Entries in H5N1 (11)

Nature's Declan Butler: Two Chinese H7N9 human clusters being investigated 

This afternoon, Nature's Declan Butler has one of the more fascinating -- and ominous -- dispatches since the H7N9 outbreak in China occurred. Nature bills itself as the international weekly journal of science.  It is one of the most respected publications of its kind in the world. 

And Declan Butler is not one to go around sounding alarms.  His articles are reasoned and insightful. SO it was with great concern that one of my IT people (shout-out Sean Nickerson) came into my office (my door is always open, insert Bob Newhart quip here).  He had just gotten an email with a link to the Nature story.

Here is a snippet:

There is still no evidence of any sustained human-to-human spread of the H7N9 virus. But the World Health Organisation confirmed on Saturday that Chinese authorities are investigating two suspicious clusters of human cases. Though these can arise by infection from a common source, they can also signal that limited human-to-human transmission has occurred.

"I think we need to be very, very concerned" about the latest developments, says Jeremy Farrar, director of the Oxford University Clinical Research Unit in Ho Chi Minh City, Vietnam.

....The Beijing Municipal Health Bureau also announced today that a 4-year-old contact of a 7-year-old girl who had been hospitalized with the virus tested positive for the virus too, despite showing no symptoms. (bold mine) This is the first asymptomatic case. Along with several mild cases already reported, it suggests that the virus might be more widespread among humans than the numbers of reported cases suggest.

Perhaps counterintuitively, such mild cases are "very worrying", says Farrar. That is because reduced virulence can often point to further genetic adaptation of the virus to infection of human beings — and thus greater potential to spread.

 Marc Lipsitch is an epidemiologist at the Harvard School of Public Health in Boston, Massachusetts. Declan quotes him:

"It's too soon to say how big a threat H7N9 poses because we don't know how many animals of which species have it, how genetically diverse it is, or what the geographic extent is," says Lipsitch, "It looks as though it will be at least as challenging as H5N1."

How will we know if H7N9 establishes itself in the USA? 

A few years ago, back in January 2009 (and six months before the swine flu pandemic),  I wrote a blog regarding H5N1 and the potential for chickens to be asymptomatic carriers of a pandemic candidate virus. 

If you performed a Find and Replace using "H7N9" for "H5N1" in that blog post, you would instantly have a very topical blog.  So please read that blog from four years ago, and change the virus subtype in your head as you go along.

Now, I vector you to today's disclosure that 64 human H7N9 cases exist in six different provinces, including two fabled cases in the city of Beijing.  There are 14 deaths.  As I mentioned in one of my earliest blogs on the subject of human H7N9, barely a week ago:

Dr. Yin of the Bill and Melinda Gates Foundation.  Apparently Dr. Yin is the Foundation's leader in China.  And it was quite satisfying, knowing Bill and Melinda are spending funds in  China, including, but not limited to, surveillance.  Dr. Yin's statement is worth paraphrasing.  He said, basically, if you don't test for H7N9, you won't find it.  But if you do test for it, you'll find it.  The inference is that there have been numerous unexplained and undiagnosed severe respiratory ailments there this season.  Retroactive testing of samples, based on Dr. Yin's inference, will yield a significant increase in the number of H7N9 human cases. 

Indeed, with more than 400 labs across China testing away, they are finding more cases in more geographic locations.  Simultaneously, more deaths are being reported.  Fortunately, the deaths are not increasing in proportion to the number of confirmed cases.  We all believed that the case fatality rate would not be as high as the initial reports would have indicated; the sample was too low and the data, therefore, did not support (yet) a high CFR.

But I found it interesting that as of this morning, the WHO has not yet established a pandemic alert system for H7N9. Dedicated Web page, yes.  But the WHO has not started an alert system. 

WHO has an alert system in place for H5N1, and had one for pH1N1, a.k.a. The Virus Formerly Known As Swine Flu.  Perhaps it is too early for such an alert system.  After all, the virus is only in one region of one nation (albeit a region that is host to more than 300,000,000 Chinese).  I also understand the reluctance the WHO must feel regarding this disease.  The WHO took significant credibility hits after swine flu, some referring to the WHO as "chicken little."  These criticisms are unfair and undeserved.  No one had any idea that pH1N1 would have been as mild as it was.

