century accounts of the plague in Europe and the Middle East [3]. Witnesses of the Black Death fueled by traveler’s stories imagined that all the known world was stricken, embellishing their writing accordingly. For the most part, modern historians have accepted their accounts of plague in China and India without scientific or historical evidence from China and India themselves. Sussman notes that McNeill’s influential Plagues and Peoples argues that plague foci in the Indian Himalayas and in central Africa are much earlier and more likely to be the source of the first plague pandemic (6th century) than the endemic strip along the Eurasian Steppe that McNeill dated to the 14th century [3]. Modern genetic diversity and biogeography points toward just the opposite with the eastern Asian steppe (Mongolia/N. China) being the original focus and the African focus dating to about the 14th-15th century [1]. There isn’t much evidence that the Indian Himalayan site is very old at all. We clearly need to learn a lot more about the Indian Ocean trade routes in Antique and Medieval periods to understand how the plague reached Pelusium in the 6th century and southern Africa by the 14th century.

So what evidence is there for plague in India before the third pandemic? During the 14th century northern and central India was ruled by Islamic sultans based in Delhi who kept close ties with the Central Asian peoples they came from and with the Middle Eastern centers of Islam [3]. They were well-connected diplomatically, economically and culturally with both Central Asia and the Middle East, areas that were both devastated by the Black Death and its successive waves. Yet there is no evidence of the plague in 14th century India [3]. Origins aside, this is strange, for there to be no record of plague even at ports makes me suspicious of the completeness of the written records. I would expect small local epidemics in ports, even if it couldn’t get traction in the countryside.  Sussman argues that the Indian subcontinent may have been the only area of Eurasia to have population growth during the 14th century [3].

Plague is unambiguously described in the Deccan of India in the early 17th century. It first came to the attention of Emperor Jahangir in Hindustan in 1616 [3]. The annals of the Emperor Jahangir record the third year of the winter plague with mad and dying rodents in January 1619 [3]. The annals include an interesting story of a cat contracting the plague from a mouse and passing it on to a girl who triggered a larger outbreak.

“After this the grain (dana) of the plague (a bubo) appeared in the girl, and from excess of temperature and increase of pain she had no rest. Her colour became changed—it was yellow inclining to black—and the fever was high (tap muhriq gardid). The next day she vomited and had motions, and died. Seven or eight people in that household died in the same way, and so many were ill that I went to the garden from that lodging. Those who were ill died in the garden, but in that place there were no buboes. In brief, in the space of eight or nine days seventeen people became travellers on the road of annihilation”.(Sussman, p. 337-338)

He is describing a case of secondary pneumonic plague that then spread throughout the household. The development of secondary pneumonic plague in a child can be especially damaging because more people will come to care for a child than an adult. In this case, mouse to cat to child to family doesn’t require any fleas at all. The cat got the plague from biting the sick mouse, the child got the plague from playing with the cat and passed it on to her family. The lack of buboes in the last people to die suggest that at some point in the transmission bubonic plague became pneumonic, probably in the child.

So plague is firmly established in 17th century India, but not in the 14th century during the Black Death pandemic. While I expect that we may yet find evidence of small outbreaks, there not does appear to have been a large epidemic. Why that was is unknown. Perhaps a combination of geographic isolation, climate, vector availability and sheer luck.  Turning to neighboring China, the picture becomes more complicated.

As I’ve already mentioned, Yersinia pestis genetic diversity and biogeography suggests that it has been in northern China long before any of the pandemics. With the wide-spread of early clones, the pandemic does not necessarily have to begin where there is the greatest genetic diversity.

Sussman notes that in the third pandemic the large northern outbreak was marmot-derived pneumonic plague while the southern outbreak was rat-derived bubonic plague [3]. This is still the case today. A marmot derived outbreak of pneumonic plague occurred in northern China as recently as 2009. If plague in northern China is usually pneumonic plague from marmots, I’m not surprised that they did not have a specific name for the disease. Pneumonic plague does not produce unique enough symptoms to differentiate from other rapidly lethal respiratory diseases.

