Influenza Virus Mashup

Influenza Virus Mashup

Archive for January, 2011

[Crof's H5N1] Greenwald down with dengue

Posted by Automator On January - 31 - 2011

Political blogger Glenn Greenwald lives in Brazil. Today in Salon.com he explains his lack of Posting. Excerpt:

Last week, I wrote that I had a bad flu and likely wouldn’t be writing for at least a few days.  As it turns out, I don’t have the flu, but rather dengue fever, combined with some still-unknown secondary problem.  

I’d strongly prefer not to write about this but I had to cancel the series of speeches I was to give this week at various California colleges and, after notifying them of the reason, at least one of the event sponsors disclosed my condition to those inquiring about the event, so it’s already been posted by well-intentioned people in various places.  

Moreover, as Andrew Sullivan pointed out when writing about the illness that prevented him from blogging all last week, it’s basically impossible to write everyday for years and then suddenly disappear without providing your readers with an explanation, as much as one might loathe writing about personal matters (as I do).

I wish him a speedy recovery.

[Crof's H5N1] Japan: Sixth B2B H5N1 outbreak

Posted by Automator On January - 31 - 2011

Via The Mainichi Daily NewsBird flu confirmed at another chicken farm in Miyazaki Pref. Excerpt:

Dead chickens found at a poultry farm in Miyazaki Prefecture were infected with a highly pathogenic avian flu virus, local officials said early Monday amid a spreading epidemic among local farms. 

The results of detailed tests on the dead birds at the farm in the town of Takanabe confirm the season’s sixth outbreak of bird flu in the prefecture and the ninth in the country. 

The prefectural government started culling Monday morning all of the 40,000 chickens at the farm, adding it will also impose a ban on transporting chickens and eggs from poultry farms within a 10-kilometer radius. 

At the farm, 90 chickens were found dead on Sunday and four out of five chickens tested were found positive in preliminary testing for bird flu.

[Avian Flu Diary] Haiti: Charting The Cholera Epidemic

Posted by Automator On January - 31 - 2011

(Mon, 31 Jan 2011 11:54:00 +0000)

 

 

# 5272

 

 

I’ve not done a lot on the Cholera outbreak in Haiti over the past few weeks, simply because Crofsblog has been extraordinarily dedicated to the story since it began.  And for daily coverage of Haiti, that’s the site to visit.

 

But from time to time - when I’ve thought I could add some value - I’ve posted on the outbreak, including:

 

MMWR: Haiti Cholera Update
Haiti: The Progression Of An Epidemic
Haiti: Updated Cholera Outbreak Map
 

Sixty days ago I posted some graphics showing the progression of the Cholera Epidemic through the end of November.  At the time, the mortality rate was listed at 2.2%.

 

image

These are just reported numbers, of course. The real numbers are likely much higher.   Also, a great many more people are assumed to be asymptomatic carriers of the bacteria.

 

Today OCHA has posted a freshly updated map, and chart of the epidemic’s progress, hosted by Reliefweb.  You can download the map in its entirety at the link below, but I’ve excerpted a couple of interesting segments to highlight.

 

Haiti: Cholera Cumulative Cases since October 2010 (as of 24 Jan 2011)

Map of 'Haiti%3A%20Cholera%20Cumulative%20Cases%20since%20October%202010%20(as%20of%2024%20Jan%202011)'

  • Date: 27 Jan 2011
  • Type: Natural Disaster
  • Keyword(s): Epidemic; Health; Natural Disaster; Affected Population
  • Format:

    map.pdfPDF *, 1218 Kb

 

 

In addition to depicting the spread of the epidemic in a series of maps, this release also charts the number of cases and fatalities. 

 

While 4000+ deaths is obviously a tragedy, the CFR (case fatality ratio) has dropped considerably over what was first reported back in October (roughly 8%).  

 

image

image

 

A goodly portion of this drop can no doubt be attributed to better surveillance and the counting of less severe cases, which may not have been included in the earliest numbers. 