And "mild" is a misnomer.  The words "mild virus" are of great consolation to virus experts, public policymakers and public health professionals who look at The Big Picture; but those words are of little consolation to the parents of children who died during the pandemic. 

A Reuters story from June of last year paints that smaller picture.

(Reuters) - The swine flu pandemic of 2009 killed an estimated 284,500 people, some 15 times the number confirmed by laboratory tests at the time, according to a new study by an international group of scientists.

The study, published on Tuesday in the London-based journal Lancet Infectious Diseases, said the toll might have been even higher - as many as 579,000 people.

The original count, compiled by the World Health Organization, put the number at 18,500....

The results paint a picture of a flu virus that did not treat all victims equally.

It killed two to three times as many of its victims in Africa as elsewhere. Overall, the virus infected children most (4 percent to 33 percent), adults moderately (0 to 22 percent of those 18 to 64) and the elderly hardly at all (0 to 4 percent).

Even though the elderly were more likely to die once infected, so few caught the virus that 80 percent of swine flu deaths were of people younger than 65.

In contrast, the elderly account for roughly 80 percent to 90 percent of deaths from seasonal influenza outbreaks. They were probably spared the worst of 2009 H1N1 because the virus resembled one that had circulated before 1957, meaning people alive then had developed some antibodies to it.

The relative youth of the victims meant that H1N1 stole more than three times as many years of life than typical seasonal flu: 9.7 million years of life lost compared to 2.8 million if it had targeted the elderly as seasonal flu does."

So swine flu was much more of a force than anyone (especially the critics) thought it was.

Here in April of 2013, we have a big problem.  No one knows how long this new H7N9 virus was circulating among wild birds, poultry and (especially) people in China.  In fact, we didn't know Diddley until March 31st, when the Chinese sprung the news upon the world.  Exactly when the Chinese knew it had H7N9 in people is cause for speculation, but I think we can excuse the Chinese for demanding confirmation before telling the whole world (to their credit) that a new pandemic candidate was emerging within their borders.

In fact, nothing may have ever been known, had the cases involving the three male family members not caused some doctor or technician to begin testing for something.  My guess is they speculated it was  seasonal influenza or H5N1 bird flu, then moved to SARS, then moved to the new novel coronavirus NCoV, and then reverse PCR testing revealed the presence of H7N9. 

Thank the Maker that someone had the curiosity and the desire to test in a wider spectrum!

Adding to the drama is the report from Beijing last week that a 4-year-old boy tested positive for H7N9.  He is not sick and displays no symptoms, yet he is an asymptomatic carrier of bird flu. This means wider testing is essential -- of humans, pigs and birds.  The testing net needs to be cast very widely in order for everyone to get their arms around the problem. 

And that, folks, is why I believe the USA's CDC opened its Emergency Operations Center at Level 2.  Since the CDC EOC alert levels only go from 3 to 1, the opening at Level 2 was considered by some to be controversial.

Knowing now what we do, and analyzing their decision in the current light, we should say this was an important and prudent decision.  Because, folks, we don't really know if this virus has come to America or not. And the only way we are going to know anytime soon is through weekly surveillance of mortality and morbidity.

From Wikipedia:

 United States

On April 9th, 2013 the Centers for Disease Control and Prevention (CDC) activated its Emergency Operations Center (EOC) in Atlanta at Level II, the second-highest level of alert.[30] Activation was prompted because the novel H7N9 avian influenza virus has never been seen before in animals or humans and because reports from China have linked it to severe human disease. EOC activation will "ensure that internal connections are developed and maintained and that CDC staff are kept informed and up to date with regard to the changing situation."[31]

From the Medscape article:

The Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia, received a specimen of the H7N9 virus from China yesterday. On April 9, the CDC activated the Emergency Operation Center (EOC) at Level 2 (there are 3 levels, with 1 as the highest) to support the management of the emerging H7N9 situation, Sharon KD Hoskins, MPH, senior press officer at the CDC told Medscape Medical News in an email.

Researchers used real-time reverse-transcriptase-polymerase-chain-reaction assays, viral culturing, and sequence analyses to test the patients' respiratory specimens for influenza and other respiratory viruses.

....In an accompanying perspective, Timothy M. Uyeki, MD, MPH, MPP, and Nancy J. Cox, PhD, from the Influenza Division, National Center for Immunization and Respiratory Diseases at the CDC, commented on the article, noting that this outbreak "is of major public health significance."

