Monday, July 26, 2010

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.

Sunday, July 25, 2010

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.

Friday, July 23, 2010

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.

Thursday, July 22, 2010


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?

Wednesday, July 21, 2010

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:

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).

Tuesday, July 20, 2010

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.)

Monday, July 19, 2010

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.

Sunday, July 18, 2010

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.

Saturday, July 17, 2010

Malaria-proof mosquito engineered

Researchers engineer malaria-proof mosquitoes.
July 17, 2010

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

Friday, July 16, 2010

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.

Thursday, July 15, 2010


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?

Wednesday, July 14, 2010

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.

Tuesday, July 13, 2010

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.

Monday, July 12, 2010

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.

Sunday, July 11, 2010

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.

Saturday, July 10, 2010

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.

Thursday, July 8, 2010

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.

Wednesday, July 7, 2010

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.

Tuesday, July 6, 2010

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.

Monday, July 5, 2010

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)

Saturday, July 3, 2010

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.

Thursday, July 1, 2010

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.