Tuesday, December 29, 2009


Welcome to the blog for EEMB40 - the Ecology of Disease - for Winter quarter 2010. It will also serve as a class website and you will find links to lectures etc. in a box at the top right imaginatively called 'links'.

You are all welcome, and encouraged to post here. To do that all you need to do is to send me an e-mail saying just that. I will then add your address and Google will send you an invitation to be an author. Just follow the simple instructions and away you go.

Postings should be relevant to the class but the blog is specifically designed to be a place where you don't need to worry about how relevant your post is. (I give you 'Basket full of puppies' as an example). I will be posting news items, research updates, interesting links and some bits that I take out of lecture (for time purposes) but that some of you may find interesting. By putting it all here you can look at it at your leisure and you know it won't be on the exam.

I try to post every day when the class is running and, where possible, the postings are relevant to the current topics we are covering in class. You can access older postings (there are nearly 400 of them) either by scrolling down the page and repeatedly hitting the 'Older posts' button at the bottom right or by using the 'Labels' (scroll down and they'll be on the right hand side) to pull up posts on particular topics.

Tuesday, September 8, 2009

Fantastically alarming

Okay this is a depressing note to end on but this was, briefly, the main story on the CNN website today.

Doctors slash vaccines due to rising costs
Health care providers say insurers don't reimburse them enough for essential vaccinations, so they're not offering them.

NEW YORK (CNNMoney.com) -- Parents who bring their kids to Dr. G. Andrew McIntosh for the chicken pox vaccine are out of luck.

The family physician, who has a solo practice in Uniontown, Ohio, doesn't offer that shot because he can't afford it. Most insurers won't sufficiently cover the cost.

"It doesn't do me any good. I am losing money on [them]," he said. The chicken pox vaccine runs about $115, but insurers only cover between $68 to $83 of that..


It's not clear exactly how widespread vaccine cutbacks are, but in a recent industry survey, 5% of pediatricians and 11% of physicians indicated that they're seriously considering no longer offering immunizations. Currently there are about 350,000 pediatricians and family physicians in the U.S.

"These are fantastically alarming numbers," said Dr. Richard Lander, a Livingston N.J.-based pediatrician who chairs a committee on administration and practices at the American Academy of Pediatricians. (AAP)

Read the full story here.

Most of you have probably not had Chicken pox because you were vaccinated against it. As someone who has had chicken pox let me tell you, in the words of Pooh Bear, it is one ******* miserable disease.

I hope you enjoyed the class. If you didn't, or it wasn't what you expected please let me know.

Monday, September 7, 2009

Infected by the Pig

Taking on Swine flu. Three videos. No comment.

Dr. Joe Bresee of the CDC takes on Swine Flu

Putnam Pig takes on Swine Flu

Elmo takes on Swine Flu

Friday, September 4, 2009

What They Say They Do and What They Actually Do

Hmmm, this sounds familiar. From a paper in this month's Journal of Environmental Health:
University Students' Hand Hygiene Practice During a Gastrointestinal Outbreak in Residence: What They Say They Do and What They Actually Do

During a 2006 norovirus outbreak at the University of Guelph in Canada researchers observed hand sanitation behavior in students. Hand sanitation stations and informational posters were stationed at the entrance to a residence hall cafeteria, where the potential for cross-contamination was high. The researchers observed that even during a high-profile outbreak, students followed recommended hand hygiene procedures just 17 percent of the time. In a self-reported survey after the outbreak had subsided, 83 of 100 students surveyed said they always followed proper hand hygiene but estimated that less than half of their peers did the same.

Hand washing is likely to reduce the chance that you will both contract influenza this winter and your chance of spreading it if you do contract it. There's no need to go all Howard Hughes but even a slight increase in hand washing rates could lead to significantly fewer sick people.

Thursday, September 3, 2009

Flu buddy

Do you have a Flu Buddy?

From the informative Pandemicflu.gov website the CDC Guidance for Responses to Influenza for Institutions of Higher Education during the 2009-2010 Academic Year

Students with a private room should remain in their room and receive care and meals from a single person. Students can establish a “flu buddy scheme” in which students pair up to care for each other if one or the other becomes ill. Additionally, staff can make daily contact by e-mail, text messaging, phone calls, or other methods with each student who is in self-isolation.

Wednesday, September 2, 2009

Swine flu latest

The President's Council of Advisors on Science and Technology said in a report last week that the virus, although moderate, could infect 30 percent to 50 percent of the U.S. population this year, put 1.8 million people into the hospital and kill anywhere between 30,000 and 90,000 people.
From a Reuters article today.

Also, interesting to see how new technologies are being used this time to track and anticipate the pandemic. The figure below shows how the discussion of 'swine flu' on Facebook is distributed geographically.

Google has been tracking flu trends for some time by analyzing people's choice of search terms. This method has been very successful and they can usually pick up trends a few weeks before the CDC data. Earlier this year a variety of workers from Google and one from the CDC published a paper in Nature describing their technique:
Detecting influenza epidemics using search engine query data.

Tuesday, September 1, 2009

National Geographic

In July 2007 National Geographic had an feature article about Malaria. This is available for free at their website and there's also a video, field notes from the writer and photographer and a gallery of the usual amazingly high quality National Geographic photographs.

Summer re-runs - part 7

One survey asked rural Africans what they would buy if they had the money. A bed net was sixth on the list. The first three items were a radio, a bicycle and, heartbreakingly, a plastic bucket.

Some Malaria postings that are well worth a read. I think everybody should read the articles in the first link. Much food for thought.
and, for fun, the Star Wars mosquito Defense System

Monday, August 31, 2009

DDT - or not...

'The U.S. and WHO encourage African countries to use DDT to fight the spread of malaria, but some Ugandans are protesting. The pesticide DDT, long banned in the United States, has made something of a comeback in Africa. DDT can be an effective weapon against malaria. The U.S. government, and the World Health Organization are encouraging African countries to use the insecticide, and say it is safe when handled properly. But in the East African nation of Uganda, DDT has provoked a fierce political battle. And the experience has taught a hard lesson: effective malaria control involves more than just fighting mosquitos.'