"The hemagglutinin (HA) sequence data suggest that these H7N9 viruses are a low-pathogenic avian influenza A virus and that infection of wild birds and domestic poultry would therefore result in asymptomatic or mild avian disease, potentially leading to a 'silent' widespread epizootic in China and neighboring countries," Drs. Uyeki and Cox write. The HPAI H5N1 virus usually causes rapid death in infected chickens.

I am not certain, but I am pretty confident that most labs in the United States are currently incapable of subtyping anything other than the prevaling seasonal flus of pH1N1, H3N2, B, and swine H3N2 (nice call, CDC). Anything other than these substrains are lumped into one or more catagories of A: "Subtyping not performed," or A "Unable to subtype."   However, the CDC is also beginning to catalog incidences of other novel influenzas.  From their April 6th report:

Novel Influenza A Virus

No new human infections with novel influenza A viruses in the United States were reported to CDC during week 14.

A total of 312 infections with variant influenza viruses (308 H3N2v viruses, 3 H1N2v viruses, and 1 H1N1v virus) have been reported from 11 states since July 2012. More information about H3N2v infections can be found at http://www.cdc.gov/flu/swineflu/h3n2v-cases.htm.

Assuming few, if any, US labs can currently quickly detect H7N9 bird flu, the only other capability the CDC has is to monitor and initiate surveillance of the public's health.  This means both ramping up a central monitoring presence dealing with day-to-day issues, and also ramping up state health departments to begin watching for unusual spikes in ILI, or Influenza-Like-Illness.
By activating their EOC at level 2, the CDC is able to pull in disparate elements and to begin the process of surveillance in earnest. Things you just cannot do sitting at a desk, you can do in a central coordinating facility, open-air, with people at their posts.  Having been in the State of Florida EOC many times, including pandemic exercises, actual hurricane tracking and the afternoon of 9/11 (and for days afterward), the ability to sort information and make decisions does not happen in a better environment.

On April 2nd, I formally activated the State of Florida CIO Association's Pandemic Committee.  It had stood in informal recess since the Swine Flu pandemic was declared over in 2010.  However, I decided that once the chickens were not doing their duty and dying, we had a real conundrum on our hands!

In fact, just last week, the Florida Department of Health announced that they were beginning monitoring the China H7N9 situation.  I suspect other state health organizations are ramping up, if for no other reason than to give the CDC timely and accurate information, should there be spikes in respiratory illness.
So what would a spike look like?  The spike would look something like this:
Hmmm.  This is the actual CDC Pneumonia and Influenza Mortality chart for April 6th, 2013. 
The top black line represents the epidemic threshhold.  The bottom black line represents the seasonal baseline.
The red line represents the actual reported cases.  As you can see, the red line is at the highest point since a spike at the beginning of calendar 2011, six months after the end of the Swine Flu Pandemic. In fact, the chart had suddenly spiked to a level higher than at any point since 2009.
Not sure of what was going on, but knowing this occurred before my rebirth as a flu blogger, I reached out to Mike Coston (again). I asked Mike about what had happened? 
Mike told me that the CDC immediately looked into the situation. In fact, he blogged on both the mortality spike and the CDC's response. Apparently, what happened is that H3N2 drifted.  If you need a primer on antigenic shift vs. antigenic drift, click here.
Anyway, what happened is that, apparently, the H3N2 seasonal flu drifted.  And seniors, who may not have been vaccinated as often as recommended, had no immunity to the drifted virus -- immunity they might have had, if they had goten regular flu shots.  H3N2 is a nasty bug for anyone, but especially for the elderly, who died in numbers sufficient to trigger the uptick that you just saw.
A similar uptick, especially coming now as flu season wanes, would trigger a pretty quick CDC response.  This is why the CDC activated.  This is why state departments of health are getting ready to ramap up their surveillance. 
To recap:
  • The chickens are not doing their duty and dying.
  • China has no real idea how widespread the virus is.
  • Nobody else does, either.
  • There is currently no reason to suspect there is H7N9 in North America.
  • That having been said, there is always the possibility that infected, asymptomatic travelers have come into the United States via any of the Pacific ports of call and airports. Unlikely, but not impossible.
  • Certainly, we would have seen the virus in Hong Kong before we would have seen it here.
  • Currently, there is no inexpensive, routine way to test in doctors' offices or public health departments in the USA for H7N9. 
  • H7N9 would appear as "Type A, Unable to subtype" or "Type A, subtyping not performed."
  • We have a long way to go with this situation.

