A virologist's take on the black death genome #microtwjc 2

The second paper in the Microbiology Twitter Journal Club (Tuesday the 22nd May 2012) is the paper out last year documenting the sequencing and assembly of the complete genome of a strain of Yersinia Pestis (plague) from a 14th Century burial site. It's open access so check it out here.


Here's a PBS news story (w/ interview with lead author as well):

Watch Reconstructing Black Death: Why Was Plague Microbe so Deadly? on PBS. See more from PBS NewsHour.

There's also an accompanying feature covering the history and background to Black Death research by Nature, here. Also includes some nice criticisms of this work too. There's also a Nature Blog article here. And here's New York Times article. There's a range of articles by Michelle Ziegler over at Contagions blog to have a look at. And finally before I forget, Vincent Racaniello's 'This Week in Microbiology' podcast covered it last year here.


Here's the video abstract from Nature:







Abstract: (emphasis my own).

Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard¹. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348–1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347–1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.

Here's a snippet from the accompanying Nature feature on this method:

"Another technology helped narrow the search. Pääbo and his team developed a technique, called targeted capture, in which they used lab-synthesized 'bait' DNA to snag ancient DNA strands from a bone sample⁷, leaving soil-microbe and other sequences behind. "It's pretty much like fishing in a pond," says Johannes Krause, a palaeogeneticist at the University of Tübingen in Germany, who worked with Pääbo on the Neanderthal genome and co-led the Black Death project with Poinar."

Here's a video showing you the basic protocol of how you do the baited sequencing: here. And also two technological reviews from the Promega blog, here and here. 

Some important points from the paper are:

Why undertook this work: "Discrepancies in epidemiological trends between the medieval disease and modern Y. pestis infections have ignited controversy over the pandemic’s aetiologic agent^5, 6. Although ancient DNA investigations have strongly implicated Y. pestis^2, 3in the ancient pandemic, genetic changes in the bacterium may be partially responsible for differences in disease manifestation and severity."

When they compared this genome to the reference strain genome ( a currently circulating isolate, which as previously stated differs pathogenically) they saw little changes: "Single-nucleotide differences between our ancient genome and the CO92 reference surprisingly consisted of only 97 chromosomal positions, and 2 and 4 positions in the pCD1 and pMT1 plasmids, respectively (Supplementary Table 3), indicating tight genetic conservation in this organism over the last 660 years."

This isolate is supposed to be very old and possibly seeded all current plague strains: "he trees place the East Smithfield sequence close to the ancestral node of all extant human pathogenic Y. pestis strains (only two differences in 1,694 positions) and at the base of branch 1 (Fig. 3b). A secure date for the East Smithfield site of 1348–1350 allowed us to assign a tip calibration to the ancient sequence and thus date the divergence time of the modern genomes and the East Smithfield genome using a Bayesian approach."

"This strain, Krause adds, probably emerged not long before the Black Death started its rampage across western Asia and Europe in the fourteenth century. "That, for me, was the biggest surprise," he says. It suggests, the authors argue, that earlier plagues were caused by either a now-extinct strain of Y. pestis or by an entirely different pathogen.

A rebuttal of this work is in the feature: 

Mark Achtman, a plague-evolution expert at University College Cork in Ireland, calls this interpretation "absolute nonsense". Krause and Poinar's team did not consider a number of modern plague strains found in central and east Asia, which are thought to have earlier origins than the East Smithfield strain, Achtman says. Genome sequences for these strains were not available to his team, says Krause, but he is eager to see how they are related."

And here's their final conclusions to the paper: "Regardless, although no extant Y. pestis strain possesses the same genetic profile as our ancient organism, our data suggest that few changes in known virulence-associated genes have accrued in the organism’s 660 years of evolution as a human pathogen, further suggesting that its perceived increased virulence in history²³ may not be due to novel fixed point mutations detectable via the analytical approach described here. At our current resolution, we posit that molecular changes in pathogens are but one component of a constellation of factors contributing to changing infectious disease prevalence and severity, where genetics of the host population²⁴, climate²⁵, vector dynamics²⁶, social conditions²⁷ and synergistic interactions with concurrent diseases²⁸ should be foremost in discussions of population susceptibility to infectious disease and host–pathogen relationships with reference to Y. pestis infections."

This is clearly a really interesting paper where the group basically dug up some bodies from a known plague (and only plague) burial ground. Using a technique known as baiting they were able to specifically detect and thus amplify/sequence Y/pestis-like sequences. This was the same tech used to find ancient human DNA. By sequencing enough of the DNA (it was heavily degraded) they assembled the entire genome of a single strain of the organism. Although they note that due to short seq. reads they were unable to accurately determine numbers of particular genes and rearrangements. They then compared this sequence data to other known genome sequences and used this info to infer the genetic basis of plague biology (pathogenicity etc). They showed very litte sequence change between their isolate (a deadly, deadly bacterium) and other less deadly strains currently circulating. This raises the possibility that the devastating effects of the black death had little to do with the pathogen per se and more to do with vector/host biology. Which I guess has been known for other pathogens for a long time. 

This paper shows just how 'easy' it can be to get your hands on ancient DNA and analyse it. So I think if anything, this work will start a rush on Y.pestis genome strains which should finally settle it's origins during the black death outbreaks. Further work should thus be done on all these final ancient DNA data to compare them with current strains which are not as pathogenic. I guess yo could use in vitro assays and alter 'safe' strains by inserting the ancient genes and do work on looking at their pathogenicity and infectivity in a range of models to see where the differences lie, if there are any. That should settle whether it does indeed involve genetic factors instead of other environmental/host or vector factors. 

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, 478 (7370), 506-510 DOI: 10.1038/nature10549