Welcome

Welcome to the blog for EEMB40 - the Ecology of Disease - for Winter 2011. 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 over 570 of them from the six 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.

Posts to the blog will be made by myself, by Erin (and possibly past TA's who do drop in occasionally), and by students in the L&S honors program. If you are not an honors student and would like to post here just send me your e-mail and I'll send you an invite.

Everyone is welcome to post comments on any posts and you don't need to be signed up to do that. If you try and add a comment on a post it will look like you need to be signed up because that's the default option but you can change it to anonymous if you wish. You will have to prove you're not a robot though. Also, because I have made commenting open to anyone it means we sometimes get hit by spam. For that reason I have comment moderation turned on. Comments will not appear immediately and will need to be moderated but unless you are trying to sell viagra or promote your nude celebrity website I'm not really vetting comments for content. 

Where's George?

Some of you might already be familiar with Google's flu trends which uses search terms to track the prevalence of flu. Although this might seem like a crude tool it is actually surprisingly accurate and gets the data much faster than the CDC does because it has such a huge volume of data to mine.

The video above shows the results from the project by Northwestern University grad students that uses data from the Where’s George? website that tracks the movement of U.S. paper currency. Again, this surprisingly crude tool is able to amass so much data (they have over 200 million bills in their system!) it has revealed valuable lessons about the movement of people and therefore for the way that diseases like flu might spread. There was an article in the New York Times about the project last year.

AIDS: the view from Africa

I thought this article from the Zambian Watchdog was an interesting perspective on AIDS in Africa: HIV/AIDS in Zambia: A Three Decade Burden.

Here is an excerpt. One in eight Zambians is now infected with the virus. Something needs to be done, but what?

There must be a total re-think of Public health policy in Zambia. We have spent millions of dollars ‘mopping’ the flooded floor while the causative leaking tap is running!

Here are a few suggestions:

1. HIV/AIDS must be declared a national disaster. I am glad that this was in the Patriotic Front Manifesto (2006). It is more than a partisan issue. We need the help of cooperating partners to deal with this, yes, but also ALL politicians and the highest office of the land must be directly involved. Awareness campaigns must extend beyond highlighting HIV infection alone, but other viral infections as well. This is why the issue of condoms is crucial.
2. Testing. When there was no treatment available, it was quiet right to be as discreet and confidential as possible while dealing with this pandemic. But now, the life saving drugs that are available, not only prolong life, but also reduce the risk of spread of infection. All gloves are off. Treatment centres can deal with the problem of confidentiality by using numbers alone for identification. These test results must be fed into a central database so that the exact extent of the problem can be known.
3. Treatment as a form of Prevention. It has been shown mathematically that treating every HIV positive person can lead to no new infections within ten years. If hospital staff were able to test universally, they could be able to commence treatment of patients, and if one million Zambians were on treatment it will go a long way in reversing our fortunes.

Review 2

Again we haven't quite covered all this material yet but:

What's the difference between:

• A dead end host and a definitive host?
• Reassortment and transformation
• An antibiotic and an antibody?
• A vector and a vaccine?
• A viral swarm and a cytokine storm?
• Antigen shift and antigen drift?

For best value try explaining these to someone else.

Review

We still have to cover influenza but some of you may find this useful for review:

Consider the following thirteen diseases, all of which we discussed, although some of them only briefly.

1. AIDS
2. Bubonic plague
3. Lyme disease
4. Cholera
5. Ebola hemorrhagic fever
6. Hantavirus cardiopulmonary syndrome
7. Measles
8. Marburg hemorrhagic fever
9. Tuberculosis
10. Malaria
11. Polio
12. Influenza
13. Yellow fever

• Four of these disease have vectors. Which are they and what are the vectors?
• Three of these diseases have rodent reservoirs. Which are they?
• Which three of these diseases have exhibited a series of truly global pandemics?
• Which of these disease are essentially incurable? What do these incurable diseases have in common?
• Which of these diseases is caused by neither a bacteria nor a virus? What is it caused by?
• Which two of these disease are transmitted by the fecal-oral route?
• Which two of these diseases are a particular problem to immunocompromised people? Why?
• Which of these disease can be vertically transmitted?
  

Extra credit

Write an Op-Ed piece as if for a major newspaper on an issue related to the course that you feel strongly about. You do not have to agree with any opinions I may have voiced - you are, for example, welcome to argue that an individual's right to decide on their own healthcare outweighs the states desire to vaccinate people even if it costs lives.

Aim for about 500 words - long enough to say something, short enough that it doesn't turn into an essay.

A maximum of 5 points are available.

You can either give me a paper copy or e-mail it to me anytime before the end of the final day of class (Wednesday 28th July).

For some advice on writing Op-Ed pieces try:

• Op-Ed Articles: How to Write and Place Them
• Writing Op Eds and Letters to the Editor
• Tips for Op-Ed Writing

By the way the Op-Ed section is often the most widely read section in the whole newspaper and you can submit your writing to a great many newspapers. Actual submission is not required for this assignment but it's a great way to get into print, get some exposure and get a cool addition to your resume.

Iron Lung

Although Radiohead used the Iron Lung as a metaphor for how something can both keep you alive and be highly restrictive I'm not sure how many people today have heard of them or are aware of just how widespread they once were (I mean Iron lungs, not Radiohead). Fortunately the Iron Lung exhibit at the University of Virginia will tell you virtually everything you need to know. Don't miss the designs to build your own!

The demise of the iron lung is due to both the decline of polio and also the use positive pressure ventilation using endotracheal tubes.