“Contagion” is a Deeply Unsettling, Haunting – and (Mostly) Realistic – Pandemic Film

Those of us who have made pandemic preparedness part of our curriculum vitae could not have been more excited about the premiere of Steven Soderbergh’s latest film, ““Contagion”.”

 And we were not disappointed.  “Contagion” is a paragon of what an intelligent biological thriller should be:  hyper-accurate, absorbing, and, most of all, a film that reminds us of our own individual responsibilities within a civilized society.

 Not to say that there’s not a little bit of Hollywood in this film.  More on that later.  First, let’s take a look at how the movie was made, the etiology of the fictional virus, and what Hollywood got right.  And in many cases, they got it absolutely right.

What “Contagion” got right 

The MEV-1 virus in the movie is the brainchild of Dr. Ian Lipkin, of Columbia University.  Dr. Lipkin directs the Center for Infection and Immunity at the Mailman School of Public Health at Columbia.    He was contacted by Soderbergh and the film’s writer, Scott Z. Burns.  He agreed to come on board the production as a paid technical and science adviser.

Dr. Lipkin created a virus for the film that is patterned after an actual virus: The Nipah virus.  Nipah was first discovered in Malaysia in 1999.  The natural reservoir of Nipah is in the Malaysian fruit bat population.  The WHO reports that Nipah has also been found in bat urine and in partially-eaten fruit in the region.  Oh, by the way:  The real-life bats in question are migratory.  Toward that end, antibodies to a virus very similar to Nipah have been found in India, Indonesia and Timor.

There is a danger in making bats the heavy in the film.  Bats are essential in such areas as insect control.  And North American bats are dying by the millions, due to “white-nose syndrome,” a fungal infection that essentially suffocates bats during their annual hibernation. 

But bats are also vectors of some of the world’s most dangerous diseases, especially Ebola – and SARS. 

While the MEV-1 virus is patterned after Nipah, the pattern of infection is modeled after the SARS virus.  How quickly we forget how threatening SARS really was.  In bookstore remainder bins all over the continent, one can find Karl Greenfield’s seminal work on the SARS epidemic, titled, “ China Syndrome: The True Story of the 21st Century's First Great Epidemic.” I highly recommend his book.

While the original vector of SARS in 2002/03 was a “civet cat,” a peculiar-looking mammal, it may be that the civet cat in question was infected by a bat.  SARS virus has been found in Brazilian bats, so the danger is not localized to Southeast Asia by any means.

Had SARS been more like influenza and less like the common cold, we would have seen a pandemic that would have made 1918’s Spanish Flu look like the common cold.  In the US, the H1N1 Spanish Flu pandemic killed 2.5% of everyone it infected.  In contrast, SARS killed 10% of those it infected, worldwide.  But luckily for us (“us” being the world), SARS infected so quickly, public health professionals got in front of the disease and eventually beat it down.  It is counterintuitive to be sure, but a disease that infects quickly is easier to corral than one with a days-long incubation period, such as influenza.

To go into how SARS infected and killed would also produce those obligatory “SPOILER ALERT!!” warnings and disclosures, which I want to avoid (where possible) in this review.  So suffice it to say that “Contagion” is disturbingly accurate when it comes to how quickly it was able to infect on a global scale.

SARS was not the exclusive province of China, Toronto or Singapore.  Two prominent Tallahassee residents (who I obviously cannot identify for HIPAA reasons) were infected by SARS during a visit to China in 2003.    The CDC and WHO were actually monitoring their health following their return to Tallahassee. By proxy, they were monitoring Tallahassee for signs of SARS infection.

So what Soberbergh, Burns and Lipkin created were a perfect fit of an established disease and historic established routes of transmission.  In other words, extremely realistic.

Dr. Lipkin also taught the cast how to correctly don protective gear, and how to speak the language of disease.

