Thursday, July 31, 2014

Ebola: Thoughts on a public health disaster

File:Ebola virus virion.jpgThe current outbreak of Ebola hemorrhagic fever in western Africa has been ongoing for months. It is a remarkable and tragic event. Sadly, there is no known cure, the case fatality proportion is high (historically 50-90%), and prevention is difficult in the areas where the virus is currently spreading.

Nations outside Africa are now recognizing the possibility of Ebola-infected travelers returning home. Importation of disease is a public health issue for other infections, such as measles, outbreaks of which are commonly sparked by visitors returning from areas where cases are prevalent. In the case of Ebola, one traveler died on the last leg of a West African trip, before returning home to Minnesota, so there's good reason to believe that importation could occur. It's probably unlikely, however, given the current level of awareness. Some African airlines, for example, have curtailed air service in affected areas and are screening passengers for signs of illness. International guidance on passenger screening is being evaluated as well. Moreover, CDC has issued interim guidance regarding Ebola for airline flight crews, cleaning personnel, and cargo personnel.

If an infected or infectious traveler does return, is it unlikely to result in the dramatic transmission currently observed in Africa. The current heightened awareness makes it very likely that travelers returning from affected areas would be evaluated for possible Ebola infection should they develop illness and present to a healthcare provider. The CDC has issued guidance advising healthcare workers to
be alert for signs and symptoms of EVD [Ebola virus disease] in patients with compatible illness who have a recent (within 21 days) travel history to countries where the outbreak is occurring, and should consider isolation of those patients meeting these criteria, pending diagnostic testing. 
Infection control procedures are standard and the necessary supplies are plentiful in Western hospitals, making it unlikely that an Ebola patient would cause secondary infections in healthcare settings.

Moreover, Ebola virus is much less transmissible than many other viruses. Measles virus, for example, has basic reproduction ratios in the range of 11-18, whereas those for Ebola have been estimated to be between 1-2. For comparison, the basic reproductive ratio for influenza is estimated to be 3-4, for rubella 6-7, and for chickenpox 10-12. The ratio for pertussis is similar to that of measles. One wonders what the basic reproduction ratio is for the current outbreak in Africa is (and if analytic approaches using social media might be helpful for estimating it).

Given that the current outbreak is so large compared to past outbreaks of Ebola, we might learn some lessons about this exotic disease. For example, are there transmission pathways that we don't know of at present? Aerosol transmission is thought to play only a minor role if any in transmission of human strains of Ebola virus, but perhaps new information will emerge from future epidemiological studies of the current outbreak.

What is for sure is that the events in Africa are a tremendous human tragedy. I hope that the desperate measures of closing schools and nonessential government services will help to control the spread of the virus. It isn't clear that it will.

(image source: Wikipedia)

Monday, July 21, 2014

Software and computing: How far we've come in a very short time

File:Computer-aj aj ashton 01.svgWhen I was in graduate school in the early 1990s, DEC and SGI Unix workstations were the hottest things around. We programmed in Fortran 77 mostly, and occasionally in Matlab® and Macsyma. As I recall, the different machines had up to a few 100 megabytes of RAM and processor speeds up to a few hundred MHz. I had grown up programming some of the first personal computers, which were very modest by comparison, and using these computers made me feel as if almost anything could be achieved computationally. Such machines cost well over $10K and the operating systems were proprietary, licensed, and expensive -- as were most of the useful applications.

Today, fast, high capacity, multi-core Linux machines are cheap. They can run Fortran and other traditional languages such as C, which are now available for free, as well as new open source packages like R and the Python language. Many of these packages are highly developed and are continuously under expansion and refinement. Libraries exist for nearly any conceivable computational problem. There are even open source analogues of Matlab® (Octave) and Macsyma (Maxima).

Very advanced methods of computation are now widely available for low cost. A major reason this has happened has been the open source software movement, the ideas of which extend now to making data and research codes used in published studies available for others to use. 25 years ago, when beginning research on a new problem, one commonly had to write new code from scratch. Today, one can turn to blogs or GitHub to look for codes that can be adapted for the problem at hand, radically shortening the code development, testing, and validation cycle. Recent work emphasizing the reproducibility and transparency of computational science promises to extend such progress farther still.

Such developments allow applications and methods to be shared and applied very broadly and across research fields. It's not uncommon for methods and codes developed for engineering, physics, and finance, for example, to be applied to problems in biology, medicine, and public health. Instead of writing code to translate abstract or unfamiliar equations into a local implementation, one often only has to install a library or find and download code (e.g., from GitHub or an online open source journal), possibly revise, and then apply to data. More time can be spent on thinking and communicating science, instead of coding and computing.

With these advances come dangers as well, but these dangers are manageable. For example, undetected bugs in codes can quickly threaten the integrity of results across multiple fields -- a frightening proposition. Similarly, it is also possible to use methods and codes in ways that are theoretically incorrect or unjustified if one doesn't understand the basis and limitations of those methods and codes. Such dangers are nothing new in science, and highlight the importance of working with others who are expert in new methods.

Current trends will only increase the computational capabilities available. It's an exciting time to work in mathematical and computational methods in biomedical science.

(image source: Wikipedia)

Sunday, July 13, 2014

Anti-vaccination movement: Nothing new

PHIL Image 14538I've always thought of the anti-vaccination movement as beginning in the aftermath of the bogus (not to mention fraudulent and retracted) 1998 paper associating vaccines with autism. Recently I've become more interested in the movement and have begun reviewing the associated literature. Perhaps what I've found shouldn't surprise me, but in reality I'm astonished: Notions against vaccination have existed for a long time, and date back to at least the British compulsory vaccination laws of the 19th Century.