Although the iron lung now appears almost medieval in appearance it is important to note that for long term use (that polio patients with paralysis would require) the iron lung leaves you able to talk, eat and drink normally which is not the case with tracheal intubation. (Not to mention that intubation is an invasive procedure with associated risks of nosocomial infection).

Healthcare on This American Life

Also from Chris here are two episodes of the This American Life radio show that deal with healthcare in America. The links take you directly to the streaming audio of the complete shows.

More is Less
An hour explaining the American health care system, specifically, why it is that costs keep rising. One story looks at the doctors, one at the patients and one at the insurance industry.

Someone Else's Money
This week, we bring you a deeper look inside the health insurance industry. The dark side of prescription drug coupons.

(If you've never explored the TAL archive before then you are in for a treat with over 400 shows, all available for free. They range from the tragic to the hilarious and a good starting point is the 'Favorites' section. My personal favorites are the ever popular Squirrel Cop segment and Scott Carrier's story of Running after Antelope.)

He not busy being born is busy dying

Chris sent me a link to this movie, The Business of Being Born, that is very relevant to our discussion today. The website contains a trailer and some interesting information in the Press Notes. Looks like you can get it from Netflix.

Among 33 industrialized nations, the United States is tied with Hungary, Malta, Poland and Slovakia with a death rate of nearly 5 per 1,000 babies, according to a new report from Save the Children (April 2006). This is the second worst newborn death rate in the developed world. The five countries with the lowest infant mortality rates in the March of Dimes report -- Japan, Singapore, Sweden, Finland and Norway – midwives were used as their main source of care for 70 percent of the birthing mothers. Cesarean section is the most commonly performed surgery in the US, at a cost of $14 billion per year. Cesarean-delivery rates are now at an all time high in the United States, standing at 1.2 million, or 29.1 percent of live births in 2004. The increase represents a 40 percent increase in the past 10 years. (In 1970 the rate was 5.5%). A new report by the World Health Organization, published in the international medical journal, Lancet, identifies complications from cesarean surgery and anesthesia as the leading causes of maternal death in developed countries, including the United States.

Disappearing needles

There's a fun set of articles in this month's Wired magazine about what happened to the future that we were dreaming of 30, 40 or 50 years ago. You can probably imagine it: where's my jetpack? where's my robot helper? and why isn't my food in pill form? It doesn't seem to be on the Wired website yet but I'm sure it will be.

However the thing about the future is that we generally try to imagine it in terms of today's technology. The real smart folks are the ones who take the latest cutting edge technology and think 'what could I use this for?'

The following press release from Georgia Tech on a paper out in Nature Medicine this week made me think of this.

Disappearing Needles: Vaccine-Delivery Patch with Dissolving Microneedles Eliminates “Sharps” Waste and Improves Protection

A new vaccine-delivery patch based on hundreds of microscopic needles that dissolve into the skin could allow persons without medical training to painlessly administer vaccines – while providing improved immunization against diseases such as influenza.

Patches containing micron-scale needles that carry vaccine with them as they dissolve into the skin could simplify immunization programs by eliminating the use of hypodermic needles – and their “sharps” disposal and re-use concerns. Applied easily to the skin, the microneedle patches could allow self-administration of vaccine during pandemics and simplify large-scale immunization programs in developing nations.

Malaria-proof mosquito engineered

Researchers engineer malaria-proof mosquitoes.
July 17, 2010. Los Angeles Times

Malaria kills nearly 1 million people a year, but it has a weakness — to infect humans, it needs mosquitoes. In a potential step toward eradicating the disease, researchers report that they have developed a genetically engineered breed of mosquito that cannot be infected by the malaria-causing parasite.

Genetically-modified mosquitoes are far from ready for use in the field, but the researchers achieved an unprecedented 100% blockage of the Plasmodium parasite, highlighting the promise of this approach, according to their study.

The actual research paper is in PLoS Pathogens: Activation of Akt Signaling Reduces the Prevalence and Intensity of Malaria Parasite Infection and Lifespan in Anopheles stephensi
Mosquitoes

More new HIV research

An important paper in the Lancet today looks like it will change the way that HIV is treated. The paper, Death rates in HIV-positive antiretroviral-naive patients with CD4 count greater than 350 cells per μL in Europe and North America: a pooled cohort observational study
is reported on by the LA Times:
HIV can be deadly even before CD4 counts fall

An infection by the virus that causes AIDS can increase risk of premature death even before the immune system has deteriorated to the point where most physicians begin antiviral therapy, British researchers reported Thursday. The finding suggests that treatment should start even earlier than it is now and supports the current plans of world bodies to begin treating HIV infections in the developing world earlier.

The most common marker of an HIV infection is the level of an immune cell called CD4 that is the target of the virus. In a healthy individual, CD4 levels are generally over 500 cells per cubic millimeter and can go as high as 1,500. A level below 200 sharply increases the risk of the infections and other illnesses that are the markers for full-blown AIDS. Most physicians in the industrial world now begin treatment when a patient's CD4 levels fall below 350. In the developing world — at least in part because of the shortage of resources — treatment has generally begun when the level falls to 200, but UNAIDS announced last week that it would now begin treatment at 350.

Shot

Knowing a little bit more about HIV/AIDS how do you feel about the information you were provided with as teenagers? The advert above comes dangerously close to scare mongering. The risk of a single act of unprotected sex is absolutely NOTHING like the risk of Russian roulette in terms of magnitude. However is that an acceptable exaggeration in order to make the point? Does the ad work? I'm actually not sure this MTV ad was used in the US. A previous YouTube posting suggested it was used in Portugal but that seems strange given the text is in English and the car number plate at the start looks British.

