Saturday, March 16, 2013


It's been fun, and I hope you've enjoyed reading the blog, but it must, sadly, go into its annual diapause.

Commas throughout the land will breath a sigh of relief.

The kitten is here because it is, somewhat surprisingly, one of the top search terms that brings people to this blog. Since I've barely ever mentioned kittens I can only presume it's because kittens is a very popular search term on the internet and a small fraction of those searching for them end up here. I would like to personally apologize to those people and provide this picture of a kitten.

Friday, March 15, 2013


Andy pointed out a couple of relevant studies in the latest Emerging Infectious Disease journal issue:

Predicting Hotspots for Influenza Virus Reassortment
The influenza pandemics of 1957 and 1968 were deadly; each killed about 1 million people. Both pandemics resulted from the mixing of genetic material of 2 types of closely related flu viruses, called reassortment. This occurs when both viruses infected the same host at the same time. This mixing produced a virus that was more lethal than either alone. This mixing could also happen again. Studies in mice have raised the possibility that mixing of the human seasonal flu virus and the bird flu virus could produce a novel virus that could spread rapidly and kill many people. To determine where such mixing is most likely to occur, researchers evaluated livestock densities and agricultural practices (looking for areas with human and bird flu viruses and high concentrations of pigs). They concluded that the areas at highest risk for a future flu pandemic are coastal and central China and the Nile Delta region of Egypt.

MRSA Infection Risk among HIV-infected Adults
Methicillin-resistant Staphylococcus aureus (MRSA) infections has emerged as an important public health problem. HIV-infected persons are at increased risk for infection and colonization (carrying the bacteria without signs of infection).  Because colonization increases risk for MRSA infection, prevention should be aimed at decreasing colonization. But where and how?  To learn where on the body these bacteria are most likely to colonize, researchers collected samples from HIV-infected patients and monitored these patients over time. Although the nose is consid­ered the primary reservoir of S. aureus, in this study the groin was also frequently colonized with MRSA, and those with groin colonization were more susceptible to developing active MRSA infection later. These data suggest that to prevent active MRSA infections, HIV-infected persons should maintain good general hygiene which includes groin hygiene and take steps to avoid potential MRSA exposures (e.g., by not sharing personal items that may become MRSA contaminated such as towels, bedding, and razors and by keeping cuts and scrapes clean and covered).

Thursday, March 14, 2013

Take it as a warning..

File under 'headlines you really don't want to see.'

6,000 Disease-Ridden Dead Pigs Found Clogging a River in Shanghai

"(S)ince the government arrested some tainted meat dealers, nobody comes to buy the stuff anymore. So it's normal that there are so many dead pigs in the river."

Although the Chinese authorities assure customers their water quality is unaffected:

6,000 Dead Pigs in River Not Affecting Shanghai's Water, Officials Insist

Concern is naturally being raised over water quality but anytime you get thousands of dead animals there's also the opportunity to ask why and to ask what warning signs we should be taking from this.

Or we could just redefine 'normal' to include thousands of dead pigs in a river

Wednesday, March 13, 2013

Put to death

The science writer Carl Zimmer addressed the question of whether our stocks of smallpox should be destroyed back in 2011, the last time this decision was made. The decision will be back up for discussion again in 2014 I think.
Should Smallpox Be Put To Death?

 Should the virus be preserved so that it can be studied? Or should the virus be destroyed, so that—in theory at least—it would become extinct and would not threaten the human species again?

For a lengthier discussion see Smallpox Virus Destruction and the Implications of a New Vaccine  by D.A. Henderson, one of the people behind the eradication of smallpox.

Tuesday, March 12, 2013

Flu Vaccine myths

From the New York Times yesterday here's a straightforward little article that addresses a number of myths about the flu vaccine.
From “The vaccine doesn’t work ” to “The vaccine causes the flu”.

The information is taken from an article in JAMA (Journal of the American Medical Association):

Monday, March 11, 2013

Why is flu season in winter?

We all know that winter is flu season - but why? That turns out to be an interesting question and some of the answers you may have heard have been shown to be incorrect.

Check out this illustrated guide from Popular Science.

Here's the bottom line but it's worth checking out the link:

Quite possibly, the flu's annual winter-time parade through our immune systems has to do with both factors: the virus survives better and transmits more easily in cooler, drier air. The case isn't closed yet--and researchers are still looking into some of those other theories, like the idea that our immune systems are weaker in winter--but, for anyone looking for ways to avoid the seasonal flu (in addition to the flu shot, of course), a portable humidifier seems like a good place to start.

Sunday, March 10, 2013

Number two

An item in the news over the last week that some of you may have seen - a second case of AIDS apparently 'cured' and by a completely different route to the first. From the New York Times:

Doctors announced on Sunday that a baby had been cured of an H.I.V. infection for the first time, a startling development that could change how infected newborns are treated and sharply reduce the number of children living with the virus that causes AIDS.

