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.

Thursday, February 28, 2013

Rare Disease Day

Today, the 28th of February is rare disease day.

On and around this day hundreds of patient organisations from more than 60 countries and regions worldwide are planning awareness-raising activities converging around the slogan “Rare Disorders without Borders” 

There are a surprisingly large number of rare diseases. Although individually they may be rare, between them they affect a lot of people and this is the 'paradox of rarity' - it is not unusual to have a rare disease. In Europe for example a 'rare' disease is defined as a disease that affects fewer than 1 in 2,000 people and yet about 30 million people, or between 6 and 8% of the European population suffer from a rare disease.

(Figures from “Rare Diseases: understanding this Public Health Priority”)

Wednesday, February 27, 2013

CJD videos

UCSF's Memory and Aging Center has a nice collection of videos on CJD and prions at their website and on their YouTube channel.

"Confronting CJD & Other Prion Disorders" is a very nice overview but there are 30 videos in total, many that might answer questions you have. From First symptoms of CJD to Is beef in the U.S. safe to eat? And then there's ' Can you have a man in a tie explain prions with plasticware'?

Tuesday, February 26, 2013

Killing prions

How do you kill something that isn't alive? With great difficulty.

The Challenge of Prion Decontamination
Iatrogenic transmission of these diseases via contaminated medical devices is considered rare, but it has been documented. In an experimental case, transmission of the disease was observed despite cleaning and decontamination of the medical device with formaldehyde. Clinically, 2 cases of TSEs have been confirmed in which transmission of the disease was due to the use of implanted depth electrodes that had been previously used on a patient with CJD and were inadequately decontaminated by cleaning with benzene and disinfecting with 70% alcohol and formaldehyde. Other cases have been linked to the use of neurosurgical instruments. These reports highlight the need for safe and effective prion decontamination methods.

The World Health Organization and the US Centers for Disease Control and Prevention recommend that instrumentation used in cases likely to have high infectivity be immediately destroyed after use; short of destruction, it is recommended that heat and chemical decontamination be used in combination to process instruments that come in contact with high-infectivity tissues.

Monday, February 25, 2013


For a wealth of fascinating historical information on Kuru check out the website for the 2009 Australian documentary Kuru: the science and the sorcery. There are trailers for the show and many outtakes, picture galleries and video clips.

The whole show has been posted to YouTube, although not officially.

The picture shows anthropologist Ronald Berndt, who proposed that Kuru was a psychosomatic disease - a reaction by the locals to European contact.

Sunday, February 24, 2013


A little off-topic but everyone should read this (part of the educated citizen thing).

Time Magazine has a big cover story on the high cost of healthcare in the US. As usual the examples are shocking.

From the high costs of basic items (aspirin with a 10,000% markup) to the high wages at "non-profits" (14 administrators at New York City’s Memorial Sloan-Kettering Cancer Center, a non-profit, who are paid over $500,000 a year, including six who make over $1 million). However the saddest part of this story is that the HIGHEST costs of healthcare are often borne by those LEAST able to pay.

If you are confused by the notion that those least able to pay are the ones singled out to pay the highest rates, welcome to the American medical marketplace.

Well worth a read. So why is the system so hard to change? Because there is so much money being made the healthcare industry as a whole not only spends the most on lobbying (the 2012 figures are below) but also come 12th, 14th and 16th for good measure. 2012 wasn't an unusual year either. Since 1998 the healthcare industry has spent 5.36 BILLION dollars on lobbying. That's more than twice as much as defense and oil & gas lobbyists combined.

Saturday, February 23, 2013

Friday's videos

If missed class on Friday here are two videos you missed. Plus a bonus video at the end if you already saw these two.

The last video shows a horsehair worm (Nematomorpha) exiting from its host.  The larvae live inside the insect and absorb nutrients directly through their skin. The adults are mostly free living in freshwater or marine environments

In Spinochordodes tellinii, which has grasshoppers and crickets as its larval host, the infection acts on the insect's brain and causes it to seek water and drown itself, thus returning the nematomorph to water. They are also able to survive the predation of their host, being able to wriggle out of the predator that has eaten the host! This manipulation of the host is documented here: Do hairworms (Nematomorpha) manipulate the water seeking behaviour of their terrestrial hosts?