The Yuan dynasty controlled China and Mongolia during the first half of the 14th century. This period coincided with a concerted withdrawal from the greater Mongolian world most of whom had by this time converted to Islam [3]. It was a time of great turbulence: famines, epidemics, natural disasters, political unrest, as the last remnants of the Mongol empire in China devolved to regional warlords and the Ming Dynasty began to develop [3]. Record keeping during this devolution is sporadic and uneven, but it does show three rounds of massive epidemic in 1330- 1350 each taking over 60% of at least regional populations. Unfortunately medical descriptions of the disease(s) have not survived [3]. Sussman’s analysis of the overall Chinese population during the early to mid 14th century is that the losses are comparable to the 25-30% loss in Europe that is directly credited to the Black Death [3]. Given the ancient foci of plague in northern China, this is where we should expect it to come from in the 14th century, and so it does appear to. On the other hand, Sussman notes that the first obvious medical description of plague in China dates to 1644.

Sussman questions whether the 14th century epidemics were plague based on some questionable criteria. He is bothered by the apparent lack of spread of the epidemic to the southwest (where the third pandemic began). He thinks a ‘virgin territory’ epidemic in densely populated China should have easily spread throughout China as it spread throughout Europe.  The European pandemic was the unusual behavior for the plague, not a regional epidemic in China where plague was more ancient than in Europe. In other words, I don’t think that Europe and China were equally ‘virgin territory’ epidemics. The importance of ‘virgin territory’ is probably also being over estimated for Yersinia pestis. Also the terrain in southwestern China is unlike northern China or Europe; it is more tropical. We need to let go of the idea that the second and third pandemic must behave the same. With a sample set of only three pandemics, we surely can not say that there must be one pattern that they will all conform. The lack of medical description also makes Sussman question if it was the plague. However, there is apparently no medical description at all to rule plague out or in. He also finds it unlikely that the plague could have traveled the length of the Eurasian steppe because much of it is so sparsely populated. Yet the first epidemic in northern China occurs in the early 1330s, surely enough time to travel the Silk Road west by caravan or Mongol horsemen. It is also possible that this clone spread along the steppe over several decades or even a century before it erupted at multiple points into large epidemics where the conditions were right and into a pandemic in the west.

Noticeably absent in this discussion is archeological evidence in either India or China. Now that we can identify Yersinia pestis aDNA in remains, hopefully this could be investigated in at least northern China. Unfortunately, I rarely hear about any medieval archaeology from India or China.

World Biomes (click to enlarge)

Plague’s normal biome is semi-arid grassland, shown on this simplified biome map as brown and yellow. From Sussman’s information it appears that the Black Death avoided tropical rainforest biomes (light green). This is not really surprising given its endemic regions. It is the opposite of the third and weakest pandemic. The endemic foci produced by the third pandemic are the usual semi-arid grasslands in the American south-west, Madagascar (which has some savanna), and Brazil.

So in conclusion, what are we left with? First, western reports of plague in the east may be more rhetoric than reality. Even if there were small unrecorded outbreaks in India, there doesn’t seem to be much evidence of population decline. For China, it would help to have more evidence of the nature of the northern epidemic. However, the coincidence and lethality of the epidemic support it being the plague. There is still a lot of work to be done on plague history in southern Asia.

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References:

[1] 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 PMID:21037571

[2] Li Y, Cui Y, Hauck Y, Platonov ME, Dai E, Song Y, Guo Z, Pourcel C, Dentovskaya SV, Anisimov AP, Yang R, & Vergnaud G (2009). Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci. PloS one, 4 (6) PMID: 19543392

[3] Sussman GD (2011). Was the black death in India and China? Bulletin of the history of medicine, 85 (3), 319-55 PMID: 22080795

Black Death Genome Fished Out of East Smithfield

Fishing just isn’t what it used to be, and neither is DNA sequencing. Reconstructing the ancient plague genome required the development of new technology that was able to enrich the sequencing sample by concentrating the Y. pestis sequence fragments from the brew of human DNA and contaminants in all aDNA extracts.