The baby, born in rural Mississippi, was treated aggressively with antiretroviral drugs starting around 30 hours after birth, something that is not usually done. If further study shows this works in other babies, it will almost certainly be recommended globally. The United Nations estimates that 330,000 babies were newly infected in 2011, the most recent year for which there is data, and that more than three million children globally are living with H.I.V.

Saturday, March 9, 2013

CDC - a hit and a miss

Speaking of the CDC, I've posted on this before but it's worthy of a repost.

Wonder why Zombies, Zombie Apocalypse, and Zombie Preparedness continue to live or walk dead on a CDC web site? As it turns out what first began as a tongue in cheek campaign to engage new audiences with preparedness messages has proven to be a very effective platform. We continue to reach and engage a wide variety of audiences on all hazards preparedness via Zombie Preparedness; and as our own director, Dr. Ali Khan, notes, "If you are generally well equipped to deal with a zombie apocalypse you will be prepared for a hurricane, pandemic, earthquake, or terrorist attack."

The graphic novel, "Preparedness 101: Zombie Pandemic" demonstrates the importance of being prepared in an entertaining way that people of all ages will enjoy. Readers follow Todd, Julie, and their dog Max as a strange new disease begins spreading, turning ordinary people into zombies. Stick around to the end for a surprising twist that will drive home the importance of being prepared for any emergency. Included in the novel is a Preparedness Checklist so that readers can get their family, workplace, or school ready before disaster strikes. You can also download the novella on Google books here or download a printable pdf version here.

The CDC got lots of press for addressing the zombie issue and it seemed to be well received. Unfortunately they decided to follow up with the CDC's guide to surviving your wedding day. Worst. Sequel. Ever. (and no longer available at their website although you can find it at the Internet Archive if you really must)

Friday, March 8, 2013

Can Polio Be Eradicated?

Here's a nice little article from the New York Times a couple of years ago that talks about whether polio really can be eradicated and, in particular, about how one expert, Donald Henderson, who worked on the eradication of smallpox has changed his mind. What caused this change of opinion was a conversation with another of the smallpox team Dr. Ciro de Quadros

While nothing has changed about the virus or the vaccine, several things Dr. de Quadros told him were persuasive, he said.

“I was unaware of how committed Gates is,” he said. “He’s saying polio is his No. 1 priority.”

I like the anecdote about Dr de Quadros's work in the field during the smallpox campaign:

“I watched him perform in Ethiopia,” said Dr. Henderson, who recruited Dr. de Quadros into the smallpox campaign. “The obstacles were unbelievable — the emperor assassinated, two revolutionary groups fighting, nine of his own teams kidnapped, even a helicopter captured and held for ransom. He kept the teams in the field — and that helicopter pilot went out and vaccinated all the rebels.”

Thursday, March 7, 2013

Close but not close enough

A textile mill in Tanzania that produces long-lasting, insecticide-treated mosquito nets.

I try to keep the figures updated in this class and, in some cases, make sure I'm giving you a good general figure and not one person's estimate. The figures on the costs of malaria eradication would be a good example. As someone pointed out we also need to know the TOTAL worldwide expenditure on malaria control not just the US contribution. I usually just double the US contribution but it looks like 2.5x would be a better figure. The Bill and Melinda Gates Foundation - who I trust to have a pretty good handle on the figures - estimate total worldwide expenditure on malaria control to now be $2 billion per year. This is an impressive increase but still well short of the $5 billion estimated to be required for eradication. The malaria page at the Gates foundation website is well worth a read.

In the past decade, funding for malaria control risen from US$300 million in 2003 to an estimated US$2 billion in 2011. This massive increase was made possible by the Global Fund to Fight AIDS, Tuberculosis and Malaria and commitments from the U.S. President’s Malaria Initiative, the UK Department for International Development, UNITAID, the World Bank, and other bilateral and multilateral agencies.

Still, the Global Malaria Action Plan estimates that an additional US$5 billion in annual funding is needed to achieve and sustain universal coverage and pursue research and development. Our strategy includes investments to encourage continued funding commitments by current major donors, mobilize new donors for malaria R&D, and support efforts to track country-level progress against malaria.

Wednesday, March 6, 2013

Nightmare bacteria

CNN today picked up on the CDC director calling antibiotic resistant strains of enterobacteria 'nightmare bacteria':

CDC: 'Nightmare bacteria' spreading

Hospitals need to take action against the spread of a deadly, antibiotic-resistant strain of bacteria, says the Centers for Disease Control and Prevention. The bacteria kill up to half of patients who are infected.