Friday, February 22, 2013

Good news everybody!

Browsing through some of the more recent papers on toxoplasmosis I came across this gem from last year:
Toxoplasma gondii Infection in the Brain Inhibits Neuronal Degeneration and Learning and Memory Impairments in a Murine Model of Alzheimer's Disease

Immunosuppression is a characteristic feature of Toxoplasma gondii-infected murine hosts. The present study aimed to determine the effect of the immunosuppression induced by T. gondii infection on the pathogenesis and progression of Alzheimer's disease (AD) in Tg2576 AD mice. 
In addition, water maze and Y-maze test results revealed retarded cognitive capacities in uninfected mice as compared with infected mice. These findings demonstrate the favorable effects of the immunosuppression induced by T. gondii infection on the pathogenesis and progression of AD in Tg2576 mice.

So it's not all bad - at least if you're a mouse. A more digesitible summary of this research appeared in the Economist magazine: It's all in your head

Thursday, February 21, 2013

Good news (for raw beef eaters anyway)

Consumption of raw or undercooked meat is a major risk factor for contracting toxoplasmosis. Somebody asked in class whether a fondness for rare steaks would doom them to a life of slightly lower reaction times.

I looked into this and the good news is that all meat is not equal. The risk is MUCH greater from pork, lamb and venison. Cows are relatively poor hosts and Toxoplasmosis is rarely found in 

In this study from Clinical infectious Disease last year they analysed several studies involving thousands of samples of retail meat and came to some interesting conclusions regarding organic meat.

An upsurge in consumer demand for “organically raised” and “free range”’ pork products has resulted in increasing numbers of pigs being raised in nonconfinement systems and several studies have shown higher rates of Toxoplasmosis infection in organically raised pigs. (eg, viable T. gondii was isolated from 17 of 33 organically raised pigs from Michigan). However pigs are not tested for T. gondii infection at slaughter.

So the conclusion would seem to be that if you must eat meat then cook it thoroughly. If you must eat undercooked meat then steak may be your best bet. 

Wednesday, February 20, 2013

Toxoplasmosis and schizophrenia

From Psychiatric News this month:

Psychiatrist Hunts for Evidence Of Infection Theory of Schizophrenia

The theory that psychotic disorders are caused by infection went for decades without receiving more than an occasional raised eyebrow from researchers, but new studies have revived interest in its validity. If the theory turns out to be correct, psychiatry could begin to find cures in antimicrobials.
The prime suspect is Toxoplasma gondii, a protozoan parasite carried primarily by cats.
“When we started, it was considered a crazy idea,” psychiatrist E. Fuller Torrey, M.D., executive director of the Stanley Medical Research Institute (SMRI), told Psychiatric News. In the early 1970s, Torrey began to suspect an infectious origin of schizophrenia. He has been on this trail for decades.

Another piece of the evidence puzzle is that T. gondii can manufacture dopamine. “We know toxoplasma has the genes to produce a precursor of dopamine,” said Torrey. Excess dopamine in the brain has long been associated with psychosis. “This idea that excess dopamine [in schizophrenia] may be coming from an outside organism is kind of mind-blowing,” he said, marveling at the “smart little organism.”

We will talk more about Toxoplasmosis and Schizophrenia next class.

Tuesday, February 19, 2013


Ralph Wiggum: At my house, we call them uh-ohs. 

It's perhaps surprising to hear that Biosafety labs in the United States only have a limited requirement to report accidents. A 2007 news article in the journal Nature, Biosafety labs urged to report accidents and near misses, based on a report from  the University of Pittsburgh's Center for Biosecurity, calls for a federal system to analyse mistakes in Biosafety Level 3 and BSL-4 laboratories to prevent future accidents.

Researchers funded by the National Institutes of Health (NIH) have to report accidents to the NIH, although there is no penalty if they neglect to do so. 

Incidents involving recombinant DNA must be reported if occurring at an institution that receives any NIH funding. 

And exposure to pathogens on the US 'select agent' list, such as anthrax, need to be reported to the Centers for Disease Control and Prevention (CDC), or the Department of Agriculture.