MTV ads that were on in the US include the FurTV ads (eg 'What is unsafe sex?'). These take a very different approach and use humor to get their point across. Is this better?

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 last 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. 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.

HIV news

Here are links to the original articles and some press reports on some of the recent research I mentioned in class, all from 2009:

A new human immunodeficiency virus derived from gorillas.
We have identified a new human immunodeficiency virus in a Cameroonian woman. It is closely related to gorilla simian immunodeficiency virus (SIVgor) and shows no evidence of recombination with other HIV-1 lineages. This new virus seems to be the prototype of a new HIV-1 lineage that is distinct from HIV-1 groups M, N and O. We propose to designate it HIV-1 group P.
Reported on CNN: Researchers identify new strain of HIV derived from gorillas

Long-Term Control of HIV by CCR5 Delta32/Delta32 Stem-Cell Transplantation
Infection with the human immunodeficiency virus type 1 (HIV-1) requires the presence of a CD4 receptor and a chemokine receptor, principally chemokine receptor 5 (CCR5). Homozygosity for a 32-bp deletion in the CCR5 allele provides resistance against HIV-1 acquisition. We transplanted stem cells from a donor who was homozygous for CCR5 delta32 in a patient with acute myeloid leukemia and HIV-1 infection. The patient remained without viral rebound 20 months after transplantation and discontinuation of antiretroviral therapy. This outcome demonstrates the critical role CCR5 plays in maintaining HIV-1 infection.
Reported in Time: Can a Bone-Marrow Transplant Halt HIV?

FGI-104: a broad-spectrum small molecule inhibitor of viral infection
The treatment of viral diseases remains an intractable problem facing the medical community. Conventional antivirals focus upon selective targeting of virus-encoded targets. However, the plasticity of viral nucleic acid mutation, coupled with the large number of progeny that can emerge from a single infected cells, often conspire to render conventional antivirals ineffective as resistant variants emerge. Compounding this, new viral pathogens are increasingly recognized and it is highly improbable that conventional approaches could address emerging pathogens in a timely manner. Our laboratories have adopted an orthogonal approach to combat viral disease: Target the host to deny the pathogen the ability to cause disease. The advantages of this novel approach are many-fold, including the potential to identify host pathways that are applicable to a broad-spectrum of pathogens. The acquisition of drug resistance might also be minimized since selective pressure is not directly placed upon the viral pathogen. Herein, we utilized this strategy of host-oriented therapeutics to screen small molecules for their abilities to block infection by multiple, unrelated virus types and identified FGI-104. FGI-104 demonstrates broad-spectrum inhibition of multiple blood-borne pathogens (HCV, HBV, HIV) as well as emerging biothreats (Ebola, VEE, Cowpox, PRRSV infection). We also demonstrate that FGI-104 displays an ability to prevent lethality from Ebola in vivo. Altogether, these findings reinforce the concept of host-oriented therapeutics and present a much-needed opportunity to identify antiviral drugs that are broad-spectrum and durable in their application.

Coughs and sneezes spread diseases.

We mentioned sneezing when we talked about TB and it will return when we talk about influenza. According to research presented July 12 at the International Conference on Emerging Infectious Diseases approximately 1 out of every 4 people observed in a public setting failed to cover their mouth when they coughed or sneezed . Even more concerning, less than 5 percent of people covered their mouth using methods recommended by public health officials.

AIDS antibodies

Well, we don't start talking about HIV and AIDS until Tuesday but this weekend saw the publication of two papers in the journal Science that are probably the most hopeful news for an eventual AIDS vaccine for a long time.

Take a deep breath and we have:

Xueling Wu, Zhi-Yong Yang, Yuxing Li, Carl-Magnus Hogerkorp, William R. Schief, Michael S. Seaman, Tongqing Zhou, Stephen D. Schmidt, Lan Wu, Ling Xu, Nancy S. Longo, Krisha McKee, Sijy O'Dell, Mark K. Louder, Diane L. Wycuff, Yu Feng, Martha Nason, Nicole Doria-Rose, Mark Connors, Peter D. Kwong, Mario Roederer, Richard T. Wyatt, Gary J. Nabel, and John R. Mascola. Rational design of envelope surface identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science, 2010.

Tongqing Zhou, Ivelin Georgiev, Xueling Wu, Zhi-Yong Yang, Kaifan Dai, Andres Finzi, Young Do Kwon, Johannes Scheid, Wei Shi, Ling Xu, Yongping Yang, Jiang Zhu, Michel C. Nussenzweig, Joseph Sodroski, Lawrence Shapiro, Gary J. Nabel, John R. Mascola, and Peter D. Kwong. Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01. Science, 2010.

Several newspapers summarized this research but the report at ScienceDaily is one of the more comprehensive.

Scientists have discovered two potent human antibodies that can stop more than 90 percent of known global HIV strains from infecting human cells in the laboratory, and have demonstrated how one of these disease-fighting proteins accomplishes this feat. According to the scientists, these antibodies could be used to design improved HIV vaccines, or could be further developed to prevent or treat HIV infection. Moreover, the method used to find these antibodies could be applied to isolate therapeutic antibodies for other infectious diseases as well.