Read the rest of the story here on Public Radio International. It's interesting and maybe not what you expect.

Alex Fokkens is a Dutch organic cotton buyer. He's worried the spraying would mean he'd no longer be able to sell the cotton to his European customers, "If they find out there are any traces of DDT, it would be sent back, and it would be a very big claim on us."

So proponents of organic agriculture mounted a vocal campaign to thwart the government's DDT plan.

Wednesday, August 26, 2009

Summer re-runs - part 6

Some nosocomial infection and antibiotic resistance favorites:

Behind Ebola/Marburg

Chris forwarded this interesting trailer/promo for an as yet unmade documentary about Ebola and Marburg virus.

Tuesday, August 25, 2009

Summer re-runs - part 5

From the abundance of HIV posts here are a few favorites. I still don't know quite what I think about the ad above. Alarmist? Yes. Too alarmist? Maybe. Effective? Possibly.

Monday, August 24, 2009

Viral Chatter

Virus hunter Nathan Wolfe is outwitting the next pandemic by staying two steps ahead: discovering deadly new viruses where they first emerge -- passing from animals to humans among poor subsistence hunters in Africa -- before they claim millions of lives.

Check out Nathan Wolfe's talk at the TED conference earlier this year. TED (Technology, Entertainment, Design) invite some of the world's most fascinating thinkers and doers, and challenge them to give the talk of their lives (in 18 minutes). The best talks and performances are available on their website. You should all check out this talk, it is very interesting, very well presented and hugely relevant to this class.

Friday, August 21, 2009


Raw scores from the midterm. Two people scored the full 300. Most people were in the B to A range or close to it. Enjoy the weekend.

Thursday, August 20, 2009

Moldy Food: When to Use, When to Discard

Tired of having your food stolen by sticky-fingered coworkers or roommates? Bullies taking your kid's lunch? Well, worry no more . . . Anti-Theft Lunch Bags are sandwich bags that have green splotches printed on both sides, making your freshly prepared lunch look spoiled. Don't suffer the injustice of having your sandwich stolen again! Protect your lunch with Anti-Theft Lunch Bags.

Okay this is barely relevant but since it is a potential health issue (albeit not an infectious disease issue) I thought I'd mention that I just discovered that the USDA has a helpful chart on 'Moldy Food: When to Use, When to Discard'. Hmm, I rather wish I'd known this some decades ago....

Tuesday, August 18, 2009

When Zombies attack

A strange increase in Zombie related news lately. First, a number of news outlets have picked up on the publication of a paper entitled 'When zombies attack!: Mathematical Modelling of an Outbreak of Zombie Infection.' For example there's a BBC article entitled 'Science ponders 'zombie attack' and a CBC Canada artcile entitled 'Zombie attack would be the death of us'. Venturing into the blogosphere reveals some criticisms of the model eg here and here. The model, by the way, should look familiar to you since it's a pretty basic SIR model.

I like the fact one of the authors is named Professor Robert Smith? - the question mark is part of his surname and not a typographical mistake.

Also making headlines, in the LA Times at least is the success of 'Pride and Prejudice and Zombies', a surprise bestseller with '85% Austen's original text and 15% brand-new blood and guts'. I bumped into this in Goleta library the other day. I must admit the premise is amusing and the cover is excellent but I found the joke wearing a bit thin after a few pages. Maybe I'll wait for the sequel: Sense and Sensibility and Sea Monsters (no, really, that is the title of the next book).

Even Austen purists admit a grudging admiration for the "Zombies" concept.
"In publishing terms, it's brilliant," said Claire Harman, a Columbia University professor and author of "Jane's Fame: How Jane Austen Conquered the World."
"Why did I spend three years writing a critical book on Austen? Why didn't I just think of that?"

Mice Invasion

There's a longer version with an annoying voice-over ('Armies of frenzied wild rodents ran amok') but I think the silent version is enough.

Monday, August 17, 2009

Lyme disease cases rising

"The number of ticks is so much more than we've seen in the past," Arias said. "It could be the humidity; it could be the moisture; it could be some biological factor out there."

A number of states are reporting another increase in the number of new cases of Lyme disease. For example the increase in Virginia was reported in the Washington post last month, and cases are also on the increase in Minnesota and Maryland.

The picture shows a device that attracts deer to corn and then uses paint rollers to apply a pesticide that kills ticks. When they lean down to get the corn, the rollers on either side touch their heads and necks, applying the pesticide. Although invented and perfected by U.S. Department of Agriculture scientists to protect cattle from lone star ticks in the Southwest it has been adapted to help reduce the number of black-legged ticks on deer in Maryland.

Summer re-runs part 4

Some Lyme disease favorites:

Sunday, August 16, 2009

Tb trivia

I was listening to the radio today and hadn't realized that Cat Stevens had suffered from tuberculosis in 1968. Near death he spent months recuperating in hospital and a year recovering. During this time Stevens began to question aspects of his life, and spirituality which, eventually, led to his conversion to Islam.
"(t)o go from the show business environment and find you are in hospital, getting injections day in and day out, and people around you are dying, it certainly changes your perspective. I got down to thinking about myself. It seemed almost as if I had my eyes shut."

Friday, August 14, 2009

Plague Years

The Black Death, one of the deadliest pandemics in human history, occurred between about 1348 and 1351.

In the centuries following the Black Death there were several further devastating outbreaks of hemorrhagic plague, particularly in European Cities. I briefly mentioned one of these, the Great Plague of London, that occurred between 1665 and 1666, and killed an estimated 100,000 people - about 20% of London's population at the time. This was the last widespread outbreak in England.

Between the 1350's and the 1660's something had happened that greatly changed our ability to understand and interpret the past - the invention of the printing press in the 1400's and the appearance and spread of books.

So our record of the Great Plague of London is much better. Perhaps the most widely known book from the period is Daniel Defoe's 'A Journal of the plague year'. However this was probably written just prior to publication in 1722 and Defoe was only 5 years old in 1665. Other books were however written at the time, such as Loimologia, or, an historical Account of the Plague in London in 1665, With precautionary Directions against the like Contagion by Dr. Nathaniel Hodges (1629–1688).