But that's about it and there's undoubtedly a lot of accidents going on that are never reported. A 2009 analysis of US government laboratories discovered  395 incidents that involved the potential release of select agents between 2003 and 2009. The most common accident was "loss of containment" with 196 cases.

Monday, February 18, 2013

Plum Island

This video, from Wired, comes from back in 2008 before the decision was made to place the new National Bio and Agro-Defense Facility (NBAF) in Manhattan Kansas. This new facility is designed to replace the Plum Island Animal Disease Center, near Long Island in New York State, and one option being considered at the time was to upgrade the Plum Island facility.

Foot-and-mouth disease is a highly infectious viral disease of cloven hoofed animals including cattle. It is not endemic to the United States and could cause billions of dollars of damage if it was released (a 2001 outbreak in the United Kingdom cost $16 billion).

Federal law stipulates that live foot-and-mouth disease virus cannot be studied on the mainland, and so Plum Island is currently the only laboratory in the U.S. studying it. Plum Island has accidentally released foot-and-mouth disease at least three times, most recently in 2004.

One of the arguments FOR locating the NBAF in Kansas is that it will be in the middle of the nation's cattle belt. What could possibly go wrong?

Hint: a second outbreak in the UK in 2007 was traced back to a strain used at the Institute for Animal Health and an examination of the 'secure' facility revealed an old, poorly maintained and defective effluent system.

Sunday, February 17, 2013


If you don't know much about the 2001 anthrax attacks on the US then the UCLA Department of Epidemiology has a nice website with lots of links.

The FBI website has a lot of images of original material and presents a fairly compelling case that U.S. Army Medical Research Institute of Infectious Disease researcher Bruce Ivins was solely responsible. However since Ivins killed himself in 2008 as the investigation closed in there was no trial and, for some people, no closure.

In response to this the FBI asked the National Academy of Sciences (NAS) to conduct an independent review of the scientific evidence that led the agency to implicate Ivins in the anthrax letter attacks. The NAS committee released its report three years later after exhaustively covering all the evidence and conducting public hearings. They concluded that it was "impossible to reach any definitive conclusion about the origins of the anthrax in the letters, based solely on the available scientific evidence". The report also challenged the FBI and U.S. Justice Department's conclusion that a single-spore batch of anthrax maintained by Ivins at his laboratory at Fort Detrick in Maryland was the parent material for the spores in the anthrax letter.

This conclusion was welcomed by various conspiracy theorists although it really only points out the weaknesses in the governments case. Of course the fact that the FBI had previously been convinced that someone else was the perpetrator doesn't exactly inspire confidence. Dr Steven Hatfill eventually sued the FBI, the Justice Department, John Ashcroft, Alberto Gonzales, and others for violating his constitutional rights and the government settled the case for $5.8 million.

Regardless of whether he was the perpetrator or not (my guess is that he was) Bruce Ivins was clearly a few sandwiches short of a full picnic which raises the question that everyone seems to overlook:

Why was a mentally disturbed person allowed to continue working with highly dangerous pathogens?

Answer: Because the army wants them to.

"Individuals will be mentally alert, mentally and emotionally stable, trustworthy, physically competent....."

This is part of the US army regulation covering scientists working on bioweapons. (Actually bioweapon 'defence' since the US doesn't work on bioweapons).

Unfortunately it appears that this modest list of conditions - which, let's face it, isn't that different to the characteristics you might look for in a date - is too much for the workers at the US Army Medical Research Institute of Infectious Diseases (USAMRIID). In 2007 the deputy commander for safety wrote:
'The possibility of losing talented and well-trained researchers to other facilities.... with less stringent programs.... may impact the ability of the Defense Threat Reduction Agency to provide research personnel to combat biological agent use.'

Saturday, February 16, 2013

"Serious" airflow problems

Headlines you don't want to see, from last June:

Air Leak Sparks Safety Fears at CDC Bioterror Lab

The Centers for Disease Control and Prevention, the federal agency charged with preventing the spread of infectious diseases has come under attack today for "serious" airflow problems in an Atlanta building that houses anthrax, SARS and monkeypox.

Documents and emails obtained by USA Today suggest that a poorly engineered airflow system in the CDC's Building 18 could expose unprotected staff and visitors to dangerous airborne pathogens.