In the movie, the Elliott Gould character, Dr. Ian Sussman (yes, a probable nod to Dr. Ian Lipkin) is able to finally grow a sample of MEV-1 to produce a vaccine candidate.  This storyline parallels the first attempts to grow H5N1 in chicken eggs to produce a vaccine.  Bird flu was killing the eggs.  That was eventually overcome.  Of course, H5N1 poultry vaccines have arguably done more harm than good, but that is a matter left to my previous blogs on the subject.

Elliott Gould’s Dr. Sussman is handling the virus in a Level 3 lab, and the CDC has already ordered all samples not contained in a Level 4 lab to be destroyed by fire.  Dr. Sussman’s on-screen disregard for CDC protocols is reminiscent of the spanking that real-life Dr. Yoshihiro Kawaoka of the University of Wisconsin received in 2007 for handling “copies” of the dreaded Ebola virus in a level-2 lab. 

Laurence Fishburne’s admonition that “We don’t want that virus leaving on the bottom of someone’s shoe” refers to a frequent and ongoing concern.  For more information, refer to my ongoing blog series, “When labs attack.”

What “Contagion” could have done better

Where the movie deviates from probability, in this reviewer’s opinion, is in its depiction of how society would react to the virus.  These deviations are all permitted, because they are clearly possible. It is just in the areas that were left out that very minor – and forgivable – faults can be found.

In less than a month, society pretty much goes over the cliff.  Garbage lies uncollected and strewn about neighborhoods.  Unions strike, rather than perform their duties.  Governors call out the National Guard and seal borders without apparently seeking consultation from Washington.  And while grocery stores are ransacked and food is extremely scarce, the lights and phones somehow stay on.

The Enemy of the People in any pandemic is the stability of the supply chain.  That just-in-time supply chain is the most fragile part of our economy.  The level of global apprehension, not to mention the Case Fatality Rate of the MEV-1 virus in the film, would have produced much more damage to the global supply chain. 

Those of us who are sought-out as experts in pandemic preparedness often point to unions as a cause for concern.  In fact, pandemic planners factor in possible union (in)actions in their calculations, but I believe that people are also capable of doing heroic things.  The public health experts in “Contagion” are justifiably viewed as heroic.  But as we saw on 9/11, and as we were reminded this past weekend, heroism is not limited to one exclusive group of people.

However, the images of public employees such as law enforcement officers abandoning their posts in New Orleans during Katrina – and even joining in the looting and pillaging, in a few cases – is also testament to our individual faults and failings.  That, too, can be seen in “Contagion,” even at the higher levels of the government.

The film did not damage the critical infrastructure enough.  In a prolonged, 1918-type pandemic, we believe ports will clog, phones will become unreliable, and power will come on and off – all because there will not be sufficient levels of people healthy enough to work to maintain them, nor will there be sufficient numbers of people to work, due to absenteeism to take care of loved ones.  And there are always those who will burn sick days just for a headache.  We have estimated that, at the height of a pandemic, as much as a third of the workforce might be absent on any given workday.

The movie attempts to display the deterioration of society in a few select scenes, but the film did not go far enough in its depiction of the degradation of the infrastructure.  It did show the requisite looting of grocery stores, and certain unsettling acts of violence, and it did an excellent job in its frequent shots of uncollected refuse.

In a real-life, lethal pandemic, the military would be called upon to perform these tasks.  That would include the National Guard, which I must believe would be Federalized early on, in order to prevent the types of actions that were undertaken by individual governors as the pandemic worsened.  Federalizing the Guard places those units under the direct control of the Pentagon.  Governors lose their Guard in that scenario.  I would have to believe that the president would exercise that authority very, very early on in this process.

Sealing the borders, for example, has been almost completely tossed as a realistic countermeasure.  The SARS epidemic and the H1N1v “swine flu” pandemic showed how border closures would be ineffective to restrain any virus. 

This point (along with the supply chain issue) was actually done very well in the TV-movie “Fatal Contact: Bird Flu in America”. In that film, the military is called home from Iraq and Afghanistan to help maintain law and order.  I would expect governors to call all their Guard units home, to assist in stabilizing the infrastructure of their states and to curtail inevitable violence.

 Other than the depiction of labor unions as petty and self-serving, “Contagion” also serves as a confirmation of the Second Amendment during a crisis.  Cops are not around when the shooting starts.  Self-defense is the order of the day.  Being armed equals being safe.  These are two curious messages to be dealt by a Hollywood director, and I found it to be refreshing.