 

Some of it, however, is undoubtedly due to the ramped up response by numerous relief agencies to the crisis.

 

 

Even assuming the vagaries of surveillance and reporting out of Haiti, and the likely undercounting of fatalities (and total cases), these numbers indicate that progress is being made.

 

That earthquake ravaged Port-au-Prince is running under a 1% mortality rate is actually quite remarkable.

 

And the (roughly) 2% CFR outside of the capital is noteworthy as well, given the pre-existing disease burdens and poor health care infrastructure that exists in rural Haiti.

 

While the cholera situation in Haiti can hardly be described as good, thankfully, it does appear that some progress is being made.

 

For some background on other diseases plaguing Haiti, you may be interested an a blog I wrote last November:

 

Haiti: Three Non-Cholera Health Threats

[Crof's H5N1] Hong Kong: Another swine flu death recorded

Posted by Automator On January - 31 - 2011

Via the Hong Kong government website, a report dated January 28: Another swine flu death recorded. Excerpt:

A 61-year-old woman has died of human swine flu, while two infected men are in critical condition.   

The Hospital Authority said the woman died at Alice Ho Miu Ling Nethersole Hospital this morning.   

The two in critical condition are a 59-year-old man who was transferred from a Mainland hospital to Tuen Mun Hospital yesterday, and 60-year-old man at Queen Elizabeth Hospital.   

Speaking after the 9th Joint Meeting of Senior Health Officials of the Mainland, Hong Kong & Macau today, Secretary for Food & Health Dr York Chow said the virus is the same H1N1 strain Hong Kong encountered in 2009, and has shown no significant change in genetic make-up.

[Crof's H5N1] Coston on B2B H5N1 in Asia

Posted by Automator On January - 31 - 2011

Mike Coston at Avian Flu Diary has one of his trademark think pieces: What Goes Around, Comes Around. It’s about the spread of B2B H5N1 as wild birds migrate from north to south, with Thailand the latest country to start watching the skies again.

[Crof's H5N1] US: How the Pentagon responded to H1N1

Posted by Automator On January - 31 - 2011

The New Yorker magazine has an Annals of Science article: The Pentagon’s War on Swine Flu. The full text is available only to subscribers (and people who pick up the current issue at a newsstand), but the abstract is pretty detailed. Excerpt:

On Tuesday night, April 28, 2009, Darrell Galloway, a senior official at the Pentagon’s Defense Threat Reduction Agency, watched a news report from Mexico City about a new strain of influenza known as swine flu that was spreading fast. That night, Galloway, a microbiologist, resolved to do something about it. 

He was authorized by the military to work on a specific set of threatening diseases that were considered potential weapons in war or in terrorism, including anthrax, smallpox, plague, and the Ebola and Marburg hemorrhagic fevers. 

Influenza was outside his focus, but the next morning, Galloway summoned his staff and announced that they were to begin work immediately on creating a new antiviral drug to combat swine flu.

[Avian Flu Diary] What Goes Around, Comes Around

Posted by Automator On January - 31 - 2011

(Sun, 30 Jan 2011 20:25:00 +0000)

 

 

# 5271

 

 

With bird flu outbreaks among poultry and wild birds increasing across South Korea and Japan (North Korea and possibly China are unknown factors), other Asian countries that see migratory bird visitations over the winter are understandably on the alert.

 

Today, a news release form the National News Bureau of Thailand, Public Relations office that reflects their concern. 

 

Bird flu fear sparks warning across the country

BANGKOK, 30 January 2011 (NNT)-Public Health Minister Jurin Laksanawisut has instructed public health services across Thailand to warn people of a possible outbreak of bird flu in human, although there has been no report on any one contracting the disease so far.

 

Following an unidentified cause of death of 100 chickens in Sam-Chuk district, Suphan Buri province, local residents fear H5N1 or commonly known as bird flu was the reason. However, an autopsy on dead chickens are still underway. Mr. Jurin has taken a precautionary step and instructed health services to coordinate with officers from the Department of Livestock and the Department of Agriculture for help.