Hodges investigated several possible cures for the plague and does not seem impressed by any, not even unicorn horn:

'The powder also of a Unicorn's horn, so much cried up for an antidote, never answered any good expectation, although I have several doses of it given me by a merchant, on purpose to try its virtues: but that which would cure pidgeons, fowls, cats and dogs, as the worthy Gentleman assured me that did, had yet no efficacy against the pestilential virulence.'

Thursday, August 13, 2009

The funny pages

I don't suppose many people read the comics in the paper anymore now that no-one is reading the newspaper. Some of them will probably continue with a healthy internet life but the fate of the interminable soap opera strips such Mary Worth or Apartment 3-G must be in doubt. One of the more bizarre soap opera strips was always 'Mark Trail' - combining outdoor folksy wisdom with a series of bizarre ongoing plots. One of the recent stories involved Sneaky, the adorable raccoon bandit.

Perhaps it was more than a coincidence that a recent Sunday nature strip set readers straight about raccoons and their rabid ways.

Wednesday, August 12, 2009

Panic in the Streets

There are a number of interesting disease movies (apart from zombie movies). I bumped into a reference to 'Panic in the streets' the other day and think I'll have to watch it again. It must be 30 years since I saw this on late night tv. Apparently the original title was 'Outbreak'

From Amazon's editorial review:

An amazingly effective film noir action movie, shot on location in New Orleans in 1950, that has twists of plot and explosions of violence that can still make audiences gasp. Elia Kazan, of all people, directed this story of a public health worker (Richard Widmark) and a police detective (Paul Douglas) who have only a few hours in which to capture some fleeing felons who may be infected with bubonic plague. The bad guys are played, with enormous relish, by Jack Palance and Zero Mostel, the latter only a few years before Kazan ratted him out to the House Un-American Activities Committee. In retrospect, this modest crime picture looks like a crucial turning point in the formation of Kazan's distinctive style, a clear precursor to the blistering location work of landmark films like On the Waterfront, Baby Doll, and America, America. --David Chute

From DVD verdict:

The trailer for Panic in the Streets promotes the film as an action/suspense thriller about preventing the spread of a nationwide biological epidemic. Reading between the lines, however, Panic in the Streets can be seen as an allegory about stopping the threat of Communism in the United States at the beginning of the Cold War.

and finally, from epinions.com

The Moral of the Story Is?

Cooperating with authorities is shown as not only a civic duty, but as necessary to self-preservation, though there are officials who are more concerned about keeping the public ignorant than about keeping it safe, and even this imperative is muddied by the movie's siding with the heroes keeping a newspaperman from reporting what is going on.

Summer re-runs part 3

Some Bubonic Plague favorites:

Tuesday, August 11, 2009

Plague outbreak in China

If you have been reading or watching the news lately you may have heard about an outbreak of the pneumonic form of Bubonic Plague in Ziketan, China.

The outbreak was first reported on August 1st, and the Chinese government has been much more open about this incident than previous diseases outbreaks (eg SARS).

The town of Ziketan, with more than 10,000 people was sealed off.

A spokeswoman for the World Health Organization, Vivian Tan, said an outbreak such as this was always a concern, but praised the Chinese for reacting quickly and for getting the situation under control.

Rapid action appears to have helped stop the outbreak in its tracks and there were only three deaths - possibly due to delayed treatment. Today there comes news that the source of the outbreak may have been a marmot. A dog that ate the plague infected marmot died and the first human victim was infected by fleas as he buried the dog.

Although this story is a good example of how rapid action can halt potential disease outbreaks there was a somewhat worrying story in the Times about how some taxi drivers have been earning a small fortune by sneaking residents around roadblocks and out of the cordoned off town.

Monday, August 10, 2009


Here's a quote I skipped in lecture for time. Nothing new, but it really brings home to me exactly how unpleasant the side effects from some second line Tuberculosis drugs are:

Nesri Padayatchi, deputy director of the Centre for the AIDS Programme of Research in South Africa, tells of 35 patients treated with a second-line drug that causes intense nausea. Eight of them, she says, "tried it and said, 'I would rather die.'"

Just a Bill

Although unanimously endorsed by public health and medical organizations, federal bills aimed at phasing out the non-therapeutic use of antibiotics in US food animal production have repeatedly failed to make it out of committee. The current version is still in committee - the 'Preservation of Antibiotics for Medical Treatment Act of 2009'.

Govtrack.us is a pretty neat site for tracking legislation. If you click on 'related legislation' you can see that legislation with the same title was introduced to the previous 3 Congress's but has never made it out of committee despite having bipartisan support (at least the sponsors include both Republicans and Democrats).

You can read the FDA's Statement before the House Committee on Rules on July 13th this year, here. A statement read into Congressional record by Rep. Jerry Moran (The expanding power of the federal government and its intrusion into America's business) gives some idea of why this Bill has trouble getting anywhere.

Other countries have, however, acted, the European Union banned the use of antibiotics as growth promotional agents in 2003.

Friday, August 7, 2009

Mmmmm Chocolate-covered bacon

Someone asked me at the start of the course once whether it was going to be a scary class. My answer was then, and is now, no. Of all the diseases we will cover I think only a single one merits being scared of (more of that in week 4 - and no it isn't AIDS or Ebola). The answer might be different if you lived in a poorer country of course....

But in the good old US of A infectious diseases are responsible for barely 5% of all deaths. If you compare that to other preventable deaths then it is dwarfed by smoking and poor diet/lack of exercise that each lead to over three times as many deaths as all infectious diseases combined in the US. The so called 'diseases of affluence'.

I'll talk about this more in the very final lecture but I was reminded of it today when I read in the news that the Wisconsin State Fair has introduced two new food items: Chocolate covered bacon, and deep fried peanut butter and jelly sandwiches.

So have a good weekend, drive/cycle/walk safely, maybe get some exercise and a nice salad......

