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Snake Bites in Kwale, Kenya: Into the Field

snakebitesWe just spent the day driving around Kwale looking for snakes, and/or people who had been bitten by snakes. As the last post showed, snakebites are a persistent problem along the Kenyan Coast, with more then 5% of the households we survey indicating that at least one person in the household had been bitten in the past two years.

It wasn’t difficult to find them.

Snakes are universally feared all over Africa and the associations with witchcraft make it a common topic of discussion. Everyone knows someone who has been bitten. They often know all the details, including where it happened and what occurred following the bite. It’s never a happy story.

We went deep into Kinango, an extremely rural area west of Kwale Town and found a friendly lady who seemed to know everything about everyone. She was incredibly jolly, pulled out some plastic chairs for us to sit under and cracked jokes the whole time. I even got to copy her collection of Sangeya music which she had recorded on her phone (another post but you can hear some of it here) at some local music festivals. In total I got more than five hours of live Sengeya and Chilewa music. In the music world, these would be called “field recordings.” Here, this is just music she cooks and cleans to.

Switching back and forth between snakes and Sengenya (in Africa it seems to be possible to have multiple conversations at once), she told us about a kid who had been bitten two days previous. She even told us where to find her, so off we went.

The child was collecting firewood around a mango tree near her home, when she was suddenly bitten by a large green snake, not once but three times on the foot. The snake bit once skated away, decided it wasn’t enough and came back and bit her twice more.

Ants had moved into the dead tree and hollowed out the area underneath. Presumably, the snake moved in previously and came out to warm up during the day.

The mother thankfully took the child immediately to Kinango Hospital and treated was administered. The child was given a three day course of antivenom injections and charcoal was wrapped around the wounds to absorb any venomous discharge. Though the child complains of some numbness in the area, it looks as if there won’t be any permanent damage. Thankfully.


Snake bite (species unknown). Note the charcoal. Victim is a 10 year old girl.

We were also told of an old woman who had been bitten more than 20 years ago, and was badly scarred, figured out where she was and off we went again.

As we pulled up a friendly young lady came out to greet us, and showed us the way to the house out back. In the distance, we could see an old lady walking with a limp. Otherwise, she was completely fit and seemed to be cutting her own firewood with a panga.

She brought us out some chairs and sat down to chat. In 1992, she had been out back collecting firewood (a pattern) and was bitten on the foot by puff adder, one of the deadliest snakes in the world. She was bitten on the foot, and became immobile for nearly a week. A series of witch doctors were brought in, who administered charcoal rubbed into small cuts in the skin.

Necrosis set in, and watery blood erupted out of the wound site. A large number of maggots appeared. Finally, someone had the good sense to take her to the hospital, where she spent an entire year.

The details were unclear, but it appeared that the gangrene was so severe that multiple infections were presents. They likely had her on intravenous antibiotics for an extended amount of time. Despite this, the foot did not heal. Some Christian missionaries came, and convinced her to convert to Christianity, which, she claimed, improved her condition. This is likely coincidental.


Puff Adder wound. Note the permanent curvature of the foot. She continues to have to wrap it and use topical medication, 24 years following the bite.

The doctors suggested a skin graft to improve the foot, but she refused. Necrosis was so deep that it permeated the bone and the foot is permanently curved as a result. The leg still shows sign of swelling even more than 24 years after the bite. In most cases, they probably would have simply amputated.

The lady was born in 1948, bore ten children, one of which was born just as she was bitten. She was unable to breast feed or care for the child. Regardless, the daughter has two children of her own now.

Snakebites are bad news. In this woman’s case, the disregard for proper medical care simply made a bad situation worse. She is truly lucky to be alive. If she had died, it is doubtful that the Mgangas would have admitted any responsibility.


Puff Adder victim, born in 1948. Ten kids. Still going strong.

Links I liked, November 18, 2014

I liked so many things I read today that, rather than clutter social media, I’ll make note of them right here:

“Falling” by William McPherson – By far, the most depressing thing I have read in a while. McPherson is a Pulitzer winning writer and former editor at the Washington Post who chose a life of curiosity and is now paying the ultimate price. It’s awful that the brightest people have to be punished for thoroughly embracing life. So many people I know are going to go this way, it is possible that I might, too.