The CNN report on the same incident also contains this gem:

There has been at least one other safety-related incident in that same building where February's air leak occurred.
In 2008, it was discovered that a high-containment lab door was sealed with duct tape. 

That one doesn't bother me too much. Duct tape is pretty good stuff.

Friday, February 15, 2013


‘Totally drug-resistant’ tuberculosis spreads in South Africa as researchers warn global outbreak would be ‘untreatable’
The world is facing outbreaks of “totally drug-resistant” tuberculosis if explosions of the bacteria in South Africa and other poorer nations are not addressed, according to a new papers published in Emerging Infectious Diseases. At this point, researchers are working to determine how the bacteria gains its invincibility, and how to isolate it.

Like the situation in India the argument over whether the South African strains are 'extensively drug-resistant or 'totally' drug resistant is beside the point. Extensively drug resistant tuberculosis (XDR-TB) is already a big enough problem. Here are some statistics from an earlier post comparing different strains of TB.

Tuberculosis (TB)
  • Cost of drug treatment: $10-$20
  • Course of treatment: 6 months
  • Side effects of treatment: generally minor but may include vomiting, nausea and loss of appetite.
Multi-drug-resistant Tuberculosis (MDR-TB)
  • Cost of drug treatment: up to $5,000 - $20,000
  • Course of treatment: 2 years
  • Side effects of treatment: side-effects are more serious and include hepatitis, depression and hallucinations.
Extensively drug-resistant Tuberculosis (XDR-TB)
  • Cost of drug treatment: cases have been dealt with individually - some have cost $500,000
  • Course of treatment: as long as it takes, many patients die
  • Side effects of treatment: severe, in South Africa many patients discontinued treatment stating that they would rather die.

Thursday, February 14, 2013

Proximity patterns

Here's a neat idea:

To investigate transmission pathways, European researchers of the SocioPatterns collaboration fitted 119 people in a ward of the Bambino Gesù Children's Hospital with radio-frequency identification (RFID) badges. The tags registered face-to-face interactions—and the potential spreading of airborne pathogens.

The original 2011 research paper is here: Close Encounters in a Pediatric Ward: Measuring Face-to-Face Proximity and Mixing Patterns with Wearable Sensors

When Scientific American reported on this research they included a series of striking diagrams that may, or may not, help interpret the results!

Wednesday, February 13, 2013

Ask a lawyer

An interesting question in class today - can you sue the hospital if you get a hospital acquired infection?

Just googling any version of this query brings up a lot of similar questions and links suggesting this is a pretty popular question.

Lets ask a lawyer:

Can I sue a hospital if I contract MRSA while in the hospital?

Answer (from an Ohio 'MRSA lawyer' !):

In order to sue a medical provider in Ohio and in many other states, you have to show that the hospital or medical facility had a duty to keep you safe, was negligent in that their treatment standard of care fell below that of an ordinary hospital in the area, and that as a result of their negligent and careless acts, you contracted MRSA or did not get treated quickly or effectively with negative consequences.

As any competent MRSA lawyer / attorney will tell you, if you want to sue a hospital or medical provider after you contract MRSA, you have to basically show they did something wrong that led to you contracting MRSA or not get treated correctly for MRSA.  As you can see these cases depend on the specific facts of each case. This breaks down to basically several theories of negligence? I will discuss four of them here.

Negligence / Failure to protect you from danger of catching MRSA
Delay in diagnosing MRSA
Delay in treatment of MRSA
Using wrong drugs to treat MRSA

So the key issue is negligence which can be difficult, but not impossible, to prove. Getting an infection and proving it came from the hospital is not sufficient. You need to prove the hospital was, in some way, negligent. The fact that some individuals have won big settlements has attracted a swarm of lawyers who are eager for cases. (I found this on one site: 'hospital infections are said to be the next asbestos'. The good news is that this may lead hospitals to improve their practices. The bad news is that it will further drive up medical costs.

Tuesday, February 12, 2013

Antibiotic-Resistant Bacteria in meat

The title of this post at Wired's Superbug blog says it all:

The Pew Campaign on Human Health and Industrial Farming (of the Pew Charitable Trusts) has been tracking this data year to year, and this year retrieved some additional data from the human side of the pharma industry to use as a comparison. They found that human-use antibiotics totaled 3.5 million kilograms, or 7.7 million pounds, in 2011.

