EID

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).

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):

Influenza Prevention Update: Examining Common Arguments Against Influenza Vaccination.

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.

Flu trends

Well in case you hadn't read the news, or noticed all the sick people, it's a pretty bad flu season this year. It's already shaping up to be worse than 2009 in terms of total cases and the virulence is actually worse as this year's strain appears to be quite nasty.

Google's flu tracker now has data by state and by cities and is a great illustration of using our search data for public good. Google can track flu trends several weeks before healthcare data is available simply by tracking the search terms people use (see 'How does this work?')

We'll talk more about influenza, why strains vary, why you need a new vaccine every year and where pandemics come from in a later class. But for now, here's a public service announcement from the executive director of UCSB student health.

Due to the increasingly serious influenza illnesses spreading across the country, we encourage all students and staff to receive a flu shot as soon as possible. Faculty & staff are encouraged to obtain their shots from their local healthcare providers, and many retail pharmacies also offer flu shots.

Student Health will be offering special times when flu shots for students can be obtained quickly without appointments in the Student Health Classroom on Tuesdays or Fridays 1:30 - 3:30pm. 

Alternatively students may obtain flu shots at our regularly scheduled Immunization Clinics Monday - Friday 10:00 am - 12:00pm & 1:30 - 3:30 pm; check in at the designated Immunization computer in the Student Health lobby. There is no additional cost for students with UC SHIP insurance, and for other students the cost is $20 and is billed to BARC.

Symptoms of flu include fever, cough, fatigue and joint aches. Medications can be prescribed to shorten the course of the illness if treatment begins within the first 48 hours, but otherwise the treatment is rest and over-the-counter painkillers. Most cases of flu don’t need to see a doctor unless there are serious symptoms, or can come in the first 2 days of illness when prescription medications may shorten the course of illness.

Please DO NOT GO TO CLASS OR WORK when you are ill to avoid spreading illness to others! The best way prevent the spread of illness is by avoiding others when ill, covering your cough and washing your hands. You should not have intimate contact or share cups or food utensils with people who are ill. Further information can be found at http://studenthealth.sa.ucsb.edu and http://www.flu.gov.             

TED talk

I came across this video of Laurie Garrett, the author of the Coming Plague, speaking at a small TED event in 2007. This was before the H1N1 swine flu of 2009 and so she is mainly talking about H5N1 avian flu. I think she makes a lot of very interesting points and the talk acts as a great review, not just for the final week but also for other topics we covered.

Swine flu (and conspiracy theories)

I just watched a whole bunch of videos about swine flu to see if there was a nice simple summary I could post here. It's amazing some of the crazy stuff that is out there. Not only is there a whole Swine flu conspiracy theory but its wrapped up with chemtrails, the new world order and probably Lee Harvey Oswald if you watch further than I did. You can get all your conspiracy theories covered in one go in this video which takes a look at some of them.

The video above is a nice simple illustration of where Swine Flu came from and reviews some of the topics we covered in class. It also simply explains why we might expect more contagious strains of flu to be less dangerous - it's all down to which part of the respiratory tract they infect.

To publish or not?

Some of you may have read about an interesting disease related debate that is going on right now and is attracting quite a lot of media attention. It concerns the H5N1 strain of influenza that appears to have a high mortality rate in people but is currently poorly transmitted between people (if it is even transmitted at all).

In 2011 two teams of scientists created mutant strains of H5N1 influenza (ie avian or bird flu) that could be more easily passed between mammals in a laboratory setting (ferrets are the animals of choice for flu studies apparently). Scientifically this is interesting research and could address several public health issues: can this strain become more easily transmitted without losing its virulence? Which changes should we watch out for? How many mutations does such a change require?

However as the papers were reviewed the US National Science Advisory Board for Biosecurity (NSABB) recommended that the results of the two studies should only be published in a redacted form. They advised that methods and details should be left out for fear the research could fall into the wrong hands and be used to create a pandemic that might kill tens of millions of people. This unprecedented move sparked a broader debate about censorship and responsibility in potentially dangerous research.