In India, Growth Breeds Waste NYT – Documenting India’s mounting problem of what to do with its waste. Europe went through their urbanization pains centuries ago. Unfortunately, developing countries are rising to the challenge fast enough. The problem, of course, is that elites are sheltered from the problems of waste and weak and corrupt government structures disallow people from demanding that their countries clean up. International environmentalists need to focus less on screaming about corporate polluting (though it is important) and need to start making demands for more boring things, like managing waste on a local level.

Stop calling me ‘the Ebola nurse’ – Kaci Hickox – This lady was a hero. She never had ebola, but was still illegally interned for having it because a few Americans don’t understand science. Anybody who supported her detainment should just stop speaking to me now. It was shocking how readily Americans were willing to lock people up simply because they were scared and even more shocking where the calls for her “arrest” came from. I give up. People like Hickox put their money where their mouths are. She did what most humans wouldn’t do and she was vilified for it. Unforgivable.

Ten Things that Anthropologists Can Do to Fight the West African Ebola Epidemic I think it should be required that every field research project include an anthropologist.

Q Fever Is Underestimated in the United States: A Comparison of Fatal Q Fever Cases from Two National Reporting Systems People are dying of Q, but much of it isn’t recorded.

Today is Jonas Salk’s 100th birthday

100 years ago today, Jonas Salk was born. As the creator of the inactivated polio vaccine, he not only changed the course of human history, he also ushered changed the field of public health forever. We can count the polio vaccines and the elimination of smallpox as probably the two great success of public health.

In its mildest form, polio causes a mild bout of diarrhea. In its worst form, the virus migrates to the spine, impedes development and causes debilitating long term paralysis. My grandfather was struck with the disease and had one of his legs stunted and weakened (though he managed to serve in WWII anyway as a Marine). A carpenter who worked for me a while back died due to long term respiratory complications from a childhood polio infection.

Polio is mostly foreign to anyone born in my generation. We were nearly all vaccinated, and the high levels of vaccination have destroyed opportunities for the virus to persist in the environment, protecting everyone, even those who don’t get the vaccine.

Unfortunately, though Salk’s achievements were great, medical care and attention to polio was hardly equitable and tainted by the racism of the time.

During the 1930s the systematic neglect of Black polio victims had become publicly visible and politically embarrassing. Most conspicuously, the polio rehabilitation center in Warm Springs, Ga, which Roosevelt, himself a polio survivor, had founded, accepted only White patients. This policy, reflecting the ubiquitous norm of race-segregated health facilities, was sustained by a persuasive scientific argument about polio itself. Blacks, medical experts insisted, were not susceptible to this disease, and therefore research and treatment efforts that focused on Black patients were neither medically necessary nor fiscally justified.[1]

It is likely true that African Americans experienced a lower burden of disease than white children. We now know that polio’s worst effect arise from the lack of acquired immunity to the disease. Repeated infections from infancy, most importantly during the first six months, when babies still have maternal antibodies to fight for them. Improvements to sanitation delayed exposure to the virus, so that children were not immune and thus more susceptible to the disease’s worst effects.

In short, polio is a disease of development, not underdevelopment. The horrible racism of the pre-civil rights medical system can’t be denied, but the observed disparities in disease incidence might have not been imagined given the disparities in sanitation and access to clean water.

Presently, we are fighting a battle to insure that all kids in Sub-Saharan Africa are vaccinated. However, there still exist pockets where the medical system so dysfunctional and the politics so chaotic, that vaccination rates are low and disease continues to flourish. In places like Afghanistan and Northern Nigeria, the hope of polio elimination is almost non-existent


1.    Rogers N: Race and the Politics of Polio: Warm Springs, Tuskegee, and the March of Dimes. American Journal of Public Health 2007, 97(5):784.


Ebola: we don’t have time to waste

Ebola is a cool disease. It transmits among fruit bats in the area in and around the Central African Republic. Apes live in and under the trees the bats live in and ingest their feces. Humans who ingest the apes pick up the virus when slaughtering the animal, or so some think. The truth is that no one really knows for sure.