It’s worth noting that this continued antibiotic use, and continued and rising appearance of resistant bacteria on meat, is happening as the FDA has abandoned attempting to regulate livestock producers’ use of antibiotics, and has switched to a voluntary approach. Given the trend, I think it’s worth asking how well that voluntary approach is going to work.

Monday, February 11, 2013

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 2009 TED conference. 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.

There's also a New Yorker article from 2010 that covers Nathan Wolfe's work although unfortunately it's behind their paywall now:

Sandrine had just finished preparing the meat for dinner. I asked her if she understood how risky it was to plunge her hands into the intestines of a dead monkey. “Yes,” she said. “I know that bushmeat is dangerous. That it can kill my children.” She was also aware that there had been an outbreak of Ebola recently in Congo. I wondered whether she or her husband had ever seen dead monkeys or gorillas in the forest. She nodded, gazing at the dark foliage as night began to fall. “What did you do when you saw them?” I asked. She turned to me and smiled. “I thanked God, picked them up, and brought them home for dinner,” she said.

Sunday, February 10, 2013

Modern-Day Typhoid Marys

A nice article on superspreaders from Slate magazine a few weeks back.

Modern-Day Typhoid Marys: Superspreaders can turn a minor outbreak into a pandemic.

Key to the disease’s spread, researchers found, was a small but crucial portion of the population that became known as “superspreaders,” people who transmitted the infection to a much greater than expected number of new hosts. The more scientists learn about superspreaders, the more they are beginning to realize that this tiny segment of the population is the driving force behind the emergence and spread of infectious diseases.

Saturday, February 9, 2013


I recently came across this somewhat shocking story from 2008.

For most people, the idea of being judged insane and held in a 1950s asylum is the stuff of nightmares. But to be locked up when you are sane would be regarded as an appalling injustice.
And yet a BBC investigation has revealed that nearly 50 women were locked in an isolation ward in a mental asylum in Surrey - not because they had a mental illness - but because they carried typhoid and were deemed a public health risk.


They were held at Long Grove Hospital - a mental asylum in Surrey - which started admitting carriers of typhoid as early as 1907 and continued through the 1940s and 1950s. Once admitted, those women never left. 

One former nurse says that many of those women - admitted sane - deteriorated mentally, driven mad by the conditions they lived in. Others remained in full possession of their senses, despite enduring conditions such as solitary isolation.
It was 1992 when Long Grove finally closed.

The woman pictured above is Rosina Bryans, who was locked up for 60 years. SIXTY YEARS!

There's a twenty minute video at the BBC site that has a lot more information.

Friday, February 8, 2013


I post this every year but I think it could lead to some interesting discussion.

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?

Thursday, February 7, 2013

The Berlin Patient

I was looking for updates on Timothy Ray Brown (aka 'The Berlin Patient' aka 'The man cured of AIDS') when I came across this interview he did with Democracy Now (which is broadcast locally on KCSB).

The interview also includes Dr. Jeffrey Laurence an AIDS researcher who clearly explains why this is a good step forward but not a cure for everyone:

(T)he way it was done in Mr. Brown is off the realm of practicality. It’s way too expensive. You’re going to need another fatal disease in order to get one of these things. The risk of dying from such a bone marrow transplant or stem cell transplant is about 20 percent in the first hundred days after the transplant, and it’s very expensive. And also, I should emphasize that finding the donors are not easy. This mutation that causes this disruption of the door, CCR5, that the AIDS virus needs to get into a cell, is found in about 1.5 percent of all Caucasians in America, about 4 or 5 percent of all Scandinavians and northern Russians, but it’s found in no African Americans, in no blacks, in no Africans, in no Oceanics, in no Asians, in no American Indians. So, it’s—for large portions of the population, it’s not even going to be helpful.

Wednesday, February 6, 2013

Tb hideout

Thanks to Mary for the tip on this report:

Stem Cells: Safe Haven For TB

Mycobacterium tuberculosis (TB) hides out in stem cells deep within bone tissue, where it avoids detection from the immune system and drugs, according to a study published last week (January 30) in Science Translational Medicine.
Ninety percent of TB infections are cleared by the body’s immune defenses or by taking anti-TB medication. In the remaining 10 percent of cases, however, TB persists as a dormant, non-replicating infection. Though latent TB infections do not cause symptoms, they can reactivate after years of hiding. An estimated one-third of the global population has latent TB, which accounts for 1.7 million deaths per year—more than any other bacterial pathogen on the planet. 