Summer re-runs part 2

Some Tuberculosis favorites:

Thursday, August 6, 2009


'Given the variable protective efficacy provided by Mycobacterium bovis bacillus Calmette-Guérin (BCG), there is an urgent need to develop new vaccines against tuberculosis. '

The BCG vaccine was the first vaccine developed for Tuberculosis. Originally developed in 1921 it is still the only vaccine available.

With the recent increase in the prevalence of Tuberculosis there are now a number of possible new vaccines in development. Since commercial firms have shown little interest in developing such drugs support has largely come from private philanthropists. The Bill and Melinda Gates foundation have a strong commitment to Tuberculosis and recently gave a $200 million grant to the Aeras Global TB Vaccine Foundation, a non-profit Product Development Partnership dedicated to the development of effective TB vaccines.

There have also been some recent developments in improving the efficacy of the BCG vaccine. A paper in the Journal of Leukocyte Biology earlier this year described the use of interferon to boost the immune response produced by the BCG vaccine and led to some inevitable headlines 'New Discovery Gives Tuberculosis Vaccine A Shot In The Arm'

Wednesday, August 5, 2009

Crimean War Photographs

I mentioned that there were photographs of the Crimean War. These are in fact some of the earliest photographs of war and were taken by Roger Fenton in 1855 He was sent to the Crimea by Prince Albert in an attempt to alter public opposition to the war and was told before he departed for the frontline: "No dead bodies."

Conveniently, the Library of Congress has a set of 263 of the 360 photographs Fenton took and you can view these at their website. Fenton's photograph of the 'Valley of the Shadow of Death' is probably the most famous but if you scan through all the images one thing really strikes you - the amazing facial hair!

I looked it up and a mustache was compulsory in the British Army until 1916! Actually that's not strictly true - army regulations forbade the shaving of the upper lip which isn't quite the same as making mustaches compulsory even though the outcome is very similar!

Summer re-runs part 1

Because not everyone has the time and patience to wade through the three hundred posts already on the blog I thought I'd highlight some of the most relevant or interesting posts for each disease we cover. Here are some Cholera favorites:

Tuesday, August 4, 2009

Choose your own apocalypse

Slate online magazine has been having an entertaining series of articles on how America might end - 'a week long though experiment on the United States' demise.'

This is quite entertaining and one article contains an impressively thorough list of 144 possible scenarios - several of which are disease related.

They also have a 'Choose your own Apocalypse' interactive feature that lets you select your most likely scenarios. This is all (vaguely) relevant to class because once you pick your scenarios you get to see what the top apocalypse scenarios are. Antibiotic resistance - our next topic is one of the top picks. Of course this is all very unscientific and most people probably picked the entertaining options (my top pick was 'Robot Overlords') but there is some food for thought there. Nevertheless I think I'll tag this 'humor'.

Monday, August 3, 2009


Even for a topical subject there were a surprising number of disease stories in the news today.

Briefly the lead item on the CNN home page was a report on a PNAS paper abut the origin of Malaria:

Today scientists reported that they have discovered the origin of malaria, one of the deadliest diseases of humanity. Chimpanzees, native to equatorial Africa, have been identified as the original source of the parasite that likely moved from them to humans via mosquitoes.

Also in the news today was a story based on a Nature Medicine paper this week that describes a new strain of HIV:

These findings indicate that gorillas, in addition to chimpanzees, are likely sources of HIV. The discovery of this novel HIV lineage highlights the need to better monitor the emergence of new HIV variants, particularly in western central Africa from where existing HIV groups have originated.

Finally, the cholera outbreak in Zimbabwe I mentioned has finally been declared over:

Zimbabwe's Health Minister yesterday said a cholera epidemic has ended, after more than 4200 deaths and 100 000 cases since last August, but gave warning new outbreaks remain a threat.

"The nation experienced the worst cholera outbreak between August 2008 and June 2009, but the epidemic has successfully been contained and has ended," Health Minister Henry Madzorera said.

International aid organisations said the cholera epidemic was the worst to hit Africa in 15 years and gave warning the disease had now entrenched itself as endemic in Zimbabwe.

Wednesday, July 29, 2009

Summer 2009

Welcome to the blog for EEMB40 - the Ecology of Disease - for Summer 2009. It will also serve as a class website and you will find links to lectures etc. in a box at the top right imaginatively called 'links'. Lecture slides will be available shortly after each lecture. They are put there for your convenience (you don't need to scribble down details of a graph because you know it will be available later) but please note that they are not designed to be lecture notes. In fact in most cases my slides would make very poor notes! In order to help you take notes I have made a glossary for the class - also linked on the right. All the terminology you will be required to know is listed in the glossary.

You are all welcome, and encouraged to post here. To do that all you need to do is to send me an e-mail saying just that. I will then add your address and google will send you an invitation to be an author. Just follow the simple instructions and away you go.

Postings to the blog should be relevant to the class but the blog is specifically designed to be a place where you don't need to worry about how relevant your post is. (I give you 'Basket full of puppies' as an example). I will be posting lots of things that I read in the news or that I take out of lecture (for time purposes) but that some of you may find interesting. By putting it here you can look at it at your leisure and you know it won't be on the exam.

I try to post every day when the class is running and, where possible, the postings are relevant to the current topics we are covering in class. You can access older postings (there are 360 (!) of them from the three previous times I have taught this class) either by scrolling down the page and repeatedly hitting the 'Older posts' button at the bottom right or by using the 'Labels' (scroll down and they'll be on the right hand side) to pull up posts on particular topics.

Wednesday, April 29, 2009

Wednesday, March 18, 2009

Thank You

A big thank you to everyone who posted to the blog this quarter. It was a happening place with multiple posts most days. It's surprising how, even though we cover a lot of historical topics, the subjects we cover are in the news.
  • From the possibility of eradicating AIDS to Antibiotic resistance and MRSA.
  • From the Pope rejecting condoms to the President acting to prevent sick cows entering the cow foodstream.
  • From pathogens in our pork to bubonic plague in our ferrets.
  • From squirrel brains to zombie snails.
If you enjoyed the class please tell your friends (I don't get paid by the student, I just honestly believe people should know this stuff). The class will run each Winter quarter AND in summer session.