Contacts between humans is increasing as settlements expand and a demand for meat increases. Lacking access to formal methods of employment, individual sellers happily take advantage of market demand and a thinly profitable trade in bushmeat profulgates. Meat equals success and in the place of professionally or pastorally raised beef, which is mostly unavailable to poor people in countries like Liberia and Sierre Leone, people eat the monkeys, chimps and many other of our cousins which are able to harbor the many of the same pathogens we do.

One person gets sick. He or she has no access to formal care because his or her government can’t or won’t provide it so he remains at home. The family consults the local herbalist who provides some medications which offer temporary psychological relief but nothing more. As time ticks on, the victim becomes even sicker until the situation becomes so serious that the family has no choice but to carry their dying loved one to a health clinic 20 km away from their house. Along the way, everyone carrying him or her touches infected feces and vomit and three weeks later the process is repeated.

This could have all been avoided if rural economies were developed enough so that a mass migration to urban areas wasn’t necessary, had there been safer sources of meat available for an affordable price, were there sufficient jobs which wouldn’t necessitate the bushmeat trade, were the governments of Liberia and Sierre Leone effective enough to place a proper health facility close by to patient 0’s house and if health care was dependable enough to be able to spot and deal with an Ebola case.

Ebola is a conflation of ecology, economics, sociology, culture and politics, all mixed together to create conditions for one of the worst health crises the African continent has seen since HIV. It’s going to erase any of the gains of the past decade and collapse the already struggling health systems of some of the poorest places on the planet.

Meanwhile, the United States is having another 9/11 moment and this is where I’m starting to get quite concerned. Panic is about to become policy. Fears of global terrorism prompted our entry into Afghanistan, which might have been justified. But it also paved the way for the invasion of Iraq, which, from the beginning, was a disaster waiting to happen. Out of 9/11, we got the Patriot Act, a massive expansion in government powers to search, seize and detain and America stood by and allowed it to happen with little debate.

I am not a Libertarian, though keep getting accused of being one. I believe in public schools, public health care and government oversight of dangerous industries. So there. John Galt wouldn’t be much into me (but I guess from the far, far left anyone looks like a Libertarian).

I am, however, despite my leftist pedigree, quite concerned with the rights of individuals and the potential for panic and ignorance to lead to a rhetoric that can quickly spiral out of control and veer seemingly caring people away from the direction that the moral compass would normally point us in. I am remembering how many Americans supported torture during Bush II and wondered how many of them would support torture were it to be practiced on their own children. Though seemingly alarmist, I think that we need to be extremely careful.

Enough about me. The reality of Ebola is that it is a man-made crisis. Forest dwelling locals have eaten bushmeat for as long as humans have lived there but there is little evidence that there has ever been a large scale outbreak like the one we are currently experiencing (though history in Africa is often obscure). As I noted earlier, many forces are at play, all of which are associated with the rapid social change that Sub-Saharan African states are currently experiencing.

Some of these forces are inevitable. Population growth, as it did in Europe and Asia before, has led to the creation of mega-cities. The connections, however, between the rural and the urban, however have not been severed. People are going to do what they do, regardless of risk, particularly if they can make a buck meeting some market demand.

Some forces, though, are avoidable. While health care did not initiate the crisis, it helped drag it along. Liberia and Sierre Leone can boast to have two of the worst health systems in the world, but their poor capabilities are hardly unique in Sub-Saharan Africa. NGOs and missionary groups work to plug some of the gaps, but the reality is that without a concerted and proactive effort from the governments of those countries, the system will never improve. International funding is too poor and weak national economies and top heavy tax structures can’t adequately fund these systems domestically. Poor funding leaves many clinics, particularly those in rural areas where these outbreaks begin, without supplies, trained staff and diagnostic equipment. In Kenya, Malawi and Tanzania, I’ve seen more than one rural clinic without power or clean water. Worse yet, Ebola outbreaks, though devastating, are infrequent so that more pressing needs like malaria, diarrheal disease and HIV eat up the brunt of the already scarce funds clinics receive. Pathogens not only compete in the wild, but also for funding and support. This leaves many rural health workers without the protective gear they need, so that they work are the highest risk for death from diseases like Ebola.

What can we do? First, we can calm down. In the United States, the reality is that one of far more likely to be killed by an oncoming car than from Ebola and the probability of sustained transmission extremely low. Though people like to view domestic transmission events such as the one in Texas as failure, the reality is that public health and medical resources move much more quickly and effectively in Texas than in troubled Liberia. Much is made over Ebola’s lethality, but a patient who is found to be infected in the United States has a vastly higher likelihood of surviving than one in Liberia.

