Category Archives: biosecurity

Plague in Surat: 20 Years Later

I can’t let 2014 pass in a few weeks without mentioning that this fall was the twentieth anniversary of the plague outbreak in Surat, India — a major turning point in modern plague history and in the development of the (re)emerging infectious disease paradigm.

In the final accounting, 53 people died of plague, mostly pneumonic, but there are over 5000 cases classified as suspected and at least half a million people fled across India. Compared to other pneumonic plague outbreaks in Africa within the last twenty years, the number of deaths was small and the mortality rate tiny (1% of suspected cases). The government response was not only woefully inadequate but also exacerbated the damage within India and scared the rest of the world.

The lessons learned from Surat are really what is important.

  • The need for a national database to keep track of seemingly isolated cases and the need for surveillance of rodents, even when there haven’t been any human cases in many years. Better surveillance established since 1994 has identified several more plague outbreaks in India and enough evidence of enduring plague foci in the country.
  • The need for transparency, willingness to accept foreign help and the futility of trying to hide the epidemic from the press.
  • The costs of unsupported allegations of biological warfare or terrorism are too high to make unless there is certainty. It ultimately does not deflect responsibility away from the government for the response. The political costs for governments who make official erroneous allegations are greater than accepting responsibility for the outbreak.

In this month’s issue of the Indian Journal of Microbiology, the full genomic sequence of Yersinia pestis collected at Surat in 1994 and at a 2002 outbreak in India was released. Four samples were sequenced and they are all four different strains. Unfortunately, they did not do a phylogenetic analysis to indicate where they fit on the Y. pestis tree.

Twenty years ago it was the double hit of plague in Surat in 1994 and the discovery of antibiotic resistant plague in Madagascar in 1995 that raised concern about re-emerging infection diseases. Antibiotic resistant strains of Yersinia pestis have continued to appear in Madagascar and now insecticide resistant fleas are a problem as well. While public health processes and surveillance are better than in 1994, there has been no improvement plague incidence or concerning resistant strains.

Ebola is currently extracting the toll that was feared of plague in Surat two decades ago. If Surat was the warning that acute pandemics are still possible, Ebola is showing how far we still have to go 20 years later. Both plague in Surat and Ebola in 2014 are also reminding us that knowing what to do to stop an epidemic is not enough, execution is everything.

Further reading on Surat:

Barrett, Ron. (2008) “The 1994 Plague in Western India: Human Ecology and the Risks of Misattribution” p. 49-71 in Terrorism, War, or Disease? Unraveling the Use of Biological Weapons. Edited by A.L. Clunan, P.B. Lavoy, and S. B. Martin. Stanford Security Studies. Stanford University Press. This is the best analysis of the Surat outbreak that I have found.

Ziegler, Michelle (2014) The Black Death and the Future of the Plague. The Medieval Globe, 1: 183-199 for an overview of plague since 1994.

Mahale, K. N., Paranjape, P. S., Marathe, N. P., Dhotre, D. P., Chowdhury, S., Shetty, S. A., et al. (2014). Draft Genome Sequences of Yersinia pestis Strains from the 1994 Plague Epidemic of Surat and 2002 Shimla Outbreak in India. Indian Journal of Microbiology, 54(4), 480–482. doi:10.1007/s12088-014-0475-7

For more on antibiotic resistant plague, see this past post and on the most recent reported pneumonic plague outbreak in Madagascar.

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.

Biosecurity Failures Round-up

Like many of you, I’ve been watching and reading all the recent biosecurity lapses at our top labs with some dismay. This really isn’t something I normally would cover here on Contagions, but a comment from a reader reminded me that not everyone gets all the stories I’ve been tweeting (or retweeting) for the last few months. So here is a partial roundup in no particular order:

CIDRAP: Wholesale roster change coming for US biosecurity board

Superbug: The Leader of the Smallpox Eradication Effort Speaks About the Virus’ Rediscovery

Superbug: Virus in Found Tubes of Smallpox Is Viable

Superbug: Enhancing flu in the lab: Are accidents inevitable?

Found: Forgotten Vials of Smallpox | Science Blogs | WIRED

Exclusive: U.S. says government lab workers possibly exposed to anthrax

After Lapses,CDC Admits a Lax Culture at Labs | NYTimes

U.S. inspectors find further anthrax violations, mishandling

Transcript of CDC Press Conference on Recent Biosafety Incidents

On biosecurity at a local level: Out of the Lab & Into the Mouth These are getting to be yearly stories!

Meanwhile, elsewhere  Ebola (another category A bioterrorism agent) is raging unchecked in western Africa….

“How to Ignore a Plague” (Ebola) by Umaru Fofana

Ebola cases in West Africa reach 964, deaths top 600

USAMRIID Providing Laboratory Support to Ebola Outbreak