My family felt that it was a little preposterous that key public health people would not continuously wear their masks and gloves, especially in public.  We have had many discussions regarding the efficacy of wearing masks in public, however, and I defer to the writer and director on this topic. 

Another concern (the most deeply-rooted one) is in the film’s conflict between the CDC and the Minneapolis public health unit.  This is where the Hollywood formula kicks in, resembling a Criminal Minds episode where the local cops resent the FBI intrusion into their bidness.  The reality is that local public health units generally work very well with the CDC, and welcome their participation when things go bad.  In my experience, the CDC is a first-rate organization, led by top-flight people.  Local public health units do the best they can do, especially in this current economy, but “overwhelmed” would be an understatement on any given workday – let alone during a pandemic.

Dr. Michael Osterholm, head of the Center for Infectious Disease Research and Policy at the University of Minnesota (and who worked at the Minnesota Department of Health for a quarter-century), alluded to this during a recent “Contagion”-inspired interview.  In fact, the Minnesota Department of Health is one of the best-run departments of its kind in the country.

The other area that the movie (which runs a brisk 106 minutes) glosses over is within the subject  of vaccine production.  Public health experts such as Dr. Osterholm have stated that the movie’s scenario for vaccine production is too rosy (my words).  Vaccine production takes months, even in a “good” viral situation such as producing an influenza vaccine.  It took every bit of six months just to produce the swine flu vaccine. 

With a new and previously-unseen virus, especially considering the repeated failures of the prototypes, it would take considerably longer.  The wait for vaccine could take almost a year, causing further destruction of the global economy and the further erosion of the critical infrastructure.  And this does not even deal with the issue of who gets vaccine and who does not. 

In another “Contagion”-imitates-life example, a Chinese group has kidnapped a WHO official, and demands -- as ransom -- vaccine produced in the West.  This is a nod to the possibility of natively-produced substandard or even counterfeit vaccine.  It is nice to hear someone demanding America vaccine –anything – because it is the best in the world.  Note, at the end of the movie, the architecture of the open-air school housing the Chinese children. 

The vaccine issue is personalized within the village, but once again, the script alludes to larger global issues.  In this case, the rural, poor demand for vaccine speaks to the problems caused by Indonesia in the fight against bird flu.  Back in 2007, the Indonesian government refused to share  human bird flu samples – or even to quickly report human bird flu cases and deaths – simply because they felt their samples would make the global pharmaceutical companies billions of dollars, and, at the end of the day, leave Indonesia without any vaccine.  It took years for the West to negotiate an agreement with Indonesia to give them vaccine in exchange for human bird flu samples.

The movie did do a good job of showing the agony involved with waiting and waiting until their vaccine lottery number was called.  I found the prospect of a “vaccine lottery” to be a curious and interesting (and fair) way to resolve the issue of who got vaccine and when. The reality is, there is a schedule of who gets vaccine, at least within the first responder community, the military and the government.  The Strategic National Stockpile has the goods.  The Department of Homeland Security and state governments have the plans.  After that, I doubt if there is a plan, so the lottery idea seems as fair as any.

Finally, we need to address the issue of the blogger character played by Jude Law.  “Blogging is graffiti with punctuation,” Elliott Gould admonishes Law’s character.  Law’s Alan Krumwiede is the worst sort of blogger, one who is only interested in promoting his “brand” at the expense of the truth, not to mention people’s very lives, by promoting an unproven homeopathic “remedy.”  He is the 21st Century snake oil salesman, shamelessly hawking an elixir that is eventually proven to be dangerously ineffective. 

Fortunately, I do not know any bloggers personally who would fit into those shoes.  My disease-blogger friends are all dedicated people who, in their minds and in mine, are performing a valuable service by alerting their readers to some very real threats and dangers.  Their surveillance uncovered the swine flu pandemic before the world’s press did, and their work on tracking H5N1 has proven to be extremely accurate.  I hope Law’s Krumwiede would not get the attention he gets in the movie.  However, having sat numerous times where Law’s character sat, in a quiet studio, in front of a television camera with an IFB in my ear, talking to a reporter or a network news anchor, I can understand how a marginal “playa” could become a fiend, mainstreamed by the press. It is up to the individual to censor him/herself and to produce accurate content.