 

According to the Health Minister, it is important that people are aware of risks and know how to protect themselves against the flu. People have also been warned not to come in contact with dead poultry. Mr. Jurin said even though Thailand has been free of the flu since 2006 ,the Ministry of Public Health will continue to monitor the disease to safeguard the health of the Thai people

 

We’ll have to wait to hear if this turns out to be anything, but it gives you an idea of how seriously officials are taking these latest outbreaks.

 

Japan, Korea, and Thailand are part of the great East Asian - Australasian Flyway. All three countries are the winter home for many species of migrating birds, many of which spend their summers in Siberia, China, and Mongolia. 

 

There are, however - overlaps between these flyways - enabling pathogens to be carried from one to another.

 

image

 

In what may turn out to be a related story, yesterday in an EID dispatch (see EID Journal: H5N1 Branching Out) we saw a report out of Qinghai, China indicating that a new (for them) clade 2.3.2  of H5N1 bird flu was reported in wild birds near major migratory nesting grounds back in 2009 (admittedly, news travels slow out of China).

 

Clade 2.3.2 isn’t new, of course. 

 

It’s been circulating - primarily among poultry in Vietnam and parts of China - since the middle of the last decade, and started showing up in wild bird surveillance a couple of years later.

 

In March of 2009, the CDC’s EID Journal published the following report.

 

Characterization of Avian Influenza Viruses A (H5N1) from Wild Birds, Hong Kong, 2004–2008

Gavin J.D. Smith,1 Dhanasekaran Vijaykrishna,1 Trevor M. Ellis, Kitman C. Dyrting, Y.H. Connie Leung, Justin Bahl, Chun W. Wong, Huang Kai, Mary K.W. Chow, Lian Duan, Allen S.L. Chan, Li Juan Zhang, Honglin Chen, Geraldine S.M. Luk, J.S. Malik Peiris, and Yi Guan

(EXCERPT)

Genetic and antigenic characterization of 47 HPAI (H5N1) viruses isolated from dead wild birds in Hong Kong showed that these isolates belonged to 2 antigenically distinct virus groups: clades 2.3.4 and 2.3.2.

 

Although research has shown that clade 2.3.4 viruses are established in poultry in Asia, the emergence of clade 2.3.2 viruses in nonpasserine birds from Hong Kong, Japan, and Russia raises the possibility that this virus lineage may have become established in wild birds.

 

 

Passerine birds encompass `perching birds’ & songbirds, while nonpasserine birds include ducks, swans, storks, ostriches, aquatic water fowl, quail, turkeys, and gulls . . . among many others.

 

In Late November of 2010, after 2 and 1/2 years without an outbreak, the H5N1 virus was detected at a poultry farm in Japan (see Japan: Bird Flu Investigation At Poultry Farm).  

 

Subsequently, the OIE WAHID follow up report # 1 identified the strain as being clade 2.3.2.  A hat tip to Ironorehopper for archiving the following information on his website:

 

Highly pathogenic avian influenza, Japan (WAHID Interface - OIE World Animal Health Information Database, Dec. 09 2010, edited

Epidemiological comments

  • It is considered that the virus was carried to the surroundings of the farm by migratory birds because the outbreak occurred in a season when migratory birds came flying from the north to Lake Nakaumi nearby the farm.

  • The virus might have invaded the affected henhouse through wild birds, wild animals or others.

  • The National Institute of Animal Health affirmed by comparison of gene sequence that the isolate is classified into clade 2.3.2 and a closely-related strain with the virus isolated from faeces of migratory wild ducks in Hokkaido in October 2010.

  • The homology between these viruses is 99.6%.

 

We’ll have to await further phylogenetic analysis from other farms in Japan, Korea, and elsewhere to know for certain .  .  .  but it certainly appears that the  2.3.2 clade has become well established in migratory birds.