Second, leaders can stop spreading and capitalizing on misinformation. While attractive, promoting hysteria only leads to bad policy. The tendency in America is to view as some kind of apocalyptic movie scenario. While fun (not to me), the reality is that there are people in the world who are dying who shouldn’t be. Moreover, closing schools because someone knows someone who knows a Liberian is just simply unwise and counterproductive in the long term.

Third, the international community needs to engage the governments of Liberia and Sierre Leone to improve their public health infrastructure. This is not an easy task. The histories of working relationships of international health bodies and developing countries governments are fraught with failure. Mutual distrust, corruption and indifference of political leaders to the plight of their constituencies has created a mostly untenable system. However, providing supplies and training come at little cost is a mostly uncontroversial affair.

How long will this last? No one knows but it is inevitable that, even if this epidemic is brought under control, it certainly won’t be the last of its kind. We don’t have time to waste.

Ebola: a poor example of disease transmission, but maybe that’s not an accident

Ebola2I’m reading through news about the American rights hijacking of the Ebola crisis for their own political gain. Did this outbreak have to occur right before the midterms, and right before a Senate election? The awful toll it will take on West African states aside, the virus couldn’t have picked a worse time (or a better, depending on how you look at it).

Ebola is a scary virus, assuming that one ever has the misfortune to come into contact with it. “Contact” in this case, means that you have to have direct contact with the blood, feces or vomit of a person infected and symptomatic with Ebola. Unfortunately for the virus, people don’t really live that long once they become symptomatic with the disease and the people who survive appear to be immune to it

This is a terrible model for an infectious pathogen. The symptoms are so severe that all around the person will immediately run away (except health workers, who bear the brunt of the risk) and the host doesn’t live very long providing only a short window with which to infect other hosts.

So the duration of infectiousness is short, the pathways are really awful and repeat infections are unlikely.

To put this into perspective, looks at the most successful pathogens out there, pathogens like influenza. Influenza transmits easily, nearly two thirds of those infected show no symptoms and thus can happily shed viral particles to everyone they know undetected. When symptoms do occur, they aren’t so bad as to keep every outside of a 5 miles radius of you. Influenza mutates at an incredible rate, so that a single infection doesn’t provide much protection against later infections. Even better, though its rapid mutation rate sometimes leads to horribly virulent strains like the 1918 flu pandemic which killed millions, in most cases influenza spares a healthy host.

It has developed an incredibly efficient and effective survival strategy (and for this reason is far scarier than Ebola).

So I’ve been thinking of how a virus like Ebola might persist in the wild, given it’s odd mode of transmission.

Now, we know that Ebola is a zoonotic disease, that is, it is transmitted from animal to humans. Since humans have not developed genetic resistance to the disease, we are at particular risk for its worst effects. Many of the scariest diseases out there are zoonoses. Examples would include HIV, SARS and, of course, influenza. While not always true, we tend to make peace with pathogens that are old and exclusively human. Many of the bacteria which live happily in your gut would be examples. As we haven’t had sufficient time to make peace with Ebola or HIV, the outcomes can be far worse than those seen in their normal hosts.

Thus, it is possible that Ebola is far less serious in whatever host it is adapted for. Nipa virus, which has a case fatality rate (the percentage of all infections of a pathogen which result in death) of more than 90% does nothing to the fruit bats it happily resides in. It is possible that Ebola is also harmless to whatever host it depends on.

However, it is possible that Ebola might be harmless in some hosts, while deadly in others, and this difference might be the result of a successful evolutionary adaptation.

Ebola has been pegged as residing in bats possibly explaining its wide range over central Africa. [1-6] Bats are a pathogens dream. They multiply quickly, providing ample opportunities for transmission and for evolutionary adaptations to the pathogen which might insure its long term survival. Better yet, they fly so that pathogens can disperse themselves quickly over a large geographic space. This is particularly useful if the pathogens wants to maintain healthy genetic diversity (though the creation of multiple sub-populations) and if it can infect multiple hosts which may or may not be all that mobile.