““Contagion”” is an incredibly well-researched, disturbingly plausible, and extremely well-made film.  With the exceptions of the vaccine production timetable and the downplaying of the damage to the economy and the critical infrastructure, Soderbergh and Burns got it right.  Soderbergh is his own cinematographer as well (under a nom de plume), and his use of “available light” in place of standard movie lighting techniques makes the film feel much more realistic -- which means, of course, much more disturbing.  The cast, without exception, is fantastic.  Gwyneth Paltrow factors heavily throughout the film, so her apparent quick departure in the film’s first act is compensated for throughout the movie. 

And equally exceptional is the villain, the MEV-1 virus.  The fact that it is based on a real virus should wake us all up to the need to engage more strenuously in personal hygiene, and remember the things Momma taught us:


  •       Wash your hands frequently.
  •       Cover your cough, not with your hands, but with your sleeve, or a handkerchief or napkin.
  •       Keep a respectable distance from strangers.


Now go put on your Level 4 gear and go see the movie!


Here are some other sites, in case you want more “Contagion” stuff:


Mike Coston’s superb Avian Flu Diary, and his entry on the movie.



An interview with Dr. Mike Osterholm on the accuracy of “Contagion”:


And a dynamite Wired blog, written by the extremely talented Maryn McKenna, featuring an interview with Dr. Ian Lipkin.  Maryn has two books in print that hypochrondriacs should not read.  Her latest is on MRSA and it is called Superbug. Find it at your local bookstore, if one still exists, or order it from Amazon.



Last, and least, an article on “Contagion” from a Palm Springs, California newspaper, with some quotes from yours truly.



FAO warns of spread of Fujian H5N1 mutation

Back in 2008, flublogia announced the origins of a new clade, or substrain, of bird flu.  And I joined right in, proclaiming that the new clade -- nicknamed "Fujian," after the province where it was subtyped -- would eventually cause major problems.  The best blog of mine that I could remember on the topic, from 2008, can be read here.  You might also be entertained by my original blog on the Chinese H2H case involving Fujian H5N1, here.  I know I was; I have forgotten half of this stuff! 

Fujian H5N1 was the cause of the father-to-son (or was it son-to-father) Chinese H2H infection back in 2008.  The arrival of simultaneous Fujian B2B and H2H bird flu was extremely troubling to all of us.

Well, it took awhile (just over three years), but Fujian H5N1 is on the lips of television announcers and copy editors the world over.  The reason?  The FAO (think WHO for animals) released a statement today, proclaiming great worry over this "new" mutant strain of bird flu, and imploring the world to monitor it carefully.

Now the timing of such stories is interesting.  We have been monitoring Fujian for years, as I mentioned earlier.  But with the release of the film "Contagion," we may be seeing where the world's public health authorities see an opportunity to raise awareness just when bird flu is about to become a household word again.

Make no mistake:  I am all about awareness.  Consider my own "pandemic fatigue" following the aftermath of the first wave of the swine flu/H1H1 pandemic of 2009-11.  This story woke me up and caused me to go back and retrace my own experiences writing about Fujian 2.3.x H5N1.  So let's review what has been happening in the months since I last blogged seriously about H5N1. 

As of August 19th of this year, there were more confirmedhuman bird flu cases than in all of 2004, 2008 or 2010.  Keep in mind that this includes an alarming increase in Egyptian human cases and accompanying deaths.  But most distressing is the sudden re-emergence of Cambodia as a bird flu incubator.  While Egypt has had 32 cases and 12 deaths to date, Cambodia has had 8 cases -- all fatal.  Of course, we shrug our shoulders at Indonesia, which continues to befuddle Western experts with its distressing lack of transparency. 

So 2011 already ranks as the fifth-worst year for human H5N1, and we have the beginnings of flu season in which to add to that total.  It would take a huge, but not impossible, acceleration of human cases to move it past 2009's 73 totals.  that is the good news.  But the FAO apparently sees a cause-and-effect relationship between the initial discovery of a new clade, the distribution of that new clade, its ability to overtake the existing clade as the dominant substrain, and then extend its reach back into humanity.  Now it is hard to calculate an accurate Case Fatality Rate (CFR) based on such low numbers, but it is safe to say that of all the documented H5N1 human cases, we are still at a reliable 50% figure, meaning that half of all human bird flu patients either die of the disease or its byproducts.  In Egypt, that figure is currently 37%; in Cambodia and Indonesia, it is much, much higher.