Another clue

A paper in the latest Journal of Vector Ecology is attracting some press and may provide an additional clue to the mysterious chronic Lyme disease. The paper:
Detection of Lyme disease spirochete, Borrelia burgdorferi sensu lato, including three novel genotypes in ticks (Acari: Ixodidae) collected from songbirds (Passeriformes) across Canada
is being used by one of the authors to explain why some patients test negative for Lyme disease but continue to show symptoms.

"In the ticks that we got from the West Coast, we found three new novel strains. This could be why Lyme disease patients are testing negative and they actually have one of these onboard and it's not showing up,"

However one of the coauthors disagrees:

Dr. Muhammad Morshed, a clinical professor in the department of pathology and laboratory medicine at the University of B. C, says Scott has reached the wrong conclusion from data he provided. Morshed's lab at UBC examined the tick-borne bacteria and identified the new strains, but says the genetic differences are not enough to throw off the current testing for Lyme disease.

So far the story has been picked up by the Vancouver Sun but I wouldn't be surprised if this one generates some more interest.

Lyme disease: The great debate

An interesting news report on this controversial topic. What do you think of the reporting in the video clip versus the reporting in the article? How is the science portrayed?

The article contains some good links to further information.

Of Mice and Man

The Center for Disease Control has a weekly podcast called 'A Cup of Health'. In a recent issue Dr. Barbara Knust discusses Hantavirus Pulmonary Syndrome. It's a bit cheesy but has some good advice

Remember, if you think you might have an infestation of rodents in or around your home, be careful not to stir up any dust or dirt that might contain the virus. Then, clean up the area with household disinfectants or bleach.

And why is this mouse pink? Well that's a completely different story from 2009:

University of Utah researchers dusted wild deer mice with fluorescent pink, blue, green, yellow and orange talcum powders to show which rodents most often fought or mated with others and thus were most likely to spread deadly hantavirus. The study identified bigger, older mice as the culprits.

Lyme - 2009 cases

Although the CDC doesn't have the 2009 Lyme disease data for the US yet (it's usually updated in August) various States are already reporting an increase in cases over those seen in 2008.

• New York - Lyme disease on the rise in New York as 20% more cases reported. Friday, June 18th 2010.
• Maryland - Lyme disease cases up in Washington Co.
• Virginia - Reports of Lyme Disease on the Rise

Squirrels are rodents too

Campground closed after ground squirrel tests positive for plague

Los Angeles County public health and U.S. Forest Service officials have closed the Los Alamos Campground in the Angeles National Forest after a California ground squirrel captured two weeks ago tested positive for plague.

The camp, between Gorman and Pyramid Lake, was closed Saturday afternoon and will remain closed for at least 10 days, said Jonathan Fielding, the county's public health director. Squirrel burrows in the area will be dusted for fleas, and further testing will be conducted before the campground is reopened.

No news on how the squirrel is doing..... (with apologies to Gary Larson)

Whooping cough vaccination

A whooping cough epidemic was recently declared in California, with 910 recorded cases of whooping cough and 5 infant deaths reported as of June 15.
Whooping cough, a highly contagious bacterial disease, also known as pertussis, is generally a minor disease for adults but can be a very unpleasant, and even deadly, disease in infants and children.

Public health officials say California's lackluster immunization rates could be a factor in the epidemic spread of whooping cough, a bacterial disease expected to take its largest toll in the state in five decades.

California is one of only 11 states that does not require middle school students to receive a booster shot against whooping cough.

Junk Science Kills

I've posted on this before but since it came up in class here are a couple of links to articles about the spurious autism-vaccine link.

One of my favorites is surprisingly in the tabloid-ish New York Post with the provocative title: Junk Science Kills which contains this gem, which I hope is one of the take home messages of this course:

It's very easy to scare people; it's very hard to unscare them.

There was also a nice Opinion article in the LA times earlier this year: The damage of the anti-vaccination movement.

Black Death

Well apparently there is a new movie out in the UK and in Germany called 'Black Death', which, perhaps not surprisingly, is set during the Black Death. Here's the summary:

In a plague-ridden medieval England, Osmund, a young monk, is charged in leading the fearsome knight Ulrich, and his group of mercenaries to a remote village where the inhabitants are unaffected by the deadly pestilence.

and some of the more entertaining reviews from rottentomatoes

'Though its title must rank as one of the most off-putting in film history, Black Death isn't as bad as you might fear.'

'Released into an era of poverty, pestilence and bad religion, Christopher Smiths historical horror-thriller Black Death fits the new Dark Ages like an bloodied iron gauntlet.'

'Dark and dirty entertainment.'

No information on a US release but you can watch a trailer. Looks like they managed to sneak some flagellants in there.

Summer reruns

I've posted both these before but I can't resist posting them again. John Stewart on Bubonic Plague and flagellation in a German Rock video.

The Daily Show With Jon StewartM - Th 11p / 10c

Bubonic Plague

Daily Show Full Episodes
Important Things With Demetri Martin

Funny Political News
Joke of the Day

Better late than never....

Mon Jun 28, 2010 from Reuters: FDA recommends new limits on livestock drugs:

To prevent development of drug-resistant bacteria that could infect people, the U.S. Food and Drug Administration recommended on Monday that livestock farmers use the drugs solely to cure or prevent disease in animals, phasing out their use to promote growth.

FDA said research showed mixing antibiotics in livestock rations or feedlot water supplies "is not in the interest of protecting or promoting public health." Over-the-counter antibiotics have been routinely used for decades to promote livestock growth and feed efficiency.