It also provoked some sensational headlines:
Controversial 'Armageddon' super virus recipe to stay secret - for now - Sydney Morning Herald

In a meeting last month the World Health organization came to a different conclusion. A panel of 22 experts  concluded that the mutant flu studies should be published in full. They argued that redaction would likely be ineffective and that the benefits outweighed the potential risks.

Nature have put together a web special on the H5N1 controversy that compiles a variety of papers, reports and commentary (and is also the source for this fantastic chicken image).

Disease Sleuths

I've posted about Google's flu tracker and how Twitter is being used to track diseases before but I thought NPR's little animation was nice. The article: Disease Sleuths Surf for Outbreaks Online expands on it and is also interesting. This type of tracking is not suitable for all diseases:

In the early days of the cholera outbreak, Twitter and HealthMap data closely matched official reports. After 100 days online activity dropped off even though the epidemic raged on. Disease is easiest to detecte when it is out of the ordinary. Regularly recurring maladies like malaria are hard to follow online.

But it's a hot topic at the moment and even has a new name 'Webidemiology'. I hadn't realized that Google had expanded its surveillance to include Dengue Fever.

Papers in limbo

We won't talk about influenza until week 10 but the theme of a paper in Science this week is very pertinent to the biosafety topic this week -
Does Forewarned = Forearmed With Lab-Made Avian Influenza Strains?

H5N1 Influenza has a human mortality rate of over 50% but does not yet spread among humans. Two groups of scientists in investigating why this is have created strains that DO spread easily among ferrets (a common model for human drug strains). Should they be able to publish the results of their work?

Papers about the studies, stuck in limbo at Science and Nature, remain unpublished while scientists, journal editors, and public health officials weigh the benefits and risks of full disclosure.

Proponents of full disclosure, including the researchers who conducted the work, contend that knowing the genetic signatures of these potentially devastating viruses might prove pivotal to shoring up surveillance measures and controlling an emerging threat.

Maybe, say opponents in the other camp, but they stress that in the predominantly poor countries where H5N1 circulates, surveillance and control systems are too rudimentary, or nonexistent, to take advantage of the new knowledge. They worry that if published, that data could provide a recipe for bioterrorists to unleash a doomsday scenario.

Thermal scanning for flu

If there is an influenza pandemic then initial attempts at isolating the outbreak, or prevent its entry into particular countries, may involve the use of infrared thermal image scanners (ITIS) at airports to detect people with elevated body temperatures characteristic of influenza. We saw this in the 2009 H1N1 (Swine Flu) pandemic. Analysis suggests that countries that adopted the policy managed to delay disease entry for 7-12 days compared to countries that did not: Entry screening to delay local transmission of 2009 pandemic influenza A (H1N1). Of course there may be other differences between these two types of countries. Correlation is not causation...

A paper in PLoS ONE in January this year, Thermal Image Scanning for Influenza Border Screening: Results of an Airport Screening Study, looked at a sample of 1275 airline passengers who agreed to be screened, have their temperature actually measured and give a respiratory sample. Six of the travellers had a fever and thirty of the travellers tested positive for influenza. But none of the influenza-positive travellers had a temperature high enough to be considered in the fever group!

Our findings therefore suggest that ITIS is unlikely to be effective for entry screening of travellers to detect influenza infection with the intention of preventing entry of the virus into a country.

I'm sure we'll see more of these thermal scanners in airports in future pandemics even if they are fairly useless. Why? Because it makes it look like somebody is doing something (even if it is useless). Just like the rest of airport security

Swine Flu Survivors Built Super Flu Antibodies

A study of antibodies in people who were infected with H1N1 swine flu suggests that a universal flu shot that could neutralize many flu strains, including swine and avian flu. Scientists believe that people who were infected with H1N1 developed a unique immune response in which antibodies that could protect them from all the seasonal H1N1 flu strains that have appeared in the last decade were produced. A universal flu vaccine could have a major impact in controlling influenza which kills anywhere from 3,300 to 49,000 people every year in the U.S. Scientists are currently working on a vaccine from antibodies isolated from nine people who were infected with the first wave of the H1N1 swine flu pandemic. Of these, five of the antibodies were cross-productive so that they are able to interfere with many different flu strains. Studies in mice show that they were protected from what is considered a lethal dose of the flu. The vaccine is currently being tested in people.