 

While that in itself may not be a game changer, it is a reminder that the bird flu virus isn’t just a moving target.

 

It is actually a half dozen (or more) moving targets.  And that just counts the H5N1 clades.

 

With myriad influenza A viruses comingling, swapping genetic material, and continually trying out new genetic combinations in order to make a better, more `fit’ virus – it is imperative that we do what we can to improve global pathogenic surveillance and reporting.

 

Because experience has shown us, diseases that go around in one part of the world, have a nasty habit of eventually coming around to the rest of the planet.

(Sun, 30 Jan 2011 16:33:00 +0000)

 

 

 

# 5270

 

 

An update to a story that first emerged last August (see Finland Suspends Use of Pandemrix Vaccine),we learn today that Finland will soon release an interim report on the potential link between the Pandemrix vaccine and an unusual spike in narcolepsy which was reported in Finland, Iceland, and Sweden.

 

While we don’t have the results at hand, we do have a report from YLE.fi where the head of Finland’s National Public Health Institute has conceded that administering the shot to children may possibly have been a mistake.

 

Exactly why these countries should experience a rise in narcolepsy, while other countries using the same vaccine have not reported similar problems, is unknown. 

 

Since I’ve not seen this Interim report, there is little I can say about today’s report. You can read it at the link below.

 

Health Official: Swine Flu Vaccinations for Children Possibly a Mistake

published today 04:40 PM, updated today 04:45 PM

 

While stating that further research is warranted (and will take months), earlier reports from regulatory agencies in Europe stated that no link has been found between the Pandemrix vaccine and recent reports of narcolepsy.

 

On September 9th, I ran a story called Sweden: No Link Between Pandemrix And Narcolepsy, which linked to a CIDRAP report on the findings of Sweden’s Medical Products Agency’s investigation into the matter.

 

And two weeks later, the European Medicines Agency (EMA) said its Committee for Medicinal Products for Human Use had reviewed all available data and found insufficient evidence to confirm a causal link between cases of narcolepsy and the vaccine.

 

We’ll simply have to wait to see if this interim report has credible evidence to the contrary.

 

The CDC published a statement on these concerns last September, part of which states:

 

Pandemrix is not licensed for use in the United States. No adjuvanted influenza vaccines are licensed in the United States. The European Medicines Agency has launched a review of Pandemrix to investigate whether there is a link between cases of narcolepsy and vaccination with Pandemrix. This vaccine has been used in at least 30.8 million Europeans.

[Avian Flu Diary] AFD Editorial Policies

Posted by Automator On January - 30 - 2011

(Sun, 30 Jan 2011 14:03:00 +0000)

 

Note: My apologies for this lengthy post in advance.

In response to several queries over the past few months as to why I do or don’t do specific things on this blog, I’ve decided to post my rationale for how I manage this blog.

 

Over five years, this blog (and blogger) have undergone a number of changes. Hopefully for the better - but that is for you, the reader - to judge. I’ve learned a great deal about infectious diseases of course, but perhaps even more about science blogging in general.

 

So today, if you’ll indulge me, an outline of the editorial policies I use when writing this blog, including  the sticky issue of`fair use’ of other people’s work.

 

These policies are specific to me, and and geared to address my personal strengths, sensitivities and foibles, and are not intended to be a guide for any other blogger but myself.

 

We each have our own style, strengths, and weaknesses. It would be a boring Internet indeed if we all wrote by the same rules.

 

# 5269

 

 

I have, admittedly, some fairly stringent self-imposed rules for writing this blog.  Since I serve as both author, and editor of AFD, they are the only safeguards I have to keep this 5-year endeavor from `jumping the shark’ (1).

 

Primarily, I try not to speculate, rant, or make this blog all about me. I also avoid, as much as possible, lifting more than a paragraph or two (with a link back) from any newspaper article.