Emergence of antibiotic-resistant bacteria poses a serious public health threat, said FDA, so it is looking for ways to reduce overuse of the drugs.

Antibiotics including penicillin and tetracyclines should be used only under the supervision of veterinarians to prevent or treat illness in livestock, FDA said in its 19-page draft.

FDA made its recommendations in a first-round version of a "guidance" document, which represents the agency's current thinking on an issue. Guidance does not carry the weight of law but generally is adopted by industry.

Mining and Tuberculosis

Dust-choked mine shafts, crowded working conditions and stifling hostels where up to 16 miners share a room — all conspire to make mining a more important contributor to tuberculosis in Africa than had been realized, a new study finds.

Rates of the illness have doubled in Africa over the past two decades, and have tripled in South Africa, which even in 1996 had the highest TB rates in the world. Until now it has been assumed that the increases were driven by Africa’s high rates of infection with the AIDS virus, which weakens the immune system, helping latent TB become active.

But researchers from Brown and Oxford Universities, the London School of Hygiene and Tropical Medicine, and the University of California, San Francisco, compared 44 African countries and found that even some with low rates of H.I.V. infection rates had high TB rates. When a country’s mines shut down, tuberculosis often fell. The study appeared in The American Journal of Public Health.

...

From an article in the New York Times last week reporting on an article in The American Journal of Public Health: Mining and Risk of Tuberculosis in Sub-Saharan Africa

More Creepy

I posted previously on the splendidly creepy Waverly Hills Sanatorium in Kentucky, complete with body chute:

The Body Chute was once used to transport the bodies of deceased TB patients from the hospital to the bottom of the hill to waiting hearses or trains. At the peak of the TB epidemic, many patients died everyday. In order to keep morale up and not upset living patients, the hospital administration decided to use the Body Chute to discretely send bodies away from the hill.

Because of the prevalence of Tuberculosis Sanataria were once quite abundant but within a few short years drug discoveries removed the need for them. There are still a number of long abandoned Sanataria out there. I think I'll continue the series with the Seaview Hospital complex.

Built between 1905 and 1938 it was, at one time, the largest tuberculosis hospital at a time when fresh air was considered the most effective treatment of "the white plague." The first drug trials leading to a cure for 'consumption' were made at Seaview Hospital.

Now it's just creepy. Let's hope (or better still plan) so we don't need them again......

'Hidden' tuberculosis raises drug-resistance fears

From a report in Nature this week:

Huge and hidden levels of tuberculosis discovered in a South African province devastated by HIV are increasing concerns about the prevalence of drug-resistant tuberculosis in Africa.

As reported in PLoS Medicine, when researchers examined newly deceased patients at Edendale hospital in the province of KwaZulu-Natal, they discovered that 50% were infected with the bacterium M. tuberculosis, the causal agent of tuberculosis, with 17% of the infected individuals carrying a multi-drug resistant (MDR) strain.

Among those with TB, only 58% had been diagnosed and started on treatment before their death. A previous study had found that only 28% of patients admitted to the same hospital were diagnosed with active tuberculosis.

In the new study, 96% of those positive for M. tuberculosis were also HIV positive, and the alarming prevalence of tuberculosis may reflect the situation in other low-income countries plagued by HIV. With weakened immunity, HIV-positive individuals are extremely vulnerable to other infections.

"This report is extremely serious," says Mario Raviglione, director of the WHO Stop TB Department in Geneva, Switzerland. "It confirms that over the last few years, multidrug-resistant tuberculosis has become rampant in people living with HIV [in Africa]".

Cholera roundup

Here are just a selected few previous posts on Cholera that you may find interesting:

• American miasma
• Dehydration
• The Ghost Map
• Preventives of Cholera

Notetaker Needed

Disabled Students Program Notetaker Needed
EEMB 40 MTW 12:30

$25 per unit (of the class)
(this will be prorated based on the number of weeks for which they are hired)

Questions: Please contact Wanda Thomas:
Phone: 893-2668
Email: thomas-w@sa.ucsb.edu

Please apply online at http://dsp.sa.ucsb.edu/services

The Stolen Bacillus

It wasn't long after the discovery of bacteria and the germ theory of disease that the use of such microbes by terrorists was suggested by H.G Wells in a short story - The Stolen Bacillus, first published in 1894.

From the Literature, Arts and Medicine database:

This story is a chilling satire about the potential role of scientists in facilitating bioterrorism. The Bacteriologist is so pleased with his own work that he gives the Anarchist access to it, and in expounding on the power of the cholera bacillus (which he feels he has in his own power), he gives the Anarchist the information he needs to recognize bioforms as an effective weapon. The Anarchist's words are all too familiar; he says that others are "blind fools to use bombs when this kind of thing is attainable"

Cholera country

The Guardian, a British newspaper, have a short video clip on their website about the Zimbabwe cholera epidemic in 2008/2009. It is well worth watching. Notice how all these people know exactly how cholera is contracted but can do nothing about it, and know what a cholera patient needs, but don't have the funds to provide it.

Summer 2010

Welcome to the blog for EEMB40 - the Ecology of Disease - for Summer 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'. 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 over 500 (!) of them from the five 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.

Supramap: Predictiong the Spread and Evolution of Viruses

By Annalee Newitz
(Not Me!)
When a pandemic breaks out, disease circles the globe, often leaping from species to species. Now scientists think they can forecast where deadly viruses will strike next, using a new tool that predicts genetic mutation.
Supramap doesn't just track the spread of viruses - it tracks how the viruses are mutating as they jump into new hosts and encounter new medicines. Using Supramap, scientists might be able to stay ahead of the virus mutation curve and figure out when to switch medicines as the microbes adapt and develop resistance.