During the early stages of the disease, active TB bacteria replicate inside human macrophages and dendritic cells. But there is no evidence these cells harbor dormant TB, and the location of the latent reservoir has remained a mystery.

The original paper is in Science Translational medicine this week: CD271+ Bone Marrow Mesenchymal Stem Cells May Provide a Niche for Dormant Mycobacterium tuberculosis.

Tuesday, February 5, 2013

Public service announcement

A repeat from 2011 but consider this a public service announcement.

Regardless of what you may have heard about chlamydia it's actually HPV, Human Papillomavirus Virus, that is the most common sexually transmitted infection in the US. One of the reasons for this is that in many cases the infected person has no signs or symptoms. Because of this the CDC estimate that by the age of 50 more than 80% of American women will have contracted at least one strain of genital HPV.

Whoa. Screechy noise. Backup.  By the age of 50 more than 80% of American women will have contracted at least one strain of genital HPV.

Although only a small percentage of these women will develop cervical cancer the fact that such large numbers of women are infected each year means that up to 1 million American women are diagnosed with cervical dysplasia each year. Cervical dysplasia, caused by HPV, is a precursor to cervical cancer and is painful and costly to treat. Of these 1 million cases each year about 11,000 subsequently develop cervical cancer and about 4,000 of these women will die. Every year.

So a safe and effective vaccine is going to be a great discovery right?

Widespread vaccination has the potential to reduce cervical cancer deaths around the world by as much as two-thirds, if all women were to take the vaccine and if protection turns out to be long-term. In addition, the vaccines can reduce the need for medical care, biopsies, and invasive procedures associated with the follow-up from abnormal Pap tests, thus helping to reduce health care costs and anxieties related to abnormal Pap tests and follow-up procedures.
—American National Cancer Institute

Because so many women are infected it is clear that women need to be vaccinated before they can become infected. The best way to do this is to vaccinate them before they become sexually active .

Oh oh. We used the sex word.
Wait, am I missing something here? We leave it up to private companies to develop vaccines and then we find it somehow sinister if they push for mandatory vaccinations when they develop an effective vaccine against a disease that kills thousands. Oh and did I mention that it is estimated (by the CDC) that at any one time 1% of sexually active adults have genital warts (also caused by HPV).

Don't make me post the genital wart pictures....

Monday, February 4, 2013

The Cow-Pock

As I mentioned in class, objectors to vaccination have been around for a long time.

In this famous cartoon from 1802, the British satirist James Gillray caricatured a scene at the Smallpox and Inoculation Hospital at St. Pancras, showing Edward Jenner administering cowpox vaccine to frightened young women, and cows emerging from different parts of people's bodies. The cartoon was inspired by the controversy over inoculating against the dreaded disease, smallpox. The inoculation agent, cowpox vaccine, was rumored to have the ability to sprout cow-like appendages. 

This is undoubtedly due to the fact that vaccination was invented prior to any understanding of immunology or even a germ theory of disease.

Sunday, February 3, 2013

Melanie's Marvelous Measles

Melanie's Marvelous Measles was written to educate children on the benefits of having measles and how you can heal from them naturally and successfully. Often today, we are being bombarded with messages from vested interests to fear all diseases in order for someone to sell some potion or vaccine, when, in fact, history shows that in industrialized countries, these diseases are quite benign and, according to natural health sources, beneficial to the body. Having raised three children vaccine-free and childhood disease-free, I have experienced many times when my children's vaccinated peers succumb to the childhood diseases they were vaccinated against. Surprisingly, there were times when my unvaccinated children were blamed for their peers' sickness. Something which is just not possible when they didn't have the diseases at all. Stephanie Messenger lives in Brisbane, Queensland, Australia, and devotes her life to educating people about vaccine dangers and supporting families in their natural health choices. She has the support of many natural therapists and natural-minded doctors.

Some Measles facts courtesy of the CDC.