If you did not enjoy the class, or it wasn't what you expected, or you have suggestions for improvement then please let me know if you haven't already.

Good luck on your finals and have a safe spring break.


AIDS in South Africa

After graduating high school, my friend Melissa left for almost a year to South Africa, where she visited children and families, helped in hospitals, set up activities, distributed Adopt-A-Bears, and so much more. I knew she was blogging her experiences, so I asked her if she had any stories of encounters with AIDS that I could share on this blog. It really makes what we are learning in the classroom come alive.

"I met ThuThukani at our small camp for orphans and other vulnerable children from Burlington- a slum community in South Africa. Whenever I saw ThuThukani, he seemed to have just one look on his face; a look that said things like, “I don’t want to be here,” or “I hate my life.” He would often sit alone, silent, never uttering a word to anyone. Despite the calming efforts of teachers, other children, or my fellow teammates, ThuThukani was angry and aggressive. If the other children were coloring, he would refuse to color until people stopped asking him to. Then, as soon as the adult left him to himself, he would slowly reach for a crayon and begin softly scribbling onto a sheet of paper. He was quiet. He was defiant. But he was constant. Anyone could tell just by looking at him that he had his own way of doing things. But what anyone observing him could not tell just by looking was that ThuThukani was dying of stage four AIDS.

In Africa, no one is too shy to term this “full-blown.” His immune system was next to nothing, and he was only twelve years old. Suddenly, all in the split second of hearing these words, ThuThukani made complete sense to me. I found myself understanding his blank stares into space while trying to look him straight in the eye and rebuke his behavior. I understood his refusal to do as he was told. Because he just didn’t see the point. At a young age, ThuThukani had to come to terms with the fact that his life would be short. A virus which was given to him during childbirth would bring the end to his life, almost before it had even begun. In his silence, defiance, and in that little face of his, he had to understand all of this. And so, I learned to understand ThuThukani.

I could not wrap my mind around AIDS ripping apart Africa. But as much as I could not understand, what I could understand was this boy. I could see his pain and frustration. Putting a face to those grim four letters, AIDS, made it all too personal to me."

Tuesday, March 17, 2009

Pope claims condoms could make African Aids crisis worse

The pontiff said condoms were not the answer to the continent's fight against HIV and Aids and could make the problem worse.

While in Africa, the pontiff is expected to talk to young people about the Aids epidemic and explain to them why the Catholic Church recommends sexual abstinence as the best way to prevent the spread of the disease.

The Pope is entitled to his opinion on the ethics of condom use however I do not believe he is entitled to make inaccurate statements about the efficacy of abstinence programs versus condom use. Since I don't believe the Pope is likely to read this I'm not going to go to go into too much detail but you may remember this study from a couple of years back:

Sex abstinence programmes do not stop risky sexual behaviour or help in the prevention of unwanted pregnancy, a research team has concluded. The Oxford University team reviewed 13 US trials involving over 15,000 people aged 10 to 21. They found abstinence programmes had no negative or positive impact on the rates of sex infections or unprotected sex, the British Medical Journal said.

Is Life a Sexually Transmitted Disease?

I got into a debate with a friend involving life as a sexually transmitted disease. According to MedTerms (www.medterms.com), a sexually transmitted infection is “an infection that can be transferred from one person to another through sexual contact. In this context, sexual contact is more than just sexual intercourse (vaginal and anal) and also includes kissing, oral-genital contact, and the use of sexual "toys," such as vibrators.” I argued that human life is not “transferred from one person to another” but rather created via fertilization. I also pointed out that there are several organisms (life forms) are asexual and do not sexually reproduce. It was an interesting topic and varies depending on everyone’s definition of life and disease.

Anyway, I thought this shirt was hilarious, even though I do not agree with it.

Monday, March 16, 2009

Prion Trio

Three prion related research stories that have come out lately:

1/ Regulation of Embryonic Cell Adhesion by the Prion Protein in PLoS Biology this week.

Researchers in Germany have shown that the regular Prion protein (the one everyone has, that isn't infectious and doesn't cause problems) plays a beneficial role for the organism by helping cells communicate with one another during embryonic development. Even though we have known that a normal prion protein in the brain can turn harmful and cause deadly illnesses like Creutzfeldt-Jakob disease (CJD) in humans, and bovine spongiform encephalopathy (BSE) in cattle we did not, until this paper, know why large amounts of this normal protein are produced by our bodies in the first place.

2/ Cellular prion protein mediates impairment of synaptic plasticity by amyloid-beta oligomers in Nature a couple of weeks ago.

The regular prion protein may contribute to nerve damage if it becomes entangled with a protein fragment that scientists consider a chief suspect as a cause for Alzheimer's disease. The prion protein, if it is involved in Alzheimer's, is probably in its normal form. There's no evidence that the disease somehow releases infectious prions.

3/ Safety and efficacy of quinacrine in human prion disease (PRION-1 study): a patient preference trial in the April issue of Lancet Neurology.

The anti-malaria drug quinacrine does not appear to extend the lives of people with the human form of mad cow disease, despite encouraging results from experiments with mice. Currently there are no drugs that prevent or reverse the disease, though quinacrine has shown promise in treating prion-infected mouse cells because it can penetrate the blood-brain barrier and the drug has been effective in treating these prion-infected mouse cells by blocking the conversion of normal proteins into the abnormal disease-causing form.

Answers to quiz 4

1. The parasite that causes malaria, Plasmodium falciparum, is most closely related to Toxoplasma gondii. Both parasites are eukaryotes, whereas Vibrio cholerae is a bacterium (prokaryote) and H5N1 influenza is a virus (non-living).

2. a. The definitive host of the malaria parasite is the mosquito.
b. The vector of the malaria parasite is also the mosquito.

3. Smallpox elimination was possible because: there are no asymptomatic carriers; the infectious period is short, and the patient is not very contagious before the rash develops; recovery leads to total immunity; there is no animal reservoir; symptoms are easily recognizable; and the vaccine is easy to transport and distribute, inexpensive, and highly effective. (You needed to name any two of these reasons.)