The Natural History Museum reports on Supramap:

"This tool has a lot of predictive power," says Ward Wheeler, curator in the Division of Invertebrate Zoology at the Museum. "If the movement of a pathogen is related to bird flyways, for example, and those routes are shifting because of something like climate change, we can predict where the disease might logically emerge next."
Operating on parallel programming on high-performance computing systems at Ohio State University and the Ohio Supercomputer Center, Supramap allows any user to input raw genetic sequences of a pathogen's strains and build an evolutionary tree based on mutations. The branches are projected onto the globe with pop-up windows to show how strains mutate over space and time and infect new hosts.

During an earlier phase in Supramap's development, one of the researchers working on it explained how it works:


This week, a paper about Supramap was published in Cladistics. The ability to predict how a virus will mutate over time could be the first step in coming up with a method to stop pandemics in their tracks - or at least, to mitigate the harm they cause by distributing medicines as effectively as possible.
Learn more about Supramap here, and start using it!
via Cladistics [spotted on Natural History Museum]

Send an email to Annalee Newitz, the author of this post, at annalee@io9.com.

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Doesn't this sound like the coolest thing EVER?

Final

Good luck tomorrow. 12 noon. The usual room (1640 Broida).
The format is not just similar to the midterm it's identical but the final is worth 50% more than the midterm.
As far as possible questions are based on material covered since the midterm BUT I have used some of the terminology that we introduced in the first half. However this should be pretty familiar by now since it is terminology we kept using (vector, prevalence, epidemic, antibiotic etc)
We'll be grading the exams pretty quickly so grades should be available before the end of the weekend but PLEASE write clearly to make our job easier

Forward harvesting

One of the grimmer terms I have come across in epidemiology is 'forward harvesting' - referring to the possibility that events like heatwaves may cause a high mortality rate but only by bringing forward the deaths of those who would have died in the short term anyway.

Although this seems likely, given that events like heatwaves and cold spells primarily affect the elderly there does not not seem to be much evidence for it. In fact there seems to be no evidence for it in cold spells and only a weak effect in some studies on hot spells. Because we have large data sets the effect, if there is one, cannot be large.

eg for the 2003 heatwave in Europe and especially France:
Impact of the 2003 Heatwave on All-Cause Mortality in 9 French Cities
There was no evidence to suggest that the extras deaths associated with the heatwave were simply brought forward in time.
and for a series of heatwaves and cold spells in Holland:
The Impact of Heat Waves and Cold Spells on Mortality Rates in the Dutch Population
The results concerning the forward displacement of deaths due to heat waves were not conclusive. However, looking at the relation between the ambient temperature and mortality over the whole period studied, our results showed compensatory effects on mortality in the longer lag periods after warm weather (average temperature above optimum temperature level). This could be an indication of a harvesting effect of warmer temperatures. However, as previously discussed, this was not clearly shown by the analysis of heat waves. We found no cold-induced forward displacement of deaths.

Acronymorama

What do the following acronyms stand for and what do they have to do with infectious disease?

• AIDS
  
• BSL
• BSE
• VRSA
• HIV
• HAART
• MDR-TB

Thirteen diseases

Consider the following thirteen diseases, all of which we discussed, although some of them only briefly.

1. AIDS
2. Bubonic plague
3. Lyme disease
4. Cholera
5. Ebola hemorrhagic fever
6. Hantavirus cardiopulmonary syndrome
7. Measles
8. Marburg hemorrhagic fever
9. Tuberculosis
10. Malaria
11. Polio
12. Influenza
13. Yellow fever

• Four of these disease have vectors. Which are they and what are the vectors?
• Three of these diseases have rodent reservoirs. Which are they?
• Which three of these diseases have exhibited a series of truly global pandemics?
• Which of these disease are essentially incurable? What do these incurable diseases have in common?
• Which of these diseases is caused by neither a bacteria nor a virus? What is it caused by?
• Which two of these disease are transmitted by the fecal-oral route?
• Which two of these diseases are a particular problem to immunocompromised people? Why?
• Which of these disease can be vertically transmitted?
  

Whale snot

Sandwiched between 'How to make a toddlers guitar hero controller' and 'How to make a cardboard horse to hide a paper tiger' (huh?) on the Make Magazine blog is the equally fascinating 'How to collect whale snot using an RC helicopter'.

With a growing interest in wildlife diseases and a desire to non-destructively collect samples from whales scientists have been interested in collecting the exudates from whale blowholes.

At the simplest level, as they explain this involves three steps:

• Find whale.
• Hold petri dish over blowhole to intercept spout.
• Return to lab, enjoy sample.

Of course holding the petri dish over the blowhole is the tricky step. Enter the RC helicopter.

Scientific report here:
"A novel non-invasive tool for disease surveillance of free-ranging whales and its relevance to conservation programs"

I've said this before, but I'll say it again, how can you not be a biologist when you could get to do things like this for a living?

HIV vaccine?

Okay, how about a review question AND an interesting news article?

There are four fundamentally different ways of making vaccines. What are they and what are the advantages and disadvantages of each?

Reported in New Scientist this week: Fight HIV with HIV: 'safe' virus proposed as vaccine from results reported last month at the 2010 annual Conference on Retroviruses and Opportunistic Infections.