Jeffrey Baker describes the history of anti-vaccine movements in a very informative paper on the pertussis vaccine controversy in Great Britain in the late 1970s and early 1980s. His study recounts and analyzes how a 1974 series of case reports describing alleged diphtheria–tetanus–pertussis (DTP) vaccine adverse reactions led to plummeting vaccination rates and a resurgence in disease. The study describes many dynamics taking place then that resonate with events surrounding the MMR vaccine recently. For example,
  • Reports of supposed vaccine injuries were published
  • Vaccine victim/anti-vaccine advocacy groups were formed
  • A number of physicians recommending against vaccination emerged as a group
These and other forces led to a sharp decline in public acceptance of the DTP vaccine then in use and an increased incidence of pertussis, the likes of which had not been observed for 20 years (which is another similarity with the current outbreaks of vaccine preventable disease in the United States).

Importantly, Baker hypothesizes that, although the press played a role in initiating the anti-DTP vaccine movement and attendant epidemics, it was not the only factor. He points out that the British medical profession was deeply divided, "reflecting quite real uncertainties surrounding the safety and efficacy of the vaccine in the 1970s." (Note that although the medical profession isn't presently divided on the issue of the MMR vaccine, there is some reason to think that younger doctors are less likely to believe that vaccines are efficacious and safe than more senior doctors are.) Moreover, he notes that
Parents in vaccine victim advocacy groups played an additional important role in sustaining the crisis. The ambivalence of both public and medical profession . . . are best understood against the background of Britain’s long history of skepticism regarding many vaccines dating back to smallpox.
Here, Baker alludes to the controversy surrounding compulsory smallpox vaccination in the late-19th century in the UK, noting that mandatory vaccination against smallpox virus
. . . represented one of the first intrusions of state public health policy into personal life, and consequently provoked considerable libertarian opposition.
Recent studies by Anna Kata of the tactics and tropes used online by the anti-vaccination movement at present, and of anti-vaccination misinformation on the Internet, reflect many facets of the anti-DTP vaccine movement nearly 40 years ago.

How could ideas opposing vaccination have persisted for well over a century? The phenomenon of groups of people opposing the best public health guidance is not limited to vaccination; other examples include the raw milk movement (which refuses to acknowledge the risk posed by bacterial contamination of raw milk and related products) and the anti-fluoridation movement (which questions the safety of fluoridating public water supplies). As I've mentioned before in this blog, it's critically important to understand such groups and how they make behavioral decisions. It may or not be possible to change their outlooks given such knowledge, but it's hard to imagine doing so without it.

(image source: CDC PHIL image ID#14538)

Sunday, July 6, 2014

Some broad threats to public health

File:Overflowepa.gifA recent Twitter thread highlighted several current threats to public health and I thought the points were sufficiently important to immortalize in a blog -- not necessarily because any one point is of primal importance (although each one alone is stunningly important for public health), but rather because we often forget to think holistically about public health. The reality is, of course, that many areas must combine in order to make good public health possible.

The thread highlighted three elements of public health that are all compromised to some extent at present: the effectiveness of antimicrobial drugs, the coverage of vaccination against vaccine preventable infectious diseases, and the preservation of sanitation infrastructure.

A few words about each of these. The specter of pathogens resistant to current antimicrobial drugs is well known. This topic is widely covered in the news media, in the scientific and medical literature, and even in political discourse. There is also a rich conversation on social media. Much has been written about the coming -- or, if you're a patient infected with a resistant pathogen, the present -- post-antibiotic era. The threat to public health is so great that the issue is now commanding economic and political attention, which hopefully will result in action soon.

And yet, antimicrobial resistance is not the only important threat to public health. The incidence of many vaccine-preventable diseases is increasing, not because pathogens are evolving and becoming mismatched to vaccines, but because significant numbers of people are electing to forgo having children vaccinated. The reasons why are varied and complex, but often they originate in mistrust between people and those who make and provide vaccines. Part of that mistrust was eroded by deeply flawed published research that has since been discredited; meanwhile, the effects and attendant impacts on human health continue. Moreover, vaccines are getting more expensive, and have been for years, which probably doesn't help the goal of increasing coverage, either.

Lastly, the sanitation infrastructure in many US cities is old, undersized, and crumbling. (It's not only the sanitation infrastructure that is failing or threatening to fail; transportation and power distribution are similar stories.) As a result, human waste is frequently released into the environment. This is remarkable for many reasons, not the least of which is that sanitation is one the oldest and most recognized cornerstones of public health. The undesirability of having human excrement handled improperly is so obvious that there's no reason to belabor the point here.

It's tempting to refer to these issues as horsemen of the public health apocalypse, but that would be bombastic and incomplete. There are other important threats, including the safety of the food supply, the high incidence of healthcare associated infections (both susceptible and drug resistant), the growing prominence of chronic diseases of the aging and the attendant demands on healthcare resources, and the continued emergence of new pathogens from nature.

To close, it's good to resurface from the depths of one's own research periodically. It can result in context and perspective, which is badly needed in any field of research. Much has been written about the use of Twitter in healthcare and biomedical research. Maybe this is another: it can force you to come up for air.

(image source: Wikipedia)