 

Of course, from time-to-time, bits of these elements do sneak in. So it isn’t a complete ban.

 

But it is a goal.

 

And then there’s the tricky minefield of what to do with conflicting science, pseudoscience, politics and individual belief systems. 

 

 

A day doesn’t pass when I don’t find some idiotic news item, blog post, or nutty idea worthy of an acidic rant. The internet is, as they say, a target rich environment. And the strong, sometimes overwhelming temptation is to go after these nutbars with devilish delight.

But I’m pretty sure my small but erudite band of loyal readers don’t need me to tell them when some idea, or policy, is inane.

 

I’d be preaching to the choir. In the end, a rant would only serve to vent my own spleen.  So while I sometimes write them (it’s therapeutic!), I rarely post them.

 

Besides, if I succumbed to the temptation often, this blog would start to sound like a broken record. So I try to resist.

 

 

As far as personal speculation or bias goes, I work constantly to remove it from my writing.

 

Why?

 

Because no one should give a flip what cockamamie ideas this aging ex-paramedic might have on avian flu, virology, or any other subject for that matter.

 

When on rare occasions I do speculate, I try to clearly label it as such.  And I must feel I have at least some credible evidence to back it up.

 

Otherwise, it’s nothing more than biased dreck, and I know it.

 

My goal is to provide context and scientific evidence, not opinion. I figure my readers are smart enough make up their own minds, without me insultingly trying to do it for them.

 

 

I also try to avoid assuming facts which are not yet in evidence.  Even if they seem `reasonable’, I side with caution.

 

Which is why, when we see suspected cases of H5N1 in Indonesia or Egypt, I don’t automatically assume them to be positive.

Or assume that negative results are always`false-negatives’.

 

When we see more than one infection in the same vicinity, and at the same time, I don’t instantly assume them to be the result of human-to-human transmission.

 

Yes, I know.

 

Someone else will likely be the first to declare that an outbreak has begun somewhere in the world. But since I know of no prize for being first to shout `Pandemic’ on the internet, I can live with that.

 

I’d rather be a day late and sure of the facts, than a day sooner and dead wrong.

 

Yes . . .you can always print a retraction, but Google never forgets. 

 

 

You’ve probably noticed I use colored text to segregate what I’m writing from excerpts or quotes by others (always in blue text).

 

Just another way to clarify who is saying what.

 

The subject of `fair use’ has come up a lot over the last year, and while I’ve always limited the amount of text I would lift from a news item (usually a linked headline, and a few paragraphs, followed by a second link), I’m taking even less today.

 

Over the past year I’ve tried to go with just the linked headline and no more than 1 or 2 paragraphs, along with my own summary of the news report.

 

Exceptions are generally press releases, state or official news releases, and of course, open access journal articles.

 

For other journal articles, I’ll give the citation, and some excerpts from the abstract, and then my own summary. 

 

Everything gets linked back to the source, of course.

 

My reasons are simple.

 

It’s no secret that newspapers, and journalists, are in financial trouble. And part of the problem is the wholesale `borrowing’ of their work, and reposting it all over the web.

 

I believe I can help them by enticing people to follow the link I provide and to read the original article with a well placed snippet or two, but I would be hurting them if I took any more than that.

 

I’ve too much respect for the talent and hard work of Maggie Fox, Helen Branswell, David Brown, Jason Gale, Lisa Schnirring, Robert Roos, David Dobbs, Maryn McKenna, and many others to ever want to scuttle their ships in order to pad my blog.

 

You’ll find that I use the very same standards when referring to another blogger’s work. And whenever I use a news item dug up by a newshound, I try to give them credit (note: I don’t use items unless linked to the original source), as well.

 

Now, I must confess that I have a personal bias when it comes to this blog.

 

I believe in promoting evidence based public health policies.

 

Unfortunately, sometimes scientific evidence is weak, anecdotal, or conflicting.  And as we all know, today’s `accepted truth’ has a bad habit of becoming tomorrow’s rejected fallacy.