Review part 1

Thank you to everyone who has posted here this quarter and thanks for being a great class. Seriously, I have enjoyed teaching the class this quarter, I thought the lectures were nicely interactive - lots of good questions from the audience.

I'll continue to post here up until the final next Friday and I'll be posting some questions for review. I will eventually post some additional exam format questions in the links on the right but I'll also post more general review type questions here. Let's see, here's some simple definitions to get you started. For best value try explaining these to someone else.

What's the difference between:

• A dead end host and a definitive host?
• Reassortment and transformation
• An antibiotic and an antibody?
• A vector and a vaccine?
• A viral swarm and a cytokine storm?
• Antigen shift and antigen drift?
  

MMWR

Morbidity and Mortality Weekly Report (MMWR) is a weekly epidemiological digest for the United States published by the Centers for Disease Control and Prevention.

You can sign up to receive it in your e-mail weekly or access the current version and the archives at the website. There's often something interesting there that isn't getting picked up by the mainstream media and when something does hit the media it's a good place to go for the plain facts.

The writing is aimed at a medical audience so there is quite a lot of jargon but there is always something interesting going on. Here are just a few items that caught my attention in the most recent reports:

• Progress Toward Poliomyelitis Eradication --- Afghanistan and Pakistan, 2009
• Jimsonweed Poisoning Associated with a Homemade Stew --- Maryland, 2008
• Outbreaks of 2009 Pandemic Influenza A (H1N1) Among Long-Term--Care Facility Residents --- Three States, 2009

Safe Patients, Smart Hospitals

This relates to the topic of nosocomial infections from a few weeks back but I thought this interview with Dr. Peter J. Pronovost, medical director of the Quality and Safety Research Group at Johns Hopkins Hospital in Baltimore, in the New York Times on Monday was interesting. Click the link for the full interview, I've just posted some snippets below. Even something as simple as making sure supplies are together and at hand can reduce infections:

At Hopkins, we tested the checklist idea in the surgical intensive care unit. It helped, though you still needed to do more to lower the infection rate. You needed to make sure that supplies — disinfectant, drapery, catheters — were near and handy. We observed that these items were stored in eight different places within the hospital, and that was why, in emergencies, people often skipped steps. So we gathered all the necessary materials and placed them together on an accessible cart. We assigned someone to be in charge of the cart and to always make sure it was stocked.

Q. WHAT CAN CONSUMERS DO TO PROTECT THEMSELVES AGAINST HOSPITAL ERRORS?

A. I’d say that a patient should ask, “What is the hospital’s infection rate?” And if that number is high or the hospital says they don’t know it, you should run. In any case, you should also ask if they use a checklist system.

Once you’re an in-patient, ask: “Do I really need this catheter? Am I getting enough benefit to exceed the risk?” With anyone who touches you, ask, “Did you wash your hands?” It sounds silly. But you have to be your own advocate.

Herd Immunity

A nice study, reported in the New York Times, demonstrating herd immunity in a Hutterite community in Canada.

Toxoplasmosis and the Future of Medicine

Toxoplasmosis killed with gold nanoparticles and lasers
Yes! This is great! This will be a great precursor to eliminating other illnesses, especially eukaryote-based diseases. Hopefully in the future, we will be able to use nanoparticles to destroy bacteria without having to use antibiotics. Then we will probably have won our battle with disease because we will not have to be constantly developing new anitbiotics, and can focus on treating infections where they occur in the body, instead of flooding a person's body with medicine or radiation. Looking good for humanity, I just wish we do not die of something extreme before we develop better technology,
But...I cannot help from being slightly skeptical, because even though we can now eliminate toxoplasmosis cysts from the brain, millions of people (and animals) are infected, and using lasers and nanoparticles can seem like an expensive waste for a non-fatal disease. But if we can develop a way to remove toxoplasmosis permanently, then I am sure it would be adopted more quickly.
My idea: nanobots with built in lasers for hunting down disease causing parasites, bacteria and viruses. For prions? Perhaps have nanobots with some storage capability as to contain the prion within itself, rendering it harmless withing the nanobots walls. If everyone has nanobots that destroy diseases as you are infected, what will happen to the human race?

ps. My favorite part of writing science-fiction is speculating, obviously.

Flu Attack! How A Virus Invades Your Body

This is a pretty nice animation. I did cringe though when he said that 'all viruses want to spread'. In terms of natural selection it is much better to think of selection as favoring those viruses that spread most successfully therefore favoring those that spread most efficiently. They've also made a very clear decision to avoid virtually all terminology and use familiar terms (locks, keys, noodly things, factories, copying machines, little chefs).

Notice all the antibodies swirling around the virus at the very end. It is the fact that these antibodies latch onto the virus (via the same lock and key mechanism) that marks the virus for destruction via the white blood cells (actual white blood cells may not actually make a slurping noise).

The answer to the final question - of why you don't usually drop dead is also rather weak. The fact you have so many cells won't keep you alive for long if a virus multiplied this fast. They actually have a better answer at the NPR website:

In our video we ask, if a flu virus inside your body can multiply by the millions within seconds, why don't we topple over and die quickly?

Here's a better, longer answer than the one in the video. First, some new viruses get caught in mucus and other fluids inside your body and are destroyed. Other viruses get expelled in coughs and sneezes. Second, lots of those new viruses are lemons. They don't work that well. Some don't have the right "keys" to invade healthy cells so they can't spread the infection. And third, as the animation shows, your immune system is busy attacking the viruses whenever and wherever possible.