The FAO is signaling that it fully expects bird flu cases in poultry and in humans to accelerate in 2011.  The efforts to vaccinate poultry, while admirable, have failed to eradicate the disease (did we ever really expect this effort to be successful?).  Pockets of H5N1 remained and pockets remain today.  While migratory wildfowl (laden with virus) are the primary culprit, humans and their myriad and almost universally bad ways of moving poultry from area to area are also culpable.    Perhaps even more so, when humans smuggle sick and dying poultry across borders, as happens hourly from the Bird Flu Ho Chi Minh Trail from Vietnam into China.

In my next blog, we will take a look at the Australian situation with Tamiflu-resistant H1N1.

Making sense of the recent flu news

It has been a long time since I blogged anything about the flu.  For starters, I am busier than ever at work, which cuts severely into my blogging time.  But also because I just have not felt the muse.  The swine flu pandemic was blessedly mild overall, although there are thousands of families still coping with the loss of a loved one due to H1N1/2009 who would harshly disagree with my assessment. But it wasn't 1918, so we breathed a sigh of relief.

There are many seemingly divergent storylines currently out there, which I will just list at random.  I am not so sure they are not somehow interconnected, however.

First has to be the continued number of human bird flu infections and deaths in Egypt.  Overlaying this ongoing problem is the sudden departure of Mubarak, the takeover by the Egyptian military, and what this portends for both transparency and NAMRU's operations within the nation. 

Second is the realization that this year's seasonal flu vaccine was way off the mark.  I began to notice last month that my employees were getting sick from flu, and I knew they had received their vaccinations in the late fall.  My deputy, in fact, was tested type A-positive last month.  That's pretty specific.  Here in Tallahassee, doc-in-the-box and emergency rooms were positively overrun with flu cases.  Things are looking better, but the WHUMP! of flu cases in January was much more severe than at the same time last year.  And last year was the dang pandemic!  Almost everyone who got flu this year who I am personally acquainted with, had, in fact, received the vaccine months prior.

Third is the ongoing Siege of Japan by H5N1 in poultry.  We all have read the articles about the culling of hundreds of thousands of birds in Japanese poultry farms.  this has spread to the mainland, especially South Korea.

What is clear to me is that the H1N1/2009 pandemic was not sufficient to push the other subtypes off the radar.  This runs contrary to previous pandemics where a dominant substrain was capable of, and able to, sufficiently supplant  the previous Big Dog of Flu.  H1N1 was replaced by H2N2, which was replaced by H3N2, and so on.  Swine flu was not able to eradicate H3N2, nor was it able to eradicate B.  for that matter, I do not know what research existed prior to the mid-1950s to actually track Influenza B.  for all I know, Influenza B has been around since the Chinese domesticated ducks some 4,000 years ago. 

Or, since B mutates more slowly than A, and is therefore not capable of producing pandemics (so says Wikipedia), it is not subject to the King of the Mountain game like Influenza A.

But someone apparently blew the call on the vaccine this season.  I get the feeling the only strain they got right was, in fact, the pandemic strain! 

The other strain that H1N1/2009 did not push off the radar is H5N1.  In fact, so far this year, bird flu activity seems to be much more intense than at the same time last year.  Human cases and deaths in Egypt seem to be at the same levels as last year, but H5N1's overrunning of the Japanese poultry industry is disconcerting.

Finally, there seems to be some concern that this year's flu outbreaks are more severe than last year's.  Again, this is not scientific, but my people got hit and hit hard by the virus.  Their symptoms were severe, with one person requiring hospitalization.  In one case Tamiflu did nothing, although there is a chance it was not administered in time.

H1N1 had a comeback in the late 1940s and early 1950s, with several epidemics (the Liverpool Flu of 1951, for instance) that were considered equal to, or more severe than, the 1918 pandemic, depending on location.  Shortly afterward, H2N2 (re)appeared, seemingly wiping H1N1 off the face of the Earth.

I openly wonder if the appearance of swine flu in 2009 was, in fact, the Beginning of the End of H1N1 as it was in the 1950s, and we are at the brink of the introduction of a different substrain of flu.


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