The bacteria, called carbapenem-resistant Enterobacteriaceae or CRE, have increased over the past decade and grown resistant to even the most powerful antibiotics, according to the CDC. In the first half of 2012, 200 health care facilities treated patients infected with CRE.

"CRE are nightmare bacteria," CDC director Dr. Tom Frieden said in a statement. "Our strongest antibiotics don't work and patients are left with potentially untreatable infections. Doctors, hospital leaders and public health must work together now to implement CDC's 'detect and protect' strategy and stop these infections from spreading."

Tuesday, March 5, 2013

Yellow fever in the Panama canal zone

 The video above looks like it is shot directly from a tv screen so it isn't the best quality but it is a really nice short introduction to the amazing work of Colonel William Gorgas and how the army conquered Yellow Fever (and also malaria since it is also spread my mosquitoes) in the Panama canal zone.

Monday, March 4, 2013

Anti-malaria pinup calendar

The radio show All Things Considered on NPR recently had a segment on How The U.S. Stopped Malaria, One Cartoon At A Time
You can listen to it at the link or read the transcript and see some awesome images.

 (T)he U.S. Army was working hard to eliminate the parasite on military bases and among the troops. They broadcasted anti-malaria jingles on the Armed Forces Radio and distributed cartoons and "pinup calendars" encouraging troops to cover up and use repellent.

Sunday, March 3, 2013


I'll talk about foreign aid a couple of times in the upcoming two weeks. Foreign Aid is one of the victims of the sequester. How you view foreign aid depends a lot on your worldview.

Here's are two commentaries on the effects of the sequester on foreign aid.

From US News and World Report: Don't Let Sequestration Cut Foreign Aid

(F)oreign assistance advances America's moral values and humanitarian interests by saving lives, fighting poverty and hunger, combating infectious diseases like HIV/AIDS, promoting education, and bolstering democratic institutions.

Foreign assistance—properly understood—is neither national bribery nor altruistic charity, but rather strategic investment. 

For a contrary view here's an opinion piece from the Washington Times: Sequester solved: Sell national parks, stop foreign aid, leave Germany

Stop all foreign aid. This one seems self-explanatory. Really, how can a government that is forced to shut down justify borrowing money to hand out to other countries that don’t have to pay it back?

Saturday, March 2, 2013

Amphibians and bats

I mainly focus on human diseases in this class but over the last week I did branch out a little. Some recently emerging diseases I did not discuss were the chytrid fungus affecting frogs and the fungus that causes white-nose syndrome in bats. Both of these are causing serious conservation problems.

The March 2013 issue of Emerging Infectious Diseases, a publication of the CDC, has a nice review:

Parallels in Amphibian and Bat Declines from Pathogenic Fungi

Pathogenic fungi have substantial effects on global biodiversity, and 2 emerging pathogenic species—the chytridiomycete Batrachochytrium dendrobatidis, which causes chytridiomycosis in amphibians, and the ascomycete Geomyces destructans, which causes white-nose syndrome in hibernating bats—are implicated in the widespread decline of their vertebrate hosts. We synthesized current knowledge for chytridiomycosis and white-nose syndrome regarding disease emergence, environmental reservoirs, life history characteristics of the host, and host–pathogen interactions. We found striking similarities between these aspects of chytridiomycosis and white-nose syndrome, and the research that we review and propose should help guide management of future emerging fungal diseases.

Friday, March 1, 2013


I've posted this before but I enjoyed listening to it again...

Whilst there is, of course, a death metal band called Rinderpest, with a song called Rinderpest, I couldn't make much headway with the 'lyrics'. Let me know if you have better luck.

More interestingly there is a South African musician who has a whole album about the Rinderpest epidemic that devastated Africa.

The Scene is the Cape Colony border, late 19th century, a terrible plague, the Rinderpest (rather like Foot & Mouth), has decimated the livestock and lives of the Boers, Brits and Amaxhosa alike. The infected animals have to be piled in pits and burned. The land is covered in smoke and weeping.

It's not easy to find but you can listen to the title song, After the Rinderpestfor free at the Last.FM website.

After the Rinderpest
There’s a wicked wind on the smoking ground
All out hopes and dreams, we had to burn them down.
And our poisoned wells took our first and best
Gave our childrens’ lives to the Rinderpest.
Sent our youths away to be militarized
And we couldn’t see into their empty eyes.
Would you have the strength, if they confessed
To what they saw, in the wilderness.
With a burying pit full of burning beasts
With the crimson coals of the heat beneath.
Holding out our hands to be cauterized
But the Rinderpest left us paralyzed.
And a tattooed child full of battle scars
With a heart of iron, hammered hard.
Do we act surprised, as though we never knew
What the sulphur air would have done to you.
There are bands of us that have survived
And all we have is how we live our lives.
As we struggle on, we must not forget,
Just what we learned, from the Rinderpest.