Blood groups and immunology

Although agglutination is a mechanism by which your body destroys attacking microorganisms, when this happens on a larger scale it can be dangerous. The human blood groups are a good illustration of the way that antibodies and antigens interact and this is well illustrated at the Nobel prize website (Karl Landsteiner's work made it possible to determine blood groups and thus paved the way for blood transfusions to be carried out safely. For this discovery he was awarded the Nobel Prize in Physiology or Medicine in 1930.)

Note that the example of human blood groups also illustrates that you do not generally have antibodies against antigens that are normally present in your body. This makes a lot of sense and this distinction between self and non-self is crucial. We see the importance of it, and the power of our immune system, when it breaks down in so-called auto-immune diseases (originally known by the splendidly gothic name of “horror autotoxicus”).

Beautiful and deadly

Deborah sent me a link to the glass artwork of Luke Jerram - transparent glass sculptures of viruses that push the boundaries of both biological knowledge and glassblowing. His website has lots of examples and a video. Everything but the cost. I'm guessing that if you have to ask, you can't afford them... Not that I need one, I was just curious.

These transparent glass sculptures were created to contemplate the global impact of each disease and to consider how the artificial colouring of scientific imagery affects our understanding of phenomena. Jerram is exploring the tension between the artworks' beauty, what they represent and their impact on humanity.

The question of pseudo-colouring in biomedicine and its use for science communicative purposes, is a vast and complex subject. If some images are coloured for scientific purposes, and others altered simply for aesthetic reasons, how can a viewer tell the difference? How many people believe viruses are brightly coloured? Are there any colour conventions and what kind of ‘presence’ do pseudocoloured images have that ‘naturally’ coloured specimens don’t? See these examples of HIV imagery. How does the choice of different colours affect their reception?

Latent AIDS infections

Researchers at the University of Michigan believe they have pinpointed the reason as to why people infected with HIV eventually develop AIDS if they cease taking medication. Scientists have found that the AIDS virus can hide in bone marrow, avoid drugs during the course of treatment, and become active later. The HIV virus can infect other cells in the bone marrow that live longer than most cells. When infected bone marrow cells are converted to blood cells, the virus reactivates and starts infecting other cells. This discovery is a crucial step toward finding a cure for HIV/AIDS; eliminating the source that is responsible for latent infections would allow HIV patients to stop treatment after the infection is over. Those in rural and poor countries where many are unable to afford medication would greatly benefit from new medications that destroy the cells responsible for latent infections. To read more about latent HIV infections click here.

Smallpox 2002

I've posted this before and I thought it worthy of repeat but I saved it for the weekend because it is a bit of a potential time sink. Smallpox 2002 is a FICTIONAL 'documentary' made in 2001 by the BBC. It was commissioned and largely completed before both the 9/11 attacks and the anthrax attack that followed. The film has been shown in the US as "Smallpox", on FX. Although the program has some flaws, on the whole I thought it was well done. If it gets people to think in advance about what will happen in the next pandemic, whether it is influenza or bioterror, then that's a good thing. What parts of the program did you find unrealistic? Do you think events would have played out differently? Do you think this program is unnecessarily fear-mongering or do you think it is a valuable warning? The tagline for the movie was, "Drama, until it happens". Good one.

The program is rather addictive and lasts 90 minutes so don't start watching if you have other things to do!

For those whose history is shaky, let me repeat, this is fiction. There wasn't a smallpox epidemic in 2002 that killed 60 million people! For reference though, the 1918 influenza pandemic killed somewhere between 20 and 100 million people worldwide.

The embedded video above is just part 1 of 9. Here's a link to the complete Playlist.

Smallpox questions

Parchment signed at Geneva on 9 December 1979, by the members of the Global Commission for Certification of Smallpox Eradication.

A couple of interesting questions during and after class that I had to look up the answers to but thought would be of enough general interest to post here.

1) Where did smallpox come from?

Human disease likely attributable to variola virus (VARV), the etiologic agent of smallpox, has been reported in human populations for >2,000 years. VARV is unique among orthopoxviruses in that it is an exclusively human pathogen....Our results show two primary VARV clades, which likely diverged from an ancestral African rodent-borne variola-like virus either ≈16,000 or ≈68,000 years before present (YBP), depending on which historical records (East Asian or African) are used to calibrate the molecular clock.
From: On the origin of smallpox: Correlating variola phylogenics with historical smallpox records
But see also: How long ago did smallpox virus emerge?

2) When was smallpox officially declared eradicated?

Both the WHO and CDC have information on their respective websites. Here is an account from the CDC website of the final years of the eradication project and the final certification of eradication which occurred two years later.

By the end of 1975, smallpox persisted only in the Horn of Africa.

Conditions were very difficult in Ethiopia and Somalia, where there were few roads. Civil war, famine, and refugees made the task even more difficult. With the interruption of smallpox transmission in Asia, more resources were made available in Africa, including more staff and transport.

An even more intensive surveillance and containment and vaccination program was initiated in the spring and summer of 1977. As a result, the world’s last indigenous patient with smallpox on earth was a hospital cook in Merka, Somalia, on October 26, 1977 with variola minor.

Searches for additional cases continued in Africa for more than 2 years, during which time thousands of rash illnesses were investigated. None proved to be smallpox.

Although 2 cases of smallpox occurred in England in 1978 as a result of a laboratory accident, smallpox was gone as a naturally transmitted disease.

The World Health Organization officially certified that smallpox had been eradicated on December 9, 1979, 2 years after the last case in Somalia. In 1980 the World Health Assembly recommended that all countries cease routine vaccination.