4. a. Viral reassortment occurs when viruses from two separate strains infect a single cell, where they exchange genetic information and create a new, hybrid viral strain.

b. Reassortment of human and bird flu strains is likely to occur in pigs.

Sunday, March 15, 2009

AIDS rate soars in nation's capital

Although, as I posted earlier, it is possible that the AIDS epidemic could be brought under control, this is not in fact the case in the US. In fact in some areas the situation is getting much worse.

Reports hitting the press today, based on a report being released tomorrow, suggest that at least 3 percent of the District of Columbia's residents have AIDS, a total that far surpasses the 1 percent threshold that constitutes a "generalized and severe" epidemic.

"Our rates are higher than West Africa," said Shannon Hader, director of the district's HIV/AIDS Administration who once led the Federal CDC's work in Zimbabwe.

'(A)lmost 30 years since the epidemic broke out in the United States, there's still a very real stigma attached to the disease.

Health officials in Washington say that stigma keeps people from getting tested, so the actual rates of HIV-AIDS in the nation's capital is probably much higher.'

Saturday, March 14, 2009

More Pork

Nicholas Kristoff continues the Pork/MRSA story in another Op-Ed piece for the New York Times today entitled 'Pathogens in our Pork'.

“We don’t give antibiotics to healthy humans,” said Robert Martin, who led a Pew Commission on industrial farming that examined antibiotic use. “So why give them to healthy animals just so we can keep them in crowded and unsanitary conditions?”

The answer is simple: politics.

Legislation to ban the nontherapeutic use of antibiotics in agriculture has always been blocked by agribusiness interests. Louise Slaughter of New York, who is the sole microbiologist in the House of Representatives, said she planned to reintroduce the legislation this coming week.

“We’re losing the ability to treat humans,” she said. “We have misused one of the best scientific products we’ve had.”

Antibodies Offer a New Path for Fighting Flu

Researchers from Harvard Medical School, the CDC, and the BuAdd Videornham Institute for Medical Research have engineered antibodies that protect against many strains of the influenza virus, including even the 1918 Spanish flu and the H5N1 bird flu, which could potentially lead to the development of a flu vaccine that would not have to be changed yearly. And, the antibodies already developed could be injected as an effective treatment, unlike drugs such as Tamiflu. Researchers estimate that the necessary clinical trials to prove that the antibodies are safe in humans could begin within three years. The researchers have the support of the National Institute of Allergy and Infectious Diseases, where they have been offered grants and access to its ferrets, which can catch human flu.


Agriculture Department Seals Cow Loopholes

Obama closed a loophole in the public health system to make it permanently illegal to slaughter 'downer' cows. These cows are too sick and weak to take care of themselves. Slaughterhouses could use these cows in the food supply for other cows as long as they collapsed after inspection of a non-neurological injury. Downer cows also have a higher chance of having BSE and they lounge in feces which makes E. coli poisoning a risk as well.


Friday, March 13, 2009

Global Warming and Disease

As we touched on in class, here are some issues concerning infectious disease and global warming:

  1. As Prof. Latto stated in lecture, insects (mosquitoes and ticks) are greatly affected by temperature. Therefore, as the temperature increases in high altitude and lower temperature areas, new epidemics of malaria may be seen in places never before affected due to the environmental changes.

  2. The flu season could be lengthen. As of now, tropical areas experience year-round influenza. As heat and tropical weather expands from the equator, more regions of the world may be susceptible to year-round influenza.]

  3. Risk to water supply. As natural catastrophes (typhoons, hurricanes, and other extreme weather) become more common and devastating, infrastructure gets damaged. With inadequate water supply and sanitation systems after extreme storms, the chances of an infectious disease spreading, such as cholera, increase greatly.

  4. Global warming will affect agriculture. With droughts and extreme weather, farmers will not be able to grow enough food to support themselves. Thus, they may move to the cities, creating a more dense cities for diseases to invade, especially in third world countries.

A lion in the village

The Cholera outbreak in Africa may finally have peaked:

The number of people dying and infected with cholera in Zimbabwe decreased for the second consecutive week, the United Nations said Wednesday.

The death toll in Zimbabwe has topped 4,000 with more than 89,000 cases since the outbreak of the waterborne disease in August. Its spread is blamed on the collapse of Zimbabwe's water and health infrastructure.


The outbreak in Zimbabwe has put strain on health infrastructure in neighboring countries.

Cholera has doubled to 12,000 cases in South Africa, with the situation along the Zimbabwean border being of particular concern, according to the U.N report. Cholera cases have also almost doubled in Namibia and Zambia.

This week's New England Journal of Medicine contains an article by CDC′s Dr. Eric Mintz, leader of the Diarrheal Diseases Epidemiology Team in the Enteric Diseases Epidemiology Branch:
A Lion in Our Village — The Unconscionable Tragedy of Cholera in Africa that details the burden of cholera in Zimbabwe and other surrounding African countries in the past year.

Unlike the severe acute respiratory syndrome, avian influenza, and other infectious-disease threats that have emerged recently, cholera is easily avoided and easily treated. The failure of the global community to mobilize the resources needed to prevent and to treat cholera among the less fortunate reflects our lack of commitment to equity and social justice. Improving access to safe drinking water, adequate sanitation, and basic health services are among the core Millennium Development Goals agreed to by all United Nations member states.

Epidemic cholera represents a fundamental failure of governance, and bold and visionary leadership is required if we are to attack its root causes. Such leadership has been demonstrated in other contexts in Africa. For example, President Yoweri Museveni of Uganda began to change public attitudes toward the human immunodeficiency virus and succeeded in reducing the rates of AIDS in his country, in part by recharacterizing the disease as similar to any other threat to the community: "When a lion comes into your village," he said, "you must raise the alarm loudly."

It is time to sound the alarm again. Whereas reported case fatality rates for cholera in the rest of the world are now well below 1%, rates in excess of 5% are still commonly reported in many African countries.