Using an Agilent Capture Array (above), a large international group led by Johannas Krause and Hendrik Poinar [1] fished ancient, degraded fragments of Yersinia pestis out of bone and teeth extracts from the East Smithfield Black Death cemetery using lures (probes) composed of short fragments of a modern Y. pestis strain. These lures (probes) are attached to the slide and the extracts are washed over the slide. Complementary ancient fragments in the extract will hybridize with the single stranded probes while the remainder of the extract is washed away. (The match does not have to be exact for these probes to hang on to the extract fragment allowing them to pull out fragments with minor sequence variants.) The fragments can then be released from the slide and sequenced. Using two of these slides (one in Canada and one in Germany?) they captured over two million unique fragments. Overlapping regions of sequence were lined up to reconstruct “93.48% of the targeted regions” (complementary to the modern CO92 strain of Yersinia pestis). All genes of the modern Y. pestis strains appear to be accounted for, although the existence of any part of the ancient genome that is completely foreign to modern strains can not be ruled out.

When they analyzed the ancient sequence they found that it is surprisingly similar to modern Y. pestis strains. It differed from modern strains at only 97 positions all of which matched the ancestral genes from Yersinia psuedotuberculosis. The most important information in this paper is that the genes of the Black Death clones do not have significant genetic differences that would make the ancient clone(s) more virulent than modern strains.

They also went on to place their reconstructed genome on the phylogenetic tree of Y. pestis relative to public sequences of modern Y. pestis strains. They placed the East Smithfield Black Death clone at the node where modern Y. pestis strains branch from the ancestral stem leading to Yersinia pseudotuberculosis, its parent species. Actually it is the primary East Smithfield clone because they also found another derivative clone in the extracts from only four people at East Smithfield. Placing the Black Death strain at the branch point is basically the same finding as Haenesh et al, 2010 [2] that I’ve discussed in a previous post. Apart from having much more sequence to compare, the finding really isn’t new. It also doesn’t really tell us anything new about the earlier, first pandemic known as the Plague of Justinian. Despite their assertion that the Plague of Justianian was “distinct from all currently circulating strains commonly associated with human infections, or it was another disease all together” [1], they can not rule out that the Black Death strain itself is not identical to or a descendant of the Justinian strain. I see no reason to think that it was another disease. Two previous groups, Drancourt’s group in Marseille [3] and Wiechmann and Grupe in Bavaria [4], have found Yersinia pestis in 6th century remains.  Further, the speed, virulence, and signs and symptoms of the Plague of Justinian match descriptions of the Black Death.

The similarity of the Black Death strain with modern Yersinia pestis strains validates modern public health and biosecurity concerns over the plague. Although this ancient strain would be susceptible to modern antibiotics — if they are administered in time, we will need all the information we can get for a potential arms race with the plague.

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[1] Bos, K., Schuenemann, V., Golding, G., Burbano, H., Waglechner, N., Coombes, B., McPhee, J., DeWitte, S., Meyer, M., Schmedes, S., Wood, J., Earn, D., Herring, D., Bauer, P., Poinar, H., & Krause, J. (2011). A draft genome of Yersinia pestis from victims of the Black Death Nature DOI: 10.1038/nature10549

[2] Haensch, S., Bianucci, R., Signoli, M., Rajerison, M., Schultz, M., Kacki, S., Vermunt, M., Weston, D., Hurst, D., Achtman, M., Carniel, E., and Bramanti, B. (2010). Distinct clones of Yersinia pestis caused the Black Death. PLoS Pathogens, 6 (10)

