Genomics of Emerging Infectious Disease PLoS Collection

If you follow me on Twitter or peruse the links in my daily Tweetlinks summaries, you may have noticed I posted several links to a new Collection at PLoS. This one is not a PLoS ONE Collection, but a PLoS-wide one, spanning six of the seven journals in the house.

The Collection Genomics of Emerging Infectious Disease, was compiled by Jonathan A. Eisen (who you probably know from his excellent blog), the Academic Editor-in-Chief at PLoS Biology.

Jonathan, together with PLoS Biology Senior Editor Catriona J. MacCallum, wrote the introductory editorial explaining what the Collection is about and I particularly like the comparison to the world of birding:

When an American robin (Turdus migratorius) showed up in London a few years ago, birders were rapidly all atwitter and many came flocking to town [22]. Why had this one bird created such a stir? For one main reason--it was out of place. This species is normally found in North America and only very rarely shows up on the other side of the "pond." Amazingly, this rapid, collective response is not that unusual in the world of birding. When a bird is out of place, people notice quickly.

This story of the errant robin gets to the heart of the subject of this collection because being out of place in a metaphorical way is what defines an emerging infectious disease. Sometimes we have never seen anything quite like the organism or the disease before (e.g., SARS, Legionella). Or perhaps, as with many opportunistic pathogens, we have seen the organism before but it was not previously known to cause disease. In other cases, such as with as pandemic H1N1 2009 or E. coli O157:H7, we have seen the organism cause disease before but a new form is causing far more trouble. And of course organisms can be literally out of place, by showing up in a location not expected (e.g., consider the anthrax letters [2]).

Historically, despite the metaphorical similarities with the robin case, the response to emerging infectious disease is almost always much slower. Clearly, there are many reasons for these differences, which we believe are instructive to consider. At least four factors are required for birders' rapid responses to the arrival of a vagrant bird: (1) knowledge of the natural "fauna" in a particular place, (2) recognition that a specific bird may be out of place, (3) positive identification of the possibly out-of-place bird, and (4) examination of the "normal" place for relatives of the identified bird.

How are these requirements achieved? Mostly through the existence of high-quality field guides that allow one to place an organism such as a bird into the context of what is known about its relatives. This placement in turn is possible because of two key components of field guides. First, such guides contain information about the biological diversity of a group of organisms. This usually includes features such as a taxonomically organized list of species with details for each species on biogeography (distribution patterns across space and time, niche preferences, relative abundance), biological properties (e.g., behavior, size, shape, etc.), and genetic variation within the species (e.g., presence of subspecies). Second, a good field guide provides information on how to identify particular types (e.g., species) of those organisms. With such information, and with a network of interested observers, an out-of-place bird can be detected with relative ease.

In much the same way, a field guide to microbes would be valuable in the study of emerging infectious diseases. The articles in this collection describe what can be considered the beginnings of species-specific field guides for the microbial agents of emerging diseases. If we want to truly gain the benefits that can come from good field guides it will be necessary to expand current efforts to include more organisms, more systematic biogeographical sampling, and more epidemiological and clinical data. But the current efforts are a great start.

On the PLoS blog, Catriona J. MacCallum explains:

The collection is a collaborative effort that combines financial support from with the editorial independence and rigor of PLoS and the expert opinion of leading researchers from several different disciplines. You can read more about's involvement in a blog post from Frank Rijsberman. In one of the articles (from PLoS Biology), Gupta et al. discuss's vision as a funding agency for how the international community might unite to best take advantage of the new technology for combating infectious disease. The challenges are large and each article ends with a section summarizing what these are and how they might be overcome.

You can also download and listen to the podcast about the Collection, in which Dr.Kirsten Sanford interviews Jonathan Eisen and two of the authors of Collection artices Siv Andersson, and Raj Gupta (both Dr.Eisen and Dr.Sanford will also attend ScienceOnline2010, for those of you interested in the event).

The press release (also here) also contains all the relevant links:

Emerging infectious diseases are caused by a wide range of organisms, but they are perhaps best typified by zoonotic viral diseases, which cross from animal to human hosts and can have a devastating impact on human health. These zoonotic diseases include monkeypox, Hendra virus, Nipah virus, and severe acute respiratory syndrome coronavirus (SARS-CoV), in addition to influenza A and the lentiviruses (HIV) that cause AIDS. As Albert Osterhaus and colleagues from the Erasmus Medical Center, Rotterdam, The Netherlands, point out in their article in the collection, the apparent increased transmission of pathogens from animals to humans over recent decades can be attributed to the unintended consequences of globalization as well as environmental factors and changes in agricultural practices.

Articles in the collection also shine a spotlight on specific pathogens, some familiar and widespread, such as the influenza A virus, some "reemerging," such as the Mycobacterium tuberculosis complex that causes tuberculosis, and some identified only relatively recently, such as the bacterium Helicobacter pylori, which is associated with peptic ulcers and gastric cancer. Others discuss the broader implications of genomics research in this area, such as what it means for researchers in developing countries or for our biosecurity. As Jacques Ravel and colleagues from the US University of Maryland School of Medicine note, genomics can and should be used proactively to build our preparedness for and responsiveness to biological threats.

On the official Google blog Frank Rijsberman writes:

The first outbreak of the new "swine flu" strain, now known as H1N1, earlier this year in Mexico caught the world by surprise. Public health officials around the world tried to stop the virus at the borders but were largely helpless. Shortly after, on the other side of the world from Mexico, I saw the health check posts in Cambodia at the airport and at a borderpost with Vietnam, right when the country found its first H1N1 cases which were flown in by US exchange students. The weapons used by the health officials to combat the spread of the virus were primarily paper survey forms and thermometers; the virus won, very quickly. Genomics is rapidly changing both the way diseases are diagnosed and the way medications and vaccines are developed - but will it give us the tools to prevent the next pandemic?

So take a look at the Genomics of Emerging Infectious Disease Collection today and read all the exciting articles in it.


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