Thursday, March 12, 2009

Donald Duck Gets Bird Flu

Always thought this was a funny picture - No Donald Ducks were harmed in the making of this image :)

What does a trillion dollars look like?

Whatever the future brings in terms of the US economy I predict that the last few months will have changed the way that we look at very large sums of money. The speed, and apparent ease, with which the government has come up with sums of two hundred billion dollars, seven hundred billion dollars etc because we cannot afford to let the banks/the auto industry/name your industry fail is going to leave people with the idea that these sums of money can be found if the situation is dire enough.

So millions of people die of dysentery/malaria/AIDS/measles/tuberculosis, not because the sums required to help them are too large but because we choose not to help them. That is a fact we always knew but it is going to become increasingly hard to ignore. I'm hardly being original in this observation, I've seen several people make similar comments already and I predict more to come.

Check out this wonderfully simple post if you have ever wondered What does one TRILLION dollars look like? The Federal Government currently raises a little over one trillion dollars in individual income taxes each and every year.

MRSA spread from pigs?

An article in the New York Times today suggests a link between MRSA and pig farming or pork. A doctor in Camden, Indiana, a small town surrounded by hog farms, found a startling number of MRSA cases, and made the link between the hog farms and the infections. He was ready to go public with the insinuations when--he died, at age 54, of a heart attack presumably (though no autopsy was done). Five years ago, some MRSA cases were linked to pig farming in the Netherlands, where a farming family became infected, as well as 8 of 10 of their pigs. In a study of American hog farmers, 45% were infected with MRSA. The article suggests that the antibiotic resistant infection likely developed in pigs due to prophylactic use of antibiotics in animal feed.

Cook your meat thoroughly, and wash your hands after dealing with raw meat!

Wednesday, March 11, 2009

The Economic Impact of Influenza

Influenza produces direct costs due to lost productivity and associated medical treatment, as well as indirect costs of preventative measures. In the United States, influenza is responsible for a total cost of over $10 billion per year, while it has been estimated that a future pandemic could cause hundreds of billions of dollars in direct and indirect costs. However, the economic impacts of past pandemics have not been intensively studied, and some authors have suggested that the Spanish influenza actually had a positive long-term effect on per-capita income growth, despite a large reduction in the working population and severe short-term depressive effects. Other studies have attempted to predict the costs of a pandemic as serious as the 1918 Spanish flu on the U.S. economy, where 30% of all workers became ill, and 2.5% were killed. A 30% sickness rate and a three-week length of illness would decrease the gross domestic product by 5%. Additional costs would come from medical treatment of 18 million to 45 million people, and total economic costs would be approximately $700 billion.
Preventative costs are also high. Governments worldwide have spent billions of U.S. dollars preparing and planning for a potential H5N1 avian influenza pandemic, with costs associated with purchasing drugs and vaccines as well as developing disaster drills and strategies for improved border controls. On 1 November 2005, United States President George W. Bush unveiled the National Strategy to Safeguard Against the Danger of Pandemic Influenza backed by a request to Congress for $7.1 billion to begin implementing the plan. Internationally, on 18 January 2006, donor nations pledged US$2 billion to combat bird flu at the two-day International Pledging Conference on Avian and Human Influenza held in China.
As of 2006, over ten billion dollars have been spent, and over two hundred million birds have been killed to try to contain H5N1 avian influenza. However, as these efforts have been largely ineffective at controlling the spread of the virus, other approaches are being tried: for example, the Vietnamese government in 2005 adopted a combination of mass poultry vaccination, disinfecting, culling, information campaigns and bans on live poultry in cities. As a result of such measures, the cost of poultry farming has increased, while the cost to consumers has gone down due to demand for poultry falling below supply. This has resulted in devastating losses for many farmers. Poor poultry farmers cannot afford mandated measures which isolate their bird livestock from contact with wild birds (among other measures), thus risking losing their livelihood altogether. Multinational poultry farming is increasingly becoming unprofitable as H5N1 avian influenza becomes endemic in wild birds worldwide. Financial ruin for poor poultry farmers, which can be as severe as threatening starvation, has caused some to commit suicide and many others to stop cooperating with efforts to deal with this virus—further increasing the human toll, the spread of the disease, and the chances of a pandemic mutation.

Quarantine for pandemic influenza

BMC Infectious Disease is an open access journal publishing research articles in all aspects of the prevention, diagnosis and management of infectious and sexually transmitted diseases in humans.

A question was asked today about whether quarantine would be effective in controlling pandemic influenza and a paper in the current issue, Quarantine for pandemic influenza control at the borders of small island nations, addresses how long a quarantine period would be necessary. They address small island nations because these are the nations most likely to be able to establish quarantine with almost all international arrivals being concentrated at one or a small number of airports.

Quarantine at the borders of island nations could contribute substantially to preventing the arrival of pandemic influenza (or at least delaying the arrival date). For small island nations we recommend consideration of quarantine alone for 9 days or quarantine for 6 days combined with using rapid diagnostic testing (if available).

Tuesday, March 10, 2009

1918 Influenza Pandemic

It's alright to learn about historical events from lecture, text books, etc, but sometimes I feel like it's more interesting to learn about it from people who lived through it. While I don't know anyone personally who lived through the Influenza Pandemic of 1918 (they'd have to be in their 90s at least!), I found a letter written by a physician who worked with soldiers in Massachusetts. He talks about the conditions in the "wards"...

The normal number of resident Drs. here is about 25 and that has been increased to over 250... We have lost an outrageous number of Nurses and Drs., and the little town of Ayer is a sight. It takes Special trains to carry away the dead. For several days there were no coffins and the bodies piled up something fierce, we used to go down to the morgue (which is just back of my ward) and look at the boys laid out in long rows...

Each man here gets a ward with about 150 beds, (Mine has 168)... I have only four day nurses and five night nurses (female) a ward-master, and four orderlies.

He also talks about the symptoms they see when they treat the infected soldiers.