[3] Drancourt M, Signoli M, Vu Dang L, Bizot B, Roux V, Tzortzis S, et al. Yersinia pestis Orientalis in remains of ancient plague patients. Emerg Infect Dis [serial on the Internet]. 2007 Feb [date cited]. Available from http://wwwnc.cdc.gov/eid/article/13/2/06-0197.htm

[4] 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

DNA of the Black Death at East Smithfield, London

It seems as though every couple of months a new paper is published reporting Yersinia pestis DNA from ancient remains. This week brought the latest installment from London’s East Smithfield Black Death cemetery. This cemetery holds a special place in the scientific investigations of the Black Death because it is so well documented as being specifically for the first wave of plague in 1348-1350 and the  recovery of so many well-preserved skeletons. This cemetery has been the subject of several bioaracheological studies, primarily by former plague skeptic Sharon DeWitte, making this one of the best characterized set of Black Death victims yet to be discovered. DeWitte is also one of the co-authors of this study.

Using a new method of ‘targeted enrichment’  and high through-put sequencing an international group led by Hendrik Poinar was able to clone and sequence relatively long stretches of Yersinia pestis DNA from recovered remains. They were given access to 100 samples (53 bones and 47 teeth) from which they found 20 positive results for Y. pestis. Unfortunately they don’t indicate how many individuals these samples represent. Although the bone yielded more aDNA, the teeth had far more positive results; 37% of teeth to only 5.7% of bones. Poinar’s group believes this is consistent with a blood-borne pathogen because the tooth pulp is more vascular than bone.

Poinar’s group has reconstructed more of the ancient genome than any group to date. They had the advantage of knowing that this burial pit was open for only a short time and specifically for plague victims. They worked under the assumption that all victims of the plague died from the same strain and were therefore able to construct a composite organism. They could not have made this assumption in a churchyard cemetery that could be open for centuries. They were able to reconstruct 99% of the pPCP1 plasmid (95% with five fold coverage) and showed that its sequence matches 11 of 14 known strains today. They were also able to reconstruct a portion of the pMT1 plasmid that contains genes for the F1 antigen and a small portion of the bacterial chromosome. The Black Death strain seems to be a variant of the Medievalis biovar, but its exact placement is unclear. This has led to premature claims that the Black Death strain is extinct. Given that they haven’t shown a single mutation/polymorphism that makes a functional change, there is no evidence yet that the medieval strain was intrinsically more virulent than modern strains.

They took great pains to close all of the possible technical questions. They obtained human remains from the cemetery of St Nicholas Shambles also in London that dates from about a century earlier to serve as negative controls. These 10 specimens remained negative throughout. They analyzed the types of DNA damage found in human mtDNA from both East Smithfield and St Nicholas Shambles, and compared the level and types of damage to the Y. pestis aDNA to prove the Y. pestis DNA was original to the remains. They followed all of the isolation and contamination prevention procedures recommended for aDNA and sent their clones to two independent high-throughput sequencing facilities to confirm the sequence. By comparing the sequences of the two facilities they were able to resolve DNA damage from true polymorphisms/point mutations.

Why is this study important? First and foremost, it confirms that a well-known Black Death burial pit was due to Yersinia pestis. They developed a method to reconstruct more of the ancient genome than has been done before that should improve our phylogenetic analysis of Y. pestis. They answered all of the technical questions  that should finally bring consensus on the cause of the plague. This does not mean that other pathogens didn’t co-circulate or that every epidemic labeled as the plague really was. Now its time to dig into the epidemiology and get to the really important questions!

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Schuenemann, V., Bos, K., DeWitte, S., Schmedes, S., Jamieson, J., Mittnik, A., Forrest, S., Coombes, B., Wood, J., Earn, D., White, W., Krause, J., & Poinar, H. (2011). PNAS Plus: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1105107108

DNA Detective Work Identifies Black Death Culprit, NPR: Science Friday, September 2, 2011. Ira Flatow interviews Hendrik Poinar and Michael McCormick. (podcast)