About 30% of measles cases develop one or more complications, including Pneumonia, which is the complication that is most often the cause of death in young children.
Ear infections occur in about 1 in 10 measles cases and permanent loss of hearing can result.
As many as 1 out of every 20 children with measles gets pneumonia, and about 1 child in every 1,000 who get measles will develop encephalitis. (This is an inflammation of the brain that can lead to convulsions, and can leave the child deaf or mentally retarded.)
For every 1,000 children who get measles, 1 or 2 will die from it.
Measles also can make a pregnant woman have a miscarriage, give birth prematurely, or have a low-birth-weight baby.
In developing countries, where malnutrition and vitamin A deficiency are common, measles has been known to kill as many as one out of four people. It is the leading cause of blindness among African children. Measles kills almost 1 million children in the world each year.

Check out some of the book reviews on Amazon from people who suffered from measles as a child.

Saturday, February 2, 2013


If you'd like to read more about the MMR-Autism issue then the American Medical Association has a fairly in depth page on its Pediatric Vaccination website: The relationship between the MMR vaccine and autism.

A couple of aspects you may find interesting:

About 90 percent of children in England received MMR at the time this paper was written. Because MMR is administered at a time when many children are diagnosed with autism, it would be expected that most children with autism would have received an MMR vaccine, and that many would have received the vaccine recently. The observation that some children with autism recently received MMR is, therefore, expected. 

Perhaps the best data examining when symptoms of autism are first evident are the "home-movie studies". These studies took advantage of the fact that many parents take movies of their children during their first birthday (before they have received the MMR vaccine). Home movies from children who were eventually diagnosed with autism and those who were not diagnosed with autism were shown to blinded eurodevelopmental specialists. Investigators were, with a very high degree of accuracy, able to separate autistic from non-autistic children at one year of age.

These studies found that subtle symptoms of autism are present earlier than some parents had suspected, and that receipt of the MMR vaccine did not precede the first symptoms of autism.

Friday, February 1, 2013

Scare stories and gutter press

It's a sad, but true, fact that it is a lot easier to scare people than it is to unscare them. Certain newspapers love to scare people with any anecdotal association they can dig up.The picture to the left is from Britain's Daily Mail.

The Daily Mail has been campaigning against the HPV vaccine for some while. But they have a right to that opinion. Except it turns out they don't even have that opinion. On the other side of the Irish Sea the Irish edition of the SAME NEWSPAPER is campaigning FOR the HPV vaccine.

From Martin Robbins at

“Are they insane?! They’re printing scare stores about the dangers of the HPV vaccine in one country, while simultaneously campaigning for its introduction in another. It’s so absurdly cynical that I can’t quite form the words to convey just how shocked I am by this. Even by the piss-poor journalistic standards of the Daily Mail, this takes quite some beating.

What this means is that those of us who believed that the Daily Mail had some editorial, ideological stance against certain vaccines (such as MMR) were in fact wrong. The Daily Mail position on vaccines is whatever sells newspapers – and if those positions are completely self-contradictory, or might cause a bit more cancer in the readership, then who cares, as long as the advertisers are happy?

In many ways, this is worse than being anti-vaccine. Anti-vaccinationists may be cranks, but at least they ultimately care about the people affected. The revelation that the Mail is pushing two contradictory positions on a major public health issue on either side of the Irish Sea, proves once and for all that they don’t give a crap about the impact such stories may have on their readers. It’s a whole new level of sick. It’s crossing the line where misguided becomes truly evil.”

Thursday, January 31, 2013

Reanimated post

It seems appropriate to reanimate this blog post from the graveyard

I introduced the basic SIR model for a simple epidemic to you. This model actually has a long history and was first described by Kermack and McKendrick in 1927.

As I indicated this model has since been expanded to include virtually every disease scenario you can imagine.

In 2009 a group of Canadian mathematicians used this SIR format as the basis for an analysis of a zombie epidemic. Their paper: WHEN ZOMBIES ATTACK!: MATHEMATICAL MODELLING OF AN OUTBREAK OF ZOMBIE INFECTION ) - somehow it seemed appropriate to keep that in capitals) - describes a model that should look basically familiar to you.