 

Which is why you’ll sometimes find I write blogs like The Temporary Immunity Hypothesis and When Studies Collide (Revisited), that look at conflicting reputable scientific studies.  

 

When I do, I try not to take sides (at least not in print).

 

But when scientific evidence favoring one side is strong enough (notice I used the word `evidence’, not `proof’), I’ll side with the preponderance of evidence. Even though I know there is a chance it may be proven wrong later.

 

Why?  

 

Because the best we can do on any given day is to base our decisions on what the best evidence indicates right now, even if absolute proof is lacking.

 

As I’ve said before, if you want a guarantee. . . buy a Craftsman.

 

Which explains why I am pro-vaccination, even though I’m aware of the (minor) risks involved and the fact that they aren’t 100% effective.  And why I don’t use this blog to actively push unproven protective regimens, like Vitamin D (a frequent question, btw), even though there is some evidence that it may be effective.

 

(Personal admission: Being a `belt and suspenders’ type of guy, every flu season I use both).

 

 

Beyond that, I try not to attack anyone personally, even if I vehemently disagree with them (their ideas are always fair game, however). I also avoid dragging politics or religion into this blog like the plague, simply because I believe they polarize the audience, and distract from the science. 

 

I’ll leave that to others, better equipped and better suited, to joust with those windmills.

 

But most importantly, I try my very best not to sensationalize, or use unnecessary hyperbole when reporting on emerging threats. I believe that to do so is both irresponsible, and unprofessional.

 

And that, I think, harkens back to my years as a paramedic (yes, I’m violating the `about me’ rule here, but this whole blog post teeters on that precipice), where maintaining calm while in the midst of chaos was ingrained into us.

 

It’s why we walked (albeit briskly) at the scene of an emergency, never ran. And its how we `handled’ dealing with a dozen horrible events every day.

 

So if you detect the hint of a detached or dispassionate voice when I report on what are admittedly terrible events around the world, you now know why.  

 

There you have it.  The basic rationale I use when writing this blog.  These are my rules, for my blog, and are not meant to apply to anyone else.

 

I’ll post this on my sidebar, so that it remains available on the front page.

 

Hopefully it will have answered any questions you may have had, and now that I’ve written it down, will make it easier for me to stick to.

 

          *             *           *           *            *

 

(1)  `Jumping the Shark’ is an American idiom that goes back to the late 1970s.  It refers to an episode of the sitcom Happy Days, where Fonzie on water skis, jumps over a shark.  It was seen as a low point in the series, and a sign that the show was running out of good ideas, and on the decline.

To `jump the shark’ now means that something that was once great, has lost its way, and is on the downhill path.

[Flu Wiki Forum] News Reports for January 30, 2011

Posted by Automator On January - 30 - 2011

(Sun, 30 Jan 2011 03:40:26 GMT)

Reminder: Please do not post whole articles, just snippets and links, and do not post articles from the Las Vegas Review-Journal. Thanks!

Japan

?  Farm Ministry Holds Emergency Meeting On Bird Flu Epidemic (Link)

?  New avian flu threat (Link)

Philippines

?  Philippines not quite prepared for flu attack (Link)

United States

?  MN: 2 flu deaths reported in Minnesota (Link)

?  OK: The Vaccinated Still Prone To Type B Flu (Link)



?  H (Link)

News for January 29, 2011 is here.


Thanks to all of the newshounds!
Special thanks to the newshound volunteers who translate international stories - thanks for keeping us all informed!

Other useful links:

WHO A(H1N1) Site

WHO H5N1 human case totals, last updated January 20, 2011
Charts and Graphs on H5N1 from WHO
Google Flu Trends (U.S.)
CDC Weekly Influenza Summary
Map of seasonal influenza in the U.S.
CIDPC (Canada) Weekly FluWatch
UK RCGP Weekly Data on Communicable and Respiratory Diseases
Flu Wiki Main Page