These men start with what appears to be an ordinary attack of LaGrippe or Influenza, and when brought to the Hosp. they very rapidly develop the most viscous type of Pneumonia that has ever been seen... It is only a matter of a few hours then until death comes, and it is simply a struggle for air until they suffocate

2008/2009 Influenza

If you got a flu shot this year in the United States you got vaccinated against the following three strains:

  • A/Brisbane/59/2007(H1N1)-like virus
  • A/Brisbane/10/2007 (H3N2)-like virus
  • B/Florida/4/2006-like virus
Currently the H1N1 strain is the most prevalent in the US and so the vaccine should give good protection. However the current strain of H1N1 is increasingly resistant to Oseltamivir, sold in the US as Tamiflu. The most recent data suggests 96.5% of H1N1 samples tested were resistant causing the CDC to issue a health advisory notice.

Recommendations are already being made for the 2009/2010 vaccine:

WHO has recommended vaccine strains for the 2009-10 Northern Hemisphere trivalent influenza vaccine, and FDA has made the same recommendations for the U.S. influenza vaccine. Both agencies recommend that the vaccine contain A/Brisbane/59/2007-like (H1N1), A/Brisbane/10/2007-like (H3N2), and B/Brisbane/60/2008-like (B/Victoria lineage) viruses. Only the influenza B component has been changed from the 2008-09 vaccine formulation. This recommendation was based on surveillance data related to epidemiology and antigenic characteristics, serological responses to 2008-09 vaccines, and the availability of candidate strains and reagents.

Monday, March 9, 2009

Final Review and Glossary

I added Erin's Final exam review sheet. I made a few very small changes to the glossary (deleted two terms and added one). The changes are listed at the end.

The end of AIDS?

Today we talked about vaccines. Although a vaccine allows us to establish herd immunity to eliminate a disease this is not our only mechanism for disease eradication. If a disease does not have an animal reservoir and only infects humans then we could, theoretically, eradicate it by preventing all transmission. We can do this by altering human behavior (see for example Guinea Worm) or by treating patients so they are no longer infectious.

Efforts to control the spread of AIDS have generally focused on altering human behavior to reduce transmission (eg practicing safe sex, providing clean needles etc). This has had success in some communities and at some times but has never been sufficient to even consider talk of elimination or eradication.

However the latest anti-retroviral drugs are so effective at reducing viral load that those patients on them are effectively no longer contagious. So if everyone with HIV were on therapy, there would be little or no transmission. This raises the fascinating possibility that with a concerted effort we could turn the tide and talk about eliminating, or at least controlling AIDS. For further discussion see the article Are we about to eliminate AIDS? in New Scientist magazine a few weeks ago. Just a couple of excerpts:

It's a simple idea, but the obstacles to implementing it worldwide are enormous. Persuading everyone with HIV to start therapy purely for public health reasons could be ethically dubious. To identify everyone who is HIV positive would require such widespread testing that some may feel it breached their civil liberties. Then there is the question of who would fund such a massive undertaking.
In 1985, when HIV testing began, no treatment for the virus existed, so a positive result was effectively a death sentence. Fear of the virus and the fact that it spread most easily among gay men and intravenous drug users meant people with HIV were shunned, as well as being barred from taking out health and life insurance. The decision to have the test was generally an agonising one and many decided it was better not to know.
What is certain is that, however and wherever it is attempted, such a scheme will be controversial. Hard-line religious groups that view AIDS as divine retribution are unlikely to help out. Some liberals, on the other hand, might resist the idea of mass testing. "Should we try a social intervention which infringes on people's civil liberties?" asks Conant. "AIDS infringes upon people too. If we're going to stop this epidemic, this is a responsibility that society has to shoulder."

and from the accompanying editorial:

Bankrolling such a long-term programme would cost serious money - initially around $3.5 billion a year in South Africa alone, rising to $85 billion in total. Huge as it sounds, however, it is peanuts compared with the estimated $1.9 trillion cost of the Iraq war, or the $700 billion spent in one go propping up the US banking sector. It also looks small beer compared with the costs of carrying on as usual, which the WHO says can only lead to spiralling cases and costs.

"Sex Positive"

This is a documentary opening March 20th about America's reaction to AIDS in the 1980's with regard to the gay community. It follows the story of activists who preached safe sex early on.

Sunday, March 8, 2009

Dr. William Foege and Smallpox

One of the key doctors that contributed to the eradication of smallpox in 1979 was Dr. William Foege, a medical missionary. In 1966, Foege was involved in a certain incident in eastern Nigeria in which there was not enough vaccine shipped in time to inoculate the entire region. After verifying that an isolated village did in fact have a few cases of smallpox, Foege realized that they would have to use a different strategy involving military tactics. They created a network of medical missionaries in an effort to establish surveillance across the region. With this intelligence, they were able to contain the disease by following the people connected to the known infected. Foege’s “surveillance/containment” strategy only vaccinated less than fifty percent of the population rather than the expected eighty to one hundred percent. However, Foege’s strategy was not immediately accepted by the CDC. Many doctors remained skeptical, including Donald Hopkins, who tried the strategy in Sierra Leone. Hopkins was able to eliminate smallpox from the disease-rich region by inoculating less than seventy percent of the population. With Foege’s help, the WHO declared smallpox eliminated from the world. Foege has worked in many sectors of public health, including the Carter Center, which aims to eradicate Guinea worm.

Details can be found here:

Won't somebody think of the ferrets?

Of relevance to both last week and next week is news this week that scientists in Hong Kong and the United States have developed an experimental H5N1 bird flu vaccine for people by inserting five key components of the H5N1 virus into the smallpox vaccine. Why smallpox?

The smallpox vaccine is very cheap, has a long shelf-life of several years and does not require highly sophisticated laboratories, making it easier for poorer countries to produce.

"Smallpox production capacity has gone down but many countries have the technology and the expertise to do it, and if necessary, it can be very quickly scaled up."
"But for other strategies (of producing H5N1 vaccines), it is not possible to rapidly set up manufacturing plants all over the world as they require very specialised plants."

However, it will take at least a few more years before the vaccine would be ready for the market. It must be tested next in ferrets, then monkeys, before human clinical trials can be carried out.