Apes would be a good example of the latter. Apes, being fairly sensitive to environmental changes, don’t like to move around a whole lot (unlike humans which are highly adaptable to just about any environment on the planet) but still might be important to the survival of the pathogen.

Ebola has been found in apes and the disease is currently devastating local populations.[4, 7-10]

And this is where I get stuck. In nature, plenty of things happen for no reason at all, but with pathogens, even accidental occurrences can have implications for survival and are often part of the tool box with which diseases evolve and persist.

A bleeding ape on a forest floor will likely kill all of its relatives in quick fashion, assuming its family doesn’t just hightail it out in which case transmission is over anyway. But the dead ape might serve an important purpose. Predators and scavengers will quickly arrive to feast on the infected corpse, transmitting the virus to carnivorous animals all around the forest. This could provide ample opportunities for transmission to other species. Even though many of these species could be poor hosts for the disease, they could also represent new opportunities for survival.

HIV would be an example of this. From HIV’s standpoint (assuming a collective viral consciousness), the jump to humans was extremely fortuitous. Humans love to have sex with multiple people, often even after having already reproduced, and physiologically they proved resistant enough to allow the virus to hang out for a few years before dying, allowing for years of transmission possibilities.

Thus, while on the surface, blood based modes of transmission seem pretty useless, they could serve a larger purpose of insuring a pathogens survival on a macro-level. In the case of HIV, humans didn’t turn into a dead end host (as they are with diseases like Brucella) but rather a new opportunity for survival.

The deadly nature of the virus in apes and humans, then might be like an insurance policy. Like a retirement portfolio, a diversified package of stocks will keep you alive in retirement much better than a portfolio with a single stock. Work has been done on pathogens which infect multiple species, and, depending on the nature of the pathogen, species diversity can either work for or against the survival of the pathogen.[11-13]

In the case of Ebola, there is no real evidence that humans play a role in sustaining transmission, but blood and predation could be sustaining something like Brucella or Q Fever in the wild.

Now, in this article, I have rambled on and bored you to death (and bless you if you made it this far) but I have to point out that I am under no illusions that pathogens act consciously, though I have like many of my colleagues present it as such. Actually, no living thing really does have a long term plan outside of its narrow goals of producing offspring. But new opportunities for transmission do present new opportunities for the long term evolutionary survival or a biological entity. These lucky occurrences are not consciously sought out, but rather enable the pathogen to do what it does successfully.

It must be said that the ecology of Ebola is somewhat of a mystery. Not much work has been done on the subject, as the pathogen hides out in some of the most inaccessible areas of the planet, and conflict and political instability in places like the Central African Republic and Northern Uganda prevent researchers from doing extensive work on the pathogen.

1. Stan D: Ebola and Fruit Bats. Clinical Infectious Diseases 2006, 42(5):V.
2. Olival KJ, Islam A, Yu M, Anthony SJ, Epstein JH, Khan SA, Khan SU, Crameri G, Wang L-F, Lipkin WI et al: Ebola virus antibodies in fruit bats, bangladesh. Emerging infectious diseases 2013, 19(2):270.
3. Hayman DTS, Yu M, Crameri G, Wang L-F, Suu-Ire R, Wood JLN, Cunningham AA: Ebola virus antibodies in fruit bats, Ghana, West Africa. Emerging infectious diseases 2012, 18(7):1207.
4. Kumulungui B, Leroy EM, Swanepoel R, Gonzalez J-P, Pourrut X, Rouquet P, Yaba P, Paweska JT, Délicat A, Hassanin A: Fruit bats as reservoirs of Ebola virus. Nature 2005, 438(7068):575.
5. Vogel G: Infectious disease. Are bats spreading Ebola across sub-Saharan Africa? Science (New York, NY) 2014, 344(6180):140.
6. Hayman DTS, Emmerich P, Yu M, Wang L-F, Suu-Ire R, Fooks AR, Cunningham AA, Wood JLN: Long-term survival of an urban fruit bat seropositive for Ebola and Lagos bat viruses. PloS one 2010, 5(8):e11978.
7. Groseth A, Feldmann H, Strong JE: The ecology of Ebola virus. Trends in microbiology 2007, 15(9):408.
8. Vogel G: Ecology. Tracking Ebola’s deadly march among wild apes. Science (New York, NY) 2006, 314(5805):1522.
9. Leroy EM, Rouquet P, Formenty P, Souquière S, Kilbourne A, Froment J-M, Bermejo M, Smit S, Karesh W, Swanepoel R et al: Multiple Ebola Virus Transmission Events and Rapid Decline of Central African Wildlife. Science 2004, 303(5656):387.
10. Walsh PD, Biek R, Real LA: Wave-like spread of Ebola Zaire. PLoS biology 2005, 3(11):e371.
11. Renwick AR, White PCL, Bengis RG: Bovine tuberculosis in southern African wildlife: a multi-species host–pathogen system. Epidemiology and Infection 2007, 135(4):529.
12. Dobson A, Meagher M: The population dynamics of brucellosis in the Yellowstone National Park. Ecology 1996, 77(4):1026.
13. Dobson A: Population Dynamics of Pathogens with Multiple Host Species. The American Naturalist 2004, 164(S5):S64.