Flu trends

Google has been tracking flu trends for some time by analyzing people's choice of search terms. This method has been very successful and they can usually pick up trends a few weeks before the CDC data. In 2009 a variety of workers from Google and one from the CDC published a paper in Nature describing their technique: Detecting influenza epidemics using search engine query data.

For epidemiologists, this is an exciting development, because early detection of a disease outbreak can reduce the number of people affected. If a new strain of influenza virus emerges under certain conditions, a pandemic could ensue with the potential to cause millions of deaths (as happened, for example, in 1918). Our up-to-date influenza estimates may enable public health officials and health professionals to better respond to seasonal epidemics and pandemics. 
 
The graph above shows, for the United States as a whole, that the peak flu season is usually in February and that we are probably past the peak this year. You can also see how unusual last year was, pandemic years are always different. The big peak in October is from 2009-2010. The same pattern was seen in California except that our peak flu season seems a bit less predictable.

PNAS

Two relevant but rather different papers in the latest Proceedings of the National Academy of Sciences (PNAS).

In the first: Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation, they describe how genomic analysis was used in the investigation of the 2001 anthrax attacks.

The paper describes how the Institute for Genome Sciences faculty and collaborators from the FBI found that the anthrax samples used in all the attacks were genetically identical. Later, another group of scientists -- also including Institute for Genome Sciences faculty -- would trace the anthrax spore used in the letters back to a flask of Bacillus anthracis and several samples taken from that flask. The primary custodian of the flask was Bruce Ivins, Ph.D., a scientist at a U.S. Army biodefense laboratory in Maryland. With this key investigative lead from the scientific team, the FBI used additional police work to conclude that Dr. Ivins was the perpetrator of the mail attacks. Dr. Ivins killed himself before the case could go to court. The FBI has since closed the Amerithrax investigation. (From a report at ScienceDaily)

In the second paper, Hybrid influenza viruses may have pandemic potential, which is relevant to this weeks discussion,  the authors describe how the H1N1 strain that caused the 2009 pandemic, but relatively few deaths, may yet turn out to be problematic. 

The H1N1 influenza virus that spawned the 2009 pandemic is now predicted to circulate as a seasonal flu. However, researchers fear it could once again present a major public health threat by recombining with the H9N2 virus, which is endemic to several bird species in Asia, and has infected pigs and humans. Yipeng Sun et al. explored this possibility by dissecting the H1N1/2009 and H9N2 influenza viruses, and systematically mixing their genes to generate 127 hybrid viruses. The authors then tested the hybrid viruses in mice to assess the likelihood that genetic reassortment between H1N1/2009 and H9N2 could create a virus of pandemic proportions. More than half of the hybrid viruses instantly infected mice and replicated as efficiently as did the parent strains. Eight of the hybrids proved more virulent and dangerous than did either of the two parent strains. Curiously, each of these eight strains carried a gene encoding part of the RNA polymerase, known as the PA gene, from the pandemic H1N1/2009 virus. The authors suggest that the pandemic PA gene may play a key role in the virus’s pathogenicity, and that screening H9 viruses for the gene might help identify influenza viruses that pose a public health risk.

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.

Flu Attack! How A Virus Invades Your Body

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

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

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

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

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

Infected by the Pig

Taking on Swine flu. Three videos. No comment.


Dr. Joe Bresee of the CDC takes on Swine Flu


Putnam Pig takes on Swine Flu


Elmo takes on Swine Flu

What They Say They Do and What They Actually Do

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

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

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

Flu buddy

Do you have a Flu Buddy?

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

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

Swine flu latest

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

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

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

Antibodies Offer a New Path for Fighting Flu

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

http://www.nytimes.com/2009/02/23/health/23flu.html?hp