Notice in their S Z R model (Z for Zombie of course) there are two extra transitions - from R back to Z (reanimation of the dead is well established in the zombie movie genre) and a movement directly from S to R (non zombie related death which can be quite high in this genre and so worth taking account of).

This is, perhaps unsurprisingly, the first mathematical analysis of an outbreak of zombie infection. While the scenarios considered are obviously not realistic, it is nevertheless instructive to develop mathematical models for an unusual outbreak. This demonstrates the flexibility of mathematical modelling and shows how modelling can respond to a wide variety of challenges in ‘biology’.

In summary, a zombie outbreak is likely to lead to the collapse of civilisation, unless it is dealt with quickly. While aggressive quarantine may contain the epidemic, or a cure may lead to coexistence of humans and zombies, the most effective way to contain the rise of the undead is to hit hard and hit often. As seen in the movies, it is imperative that zombies are dealt with quickly, or else we are all in a great deal of trouble.

Wednesday, January 30, 2013

Coming back to bite you

Would Bubonic Plague make a good weapon?

A 1970 World Health Organization assessment asserted that in a worst-case scenario a dissemination of 50 kg of Yersinia pestis in an aerosol cloud over a city of 5 million might result in 150,000 cases of pneumonic plague. Of those, 80,000 to 100,000 cases would require hospitalization, and 36,000 victims would be expected to die.

Of course there are numerous difficulties involved in getting 50kg of bacteria into an aerosol cloud. You could just breed infected fleas instead but, as the video says, they may well come back to bite you...


Tuesday, January 29, 2013

Got Plague?

In 1914, three men in New Orleans examine rats to determine if they are carrying bubonic plague.  

This article from Discovery news this week has a slightly alarmist headline but makes some good points.

Plague, in humans, doesn't pop up a lot. Generally there are between one and seventeen cases per year in the United States, and only about a thousand in total since 1900. 
Remembering, and mentioning, exposure to dead or dying animals is key. As for efforts to eliminate it completely - although they've been considered, it would take too much extensive trapping and  it would take too much extensive trapping and testing of animals to be easily accomplished while the plague is still so rare. It looks like we'll continue getting the plague for the foreseeable future.

Monday, January 28, 2013

Traditional videos

The posting of the following videos has become traditional during the Bubonic Plague section of the course. The first one isn't strictly bubonic plague related, it's just included because of the flagellants.

The Daily Show with Jon StewartMon - Thurs 11p / 10c
Bubonic Plague
Daily Show Full EpisodesPolitical Humor & Satire BlogThe Daily Show on Facebook

Sunday, January 27, 2013

Lizard loss

If lizards are so important in keeping California relatively Lyme disease free then what would happen if we were to lose the lizards from an area? This is the sort of thing that might happen with a dramatic change in habitat.

Well this has been tested experimentally and the results are a little surprising.

“Our expectation going into this study was that removing the lizards would increase the risk of Lyme disease, so we were surprised by these findings,” said study lead author Andrea Swei, who conducted the study while she was a Ph.D. student in integrative biology at UC Berkeley. “Our experiment found that the net result of lizard removal was a decrease in the density of infected ticks, and therefore decreased Lyme disease risk to humans.”

The researchers found that in plots where the lizards had been removed, ticks turned to the female woodrat as their next favorite host. On average, each female woodrat got an extra five ticks for company when the lizards disappeared.

However, the researchers found that 95 percent of the ticks that no longer had lizard blood to feast on failed to latch on to another host.

“One of the goals of our study is to tease apart the role these lizards play in Lyme disease ecology,” said Swei, who is now a post-doctoral associate at the Cary Institute of Ecosystem Studies in New York. “It was assumed that these lizards played an important role in reducing Lyme disease risk. Our study shows that it’s more complicated than that.”

Notwithstanding the results in this new study, Lane pointed out that the Western fence lizard are key to keeping infection rates down among adult ticks. “This study focused only on the risk from juvenile ticks, specifically those in the nymphal stage,” he said. “The earlier finding that adult ticks have lower infection rates because they feed predominantly on the Western fence lizard at the nymphal stage still holds.”

For more information check out this press release from UC Berkeley: Tick population plummets in absence of lizard hosts or the original article here: Impact of the experimental removal of lizards on Lyme disease risk.