The Jigger flea: a neglected scourge

Jigger infestation of the hands. I picked the least awful picture I could find. Note the deformity of the hands. This person has likely been suffering from infections since childhood.

Jigger infestation of the hands. I picked the least awful picture I could find. Note the deformity of the hands. This person has likely been suffering from infections since childhood.

I just learned about probably one of the most horrible dieases I’ve ever seen: the jigger. Tunga penetrans is one of the smallest fleas around, less than 1 mm in length. The gravid female attaches itself to a mammalian host, burrows into the skin head first leaving its read end exposed for breathing and defecation. It feeds on blood from the subcutaneous capillaries and proceeds to produce anywhere from 20-200 eggs. Under the skin it can grow to nearly 1 cm in width.

Tunga penetrans is native to South America, was brought to West Africa through the slave trade. In the mid 19th century it was brought on an English shipping vessel and made its way through trade routes and is now found everywhere throughout the continent.

Bacteria opportunistically invades the site and super-infections (multiple pathogens) are common. Victims suffer from itching and pain and multiple fleas are common. Due to the location of the bite, people often have trouble walking and due to the disgusting nature of the infection, victims are stigmatized and marginalized. Worse yet, the site can becomes gangrenous and auto-amputations of digits and feet and eventually death are not uncommon.

The Parliaments of both Kenya and Uganda have introduced bills in the past calling for the arrest of people suffering from jiggers. Of course, these ridiculous bills don’t come with public health actions to control the disease.

Jiggers are entirely preventable, treatable through either surgical excision or through various medications but risk factors for it are mostly unknown and the data contradictory and mostly inconclusive.

It sometimes occurs in travelers and is easily treated in a clinic on an outpatient basis but is a debilitating infection for poor communities. Thus, it is not taken seriously by international public health groups who choose to focus on big issues like HIV and malaria.

Jiggers are a classic example of the neglected tropical disease: it devastates the poorest of the poor but gets almost no attention from donors or the international press.

We gathered some data on jiggers back in 2011 along the coast of Kenya. Without presenting these results as official, I was drawn to the attached map.

Animals of various species have been implicated as reservoirs for the disease, most notably pigs and dogs. Less understood is the role of wildlife in maintaining transmission. On the map below, the large yellow dots represent cases. Note that they are nearly all located along the Shimba Hills Wildlife Reserve. I calculated the distance of each household to the park’s border (see the funny graph at the bottom), and found a graded relationship between distance and jiggers infections. Past 5km away from the park, the risk of jiggers is nearly zero.

What does this mean? I have ruled out domesticated animals, at least as a primary reservoir. People in this area tend to all own the same types and numbers of animals. Being Islamic, there are no pigs here, but dogs are found everywhere. Despite this, there are distinct spatial patterns which are associated with the park. Note that all of the cases are found between the parks border and a set of lakes, perhaps implying that certain wild animals are traveling there for water and food.

The ecology of jiggers is very poorly understood and, like many pathogens (like Ebola, for example), wildlife probably play an important role.

It’s worth paying me a lot of money to study it.

Locations of jiggers cases. note the proximity to the park.

Locations of jiggers cases. note the proximity to the park.

Distance to wildlife reserve and jiggers risk. Note that risk drops until 5km, then becomes nearly zero.

Distance to wildlife reserve and jiggers risk. Note that risk drops until 5km, then becomes nearly zero.

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